RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1680
(227 letters)
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic
translation initiation factor 4H (eIF-4H) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4H, also termed Williams-Beuren syndrome
chromosomal region 1 protein, which, together with
elf-4B/eIF-4G, serves as the accessory protein of RNA
helicase eIF-4A. eIF-4H contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It
stimulates protein synthesis by enhancing the helicase
activity of eIF-4A in the initiation step of mRNA
translation. .
Length = 76
Score = 110 bits (277), Expect = 1e-31
Identities = 45/77 (58%), Positives = 58/77 (75%), Gaps = 1/77 (1%)
Query: 13 PYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
P+TAFVGNLP QGD++ F + + SVRLV+DKETD+FKGFCYVEF DVE+L++AL
Sbjct: 1 PFTAFVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE 60
Query: 73 KDGRITVDGLQVRLDIA 89
DG + D +R+DIA
Sbjct: 61 YDGAL-FDDRSLRVDIA 76
Score = 65.4 bits (160), Expect = 2e-14
Identities = 27/40 (67%), Positives = 35/40 (87%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI 222
++ SVRLV+DKETD+FKGFCYVEF DVE+L++AL DG +
Sbjct: 26 SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGAL 65
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic
translation initiation factor 4B (eIF-4B) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4B, a multi-domain RNA-binding protein that has
been primarily implicated in promoting the binding of
40S ribosomal subunits to mRNA during translation
initiation. It contains two RNA-binding domains; the
N-terminal well-conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), binds the 18S rRNA of the
40S ribosomal subunit and the C-terminal basic domain
(BD), including two arginine-rich motifs (ARMs), binds
mRNA during initiation, and is primarily responsible
for the stimulation of the helicase activity of eIF-4A.
eIF-4B also contains a DRYG domain (a region rich in
Asp, Arg, Tyr, and Gly amino acids) in the middle,
which is responsible for both, self-association of
eIF-4B and binding to the p170 subunit of eIF3.
Additional research indicates that eIF-4B can interact
with the poly(A) binding protein (PABP) in mammalian
cells, which can stimulate both, the eIF-4B-mediated
activation of the helicase activity of eIF-4A and
binding of poly(A) by PABP. eIF-4B has also been shown
to interact specifically with the internal ribosome
entry sites (IRES) of several picornaviruses which
facilitate cap-independent translation initiation. .
Length = 77
Score = 67.8 bits (166), Expect = 3e-15
Identities = 33/79 (41%), Positives = 50/79 (63%), Gaps = 4/79 (5%)
Query: 13 PYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQAL 71
PYTA++GNLP +T+ D++ FF + SVRL ++ + R +GF Y EF D ++L QAL
Sbjct: 1 PYTAYLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL 60
Query: 72 -LKDGRITVDGLQVRLDIA 89
L D + ++R+DIA
Sbjct: 61 SLNDESLK--NRRIRVDIA 77
Score = 37.7 bits (88), Expect = 3e-04
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 7/49 (14%)
Query: 184 LVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQAL------LKDGRITVD 225
+ SVRL ++ + R +GF Y EF D ++L QAL LK+ RI VD
Sbjct: 27 VSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRIRVD 75
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 63.6 bits (155), Expect = 1e-13
Identities = 31/61 (50%), Positives = 39/61 (63%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
T ++GNL IT+ DV FF ++ SVRL DKET FKGF +V+F D E+L AL D
Sbjct: 1 TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60
Query: 75 G 75
G
Sbjct: 61 G 61
Score = 45.1 bits (107), Expect = 6e-07
Identities = 21/35 (60%), Positives = 24/35 (68%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
SVRL DKET FKGF +V+F D E+L AL DG
Sbjct: 27 SVRLATDKETGEFKGFGHVDFADEESLDAALKLDG 61
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 62.6 bits (153), Expect = 2e-13
Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FVGNLP T+ ++ F K+ SVRLV+DKET + KGF +VEF E+ +AL
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 74 DGRITVDGLQVRL 86
+DG +++
Sbjct: 61 LNGKELDGRPLKV 73
Score = 44.5 bits (106), Expect = 1e-06
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ SVRLV+DKET + KGF +VEF E+ +AL +DG
Sbjct: 25 KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM2 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 73
Score = 60.8 bits (148), Expect = 1e-12
Identities = 29/72 (40%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGNL + + F E ++ SVRL D ++ R KGF YVEF E + AL G
Sbjct: 2 FVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALG 61
Query: 76 RITVDGLQVRLD 87
+ G VRLD
Sbjct: 62 GTDLLGRPVRLD 73
Score = 38.5 bits (90), Expect = 2e-04
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
SVRL D ++ R KGF YVEF E + AL
Sbjct: 26 SSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 57.3 bits (139), Expect = 2e-11
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FVGNL Q D+E FF E ++V VR+ +D + R KGF +VEF E ++AL K
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEK 59
Query: 74 DGRITVDGLQVRLDIA 89
G + G ++R+D+A
Sbjct: 60 SGE-ELLGREIRVDLA 74
Score = 32.7 bits (75), Expect = 0.026
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 221
+V VR+ +D + R KGF +VEF E ++AL K G
Sbjct: 25 EVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKSGE 62
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of
RBM23 remains unclear, it shows high sequence homology
to RBM39 and contains two RRMs. It may possibly
function as a pre-mRNA splicing factor. .
Length = 73
Score = 56.8 bits (138), Expect = 4e-11
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FV L + + D+ FF + K+ VR+++D+ + R KG YVEF D E++ AL
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60
Query: 74 DGRI 77
G+
Sbjct: 61 TGQR 64
Score = 43.0 bits (102), Expect = 4e-06
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI 222
VR+++D+ + R KG YVEF D E++ AL G+
Sbjct: 28 DVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTGQR 64
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 56.5 bits (137), Expect = 5e-11
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
+VGNLP +T+ D++ F ++ S R++ D+ET R +GF +VE E A+ K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 74 DGRITVDGLQVRLDIA 89
G + ++ A
Sbjct: 61 LNGTDFGGRTLTVNEA 76
Score = 40.3 bits (95), Expect = 4e-05
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
+ S R++ D+ET R +GF +VE E A+
Sbjct: 25 EVTSARVITDRETGRSRGFGFVEMETAEEANAAI 58
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 55.8 bits (135), Expect = 8e-11
Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL- 71
+ FVGNLP T D+ F SVRL+ DK+T + KG +VEF E + +AL
Sbjct: 1 FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60
Query: 72 -----LKDGRITVD 80
LK +I V+
Sbjct: 61 LHHTLLKGRKINVE 74
Score = 39.6 bits (93), Expect = 6e-05
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQAL------LKDGRITVD 225
SVRL+ DK+T + KG +VEF E + +AL LK +I V+
Sbjct: 28 PSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKINVE 74
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 72
Score = 55.7 bits (135), Expect = 1e-10
Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FV NL + + ++ + F + + VRLVK+ + + KG+ YVEF + E++++AL
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEESVQEALKL 59
Query: 74 DGRITVDG 81
D R + G
Sbjct: 60 D-RELIKG 66
Score = 45.3 bits (108), Expect = 7e-07
Identities = 17/44 (38%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ VRLVK+ + + KG+ YVEF + E++++AL D R + G
Sbjct: 25 EITDVRLVKNYKG-KSKGYAYVEFENEESVQEALKLD-RELIKG 66
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 54.1 bits (131), Expect = 3e-10
Identities = 29/70 (41%), Positives = 42/70 (60%), Gaps = 3/70 (4%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
+V NLP +T+ D+ FF P K+ VRLV++K DR +GF +VEF E+ AL K
Sbjct: 2 YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKLN 59
Query: 76 RITVDGLQVR 85
+ +DG +R
Sbjct: 60 GLVLDGRTLR 69
Score = 38.3 bits (90), Expect = 2e-04
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ VRLV++K DR +GF +VEF E+ AL K + +DG
Sbjct: 24 KVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKLNGLVLDG 65
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 54.1 bits (131), Expect = 4e-10
Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 2/73 (2%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
+ FVGNLP I + ++ + F + V +VR+V+D++T KGF YV F +++ AL
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60
Query: 74 DGRITVDGLQVRL 86
+G I + G ++R+
Sbjct: 61 NG-IKLKGRKIRV 72
Score = 36.8 bits (86), Expect = 8e-04
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
+VR+V+D++T KGF YV F +++ AL +G
Sbjct: 28 AVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands
and two helices arranged in an alpha/beta sandwich,
with a third helix present during RNA binding in some
cases The C-terminal beta strand (4th strand) and final
helix are hard to align and have been omitted in the
SEED alignment The LA proteins have an N terminal rrm
which is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 52.2 bits (126), Expect = 1e-09
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGNLP T+ D++ F + + S+R+V+D ET R KGF +VEF D E+ +AL
Sbjct: 2 FVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 76 RITVDGLQVR 85
+ G ++R
Sbjct: 61 GKELGGRELR 70
Score = 34.1 bits (79), Expect = 0.006
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
S+R+V+D ET R KGF +VEF D E+ +AL + G
Sbjct: 26 ESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALNGKELGG 66
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes
including mRNA and rRNA processing, RNA export, and RNA
stability. This domain is 90 amino acids in length and
consists of a four-stranded beta-sheet packed against
two alpha-helices. RRM usually interacts with ssRNA,
but is also known to interact with ssDNA as well as
proteins. RRM binds a variable number of nucleotides,
ranging from two to eight. The active site includes
three aromatic side-chains located within the conserved
RNP1 and RNP2 motifs of the domain. The RRM domain is
found in a variety heterogeneous nuclear
ribonucleoproteins (hnRNPs), proteins implicated in
regulation of alternative splicing, and protein
components of small nuclear ribonucleoproteins
(snRNPs).
Length = 72
Score = 51.9 bits (125), Expect = 2e-09
Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGNLP T+ D+ F + ++ SVR+V+DK + KGF +VEF E+ +AL
Sbjct: 2 FVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEALN 60
Query: 76 RITVDGLQVRLD 87
+DG ++++
Sbjct: 61 GKELDGRKLKVS 72
Score = 35.0 bits (81), Expect = 0.004
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ SVR+V+DK + KGF +VEF E+ +AL +DG
Sbjct: 24 EIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEALNGKELDG 66
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 55.7 bits (133), Expect = 3e-09
Identities = 35/170 (20%), Positives = 63/170 (37%), Gaps = 4/170 (2%)
Query: 9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 67
E T FVGNLP +T+ D+ F + + VRLV+D+ET + +GF +VEF E+
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESA 170
Query: 68 RQALLKDGRITVDGLQVRLDIA---DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGG 124
+A+ + ++G +R+ A R++ + + G + + +
Sbjct: 171 EKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYV 230
Query: 125 SFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDH 174
S G S G + + + D
Sbjct: 231 GNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDA 280
Score = 33.0 bits (74), Expect = 0.10
Identities = 15/42 (35%), Positives = 26/42 (61%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
VRLV+D+ET + +GF +VEF E+ +A+ + ++G
Sbjct: 143 KRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG 184
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 49.9 bits (120), Expect = 2e-08
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 8/72 (11%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD-------VENLR 68
++G LP +T+GD+ F + ++V + LV+DK+T + KGF ++ + D V+NL
Sbjct: 13 YIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLN 72
Query: 69 QALLKDGRITVD 80
L I VD
Sbjct: 73 GIKLLGRTIRVD 84
Score = 36.1 bits (84), Expect = 0.002
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVD-------VENLRQALLKDGRITVD 225
V + LV+DK+T + KGF ++ + D V+NL L I VD
Sbjct: 37 VDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRVD 84
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins.
This subfamily includes the RRM1 and RRM2 of
RNA-binding protein 5 (RBM5 or LUCA15 or H37) and
RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). These RBMs share high sequence homology and may
play an important role in regulating apoptosis. RBM5 is
a known modulator of apoptosis. It may also act as a
tumor suppressor or an RNA splicing factor. RBM6 has
been predicted to be a nuclear factor based on its
nuclear localization signal. Both, RBM6 and RBM5,
specifically bind poly(G) RNA. RBM10 is a paralog of
RBM5. It may play an important role in mRNA generation,
processing and degradation in several cell types. The
rat homolog of human RBM10 is protein S1-1, a
hypothetical RNA binding protein with poly(G) and
poly(U) binding capabilities. All family members
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a
G-patch/D111 domain. .
Length = 84
Score = 47.9 bits (115), Expect = 8e-08
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 20 NLPNGITQGDVERFF---PEQKLVSVRLVKDKETDRFKGFCYVEFVDVEN---LRQALLK 73
L T+ D+ + + VRL++DK T +GF +VEF +E+ AL
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 74 DGRITVDGLQVRLDIA 89
+DG VR+ A
Sbjct: 69 LDPFVIDGRVVRVSYA 84
Score = 43.3 bits (103), Expect = 4e-06
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVEN---LRQALLKDGRITVDG 226
+ VRL++DK T +GF +VEF +E+ AL +DG
Sbjct: 30 PIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDG 76
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 46.9 bits (112), Expect = 2e-07
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 15 TAFVGNLPNGITQGDVER-FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T ++G+L + + + F ++ SV+++++K+T + G+ +VEF E QAL
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
Score = 41.5 bits (98), Expect = 2e-05
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 179 TEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
E + SV+++++K+T + G+ +VEF E QAL
Sbjct: 21 AECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM1 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 46.5 bits (111), Expect = 3e-07
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FV NLP T +E FF E + +VKDK + + +GF YV F E+ ++AL +
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
Query: 74 DGRITVDGLQVRLDIADGK 92
+ G ++ ++ A K
Sbjct: 61 KKKTKFGGRKIHVEFAKKK 79
Score = 29.1 bits (66), Expect = 0.43
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 189 LVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+VKDK + + +GF YV F E+ ++AL + + G
Sbjct: 31 VVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGG 68
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 46.2 bits (110), Expect = 3e-07
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FVGNL + ++ F + +V R++ D+ET R +GF YV+F E+ ++A+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 74 DGRITVDGLQVRLDIA 89
+DG + +D +
Sbjct: 61 MDGKELDGRPINVDFS 76
Score = 36.2 bits (84), Expect = 0.001
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
T+V R++ D+ET R +GF YV+F E+ ++A+ +DG
Sbjct: 25 TVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDG 68
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed
in all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64
at U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation
in a more limited set of tissues and cell types,
largely in meiotic and postmeiotic male germ cells, and
to a lesser extent in brain. The loss of CSTF2T will
cause male infertility, as it is necessary for
spermatogenesis and fertilization. Moreover, CSTF2T is
required for expression of genes involved in
morphological differentiation of spermatids, as well as
for genes having products that function during
interaction of motile spermatozoa with eggs. It
promotes germ cell-specific patterns of polyadenylation
by using its RRM to bind to different sequence elements
downstream of polyadenylation sites than does CstF64.
The family also includes yeast ortholog mRNA
3'-end-processing protein RNA15 and similar proteins.
RNA15 is a core subunit of cleavage factor IA (CFIA),
an essential transcriptional 3'-end processing factor
from Saccharomyces cerevisiae. RNA recognition by CFIA
is mediated by an N-terminal RRM, which is contained in
the RNA15 subunit of the complex. The RRM of RNA15 has
a strong preference for GU-rich RNAs, mediated by a
binding pocket that is entirely conserved in both yeast
and vertebrate RNA15 orthologs.
Length = 75
Score = 45.7 bits (109), Expect = 5e-07
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGN+P T+ + F E +VS RLV D++T + KG+ + EF D+E A+
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 76 RITVDGLQVRLDIA 89
+G +R+D A
Sbjct: 62 GYEFNGRALRVDFA 75
Score = 36.4 bits (85), Expect = 0.001
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 180 EVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
EV +VS RLV D++T + KG+ + EF D+E A+
Sbjct: 21 EVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 48.0 bits (114), Expect = 1e-06
Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FV L + D+ FF + K+ V+ +KD+ + R KG YVEF DVE++ +AL
Sbjct: 91 TVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALAL 150
Query: 74 DG 75
G
Sbjct: 151 TG 152
Score = 43.7 bits (103), Expect = 3e-05
Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)
Query: 3 RNQKTLPTEPP--YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYV 59
+ P + P +VGNL IT+ ++ + F P + V+L +D ET R KGF ++
Sbjct: 174 KAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI 233
Query: 60 EFVDVENLRQALLKDGRITVDGLQVRLDIADG--KRNDNKGGFNNKQNRGGGSGGMGGNK 117
+F D E ++AL + G +++ A D F + + + +
Sbjct: 234 QFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEE 293
Query: 118 YNQHQGGSFNRDNMRNNSRGGGASSGGG-----FNDFSRGGEGPGGFR 160
Q R++ GG G G R G
Sbjct: 294 REQ-----LMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIP 336
Score = 36.0 bits (83), Expect = 0.012
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 179 TEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
++V + V+ +KD+ + R KG YVEF DVE++ +AL G
Sbjct: 111 SKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTG 152
Score = 32.2 bits (73), Expect = 0.22
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
+ V+L +D ET R KGF +++F D E ++AL
Sbjct: 213 IEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 44.4 bits (105), Expect = 2e-06
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T FV NL +TQ D+ FF + + +V D ET +G+ +V F +E+ ++AL K
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 74 DGRITVDGLQVRLDIA 89
+ G +RLDIA
Sbjct: 61 LKNKKLHGRILRLDIA 76
Score = 27.1 bits (60), Expect = 2.3
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 189 LVKDKETDRFKGFCYVEFVDVENLRQALLK 218
+V D ET +G+ +V F +E+ ++AL K
Sbjct: 31 VVTDPETGESRGYGFVTFAMLEDAQEALAK 60
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Although
the cellular function of RBM23 remains unclear, it
shows high sequence homology to RBM39 and contains two
RRMs. It may possibly function as a pre-mRNA splicing
factor. .
Length = 73
Score = 44.2 bits (105), Expect = 2e-06
Identities = 22/56 (39%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
+VGNL IT+ D+ F P ++ V+L +D ET R KG+ +++F D E+ ++AL
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57
Score = 34.5 bits (80), Expect = 0.005
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
V+L +D ET R KG+ +++F D E+ ++AL
Sbjct: 27 FVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 44.2 bits (105), Expect = 2e-06
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
FVGNLP + +++ +F + K+ S + DKET KG+ +V F + L AL K
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 74 DGRITVDG--LQVR 85
+ ++G LQV+
Sbjct: 61 Q-KHILEGNKLQVQ 73
Score = 33.0 bits (76), Expect = 0.017
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
S + DKET KG+ +V F + L AL K + ++G
Sbjct: 27 KSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ-KHILEG 67
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 43.4 bits (103), Expect = 3e-06
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 16 AFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
FV NLP T+ ++ F ++ V L DKET R KGF +V F+ E+ +A +
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 75 GRITVDG 81
G
Sbjct: 62 DGSIFQG 68
Score = 33.0 bits (76), Expect = 0.015
Identities = 15/44 (34%), Positives = 21/44 (47%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ V L DKET R KGF +V F+ E+ +A + G
Sbjct: 25 EISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQG 68
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 42.7 bits (101), Expect = 5e-06
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
T +V NLP +T D+ + F K+V V +VKDKET + KG ++ F+D E+ +
Sbjct: 3 TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59
Score = 30.4 bits (69), Expect = 0.18
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 215
+V V +VKDKET + KG ++ F+D E+ +
Sbjct: 27 KVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L)
and similar proteins. PABPs are highly conserved
proteins that bind to the poly(A) tail present at the
3' ends of most eukaryotic mRNAs. They have been
implicated in the regulation of poly(A) tail length
during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping.
ePABP-2 is predominantly located in the cytoplasm and
PABP-2 is located in the nucleus. In contrast to the
type I PABPs containing four copies of RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), the type II PABPs
contains a single highly-conserved RRM. This subfamily
also includes Saccharomyces cerevisiae RBP29 (SGN1,
YIR001C) gene encoding cytoplasmic mRNA-binding protein
Rbp29 that binds preferentially to poly(A). Although
not essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 42.7 bits (101), Expect = 6e-06
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGN+ G T +++ F ++ + ++ DK T + KGF Y+EF+D ++ ALL +
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
Score = 36.5 bits (85), Expect = 9e-04
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
T+ + ++ DK T + KGF Y+EF+D ++ ALL +
Sbjct: 25 TINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 42.4 bits (100), Expect = 8e-06
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 74
FV NLP + D+E+ F +L V + DK++ + KGF YV F+D E+ +A + D
Sbjct: 6 FVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELD 65
Query: 75 GRI 77
G++
Sbjct: 66 GKV 68
Score = 31.2 bits (71), Expect = 0.078
Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 187 VRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DGRI 222
V + DK++ + KGF YV F+D E+ +A + DG++
Sbjct: 32 VHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKV 68
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM3 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 41.4 bits (98), Expect = 2e-05
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 8/82 (9%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVEN----LR 68
T F+ NLP T+ +++ F Q ++ R+VKDK T KG +V+F E+ L
Sbjct: 2 TVFIRNLPFDATEEELKELF-SQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 69 QAL-LKDGRITVDGLQVRLDIA 89
A +D +++DG ++ + +A
Sbjct: 61 AADNAEDSGLSLDGRRLIVTLA 82
Score = 31.0 bits (71), Expect = 0.091
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVEN----LRQAL-LKDGRITVDG 226
R+VKDK T KG +V+F E+ L A +D +++DG
Sbjct: 29 YARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDG 74
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation
factor 64 kDa subunit (CstF64), is the vertebrate
conterpart of yeast mRNA 3'-end-processing protein
RNA15. It is expressed in all somatic tissues and is
one of three cleavage stimulatory factor (CstF)
subunits required for polyadenylation. CstF64 contains
an N-terminal RNA recognition motif (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a CstF77-binding domain, a repeated MEARA
helical region and a conserved C-terminal domain
reported to bind the transcription factor PC-4. During
polyadenylation, CstF interacts with the pre-mRNA
through the RRM of CstF64 at U- or GU-rich sequences
within 10 to 30 nucleotides downstream of the cleavage
site. CSTF2T, also termed tauCstF64, is a paralog of
the X-linked cleavage stimulation factor CstF64 protein
that supports polyadenylation in most somatic cells. It
is expressed during meiosis and subsequent haploid
differentiation in a more limited set of tissues and
cell types, largely in meiotic and postmeiotic male
germ cells, and to a lesser extent in brain. The loss
of CSTF2T will cause male infertility, as it is
necessary for spermatogenesis and fertilization.
Moreover, CSTF2T is required for expression of genes
involved in morphological differentiation of
spermatids, as well as for genes having products that
function during interaction of motile spermatozoa with
eggs. It promotes germ cell-specific patterns of
polyadenylation by using its RRM to bind to different
sequence elements downstream of polyadenylation sites
than does CstF64. .
Length = 75
Score = 41.3 bits (97), Expect = 2e-05
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGN+P T+ ++ F E +VS RLV D+ET + KG+ + E+ D E A+
Sbjct: 2 FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLN 61
Query: 76 RITVDGLQVRLDIA 89
++G Q+R+D A
Sbjct: 62 GYELNGRQLRVDNA 75
Score = 31.3 bits (71), Expect = 0.076
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 179 TEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
+EV +VS RLV D+ET + KG+ + E+ D E A+
Sbjct: 20 SEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 41.5 bits (98), Expect = 2e-05
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 11 EPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
+P T FVG L T+ + F + +RLV+D T KG+ +VE+ + +
Sbjct: 1 DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60
Query: 70 ALLKDGRITVDGLQVRLD 87
A ++ +DG ++ +D
Sbjct: 61 AYRDAHKLVIDGSEIFVD 78
Score = 30.3 bits (69), Expect = 0.19
Identities = 12/44 (27%), Positives = 23/44 (52%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ +RLV+D T KG+ +VE+ + +A ++ +DG
Sbjct: 29 DIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDG 72
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 40.6 bits (96), Expect = 3e-05
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
+VG+L +T+ + F P ++S+R+ +D T R G+ YV F + + +AL
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERAL 58
Score = 28.3 bits (64), Expect = 0.75
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
++S+R+ +D T R G+ YV F + + +AL
Sbjct: 25 PVLSIRVCRDLITRRSLGYAYVNFQNPADAERAL 58
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 40.5 bits (95), Expect = 4e-05
Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
+ FV LP +T+ ++E+ F + + SVRLV ++ + + KG YVE+ + + QA+
Sbjct: 2 KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60
Query: 72 LKDGRITVDGLQVR 85
LK +DG +++
Sbjct: 61 LK-----MDGTEIK 69
Score = 28.5 bits (64), Expect = 0.84
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ SVRLV ++ + + KG YVE+ + + QA+LK +
Sbjct: 28 VVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKMDGTEIKE 70
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 40.6 bits (95), Expect = 4e-05
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 17 FVGNLP-NGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGNL + +G F + VR+V+D +T+ KGF YV+F D + +ALL +
Sbjct: 3 FVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNE 62
Query: 76 R 76
+
Sbjct: 63 K 63
Score = 35.2 bits (81), Expect = 0.003
Identities = 15/36 (41%), Positives = 24/36 (66%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 221
VR+V+D +T+ KGF YV+F D + +ALL + +
Sbjct: 28 YVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEK 63
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 40.6 bits (95), Expect = 4e-05
Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
F+G L + +E+ F + +S V +VKD+ET R +GF +V F + ++ + A++
Sbjct: 4 FIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMN 63
Query: 76 RITVDGLQVRLDIA 89
+VDG Q+R+D A
Sbjct: 64 GKSVDGRQIRVDQA 77
Score = 31.4 bits (71), Expect = 0.075
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 187 VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
V +VKD+ET R +GF +V F + ++ + A++ +VDG
Sbjct: 30 VVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDG 69
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 39.9 bits (94), Expect = 6e-05
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FV L T+ ++E F ++ V L+KD ET +GF +V F VE+ A+
Sbjct: 5 FVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLN 64
Query: 76 RITVDGLQVRLDIA 89
++G ++++ A
Sbjct: 65 GKELEGRVIKVEKA 78
Score = 28.0 bits (63), Expect = 1.3
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVE 210
+ V L+KD ET +GF +V F VE
Sbjct: 27 RVEEVLLMKDPETGESRGFGFVTFESVE 54
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the
RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. SRSF12, also
termed 35 kDa SR repressor protein (SRrp35), or
splicing factor, arginine/serine-rich 13B (SFRS13B), or
splicing factor, arginine/serine-rich 19 (SFRS19), is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice
site of the adenovirus E1A pre-mRNA in vivo. Both,
SRSF10 and SRSF12, contain a single N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a C-terminal RS domain rich in serine-arginine
dipeptides. .
Length = 84
Score = 40.0 bits (94), Expect = 6e-05
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
+ +V N+ + D+ R F + +V V + D T R +GF YV+F DV + AL
Sbjct: 2 SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61
Query: 74 DGRITVDGLQVRLDIADGKR 93
R G ++ + A G R
Sbjct: 62 LDRTRFLGREIEIQFAQGDR 81
Score = 27.7 bits (62), Expect = 1.4
Identities = 16/43 (37%), Positives = 21/43 (48%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+V V + D T R +GF YV+F DV + AL R G
Sbjct: 27 IVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLG 69
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar
protein interacting with the FHA domain of pKI-67
(NIFK) and similar proteins. This subgroup corresponds
to the RRM of NIFK and Nop15p. NIFK, also termed MKI67
FHA domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also
includes Saccharomyces cerevisiae YNL110C gene encoding
ribosome biogenesis protein 15 (Nop15p), also termed
nucleolar protein 15. Both, NIFK and Nop15p, contain an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 39.5 bits (93), Expect = 9e-05
Identities = 16/51 (31%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 17 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVE 65
++G+LP+G + ++ ++F Q + +RL + K+T + KG+ +VEF E
Sbjct: 3 YIGHLPHGFYEPELRKYF-SQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52
Score = 30.6 bits (70), Expect = 0.099
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 174 HGLMVTEVT-------TLVSVRLVKDKETDRFKGFCYVEFVDVE 210
HG E+ T+ +RL + K+T + KG+ +VEF E
Sbjct: 9 HGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP
complex, which is one of the key factors facilitating
the splicing of pre-mRNA via interaction at the 5'
splice site, and is involved in regulation of
polyadenylation of some viral and cellular genes,
enhancing or inhibiting efficient poly(A) site usage.
U1-70K plays an essential role in targeting the U1
snRNP to the 5' splice site through protein-protein
interactions with regulatory RNA-binding splicing
factors, such as the RS protein ASF/SF2. Moreover,
U1-70K protein can specifically bind to stem-loop I of
the U1 small nuclear RNA (U1 snRNA) contained in the U1
snRNP complex. It also mediates the binding of U1C,
another U1-specific protein, to the U1 snRNP complex.
U1-70K contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region at the N-terminal half, and two
serine/arginine-rich (SR) domains at the C-terminal
half. The RRM is responsible for the binding of
stem-loop I of U1 snRNA molecule. Additionally, the
most prominent immunodominant region that can be
recognized by auto-antibodies from autoimmune patients
may be located within the RRM. The SR domains are
involved in protein-protein interaction with SR
proteins that mediate 5' splice site recognition. For
instance, the first SR domain is necessary and
sufficient for ASF/SF2 Binding. The family also
includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but
its SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 39.5 bits (93), Expect = 1e-04
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL-L 72
T FV L T+ + R F E + +RLV+DK+T + +G+ ++EF +++ A
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62
Query: 73 KDGRITVDGLQVRLDIADGK 92
DG +DG +V +D+ G+
Sbjct: 63 ADG-KKIDGRRVLVDVERGR 81
Score = 32.2 bits (74), Expect = 0.040
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQAL-------LKDGRITVD 225
+RLV+DK+T + +G+ ++EF +++ A + R+ VD
Sbjct: 30 RIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGRRVLVD 76
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 38.8 bits (91), Expect = 1e-04
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
FVG L +T+ D+ +F + + SV +V DKET + +GF +V F D + + + +L+
Sbjct: 3 FVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Score = 32.6 bits (75), Expect = 0.023
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
+ SV +V DKET + +GF +V F D + + + +L+
Sbjct: 25 NVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 38.8 bits (90), Expect = 2e-04
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
FVG++P IT+ +V F E ++ V ++KDK T +G C+V++ + +A+
Sbjct: 3 FVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
Score = 26.9 bits (59), Expect = 3.1
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 177 MVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
M E ++ V ++KDK T +G C+V++ + +A+
Sbjct: 19 MFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 77
Score = 38.4 bits (90), Expect = 2e-04
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
F+G LPN +++ V E KL + LVKD T KG+ + E++D
Sbjct: 4 FIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPS 53
Score = 30.3 bits (69), Expect = 0.17
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVE 210
L + LVKD T KG+ + E++D
Sbjct: 27 LKAFNLVKDSATGLSKGYAFCEYLDPS 53
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2),
TRA2-alpha, TRA2-beta (also termed SFRS10), and similar
proteins found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent
GnRH pre-mRNA splicing. TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. Both, TRA2-alpha and TRA2-beta, contains a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), flanked by the N- and C-terminal
arginine/serine (RS)-rich regions. .
Length = 78
Score = 38.4 bits (90), Expect = 2e-04
Identities = 19/59 (32%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 31 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 89
R+ P +K V++V D++T R +GF +V F VE+ ++A + + +DG ++R+D +
Sbjct: 21 SRYGPIEK---VQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 76
Score = 32.2 bits (74), Expect = 0.034
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
V++V D++T R +GF +V F VE+ ++A + + +DG
Sbjct: 28 KVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDG 68
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0, a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. It has also been identified
as an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 38.1 bits (89), Expect = 3e-04
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVG L T+ + +F + +V + L DK+T++ +GFC++ F D E + +L+
Sbjct: 3 FVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF-DSEEPVKKILETQ 61
Query: 76 RITVDGLQVRLDIA 89
+ G +V + A
Sbjct: 62 FHVIGGKKVEVKKA 75
Score = 28.1 bits (63), Expect = 0.91
Identities = 12/35 (34%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
+V + L DK+T++ +GFC++ F D E + +L+
Sbjct: 26 IVEIELPMDKKTNKRRGFCFITF-DSEEPVKKILE 59
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 37.7 bits (88), Expect = 3e-04
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T VG + +++ D++ FF V+ VRL D++ F +VEF D E+ AL
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHS--ARFAFVEFADAESALSALNL 59
Query: 74 DG 75
G
Sbjct: 60 SG 61
Score = 25.8 bits (57), Expect = 6.3
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
VRL D++ F +VEF D E+ AL G
Sbjct: 28 TRVRLCGDRQHS--ARFAFVEFADAESALSALNLSG 61
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 37.2 bits (87), Expect = 4e-04
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
T V NLP T+ + +FF + +R VK E++ +EF + AL KD
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCG--EIREVKIVESEGGL-VAVIEFETEDEALAALTKD 58
Query: 75 GR 76
+
Sbjct: 59 HK 60
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM2 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal, highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 80
Score = 37.8 bits (87), Expect = 4e-04
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
+ FVG+L IT D++ F P K+ R+VKD T + KG+ +V F + + A++
Sbjct: 2 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61
Query: 73 KDGRITVDGLQVRLDIA 89
G + G Q+R + A
Sbjct: 62 HMGGQWLGGRQIRTNWA 78
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33
(Cyp33) and similar proteins. This subfamily
corresponds to the RRM of Cyp33, also termed
peptidyl-prolyl cis-trans isomerase E (PPIase E), or
cyclophilin E, or rotamase E. Cyp33 is a nuclear
RNA-binding cyclophilin with an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal PPIase domain. Cyp33 possesses RNA-binding
activity and preferentially binds to polyribonucleotide
polyA and polyU, but hardly to polyG and polyC. It
binds specifically to mRNA, which can stimulate its
PPIase activity. Moreover, Cyp33 interacts with the
third plant homeodomain (PHD3) zinc finger cassette of
the mixed lineage leukemia (MLL) proto-oncoprotein and
a poly-A RNA sequence through its RRM domain. It
further mediates downregulation of the expression of
MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a
proline isomerase-dependent manner. Cyp33 also
possesses a PPIase activity that catalyzes cis-trans
isomerization of the peptide bond preceding a proline,
which has been implicated in the stimulation of folding
and conformational changes in folded and unfolded
proteins. The PPIase activity can be inhibited by the
immunosuppressive drug cyclosporin A. .
Length = 73
Score = 37.2 bits (87), Expect = 5e-04
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
+VG L + + + F P + +++ D ET + +GF +VEF + E+ A+
Sbjct: 2 YVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57
Score = 31.4 bits (72), Expect = 0.051
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
+ +++ D ET + +GF +VEF + E+ A+
Sbjct: 25 IKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 37.7 bits (87), Expect = 5e-04
Identities = 21/50 (42%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVD 63
T F L I D+E FF K+ VR++ D+ + R KG YVEFVD
Sbjct: 3 TVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVD 52
Score = 30.8 bits (69), Expect = 0.15
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 187 VRLVKDKETDRFKGFCYVEFVD 208
VR++ D+ + R KG YVEFVD
Sbjct: 31 VRMISDRNSRRSKGIAYVEFVD 52
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the
RRM of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). This
family also includes yeast eIF3-p33, a homolog of
vertebrate eIF-3G, plays an important role in the
initiation phase of protein synthesis in yeast. It
binds both, mRNA and rRNA, fragments due to an RRM near
its C-terminus. .
Length = 77
Score = 37.1 bits (87), Expect = 5e-04
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 18 VGNLPNGITQGDVER-FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DG 75
V NL + D+ F P + V L KDKET + +GF +V F E+ +A+ K +G
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Query: 76 R 76
Sbjct: 64 F 64
Score = 32.1 bits (74), Expect = 0.033
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 187 VRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DGR 221
V L KDKET + +GF +V F E+ +A+ K +G
Sbjct: 29 VYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 37.2 bits (87), Expect = 6e-04
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 17 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
FVG LP T + ++F Q ++ ++ D++T + +G+ +V F D E+ +A KD
Sbjct: 4 FVGGLPYHTTDDSLRKYF-SQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA-CKD 61
Query: 75 GRITVDG 81
+DG
Sbjct: 62 PNPIIDG 68
Score = 31.0 bits (71), Expect = 0.086
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 189 LVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
++ D++T + +G+ +V F D E+ +A KD +DG
Sbjct: 32 VITDRQTGKSRGYGFVTFKDKESAERA-CKDPNPIIDG 68
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 37.1 bits (86), Expect = 7e-04
Identities = 12/52 (23%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
++G+LP+G + +++++F + + +VR+ + K+T K + +++F++ E
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPE 52
Score = 28.6 bits (64), Expect = 0.63
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 174 HGLMVTEVTTLVS-------VRLVKDKETDRFKGFCYVEFVDVE 210
HG + E+ S VR+ + K+T K + +++F++ E
Sbjct: 9 HGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPE 52
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein
42 (RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 83
Score = 36.8 bits (86), Expect = 8e-04
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 14 YTAFVGNLPNGITQGDVERFFPEQK-LVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
+ FVG+L N +T + R F + ++V+DK T + KG+ +V F D + +A+
Sbjct: 7 FRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAM 65
Score = 28.3 bits (64), Expect = 0.81
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 182 TTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
+ ++V+DK T + KG+ +V F D + +A+
Sbjct: 31 PSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAM 65
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 36.5 bits (85), Expect = 9e-04
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 20 NLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
N+P +T+G+V FF + + ++ DK T + G YVEFV E+ +A
Sbjct: 6 NIPFDVTKGEVLAFFAGIAIAEQGIHILYDK-TGKTLGEAYVEFVSEEDAMRAE 58
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 36.6 bits (84), Expect = 0.001
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
+ FVG+L IT D++ F P ++ R+VKD T + KG+ +V F + + A+
Sbjct: 2 FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61
Query: 73 KDGRITVDGLQVRLDIA 89
+ G + G Q+R + A
Sbjct: 62 QMGGQWLGGRQIRTNWA 78
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM2 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 80
Score = 36.5 bits (85), Expect = 0.001
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 14 YTAFVGNLPNGITQGDVERFFPEQKLVSVRLVK---DKETDRFKGFCYVEFVDVENLRQA 70
++ FVG+L +T ++ F + SVR K D T R KG+ +V F D + +A
Sbjct: 2 HSIFVGDLAPDVTDYMLQETF-RARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60
Query: 71 L 71
L
Sbjct: 61 L 61
Score = 29.2 bits (66), Expect = 0.38
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 172 NDHGLMVTEVTTLVSVRLVK---DKETDRFKGFCYVEFVDVENLRQAL 216
D+ L T SVR K D T R KG+ +V F D + +AL
Sbjct: 14 TDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds
to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share
high sequence similarity and are expressed in a wide
variety of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains. This subfamily also
includes a yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1, termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein, which has been identified as
both a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP).
It may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. PUB1 is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it
is one of the major cellular proteins cross-linked by
UV light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there
is no strong evidence implicating PUB1 in the mechanism
of DNA replication. PUB1 contains three RRMs, and a GAR
motif (glycine and arginine rich stretch) that is
located between RRM2 and RRM3. .
Length = 73
Score = 36.1 bits (84), Expect = 0.001
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 7/48 (14%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEF 61
T +VGNLP+G+T+ +++R F + VR+ KD KG+ +V F
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRF 43
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins.
This subgroup corresponds to the RRM1 of SF2, also
termed SR1 protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal domain rich in proline, serine
and lysine residues (PSK domain), a composition
reminiscent of histones. This PSK domain harbors a
putative phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 35.9 bits (83), Expect = 0.002
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 15 TAFVGNLPNGITQGDVER-FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T +VGNLP I + +VE F+ +V + L K R G+ ++EF D + A+
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57
Query: 74 DGRITVDGLQVRLDI 88
DG ++R+++
Sbjct: 58 RDGYDFDGQRLRVEL 72
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 35.6 bits (83), Expect = 0.002
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 20 NLPNGITQGDVERFF--PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
LP T+ D+ FF + + +V D + R G YVEF E+ R+AL K
Sbjct: 6 GLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDG-RPTGEAYVEFASPEDARRALRKHNN 63
Score = 29.8 bits (68), Expect = 0.19
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 221
+ +V D + R G YVEF E+ R+AL K
Sbjct: 29 GIHIVYDDDG-RPTGEAYVEFASPEDARRALRKHNN 63
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 82
Score = 36.0 bits (84), Expect = 0.002
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 19/82 (23%)
Query: 17 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 64
+VGNLP GIT+ ++ FF P ++SV++ +K F +VEF V
Sbjct: 5 YVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN------FAFVEFRTV 58
Query: 65 ENLRQALLKDGRITVDGLQVRL 86
E AL DG I G +++
Sbjct: 59 EEATAALALDG-IIFKGQPLKI 79
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19). SRSF12 is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates
distal alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. SRSF12 contains a single N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
followed by a C-terminal RS domain rich in
serine-arginine dipeptides. .
Length = 84
Score = 35.8 bits (82), Expect = 0.002
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FV N+ + D+ R F +V V + D T R +GF Y++F DV + AL
Sbjct: 4 FVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLN 63
Query: 76 RITVDGLQVRLDIADGKR 93
R V G Q+ + A G R
Sbjct: 64 RKWVCGRQIEIQFAQGDR 81
Score = 25.7 bits (56), Expect = 8.7
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+V V + D T R +GF Y++F DV + AL R V G
Sbjct: 27 IVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKWVCG 69
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 35.6 bits (83), Expect = 0.002
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ--KLVSVRL--VKDKETDRFKGFCYVEFVDVENLRQA 70
T +V N P Q D+ F EQ +++S+R ++ +T RF CYV+F E+ A
Sbjct: 2 TLWVTNFPPSFDQSDIRDLF-EQYGEILSIRFPSLRFNKTRRF---CYVQFTSPESAAAA 57
Query: 71 LLKDGRITVDG--LQVRL 86
+ +G L V++
Sbjct: 58 VALLNGKLGEGYKLVVKI 75
Score = 26.4 bits (59), Expect = 3.6
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 180 EVTTLVSVRL--VKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL 227
+ ++S+R ++ +T RF CYV+F E+ A+ +G
Sbjct: 23 QYGEILSIRFPSLRFNKTRRF---CYVQFTSPESAAAAVALLNGKLGEGY 69
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate
probable RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 35.8 bits (82), Expect = 0.002
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
T F L I D+E FF K+ VR++ D+ + R KG YVEF +++++ A+
Sbjct: 3 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60
Score = 29.2 bits (65), Expect = 0.43
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 187 VRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
VR++ D+ + R KG YVEF +++++ A+
Sbjct: 31 VRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of SRSF10, also termed 40 kDa SR-repressor protein
(SRrp40), or FUS-interacting serine-arginine-rich
protein 1 (FUSIP1), or splicing factor SRp38, or
splicing factor, arginine/serine-rich 13A (SFRS13A), or
TLS-associated protein with Ser-Arg repeats (TASR).
SRSF10 is a serine-arginine (SR) protein that acts as a
potent and general splicing repressor when
dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. It contains a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 35.7 bits (82), Expect = 0.002
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FV N+ + D+ R F +V V + D T R +GF YV+F DV + AL
Sbjct: 4 FVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLD 63
Query: 76 RITVDGLQVRLDIADGKR 93
R + G Q+ + A G R
Sbjct: 64 RKWICGRQIEIQFAQGDR 81
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway; it binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 75
Score = 34.7 bits (80), Expect = 0.004
Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVG LP +T+ + + +F + K+V +L++D +T R +GF +V F D E+ + + G
Sbjct: 3 FVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSAG 61
Query: 76 RITVDGLQV 84
+ + G QV
Sbjct: 62 MLELGGKQV 70
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM1 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 91
Score = 34.9 bits (81), Expect = 0.005
Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 21/92 (22%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRL----------------VKDKETDRFKGFC 57
T FVGNLP + D+++ F + + SVR +K K D+ K
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDK-KDNV 60
Query: 58 --YVEFVDVENLRQALLKDGRITVDGLQVRLD 87
YV F + E+ +AL +G +G +R+D
Sbjct: 61 NAYVVFKEEESAEKALKLNGT-EFEGHHIRVD 91
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 34.4 bits (79), Expect = 0.006
Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
+VGN+ G T ++E F V+ V ++ DK + KGF Y+EF D E++R AL D
Sbjct: 3 YVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDE 62
Query: 76 RI 77
+
Sbjct: 63 SL 64
Score = 30.5 bits (69), Expect = 0.14
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 187 VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI 222
V ++ DK + KGF Y+EF D E++R AL D +
Sbjct: 29 VTILCDKFSGHPKGFAYIEFSDKESVRTALALDESL 64
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2
protein homolog alpha (TRA-2 alpha) and similar
proteins. This subgroup corresponds to the RRM of
TRA2-alpha or TRA-2-alpha, also termed transformer-2
protein homolog A, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein (SRp40) that
specifically binds to gonadotropin-releasing hormone
(GnRH) exonic splicing enhancer on exon 4 (ESE4) and is
necessary for enhanced GnRH pre-mRNA splicing. It
strongly stimulates GnRH intron A excision in a
dose-dependent manner. In addition, TRA2-alpha can
interact with either 9G8 or SRp30c, which may also be
crucial for ESE-dependent GnRH pre-mRNA splicing.
TRA2-alpha contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 79
Score = 34.6 bits (79), Expect = 0.006
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 26 TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV 84
T+ D+ F L V +V D+ T R +GF +V F +++ ++A+ + +DG ++
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71
Query: 85 RLD 87
R+D
Sbjct: 72 RVD 74
Score = 28.8 bits (64), Expect = 0.54
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
L V +V D+ T R +GF +V F +++ ++A+ + +DG
Sbjct: 26 LAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDG 68
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has
been identified as a regulator of the hematopoietic
stem cell (HSC) compartment and of leukemic stem cells
after transplantation of cells with loss and gain of
function of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 34.3 bits (79), Expect = 0.007
Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEF 61
FVG L T+ DV+++F + K+ L+ DK+T+R +GF +V F
Sbjct: 3 FVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 34.1 bits (79), Expect = 0.008
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 18 VGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFV---DVENLRQAL 71
V N+P T+ ++ F P ++ SVRL K K +GF +VEFV + +N +AL
Sbjct: 5 VRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEAL 61
Score = 29.9 bits (68), Expect = 0.21
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFV---DVENLRQAL 216
+ SVRL K K +GF +VEFV + +N +AL
Sbjct: 26 QVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEAL 61
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding
protein 19 (RBM19) and similar proteins. This
subfamily corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 33.5 bits (77), Expect = 0.009
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 21 LPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
P + + + FF K V++R+VK+ + GF +V+ E+L++AL ++
Sbjct: 8 APFNVKEKHIREFFSPLKPVAIRIVKNDHGRK-TGFAFVDLKSEEDLKKALKRNK 61
Score = 26.2 bits (58), Expect = 4.5
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
V++R+VK+ + GF +V+ E+L++AL ++
Sbjct: 25 KPVAIRIVKNDHGRK-TGFAFVDLKSEEDLKKALKRNK 61
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic
RNA-binding protein 25 and similar proteins. This
subfamily corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or
protein S164, or RNA-binding region-containing protein
7, an evolutionary-conserved splicing coactivator
SRm160 (SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif.
It localizes to the nuclear speckles and associates
with multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors.
It can activate proapoptotic Bcl-xS 5'ss by binding to
the exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 34.1 bits (79), Expect = 0.009
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
T FVGN+P G++ + + + K++S + VKD T + K F + EF D E +AL
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRAL 59
Score = 25.6 bits (57), Expect = 8.0
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
++S + VKD T + K F + EF D E +AL
Sbjct: 27 VLSWKRVKDPSTGKLKAFGFCEFEDPEGALRAL 59
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 81
Score = 33.5 bits (77), Expect = 0.011
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 12 PPYTAFVGNLPNGITQGD----VERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
P T + LP +T+ D + E K VRL++ K T +GF +VEF+ +E
Sbjct: 1 PNNTIMLRGLPLSVTEEDIRNALVSHGVEPK--DVRLMRRKTTGASRGFAFVEFMSLE 56
Score = 32.0 bits (73), Expect = 0.047
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVE 210
N++ HG+ VRL++ K T +GF +VEF+ +E
Sbjct: 21 NALVSHGV------EPKDVRLMRRKTTGASRGFAFVEFMSLE 56
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 35.9 bits (83), Expect = 0.012
Identities = 18/74 (24%), Positives = 25/74 (33%), Gaps = 8/74 (10%)
Query: 101 NNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEG--PGG 158
N +Q RGGG G GG + Q R R AS+ R G+ G
Sbjct: 389 NGRQQRGGGGRGQGG---GRGQQQGQPR---RGEGGAKSASAKPAEKPSRRLGDAKPAGE 442
Query: 159 FRNNNGPNRSNSMN 172
+ P + +
Sbjct: 443 QQRRRRPRKPAAAQ 456
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate
nucleolin. This subfamily corresponds to the RRM2 of
ubiquitously expressed protein nucleolin, also termed
protein C23, a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines.RRM2,
together with RRM1, binds specifically to RNA
stem-loops containing the sequence (U/G)CCCG(A/G) in
the loop. .
Length = 77
Score = 33.7 bits (77), Expect = 0.012
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
T FV NLP IT +++ F + V +RL K+ KG Y+EF +AL +
Sbjct: 5 TLFVKNLPYNITVDELKEVF--EDAVDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALEEK 61
Query: 75 GRITVDGLQVRLD 87
VDG + +D
Sbjct: 62 QGAEVDGRSIVVD 74
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 33.5 bits (77), Expect = 0.013
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
F+ NL T+ D+E+ F + L V L DK T + KGF +V ++ E+ +A
Sbjct: 6 FIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 33.5 bits (77), Expect = 0.013
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 12 PPYTAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
PP + +T+ D+ E F P ++ + +VKDK+T KG YV+F
Sbjct: 1 PPNSRLFIVCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF 51
Score = 30.4 bits (69), Expect = 0.17
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 186 SVRLVKDKETDRFKGFCYVEF 206
+ +VKDK+T KG YV+F
Sbjct: 31 DIWVVKDKQTKESKGVAYVKF 51
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 33.5 bits (77), Expect = 0.014
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
T +V LP T ++ F + V V L + K T KGF ++EF E ++A
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58
Score = 29.3 bits (66), Expect = 0.35
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
T+V V L + K T KGF ++EF E ++A
Sbjct: 25 TVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate
nucleolin. This subfamily corresponds to the RRM4 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 78
Score = 33.4 bits (76), Expect = 0.015
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA--LL 72
T FV L T+ ++ F ++ R+V D++T KGF +V+F E+ + A +
Sbjct: 2 TLFVKGLSEDTTEETLKESF--DGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 73 KDGRITVDGLQVRLDIADGK 92
+DG I DG +V LD A K
Sbjct: 60 EDGEI--DGNKVTLDFAKPK 77
Score = 27.2 bits (60), Expect = 1.8
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQA--LLKDGRI 222
++ R+V D++T KGF +V+F E+ + A ++DG I
Sbjct: 25 IAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEI 64
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 35.6 bits (82), Expect = 0.016
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 17 FVGNLPNGITQGDV----ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
++GNLP + + + E F L + L+KD T KG+ + E+ D A+
Sbjct: 299 YIGNLPLYLGEDQIKELLESFGD---LKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354
Score = 34.9 bits (80), Expect = 0.032
Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 9/69 (13%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRF--------KGFCYVEFVDVENLR 68
+VG +P + V FF +++ K ++ K F ++EF VE
Sbjct: 179 YVGGIPPEFVEEAVVDFF-NDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEAT 237
Query: 69 QALLKDGRI 77
A+ D I
Sbjct: 238 FAMALDSII 246
Score = 28.7 bits (64), Expect = 2.6
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
L + L+KD T KG+ + E+ D A+
Sbjct: 322 LKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 33.8 bits (77), Expect = 0.016
Identities = 27/84 (32%), Positives = 33/84 (39%), Gaps = 9/84 (10%)
Query: 14 YTAFVGNLPNGITQGDVERFFPEQKLVSVR---LVKDKETDRFKGFCYVEFVDVENLRQA 70
+T FV NLP T+ + F K SVR V DK T R KG +V F D
Sbjct: 2 FTLFVRNLPYDATEESLAPHF--SKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59
Query: 71 LLKDGRI----TVDGLQVRLDIAD 90
L + G + DI D
Sbjct: 60 LKNAPAAGSTSLLSGSSLTADIGD 83
Score = 27.6 bits (61), Expect = 2.2
Identities = 11/29 (37%), Positives = 12/29 (41%)
Query: 188 RLVKDKETDRFKGFCYVEFVDVENLRQAL 216
V DK T R KG +V F D L
Sbjct: 32 LPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 33.2 bits (76), Expect = 0.016
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 7/70 (10%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-- 73
FVG L TQ + R+F + ++V ++KDK T+R +GF +V+F D + L
Sbjct: 3 FVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGP 62
Query: 74 ---DGRITVD 80
DGR T+D
Sbjct: 63 HTLDGR-TID 71
Score = 26.7 bits (59), Expect = 3.1
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 189 LVKDKETDRFKGFCYVEFVDVENLRQALLK-----DGRITVD 225
++KDK T+R +GF +V+F D + L DGR T+D
Sbjct: 31 IMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGR-TID 71
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 34.2 bits (78), Expect = 0.019
Identities = 25/100 (25%), Positives = 45/100 (45%), Gaps = 1/100 (1%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
F+G L G + F +V +++ D+ET R +GF +V F D A+ +
Sbjct: 38 FIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMD 97
Query: 76 RITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGG 115
++G +R++ A+ + + + GGG G GG
Sbjct: 98 GKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGG 137
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is ubiquitously expressed Hu family member. It has
a variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the
cytoplasm, Hu proteins recognize and bind to AU-rich
RNA elements (AREs) in the 3' untranslated regions
(UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. This family
also includes the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own
pre-mRNA and promotes female-specific alternative
splicing. It contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 77
Score = 32.7 bits (75), Expect = 0.022
Identities = 18/69 (26%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 18 VGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
V LP +TQ ++ F + S ++V+D+ T + G+ +V++VD + ++A+
Sbjct: 5 VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN---- 60
Query: 77 ITVDGLQVR 85
T++G ++R
Sbjct: 61 -TLNGFEIR 68
Score = 27.7 bits (62), Expect = 1.4
Identities = 9/31 (29%), Positives = 22/31 (70%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
S ++V+D+ T + G+ +V++VD + ++A+
Sbjct: 29 SCKIVRDRITGQSLGYGFVDYVDENDAQKAI 59
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 80
Score = 32.7 bits (75), Expect = 0.023
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVG LP +T+ D+ ++F + V+ V ++ D E R +GF ++ F +++ Q + +
Sbjct: 6 FVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE-H 64
Query: 76 RITVDGLQV 84
++G +V
Sbjct: 65 FHDINGKKV 73
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 32.7 bits (75), Expect = 0.025
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 11/57 (19%)
Query: 28 GDVERFFPE-----------QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
GD+E + E + ++SV+++++K T G+C+VEF D + L K
Sbjct: 5 GDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61
Score = 32.3 bits (74), Expect = 0.041
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
T++SV+++++K T G+C+VEF D + L K
Sbjct: 26 TVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 32.7 bits (74), Expect = 0.027
Identities = 17/65 (26%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 26 TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV 84
T+ D+ F + + V +V D+++ R +GF +V F +V++ ++A + + +DG ++
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81
Query: 85 RLDIA 89
R+D +
Sbjct: 82 RVDFS 86
Score = 27.3 bits (60), Expect = 2.4
Identities = 12/43 (27%), Positives = 27/43 (62%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+ V +V D+++ R +GF +V F +V++ ++A + + +DG
Sbjct: 36 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 78
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 of Nop13p
encoded by YNL175c from Saccharomyces cerevisiae. It
shares high sequence similarity with nucleolar protein
12 (Nop12p). Both, Nop12p and Nop13p, are not essential
for growth. However, unlike Nop12p that is localized to
the nucleolus, Nop13p localizes primarily to the
nucleolus but is also present in the nucleoplasm to a
lesser extent. Nop13p contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 85
Score = 32.5 bits (74), Expect = 0.028
Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 12/67 (17%)
Query: 17 FVGNLPNGITQGDVERFF---------PEQ-KLVSVRLVKDKETDRF--KGFCYVEFVDV 64
++GNL T+ + +FF EQ V + K K KGF YV+F
Sbjct: 2 WIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTSQ 61
Query: 65 ENLRQAL 71
E + A+
Sbjct: 62 EATKAAI 68
Score = 27.9 bits (62), Expect = 1.3
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 172 NDHGLMVTEVTTLVSVRLVKDKETDRF--KGFCYVEFVDVENLRQAL 216
+ E T V + K K KGF YV+F E + A+
Sbjct: 22 KSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTSQEATKAAI 68
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 32.1 bits (74), Expect = 0.031
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 38 KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL--LKDGRITVDGLQVR 85
+ V L D+E + +G+ YVEF E+ +A+ + G+I DG +V
Sbjct: 24 TVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQI--DGQEVT 71
Score = 30.6 bits (70), Expect = 0.13
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
T+ V L D+E + +G+ YVEF E+ +A+
Sbjct: 24 TVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAI 57
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 32.3 bits (73), Expect = 0.033
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
FVG L T+ ++ +F ++ ++ L D +T+ +GFC+V + D E +++ L
Sbjct: 3 FVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL 58
Score = 26.9 bits (59), Expect = 2.7
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
++ L D +T+ +GFC+V + D E +++ L
Sbjct: 28 NIELPMDTKTNERRGFCFVTYTDEEPVQKLL 58
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It binds with high affinity
to A/U-rich stretches of RNA, and to A/T-rich DNA
sequences, and functions as a regulator of cytoplasmic
activity. RBMS3 contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 80
Score = 32.5 bits (73), Expect = 0.034
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
++ LP G T D+ + P K+VS + + DK T++ KG+ +V+F
Sbjct: 8 YIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDF 53
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 32.0 bits (73), Expect = 0.035
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVG+L I + F P ++ R+VKD +T + KG+ +V FV E+ A+
Sbjct: 3 FVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMN 62
Query: 76 RITVDGLQVR 85
+ G +R
Sbjct: 63 GQWLGGRAIR 72
Score = 25.8 bits (57), Expect = 5.8
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 186 SVRLVKDKETDRFKGFCYVEFV---DVEN 211
R+VKD +T + KG+ +V FV D EN
Sbjct: 28 DARVVKDMQTGKSKGYGFVSFVKKEDAEN 56
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise
role of PPIase remains unclear. PPIase contains a
conserved N-terminal peptidyl-prolyl cistrans isomerase
(PPIase) motif, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 32.2 bits (74), Expect = 0.036
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 12 PPYTAFVGNLPNGITQ-GDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
P FV L N +T D+E F K+ S +++DK+T + ++EF E+ +
Sbjct: 2 PENVLFVCKL-NPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60
Query: 70 ALLK-------DGRITVD 80
A K D RI VD
Sbjct: 61 AYFKMDNVLIDDRRIHVD 78
Score = 30.3 bits (69), Expect = 0.17
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 7/50 (14%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-------DGRITVD 225
+ S +++DK+T + ++EF E+ +A K D RI VD
Sbjct: 29 KIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHVD 78
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 32.3 bits (74), Expect = 0.036
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 11/73 (15%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVK--DKETDRFKGFCYVEFVDVENLRQAL- 71
T +VGNL T + FF + V+ V+ ET + +VEF + ++ AL
Sbjct: 6 TIYVGNLDPTTTADQLLEFF--SQAGEVKYVRMAGDETQ-PTRYAFVEFAEQTSVINALK 62
Query: 72 -----LKDGRITV 79
+ V
Sbjct: 63 LNGAMFGGRPLKV 75
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to
the RRM domain in the G3BP family of RNA-binding and
SH3 domain-binding proteins. G3BP acts at the level of
RNA metabolism in response to cell signaling, possibly
as RNA transcript stabilizing factors or an RNase.
Members include G3BP1, G3BP2 and similar proteins.
These proteins associate directly with the SH3 domain
of GTPase-activating protein (GAP), which functions as
an inhibitor of Ras. They all contain an N-terminal
nuclear transfer factor 2 (NTF2)-like domain, an acidic
domain, a domain containing PXXP motif(s), an RNA
recognition motif (RRM), and an Arg-Gly-rich region
(RGG-rich region, or arginine methylation motif).
Length = 81
Score = 32.0 bits (73), Expect = 0.041
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
FVGNLP+ IT+ +++ FF E ++ VR+ R F +V F D E +++ L
Sbjct: 7 FVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 31.8 bits (73), Expect = 0.042
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 17 FVGNLPNGITQGD-VERFFPEQKLVSVRLVKDKETDRFKGFCYVEF-VDVENLRQAL 71
FVG L +T+ D ERF + V ++K K+ +GF Y++ L++
Sbjct: 3 FVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCK 59
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 34.3 bits (78), Expect = 0.046
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 89 ADGKRND---NKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGG 145
A+GK N+ K +N Q + G G +K Q GG R R RGGG G G
Sbjct: 481 ANGKGNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGG---RGRTRGRGRGGGGGRGRG 537
Query: 146 FN 147
+N
Sbjct: 538 YN 539
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p
encoded by YNL175c from Saccharomyces cerevisiae. It
shares high sequence similarity with nucleolar protein
12 (Nop12p). Both Nop12p and Nop13p are not essential
for growth. However, unlike Nop12p that is localized to
the nucleolus, Nop13p localizes primarily to the
nucleolus but is also present in the nucleoplasm to a
lesser extent. Nop13p contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 73
Score = 31.6 bits (72), Expect = 0.046
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
FVGNL T+ ++ F ++ VR++ +++ + KGF +V+F ++E AL
Sbjct: 2 FVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate
nucleolin. This subfamily corresponds to the RRM3 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 72
Score = 31.4 bits (71), Expect = 0.054
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
V NL ++ ++ F +K S+R+ ++ R KG+ +VEF E+ ++AL
Sbjct: 3 VLVVNNLSYSASEDSLQEVF--EKATSIRIPQNN--GRPKGYAFVEFESAEDAKEALNSC 58
Query: 75 GRITVDGLQVRLD 87
++G +RL+
Sbjct: 59 NNTEIEGRSIRLE 71
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 77
Score = 31.5 bits (72), Expect = 0.060
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
+V ++ +++ D++ F K+ S L D ET + KG+ ++E+ EN + A
Sbjct: 4 YVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEY---ENPQSA 55
Score = 28.0 bits (63), Expect = 1.1
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQA 215
S L D ET + KG+ ++E+ EN + A
Sbjct: 28 KSCSLAPDPETGKHKGYGFIEY---ENPQSA 55
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in
muscle differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 31.6 bits (72), Expect = 0.064
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 18 VGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
V LP +TQ ++ F ++ S +L++DK T + G+ +V +VD E+ +A+
Sbjct: 6 VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60
Score = 25.5 bits (56), Expect = 9.0
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
S +L++DK T + G+ +V +VD E+ +A+
Sbjct: 30 SCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically bind mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone and play a key role in
cell growth and differentiation. DND1 is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two
RRMs. .
Length = 82
Score = 31.5 bits (72), Expect = 0.072
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 17 FVGNLPNGITQGDVERFFPEQK--LVSVRLVKD-KETDRFKGFCYVEFVDVENLRQAL-- 71
FVG +P T+ ++ F + +V V + + + ++ +GF +VE+ A
Sbjct: 5 FVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARRK 64
Query: 72 LKDGRITVDGLQVRLDIA 89
L GRI + G +V +D A
Sbjct: 65 LVPGRILLWGHEVAVDWA 82
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 33.5 bits (76), Expect = 0.077
Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 9/109 (8%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
+V NLP IT ++ F + ++V +++DK T +G +V F E ++A+
Sbjct: 197 YVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256
Query: 76 RITVDG----LQVRLDIADGKRND----NKGGFNNKQNRGGGSGGMGGN 116
+ +G L VRL GK ++ G N N G G+ GM G
Sbjct: 257 NVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGHGNMGMAGG 305
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 31.2 bits (71), Expect = 0.083
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 16/73 (21%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVD-------VENL 67
++GNL + + + D+ + F E K+ SV + K G+ +V+ D +E L
Sbjct: 2 YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDCPDQSWADKAIEKL 54
Query: 68 RQALLKDGRITVD 80
+L+ I V+
Sbjct: 55 NGKILQGKVIEVE 67
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 31.0 bits (71), Expect = 0.084
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 11/64 (17%)
Query: 17 FVGNLP-NGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 73
FVGNL + +++ D+E F K++ + L KG+ +V+F + E+ R A+
Sbjct: 4 FVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAGE 55
Query: 74 DGRI 77
+GR
Sbjct: 56 NGRE 59
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La
or LARP3) and similar proteins. This subfamily
corresponds to the RRM1 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also possesses a short
basic motif (SBM) and a nuclear localization signal
(NLS) at the C-terminus. .
Length = 72
Score = 31.0 bits (71), Expect = 0.092
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
T +V P T D++ FF K+ ++R+ +D + FKG +VEF
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKK-FKGSVFVEF 47
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 30.8 bits (70), Expect = 0.11
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 16 AFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
+VG +P T+ ++ +F ++ + L+ +T RF+G ++ F E ++AL D
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60
Query: 75 G 75
G
Sbjct: 61 G 61
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 30.6 bits (70), Expect = 0.12
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 17 FVGNLPNGITQGDVERFFPEQK---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
F+G L T+ + +F K +V ++KD T R +GF +V F D ++ +L
Sbjct: 2 FIGGLSWDTTEESLREYF--SKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSV-DKVLA 58
Query: 74 DGRITVDGLQV 84
+DG ++
Sbjct: 59 AKPHVLDGREI 69
Score = 29.1 bits (66), Expect = 0.38
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
+V ++KD T R +GF +V F D ++ +L +DG
Sbjct: 24 EVVDCVIMKDPITGRSRGFGFVTFADPSSV-DKVLAAKPHVLDG 66
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 32.6 bits (74), Expect = 0.12
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 11 EPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
E V LP +TQ ++ F ++ S +LV+DK T + G+ +V +V E+ +
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
Query: 70 AL 71
A+
Sbjct: 61 AV 62
Score = 31.1 bits (70), Expect = 0.49
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
+V LP +TQ ++E F P ++++ R++ D T KG ++ F
Sbjct: 93 YVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF 138
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 30.4 bits (69), Expect = 0.14
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 18 VGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
V NLP GI + + + F + V+L K+ +F+ F +V + E ++AL
Sbjct: 5 VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKAL 58
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 30.4 bits (69), Expect = 0.14
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 180 EVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
+ V + D+ET KGF Y+EF V+ + +AL DG
Sbjct: 26 SCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDG 66
Score = 30.1 bits (68), Expect = 0.19
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 31 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
E F ++ V + D+ET KGF Y+EF V+ + +AL DG
Sbjct: 22 EHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDG 66
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to
the RRM1 of hnRNP A0 which is a low abundance hnRNP
protein that has been implicated in mRNA stability in
mammalian cells. It has been identified as the
substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 79
Score = 30.5 bits (69), Expect = 0.16
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVG L + + R F KL ++ D T R +GF ++ F + +A+
Sbjct: 6 FVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQP 65
Query: 76 RITVDGLQVRL 86
+DG Q+ L
Sbjct: 66 HS-IDGNQIEL 75
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 86
Score = 30.6 bits (69), Expect = 0.17
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 12/55 (21%)
Query: 41 SVRLVKDKETDRFKGFCYVEF---VDVENLRQALLKDGRITVDGLQVRLDIADGK 92
++RL+KDK+T + +GF +V+ ++ L Q L L L I DGK
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQIL--------QALHPPLKI-DGK 78
Score = 29.1 bits (65), Expect = 0.62
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 11/51 (21%)
Query: 186 SVRLVKDKETDRFKGFCYVEF---VDVENLRQAL------LK-DGR-ITVD 225
++RL+KDK+T + +GF +V+ ++ L Q L LK DG+ I VD
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGVD 83
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 30.3 bits (68), Expect = 0.18
Identities = 13/56 (23%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
+V LP +TQ ++E+ F + ++++ R+++D+ T +G ++ F +A+
Sbjct: 4 YVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 71
Score = 29.9 bits (68), Expect = 0.19
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 17 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
FVG L +T+ D+ ++F Q ++ V + K F+ F +V F D E + Q+L +
Sbjct: 4 FVGRLTEDMTEEDLRQYF-SQFGEVTDVYIPKP-----FRAFAFVTFADPE-VAQSLCGE 56
Query: 75 GRITVDGLQVRLDIAD 90
I + G+ V + A+
Sbjct: 57 DHI-IKGVSVHVSNAE 71
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 30.4 bits (68), Expect = 0.19
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 8/79 (10%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 74
+VGNL N + ++ER F L SV + ++ GF +VEF D + A+ + D
Sbjct: 8 YVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRELD 62
Query: 75 GRITVDGLQVRLDIADGKR 93
GR T+ G +VR+++++G++
Sbjct: 63 GR-TLCGCRVRVELSNGEK 80
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein
zinc fingers (zf-RanBP), and an asparagine-rich region.
It may possess RNA-binding and zinc ion binding
activities. Additional research had indicated that ARP
may function as a factor involved in the stress
response. .
Length = 88
Score = 30.5 bits (69), Expect = 0.19
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFK-------GFCYVEFVDVENLRQ 69
++ NLP TQ ++E +F + + V K D + F E +
Sbjct: 4 YISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAME 63
Query: 70 ALLKDGRITVD 80
AL +GR +
Sbjct: 64 ALALNGRCLGE 74
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells, and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1) and has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
It represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 30.0 bits (67), Expect = 0.20
Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEF 61
FVG L T DV+++F + K+ L+ DK T+R +GF +V F
Sbjct: 3 FVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads and is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 83
Score = 30.1 bits (67), Expect = 0.20
Identities = 19/69 (27%), Positives = 41/69 (59%), Gaps = 6/69 (8%)
Query: 18 VGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
V LP +TQ +++ F ++ S +LV+DK T + G+ +V ++D ++ +A+
Sbjct: 9 VNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI----- 63
Query: 77 ITVDGLQVR 85
T++GL+++
Sbjct: 64 NTLNGLRLQ 72
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 86
Score = 30.2 bits (67), Expect = 0.20
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
++ LP T D+ + P K+VS + + DK T++ KG+ +V+F
Sbjct: 11 YIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 56
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 87
Score = 30.4 bits (68), Expect = 0.22
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 41 SVRLVKDKETDRFKGFCYVEF---VDVENLRQALLK-DGRITVDGLQVRLDIADG 91
+VR++KDK+T +GF +++ V+ L Q L +++DG + ++ A G
Sbjct: 33 NVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLSIDGKTINVEFAKG 87
Score = 27.3 bits (60), Expect = 2.2
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
+VR++KDK+T +GF +++ + Q L
Sbjct: 33 NVRVIKDKQTQLNRGFAFIQLSTIVEAAQLL 63
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 2 (Musashi-2) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 79
Score = 30.0 bits (67), Expect = 0.23
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 61
FVG L DV+++F + K+ L+ DK T+R +GF +V F
Sbjct: 7 FVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM4 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 79
Score = 29.8 bits (67), Expect = 0.23
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
P V NLP+ +T+ DV E +V+V++ + + VEF E +A
Sbjct: 6 PTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQ----ALVEFATEEQATEA 61
Query: 71 LLKDGRITVDGLQVRL 86
L +++G +RL
Sbjct: 62 LACKHASSLNGSTIRL 77
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 30.1 bits (68), Expect = 0.24
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLV---------SVRLVKDKETDRFKGFCYVEFVD 63
FV NLP T+ D+ F ++ + L KDK+T KG V + D
Sbjct: 2 FVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDD 57
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 32.2 bits (74), Expect = 0.25
Identities = 20/99 (20%), Positives = 33/99 (33%), Gaps = 5/99 (5%)
Query: 90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDF 149
D R D + + ++ RG GG + RD +++R G +
Sbjct: 202 DRDRRDRREQGDRREERGRRDGG----DRRGRRRRRDRRDARGDDNREDRGDRDGDDGEG 257
Query: 150 SRGGEGP-GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSV 187
G G R+ G + N+ + E LV V
Sbjct: 258 RGGRRGRRFRDRDRRGRRGGDGGNEREPELREDDVLVPV 296
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 29.9 bits (67), Expect = 0.25
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVD 63
FVG L + +GD+ F + V ++ DK+T + +GF +V F +
Sbjct: 3 FVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN 50
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 29.7 bits (67), Expect = 0.26
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 10/77 (12%)
Query: 15 TAFVGNL-PNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
T FV P + D+E+ F P LV + K F +VEF D E+ +AL
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALE 52
Query: 73 KDGRITVDGLQVRLDIA 89
+DG + ++
Sbjct: 53 ALHGSRIDGSVLTVEFV 69
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 29.5 bits (67), Expect = 0.27
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
+VGNL +T+ + E F +V+V + KD+ T +G+ +VEF
Sbjct: 2 YVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEF 47
Score = 28.3 bits (64), Expect = 0.66
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 185 VSVRLVKDKETDRFKGFCYVEF 206
V+V + KD+ T +G+ +VEF
Sbjct: 26 VNVHIPKDRVTQAHQGYGFVEF 47
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 29.6 bits (66), Expect = 0.27
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 74
+VGNL G +G++ER F L +V + ++ GF +VEF D + A+ D
Sbjct: 3 YVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGLD 57
Query: 75 GRITVDGLQVRLDIADG 91
G++ + G +VR++++ G
Sbjct: 58 GKV-ICGSRVRVELSTG 73
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup
corresponds to the RRM2 of RBM5, also termed protein
G15, or putative tumor suppressor LUCA15, or renal
carcinoma antigen NY-REN-9, a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor. RBM5 shows high sequence
similarity to RNA-binding protein 6 (RBM6 or NY-LU-12
or g16 or DEF-3). Both, RBM5 and RBM6, specifically
bind poly(G) RNA. They contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), two C2H2-type zinc
fingers, a nuclear localization signal, and a
G-patch/D111 domain. .
Length = 86
Score = 29.5 bits (66), Expect = 0.33
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 41 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGK 92
++RL+KDK+T + +GF +V+ Q L + L L I DGK
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ-----ILQSLHPPLKI-DGK 78
Score = 28.8 bits (64), Expect = 0.72
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 186 SVRLVKDKETDRFKGFCYVEF---VDVENLRQAL 216
++RL+KDK+T + +GF +V+ ++ L Q L
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQIL 66
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM2 of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Overexpression of hnRNP A2/B1 has been described in
many cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 29.7 bits (66), Expect = 0.33
Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
FVG + + + +F E K+ ++ ++ D+++ + +GF +V F D + + + +L+
Sbjct: 4 FVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 31.2 bits (71), Expect = 0.34
Identities = 20/62 (32%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 106 RGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP 165
GG GG GG G RGGG GGG GG G G GP
Sbjct: 3 GGGFGGGRGGG------RGGGGGGGRGGGGRGGG--RGGGRGRGRGGGGGGRGGGGGGGP 54
Query: 166 NR 167
+
Sbjct: 55 GK 56
Score = 29.7 bits (67), Expect = 1.0
Identities = 19/63 (30%), Positives = 19/63 (30%), Gaps = 6/63 (9%)
Query: 100 FNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGF 159
GG GG GG GG RG G GG RGG G GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGG------RGGGGGGGP 54
Query: 160 RNN 162
Sbjct: 55 GKV 57
Score = 28.5 bits (64), Expect = 2.6
Identities = 17/55 (30%), Positives = 20/55 (36%), Gaps = 10/55 (18%)
Query: 91 GKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGG 145
G R +GG GGG GG G + +GG GG GGG
Sbjct: 8 GGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGG----------GGGGRGGGGGG 52
Score = 27.0 bits (60), Expect = 8.0
Identities = 12/36 (33%), Positives = 12/36 (33%)
Query: 130 NMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP 165
M GG GG RGG G GG R
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRG 36
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM1 of RBM40, also known
as RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of
the U12 small nuclear RNA (snRNA). The proline-rich
region might be involved in protein-protein
interactions. .
Length = 73
Score = 29.1 bits (66), Expect = 0.34
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T V +LP +++ D E SVR++ + + K + F + + QAL +
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRR--GKLKNTAFATFDNEQAASQALSR 57
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or
CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3,
or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1
and ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
family of RNA-binding proteins that have been
implicated in regulation of pre-mRNA splicing, and
control of mRNA translation and deadenylation. CELF-1
is strongly expressed in all adult and fetal tissues
tested. The human CELF-1 is a nuclear and cytoplasmic
RNA-binding protein that regulates multiple aspects of
nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element
involved in translational control of oskar mRNA in
Drosophila, and share sequence similarity to Bruno, the
Drosophila protein that mediates this process. The
Xenopus homolog embryo deadenylation element-binding
protein (EDEN-BP) mediates sequence-specific
deadenylation of Eg5 mRNA. It binds specifically to the
EDEN motif in the 3'-untranslated regions of maternal
mRNAs and targets these mRNAs for deadenylation and
translational repression. CELF-1 contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. This
subgroup also includes Drosophila melanogaster Bruno
protein, which plays a central role in regulation of
Oskar (Osk) expression in flies. It mediates repression
by binding to regulatory Bruno response elements (BREs)
in the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 84
Score = 29.4 bits (66), Expect = 0.34
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRF--KGFCYVEF 61
FVG +P ++ D+ F + V + +++D+ + KG C+V F
Sbjct: 5 FVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and
plant flowering time control protein FCA. This
subfamily corresponds to the RRM1 and RRM2 domains of
the CUGBP1 and ETR-3-like factors (CELF) as well as
plant flowering time control protein FCA. CELF, also
termed BRUNOL (Bruno-like) proteins, is a family of
structurally related RNA-binding proteins involved in
regulation of pre-mRNA splicing in the nucleus, and
control of mRNA translation and deadenylation in the
cytoplasm. The family contains six members: CELF-1
(also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP),
CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2,
NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1,
CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5)
and CELF-6 (BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both, sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 29.4 bits (67), Expect = 0.35
Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEF 61
FVG LP T+ DV F E + V +++DK+T + KG +V+F
Sbjct: 3 FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKF 48
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 30.9 bits (70), Expect = 0.38
Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 103 KQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFR 160
+ GGG GG Y GG + S GGG + GG GG G G R
Sbjct: 111 RGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGG----GGGGAGGGASR 164
Score = 28.6 bits (64), Expect = 2.1
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 98 GGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGAS-----SGGGFNDF 149
GG GGG GG G ++ GG GGGAS +GGGF++
Sbjct: 120 GGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGGGFDEM 176
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in
the system using SV40 DNA. MSSP-2 is identical with
Scr3, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-2 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 75
Score = 29.3 bits (65), Expect = 0.39
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
++ L G T D+ + P K+VS + + DK T++ KG+ +V+F
Sbjct: 5 YIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 50
>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM2 of hnRNP R, a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. It contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif. hnRNP R binds RNA through its RRM domains. .
Length = 85
Score = 29.3 bits (65), Expect = 0.43
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 9/81 (11%)
Query: 17 FVGNLPNGITQGDVERFFPE--QKLVSVRLV---KDKETDRFKGFCYVEFVDVENLRQA- 70
FVG++P T+ ++ F + + LV V L DK+ +R GFC++E+ D ++ QA
Sbjct: 6 FVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNR--GFCFLEYEDHKSAAQAR 63
Query: 71 -LLKDGRITVDGLQVRLDIAD 90
L G++ V G V ++ AD
Sbjct: 64 RRLMSGKVKVWGNVVTVEWAD 84
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 30.5 bits (69), Expect = 0.45
Identities = 12/39 (30%), Positives = 14/39 (35%)
Query: 135 SRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMND 173
GG GG F GP + G N S M+D
Sbjct: 124 GGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSRDMDD 162
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 28.8 bits (65), Expect = 0.51
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 61
Y+ FVG L +T+ ++ F K++ V L+K F +++F
Sbjct: 3 KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN--AFAFIKF 50
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types
1, 2, 3, 4 family. These eukaryotic proteins recognize
the poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are
four paralogs in Homo sapiens which are expressed in
testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4
), broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 30.9 bits (70), Expect = 0.52
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 17 FVGNLPNGITQGD-VERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
+VG+L +T+ + F P ++SVR+ +D T R G+ YV F + + +AL
Sbjct: 4 YVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMN 63
Query: 76 RITVDGLQVRL 86
+ G +R+
Sbjct: 64 FKRLGGKPIRI 74
Score = 29.8 bits (67), Expect = 1.1
Identities = 12/54 (22%), Positives = 24/54 (44%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
+V NL + + + F + ++ V + R +GF +V F E+ +A
Sbjct: 182 YVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. This subfamily also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 28.8 bits (65), Expect = 0.53
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDK 48
FVGNLPN IT+ + + F ++ V L K+K
Sbjct: 5 FVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK 37
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This
subgroup corresponds to the RRM3 of the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
proteins, a family of structurally related RNA-binding
proteins involved in the regulation of pre-mRNA
splicing in the nucleus and in the control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or
NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or
ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed
BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also
termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts. .
Length = 73
Score = 28.8 bits (65), Expect = 0.58
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 11/78 (14%)
Query: 17 FVGNLPNGITQGD-VERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
F+ +LPN T D + F P ++S ++ DK T + K F +V + + E+ + A+
Sbjct: 2 FIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIK--- 58
Query: 76 RITVDGLQVRLDIADGKR 93
++G QV GKR
Sbjct: 59 --AMNGFQV-----GGKR 69
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. The hnRNP H protein family
includes hnRNP H (also termed mcs94-1), hnRNP H2 (also
termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also
termed hnRNP 2H9), which represent a group of nuclear
RNA binding proteins that are involved in pre-mRNA
processing. These proteins have similar RNA binding
affinities and specifically recognize the sequence
GGGA. They can either stimulate or repress splicing
upon binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements
downstream of the 5' splice site in the transcripts of
c-src, human immunodeficiency virus type 1 (HIV-1),
Bcl-X, GRIN1, and myelin. It silences exons when bound
to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
hnRNP H3 may be involved in the splicing arrest induced
by heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and they play an important role in
efficiently silencing the exon. For instance, members
in this family can regulate the alternative splicing of
the fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced
silencing activity within hnRNP H3. In addition, the
family members have an extensive glycine-rich region
near the C-terminus, which may allow them to homo- or
heterodimerize. The family also includes a cytoplasmic
poly(A)+ mRNA binding protein, GRSF-1, which interacts
with RNA in a G-rich element-dependent manner. It may
function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. GRSF-1 also contains three potential RRMs
responsible for the RNA binding, and two auxiliary
domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 28.8 bits (65), Expect = 0.58
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 21 LPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
LP T+ D+ FF V+VR+ + + R G VEF E+ A+ KD
Sbjct: 8 LPYRATENDIFEFFSPLNPVNVRIEYNAD-GRATGEADVEFATHEDAVAAMSKD 60
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 31.0 bits (70), Expect = 0.61
Identities = 17/69 (24%), Positives = 24/69 (34%), Gaps = 10/69 (14%)
Query: 105 NRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNG 164
R GG G GG + + G +F+ + R GG G FS R ++
Sbjct: 570 ERRGGGRGFGGER--REGGRNFSGER-----REGG---RGDGRRFSGERREGRAPRRDDS 619
Query: 165 PNRSNSMND 173
R D
Sbjct: 620 TGRRRFGGD 628
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 77
Score = 28.5 bits (64), Expect = 0.69
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 18 VGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
V LP T+ D++ +F +L+ V++ KD +T + KGF +V F D E+ + L R
Sbjct: 4 VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL--SQR 61
Query: 77 ITVDGLQVRLDIADGK 92
+DG + I + K
Sbjct: 62 HMIDGRWCDVKIPNSK 77
Score = 25.4 bits (56), Expect = 8.6
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 184 LVSVRLVKDKETDRFKGFCYVEFVDVEN----LRQALLKDGRI 222
L+ V++ KD +T + KGF +V F D E+ L Q + DGR
Sbjct: 26 LLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMIDGRW 68
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3'
processing machinery that functions in UGUA-mediated
poly(A) site recognition, the regulation of alternative
poly(A) site selection, mRNA export, and mRNA splicing.
It is a complex composed of a small 25 kDa (CFIm25)
subunit and a larger 59/68/72 kDa subunit. Two separate
genes, CPSF6 and CPSF7, code for two isoforms of the
large subunit, CFIm68 and CFIm59. Structurally related
CFIm68 and CFIm59, also termed cleavage and
polyadenylation specificity factor subunit 6 (CPSF7),
or cleavage and polyadenylation specificity factor 59
kDa subunit (CPSF59), are functionally redundant. Both
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. Their
N-terminal RRM mediates the interaction with CFIm25,
and also serves to enhance RNA binding and facilitate
RNA looping. .
Length = 76
Score = 28.4 bits (64), Expect = 0.78
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVK---DKETDRFKGFCYVEFVDVENLRQALLK 73
+VGNL T D+E E +V V+ +K K + KGF YVEF K
Sbjct: 2 YVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEK 61
Query: 74 DGRITVDG 81
+G
Sbjct: 62 LEGREFNG 69
Score = 26.5 bits (59), Expect = 3.6
Identities = 12/46 (26%), Positives = 18/46 (39%)
Query: 181 VTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
V + S++ + K + KGF YVEF K +G
Sbjct: 24 VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNG 69
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 28.5 bits (64), Expect = 0.80
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFK-------GFCYVEFVDVENLRQ 69
++ NL ++ D+E F + + VSV L+ + F+ G Y EF E +
Sbjct: 3 YISNLSYSSSEEDLEEFLKDFEPVSV-LIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61
Query: 70 AL 71
+
Sbjct: 62 VV 63
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM2 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 28.3 bits (63), Expect = 0.81
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 14 YTAFVGNLPNGITQGDVERFF--PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
Y+ FVG+L + + D+ F S +++ D T +G+ +V F D + ++AL
Sbjct: 2 YSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRAL 61
Query: 72 L 72
+
Sbjct: 62 I 62
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit
2 (NCBP2), or cell proliferation-inducing gene 55
protein, or NCBP-interacting protein 1 (NIP1). CBP20 is
the small subunit of the nuclear cap binding complex
(CBC), which is a conserved eukaryotic heterodimeric
protein complex binding to 5'-capped polymerase II
transcripts and plays a central role in the maturation
of pre-mRNA and uracil-rich small nuclear RNA (U
snRNA). CBP20 is most likely responsible for the
binding of capped RNA. It contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and interacts with the
second and third domains of CBP80, the large subunit of
CBC. .
Length = 78
Score = 28.3 bits (64), Expect = 0.87
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 47 DKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD 87
D+ T GFC+VE+ E+ A+ +D +R+D
Sbjct: 33 DRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRVD 73
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells, as well as the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 28.5 bits (63), Expect = 0.91
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 18 VGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
V LP +TQ + F ++ S +LV+DK T + G+ +V ++D ++ +A+
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 28.3 bits (64), Expect = 0.92
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFK-----GFCYVEFVDVENLR 68
T FV NL T+ +++ F + + SV + K K+ G+ +VEF E +
Sbjct: 2 TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 69 QALLKDGRITVDGLQVRLDI 88
+AL + +DG + L +
Sbjct: 62 KALKRLQGTVLDGHALELKL 81
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 of SRSF1, also termed alternative-splicing factor
1 (ASF-1), or pre-mRNA-splicing factor SF2, P33
subunit. SRSF1 is a splicing regulatory serine/arginine
(SR) protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich
in serine-arginine dipeptides. .
Length = 73
Score = 27.8 bits (62), Expect = 1.0
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
+VGNLP I D+E F K ++R + D + R F +VEF D + A+
Sbjct: 3 YVGNLPPDIRTKDIEDLF--YKYGAIRDI-DLKNRRGPPFAFVEFEDPRDAEDAVYGRDG 59
Query: 77 ITVDGLQVRLD 87
DG ++R++
Sbjct: 60 YDYDGYRLRVE 70
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras
GTPase-activating protein-binding protein 2 (G3BP2) and
similar proteins. This subgroup corresponds to the RRM
of G3BP2, also termed GAP SH3 domain-binding protein 2,
a cytoplasmic protein that interacts with both
IkappaBalpha and IkappaBalpha/NF-kappaB complexes,
indicating that G3BP2 may play a role in the control of
nucleocytoplasmic distribution of IkappaBalpha and
cytoplasmic anchoring of the IkappaBalpha/NF-kappaB
complex. G3BP2 contains an N-terminal nuclear transfer
factor 2 (NTF2)-like domain, an acidic domain, a domain
containing five PXXP motifs, an RNA recognition motif
(RRM domain), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif). It binds to the
SH3 domain of RasGAP, a multi-functional protein
controlling Ras activity, through its N-terminal
NTF2-like domain. The acidic domain is sufficient for
the interaction of G3BP2 with the IkappaBalpha
cytoplasmic retention sequence. Furthermore, G3BP2
might influence stability or translational efficiency
of particular mRNAs by binding to RNA-containing
structures within the cytoplasm through its RNA-binding
domain.
Length = 83
Score = 28.0 bits (62), Expect = 1.1
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
FVGNLP+ I + +++ FF +V +R+ + F +V F D E +++ L
Sbjct: 9 FVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILGAK- 67
Query: 76 RITVDGLQVRLDIADGK 92
I G +VRL++ + K
Sbjct: 68 PIMFRG-EVRLNVEEKK 83
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell
surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or
ENOX) proteins. This subgroup corresponds to the
conserved RNA recognition motif (RRM) in ECTO-NOX
proteins (also termed ENOX), comprising a family of
plant and animal NAD(P)H oxidases exhibiting both,
oxidative and protein disulfide isomerase-like,
activities. They are growth-related and drive cell
enlargement, and may play roles in aging and
neurodegenerative diseases. ENOX proteins function as
terminal oxidases of plasma membrane electron transport
(PMET) through catalyzing electron transport from
plasma membrane quinones to extracellular oxygen,
forming water as a product. They are also hydroquinone
oxidases that oxidize externally supplied NADH, hence
NOX. ENOX proteins harbor a di-copper center that lack
flavin. ENOX proteins display protein disulfide
interchange activity that is also possessed by protein
disulfide isomerase. In contrast to the classic protein
disulfide isomerases, ENOX proteins lack the double
CXXC motif. This family includes two ENOX proteins,
ENOX1 and ENOX2. ENOX1, also termed candidate
growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous
and refractory to drugs. ENOX2, also termed APK1
antigen, or cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role
in cell proliferation and tumor progression. In
contrast to ENOX1, ENOX2 is drug-responsive and harbors
a drug binding site to which the cancer-specific
S-peptide tagged pan-ENOX2 recombinant (scFv) is
directed. Moreover, ENOX2 is specifically inhibited by
a variety of quinone site inhibitors that have
anticancer activity and is unique to the surface of
cancer cells. ENOX proteins contain many functional
motifs.
Length = 84
Score = 28.1 bits (63), Expect = 1.2
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 16/74 (21%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
T FVG LP T+ + F EQ +++++R+ K K FC++ F + +
Sbjct: 8 TVFVGGLPENATEEIIREVF-EQCGEIIAIRMSK-------KNFCHIRFAEEFAV----- 54
Query: 73 KDGRITVDGLQVRL 86
D I + G +VR+
Sbjct: 55 -DKAIYLSGYRVRI 67
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM1 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two of which are followed by a glutamine-rich
stretch that may be involved in transcriptional
activity. In addition, NGR1 has an asparagine-rich
region near the carboxyl terminus which also harbors a
methionine-rich region. The subgroup also includes
NAM8, a putative RNA-binding protein that acts as a
suppressor of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 81
Score = 27.8 bits (62), Expect = 1.2
Identities = 13/63 (20%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 15 TAFVGNLPNGITQGDVERFFP--EQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
T ++G+L + + +++ + + V+V++++ + + G+C+VEF + AL
Sbjct: 1 TLWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS 60
Query: 73 KDG 75
+G
Sbjct: 61 LNG 63
Score = 27.8 bits (62), Expect = 1.4
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
V+V++++ + + G+C+VEF + AL +G
Sbjct: 28 VNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALSLNG 63
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function
in RNA packaging, stabilization of RNA secondary
structure, or other macromolecular interactions. GRSF-1
contains three potential RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 27.8 bits (62), Expect = 1.2
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 21 LPNGITQGDVERFFPEQKLVSVRLVKDKET-DRFKGFCYVEFVDVENLRQALLKD 74
LP T+ D+ FF +V +V R G YV+F E +ALLK
Sbjct: 9 LPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKH 63
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 27.9 bits (63), Expect = 1.2
Identities = 20/70 (28%), Positives = 24/70 (34%), Gaps = 29/70 (41%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGF-------------CYVEF 61
T FV NL T E++L + R GF C+VEF
Sbjct: 4 TLFVANLGPNTT---------EEELRQL-------FSRQPGFRRLKMHNKGGGPVCFVEF 47
Query: 62 VDVENLRQAL 71
DV QAL
Sbjct: 48 EDVSFATQAL 57
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), in the middle and
an RGG box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 27.7 bits (61), Expect = 1.2
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
FVG L + + +F ++ S+ L D +T++ +GFC++ F + E +++ + K
Sbjct: 3 FVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 25.7 bits (56), Expect = 7.1
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
S+ L D +T++ +GFC++ F + E +++ + K
Sbjct: 28 SIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM1 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single-
and double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. It forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manneras well as with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 27.5 bits (61), Expect = 1.2
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 17 FVGNLPNGITQGDVERFF 34
FVGNLP IT+ ++ + F
Sbjct: 5 FVGNLPPDITEEEMRKLF 22
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 29.6 bits (67), Expect = 1.3
Identities = 14/41 (34%), Positives = 15/41 (36%), Gaps = 7/41 (17%)
Query: 105 NRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGG 145
R S G GG G + GGG SSGGG
Sbjct: 232 GRRRRSSGSGG-------SGGSGGGSSGGGFSGGGGSSGGG 265
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 27.7 bits (62), Expect = 1.4
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 18 VGNLPNGITQGDVERFF-PEQKLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQA 70
V N+P T ++ F +L +VRL K T +GF +V+F+ ++ ++A
Sbjct: 5 VRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59
>gnl|CDD|240354 PTZ00310, PTZ00310, AMP deaminase; Provisional.
Length = 1453
Score = 29.8 bits (67), Expect = 1.5
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 67 LRQALLKDG---RITVDGLQVRLDIADGKRNDNKGGFNNKQN 105
L Q K G +TVD L V+ D +R DN FN+K N
Sbjct: 888 LGQLFSKYGITPNLTVDQLNVQADHTLFERFDN---FNSKYN 926
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 27.7 bits (61), Expect = 1.6
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
++ LP +TQ DVE F ++++ R++ D+ T +G ++ F
Sbjct: 4 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRF 49
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 85
Score = 27.7 bits (61), Expect = 1.6
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 21 LPNGITQGDVERFFPEQKLVS--VRLVKDKETDRFKGFCYVEF 61
LP T+ D+ E + VRL+++K + + +GF +VEF
Sbjct: 10 LPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEF 52
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 27.2 bits (61), Expect = 1.8
Identities = 18/56 (32%), Positives = 22/56 (39%), Gaps = 19/56 (33%)
Query: 17 FVGNLPNGITQ----------GDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
VGNLP T G VER F LV + T KG+ +VE+
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAVERCF---------LVYSESTGESKGYGFVEYA 49
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 27.4 bits (61), Expect = 1.8
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
T +VGN+P TQ D+ F ++ R D +GF +V+
Sbjct: 2 TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKL 43
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C), and plant pre-mRNA-splicing factor SF2
(SR1). SRSF1 is a shuttling SR protein involved in
constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation.
SRSF9 has been implicated in the activity of many
elements that control splice site selection, the
alternative splicing of the glucocorticoid receptor
beta in neutrophils and in the gonadotropin-releasing
hormone pre-mRNA. It can also interact with other
proteins implicated in alternative splicing, including
YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both,
SRSF1 and SRSF9, contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
RS domains rich in serine-arginine dipeptides. In
contrast, SF2 contains two N-terminal RRMs and a
C-terminal PSK domain rich in proline, serine and
lysine residues. .
Length = 72
Score = 27.4 bits (61), Expect = 1.8
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVD 63
+VGNLP I + D+E F K ++ + K R F +VEF D
Sbjct: 3 YVGNLPGDIRERDIEDLF--YKYGPIKAIDLKNRRRGPPFAFVEFED 47
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 27.3 bits (61), Expect = 1.9
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDV 64
++G LP + DVERFF + +E + GF +VEF D
Sbjct: 3 YIGRLPYRARERDVERFFKGYG-------RIREINLKNGFGFVEFEDP 43
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 27.3 bits (60), Expect = 2.0
Identities = 11/48 (22%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD 63
FVG + + + +F + K+ ++ +++D+++ + +GF +V F D
Sbjct: 4 FVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDD 51
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 29.0 bits (65), Expect = 2.0
Identities = 26/73 (35%), Positives = 31/73 (42%), Gaps = 14/73 (19%)
Query: 101 NNKQNR--------GGGSGGMGGNKYNQHQGGSFNRDNMRNNSR-----GGGASSGGGFN 147
NN Q+R GG SGG GNK + QG D R S+ GGG +G G
Sbjct: 8 NNGQDRDPWGSSKPGGNSGG-NGNKGGRDQGPPDLDDIFRKLSKKLGGLGGGKGTGSGGG 66
Query: 148 DFSRGGEGPGGFR 160
S+G G R
Sbjct: 67 SSSQGPRPQLGGR 79
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a major
component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 28.7 bits (64), Expect = 2.1
Identities = 20/67 (29%), Positives = 23/67 (34%), Gaps = 12/67 (17%)
Query: 92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSR 151
KR GG+N +R G G GGN+Y GG G GG
Sbjct: 2 KRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGG------------WGQPHGGGWGQPHGG 49
Query: 152 GGEGPGG 158
G P G
Sbjct: 50 GWGQPHG 56
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 27.0 bits (60), Expect = 2.3
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 9/34 (26%)
Query: 28 GDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
GD+E V +VKDK T KGF YV+F
Sbjct: 25 GDIE---------YVSIVKDKNTGESKGFGYVKF 49
Score = 26.6 bits (59), Expect = 3.3
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 186 SVRLVKDKETDRFKGFCYVEF 206
V +VKDK T KGF YV+F
Sbjct: 29 YVSIVKDKNTGESKGFGYVKF 49
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 26.7 bits (60), Expect = 2.3
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 12/50 (24%)
Query: 38 KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL-------LKDGRITVD 80
+ ++L+K K GF +VEF E +A+ + VD
Sbjct: 10 NVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
Score = 26.3 bits (59), Expect = 2.8
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 12/50 (24%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL-------LKDGRITVD 225
+ ++L+K K GF +VEF E +A+ + VD
Sbjct: 10 NVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear
molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 26.9 bits (60), Expect = 2.4
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 13 PYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
+ FV NLP + + + F P + +V++++D T++ KG+ +V + E
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE 54
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 27.0 bits (60), Expect = 2.4
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
T +V ++ +T+ + F ++V R+ D + F ++EF D E R AL
Sbjct: 4 TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAALSL 61
Query: 74 DG 75
G
Sbjct: 62 SG 63
>gnl|CDD|239745 cd03776, MATH_TRAF6, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily,
TRAF domain, C-terminal MATH subdomain; composed of
proteins with similarity to human TRAF6, including the
Drosophila protein DTRAF2. TRAF molecules serve as
adapter proteins that link TNFRs and downstream kinase
cascades resulting in the activation of transcription
factors and the regulation of cell survival,
proliferation and stress responses. TRAF6 is the most
divergent in its TRAF domain among the mammalian TRAFs.
In addition to mediating TNFR family signaling, it is
also an essential signaling molecule of the
interleukin-1/Toll-like receptor superfamily. Whereas
other TRAF molecules display similar and overlapping
TNFR-binding specificities, TRAF6 binds completely
different sites on receptors such as CD40 and RANK.
TRAF6 serves as a molecular bridge between innate and
adaptive immunity and plays a central role in
osteoimmunology. DTRAF2, as an activator of nuclear
factor-kappaB, plays a pivotal role in Drosophila
development and innate immunity. TRAF6 contains a RING
finger domain, five zinc finger domains, and a TRAF
domain. The TRAF domain can be divided into a more
divergent N-terminal alpha helical region (TRAF-N), and
a highly conserved C-terminal MATH subdomain (TRAF-C)
with an eight-stranded beta-sandwich structure. TRAF-N
mediates trimerization while TRAF-C interacts with
receptors.
Length = 147
Score = 28.1 bits (63), Expect = 2.5
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 54 KGFCYVEFVDVENLRQAL-LKDGRITV 79
KGF YVEF +E+L Q +K+ + +
Sbjct: 116 KGFGYVEFAHIEDLLQRGFVKNDTLLI 142
Score = 28.1 bits (63), Expect = 2.5
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 199 KGFCYVEFVDVENLRQAL-LKDGRITV 224
KGF YVEF +E+L Q +K+ + +
Sbjct: 116 KGFGYVEFAHIEDLLQRGFVKNDTLLI 142
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 28.5 bits (64), Expect = 2.5
Identities = 13/35 (37%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 131 MRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP 165
R + GGG GGGF GG GG G
Sbjct: 118 TRASRGGGGGGGGGGFG--GGGGGSGGGGGGGGGG 150
>gnl|CDD|234269 TIGR03588, PseC, UDP-4-keto-6-deoxy-N-acetylglucosamine
4-aminotransferase. This family of enzymes are
aminotransferases of the pfam01041 family involved in
the biosynthesis of pseudaminic acid. They convert
UDP-4-keto-6-deoxy-N-acetylglucosamine into
UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic
acid has a role in surface polysaccharide in Pseudomonas
as well as in the modification of flagellin in
Campylobacter and Helicobacter species.
Length = 380
Score = 28.4 bits (64), Expect = 2.8
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 59 VEFVDVENLRQALLKDGRITVDGLQVRLDIADGKR 93
V+FVD++ G I D L+ +L A GK
Sbjct: 93 VDFVDIDP------DTGNIDEDALEKKLAAAKGKL 121
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the
RRM of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved
in termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
Its localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 26.8 bits (60), Expect = 2.9
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 74
+VGNL T+ ++E F + L SV + + GF +VEF D + A+ D
Sbjct: 3 YVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRALD 57
Query: 75 GRITVDGLQVRLDIADG 91
GR + G +VR++++ G
Sbjct: 58 GR-RICGNRVRVELSRG 73
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of
Oskar (Osk) expression. It mediates repression by
binding to regulatory Bruno response elements (BREs) in
the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 79
Score = 26.9 bits (59), Expect = 3.0
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
F+ +LP T D+ + F P ++S ++ DK+T+ K F +V +
Sbjct: 8 FIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSY 53
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation.
G3BP1 also contains an N-terminal nuclear transfer
factor 2 (NTF2)-like domain, an RNA recognition motif
(RRM domain), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif). The RRM domain
and RGG-rich region are canonically associated with RNA
binding. G3BP1 co-immunoprecipitates with mRNAs. It
binds to and cleaves the 3'-untranslated region
(3'-UTR) of the c-myc mRNA in a
phosphorylation-dependent manner. Thus, G3BP1 may play
a role in coupling extra-cellular stimuli to mRNA
stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of
G3BP1 regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 26.8 bits (59), Expect = 3.0
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
FVGNLP+ + + +++ FF Q+ +V ++ + F +V F D E + Q +L +
Sbjct: 7 FVGNLPHDVDKSELKEFF--QQYGNVVELRINSGGKLPNFGFVVFDDSEPV-QKILSNRP 63
Query: 77 ITVDGLQVRLDIADGK 92
I G VRL++ + K
Sbjct: 64 IMFRG-DVRLNVEEKK 78
>gnl|CDD|217494 pfam03325, Herpes_PAP, Herpesvirus polymerase accessory protein.
The same proteins are also known as polymerase
processivity factors.
Length = 268
Score = 28.3 bits (63), Expect = 3.1
Identities = 29/122 (23%), Positives = 44/122 (36%), Gaps = 18/122 (14%)
Query: 41 SVRLVKDKETDRF----KGFCYVE-FVDVENLRQALLKDGRITVDGLQVRLDIADGKRND 95
++R+V D ET + G VE F+ E ++ + R + + + ND
Sbjct: 126 TLRVVTDHETKLYVSSKNGLFTVENFLTEEPFQRGDPRFERNGKQDDGLAVANSGESHND 185
Query: 96 N-----KGGFNNKQNRGGGSGGMGG----NKYNQHQGGSFNRDNMRNNSRGGGASSGGGF 146
K N++ G G NKY QH+ S+ M GG F
Sbjct: 186 AEPVPKKHERANRKKGDGDHKNEDGSNSKNKYEQHKITSY----MVPKGAGGAGERSNYF 241
Query: 147 ND 148
ND
Sbjct: 242 ND 243
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells and also regulates the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 27.0 bits (59), Expect = 3.2
Identities = 12/46 (26%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 61
+V LP +TQ ++E+ F + ++++ R++ D+ T +G ++ F
Sbjct: 6 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 51
>gnl|CDD|178574 PLN02995, PLN02995, Probable pectinesterase/pectinesterase
inhibitor.
Length = 539
Score = 28.5 bits (63), Expect = 3.5
Identities = 29/115 (25%), Positives = 44/115 (38%), Gaps = 26/115 (22%)
Query: 73 KDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDN-- 130
KDG + +Q +D+A G+R G F RG Y ++ N D+
Sbjct: 229 KDGSGHFNTVQAAIDVA-GRRKVTSGRFVIYVKRG---------IYQENINVRLNNDDIM 278
Query: 131 -----MRNNSRGGGASSGGGFNDFSRGGEGPGG---------FRNNNGPNRSNSM 171
MR+ GG S GG+ ++ G G FRN GP + ++
Sbjct: 279 LVGDGMRSTIITGGRSVKGGYTTYNSATAGIEGLHFIAKGITFRNTAGPAKGQAV 333
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 28.2 bits (63), Expect = 3.7
Identities = 23/77 (29%), Positives = 28/77 (36%), Gaps = 15/77 (19%)
Query: 98 GGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFND-----FSRG 152
GGF R GG G G FN +++ + G GGG D F+RG
Sbjct: 81 GGFGG---RRFDGGGGFGGFGTGGDGAEFNLNDLFD---AAGRGGGGGIGDLFGGLFNRG 134
Query: 153 GEGPGGFRNNNGPNRSN 169
G R P R N
Sbjct: 135 GGSARPSR----PRRGN 147
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 26.4 bits (59), Expect = 3.8
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 21 LPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV 79
LP T D+E+ P K++S + + DK+T++ KG+ FVD ++ AL +
Sbjct: 8 LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGY---GFVDFDSPEAAL-----KAI 59
Query: 80 DGLQ 83
+GL
Sbjct: 60 EGLN 63
Score = 25.7 bits (57), Expect = 6.1
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 170 SMNDHGL--MVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 217
+ D L + ++S + + DK+T++ KG+ FVD ++ AL
Sbjct: 11 NTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGY---GFVDFDSPEAALK 57
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 26.5 bits (58), Expect = 3.9
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLV-KDKETDRFKGFCYVEFVDVENLRQAL 71
F+G L TQ + +F + V LV +D T R +GF +V F+D + + L
Sbjct: 4 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family. This subfamily corresponds to the RRM2
of hnRNP H protein family which includes hnRNP H (also
termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP
H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA
only in the presence of cap-binding proteins.
Furthermore, hnRNP H and hnRNP H2 are almost identical;
both have been found to bind nuclear-matrix proteins.
hnRNP H activates exon inclusion by binding G-rich
intronic elements downstream of the 5' splice site in
the transcripts of c-src, human immunodeficiency virus
type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences
exons when bound to exonic elements in the transcripts
of beta-tropomyosin, HIV-1, and alpha-tropomyosin.
hnRNP H2 has been implicated in pre-mRNA 3' end
formation. hnRNP H3 may be involved in the splicing
arrest induced by heat shock. Most family members
contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. In addition, the family members have an extensive
glycine-rich region near the C-terminus, which may
allow them to homo- or heterodimerize. .
Length = 77
Score = 26.6 bits (59), Expect = 4.0
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 21 LPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
LP G ++ ++ +FF ++V + L D R G YV+F E+ +AL K
Sbjct: 8 LPFGCSKEEIAQFFSGLEIVPNGITLPMDYRG-RSTGEAYVQFASQESAERALGKH 62
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 27.9 bits (62), Expect = 4.1
Identities = 21/78 (26%), Positives = 25/78 (32%), Gaps = 10/78 (12%)
Query: 87 DIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGF 146
D A+G R++ N N G GG GG GG GG GG
Sbjct: 168 DAANGVRDN----VLNNLNNAPGGGGYGG------GGGGMGGGGGGGMGEMGGMGPQGGG 217
Query: 147 NDFSRGGEGPGGFRNNNG 164
+ G G N G
Sbjct: 218 GGYGGMGAPGQGNAYNQG 235
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 26.4 bits (58), Expect = 4.1
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
+ +VGN+ G T ++E F ++ V ++ DK + KG+ Y+EF +++ A+
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60
Query: 74 D 74
D
Sbjct: 61 D 61
>gnl|CDD|235801 PRK06443, PRK06443, chorismate mutase; Validated.
Length = 177
Score = 27.6 bits (61), Expect = 4.2
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 59 VEFVDVENLRQALLKDGRITVDGLQVRLDIA 89
V F+D+E+LR +L++ ++ ++ R ++A
Sbjct: 2 VHFIDMEDLRSEILENTMDIIELIEKRRELA 32
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 90
Score = 26.7 bits (58), Expect = 4.3
Identities = 12/46 (26%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 61
+V LP +TQ ++E+ F + ++++ R++ D+ T +G ++ F
Sbjct: 9 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 54
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 26.4 bits (58), Expect = 4.4
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
FVG L T+ D++ +F + ++V + D T R +GF +V F D ++ + L
Sbjct: 2 FVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL 57
>gnl|CDD|218573 pfam05387, Chorion_3, Chorion family 3. This family consists of
several Drosophila chorion proteins S36 and S38. The
chorion genes of Drosophila are amplified in response to
developmental signals in the follicle cells of the
ovary.
Length = 277
Score = 27.8 bits (61), Expect = 5.1
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 108 GGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGG 144
GG GG G +Y G S + N + GG SGG
Sbjct: 24 GGGGGHGSGQYGA--GASAGLEEYVNAAAGGAQPSGG 58
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 27.8 bits (62), Expect = 5.4
Identities = 20/71 (28%), Positives = 22/71 (30%), Gaps = 7/71 (9%)
Query: 91 GKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQG---GSFNRDNMRNNSRGGGASSGGGFN 147
G + G+ GGG GG GG G F G G SSG G
Sbjct: 185 GGPRPERAGYG----GGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSG 240
Query: 148 DFSRGGEGPGG 158
G G G
Sbjct: 241 GTRSGQGGWGP 251
Score = 27.0 bits (60), Expect = 9.4
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 2/49 (4%)
Query: 119 NQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR 167
+GG GGG GGG S G P GF+++ P
Sbjct: 181 GGVRGGPRPERA--GYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPY 227
>gnl|CDD|216952 pfam02264, LamB, LamB porin. Maltoporin (LamB protein) forms a
trimeric structure which facilitates the diffusion of
maltodextrins across the outer membrane of Gram-negative
bacteria. The membrane channel is formed by an
antiparallel beta-barrel.
Length = 399
Score = 27.5 bits (61), Expect = 5.6
Identities = 20/105 (19%), Positives = 35/105 (33%), Gaps = 5/105 (4%)
Query: 58 YVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNK 117
Y +V +LR A + + + + ND K +N G M G +
Sbjct: 157 YQTNNNVFDLRLAGIP----LWPDGSLEVSGDYARANDEKDDYNL-NYGAAKDGWMFGAE 211
Query: 118 YNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNN 162
Q FN+ + + G + G + ++ G RN
Sbjct: 212 LTQGLLNGFNKFVFQYGTAGTALNFGHFWGAGTKYNGSGGEARNG 256
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 25.8 bits (57), Expect = 5.8
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 15 TAFVGNLPNGITQGDVERFF 34
T F+GNL T D+ F
Sbjct: 4 TLFIGNLEKTTTYSDLREAF 23
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 25.9 bits (57), Expect = 6.2
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 13/54 (24%)
Query: 17 FVGNLPNGITQG----DVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVEN 66
++GNLP ++ D+E+F P + +++VK+ K +V F+ + N
Sbjct: 7 YIGNLPESYSEEELREDLEKFGP---IDQIKIVKE------KNIAFVHFLSIAN 51
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 26.0 bits (58), Expect = 6.4
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 16/68 (23%)
Query: 20 NLPNGITQGDVERFF----------PEQKLVSVRLVKDKE------TDRFKGFCYVEFVD 63
NLP + + ++ F + K+ V++++D + + KG+ +VEF +
Sbjct: 7 NLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTN 66
Query: 64 VENLRQAL 71
E+ +AL
Sbjct: 67 HEHALKAL 74
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia
(DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE.
This subfamily corresponds to the RRM domain of two
Deleted in AZoospermia (DAZ) autosomal homologs, DAZL
(DAZ-like) and BOULE. BOULE is the founder member of
the family and DAZL arose from BOULE in an ancestor of
vertebrates. The DAZ gene subsequently originated from
a duplication transposition of the DAZL gene.
Invertebrates contain a single DAZ homolog, BOULE,
while vertebrates, other than catarrhine primates,
possess both BOULE and DAZL genes. The catarrhine
primates possess BOULE, DAZL, and DAZ genes. The family
members encode closely related RNA-binding proteins
that are required for fertility in numerous organisms.
These proteins contain an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a varying number of
copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 25.7 bits (57), Expect = 6.4
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 13 PYTAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
P FVG +P T+ ++ FF V V+++ D+ KG+ +V F E+ + +
Sbjct: 2 PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDA-EKI 59
Query: 72 LKDGRITVDGLQVRL 86
L G + G ++ +
Sbjct: 60 LAMGNLNFRGKKLNI 74
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 27.6 bits (62), Expect = 6.5
Identities = 12/37 (32%), Positives = 12/37 (32%), Gaps = 1/37 (2%)
Query: 137 GGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMND 173
G GG F D G GG PNR D
Sbjct: 82 FGFGGFGGDFGDIFEDFFG-GGGGGRRRPNRPRRGAD 117
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 76
Score = 25.9 bits (57), Expect = 6.5
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEF 61
+VG++ + + + + F P + S+ + D T + KGF +VE+
Sbjct: 4 YVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEY 49
>gnl|CDD|187695 cd07182, RNase_HII_bacteria_HII_like, bacterial Ribonuclease
HII-like. Ribonuclease H (RNase H) is classified into
two families, type I (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type II (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H
endonucleolytically hydrolyzes an RNA strand when it is
annealed to a complementary DNA strand in the presence
of divalent cations, in DNA replication and repair.
Bacterial RNase HII has a role in primer removal based
on its involvement in ribonucleotide-specific catalytic
activity in the presence of RNA/DNA hybrid substrates.
Several bacteria, such as Bacillus subtilis, have two
different type II RNases H, RNases HII and HIII; double
deletion of these leads to cellular lethality. It
appears that type I and type II RNases H also have
overlapping functions in cells, as over-expression of
Escherichia coli RNase HII can complement an RNase HI
deletion phenotype.
Length = 179
Score = 27.0 bits (61), Expect = 6.7
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 55 GFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA--DGKRNDN 96
G VE +D N+ QA L + V+GL+V+ D+ DG R
Sbjct: 59 GIASVEEIDRINILQATLLAMKRAVEGLKVKPDLVLVDGNRLPP 102
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 25.8 bits (56), Expect = 6.8
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
F+ NL +G + + F P + +V++++D T++ KGF +V + E A+
Sbjct: 5 FIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 26.2 bits (58), Expect = 7.5
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 134 NSRGGGASSGGGFNDF--SRGGEGPGGFRNNNG 164
N G G +GG + GG G GG+ N G
Sbjct: 75 NGGGRGWGNGGSGGGWVNGGGGWGNGGWVNGGG 107
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 25.3 bits (55), Expect = 7.7
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DG 75
F+G L + DVERFF + ++ D +GF +VEF D + A+ + DG
Sbjct: 3 FIGRLNPAAREKDVERFFKGYGRI-------RDIDLKRGFGFVEFDDPRDADDAVYELDG 55
Query: 76 R 76
+
Sbjct: 56 K 56
>gnl|CDD|240954 cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM1 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 74
Score = 25.3 bits (56), Expect = 7.8
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 54 KGFCYVEFVDVENLRQALLKDGRITVDGLQVRL 86
G ++ F E+ R A+ +DG+ T+ G +V+L
Sbjct: 39 MGEAFIAFATDEDARLAMSRDGQ-TIKGSKVKL 70
>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 85
Score = 25.8 bits (56), Expect = 8.0
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 17 FVGNLPNGITQGDVERFFPE--QKLVSVRLV---KDKETDRFKGFCYVEFVDVENLRQA- 70
FVG++P T+ + F + + L V L DK+ +R GFC++E+ D + QA
Sbjct: 6 FVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNR--GFCFLEYEDHKTAAQAR 63
Query: 71 -LLKDGRITVDG 81
L G++ V G
Sbjct: 64 RRLMSGKVKVWG 75
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 26.8 bits (60), Expect = 8.6
Identities = 20/62 (32%), Positives = 26/62 (41%)
Query: 98 GGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPG 157
GG +N N GG+ GG + G F N GGG GGG ++ GG G
Sbjct: 135 GGTSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNGGGGGGGYFGGGGGHYAGGGGGGS 194
Query: 158 GF 159
+
Sbjct: 195 SY 196
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 25.5 bits (56), Expect = 9.8
Identities = 15/44 (34%), Positives = 17/44 (38%)
Query: 102 NKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGG 145
GGG GG GG + GG + GGG GGG
Sbjct: 41 QDDKYGGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGG 84
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.139 0.411
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,708,980
Number of extensions: 1103406
Number of successful extensions: 1559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1339
Number of HSP's successfully gapped: 378
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 57 (25.6 bits)