Citrus Sinensis ID: 030341

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18

MADGYWRYSDARQPQSALPSLVSKRPRTDYDVPSGHELSSYYTRDDDRGALRGMRDTDSLGASYDRYLRSAQISSYSGGQSARHMSGGMPSRPVDDPRIVGIGGMDPGPSAKDRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLLF

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccHHHHHHHHccccccccEEEEEEccccccccEEEEc

cccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHccccccEEEEEEEcccccccEEEEcc

madgywrysdarqpqsalpslvskrprtdydvpsghelssyytrdddrgalrgmrdtdslgasYDRYLRSAqissysggqsarhmsggmpsrpvddprivgiggmdpgpsakdralglgggrsevplppdasstlfveglpsdcsrrevahifrpfvgykEVRLVSKESRHVSMIFLLF

madgywrysdarqpqsalpslvskrprtdydvpsghelssyytrdddrgalrGMRDTDSLGASYDRYLRSAQISSYSGGQSARHMSGGMPSRPVDDPRIVGIGGMDPGPSAKDRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHifrpfvgykevrlvskesrhvsmifllf

MADGYWRYSDARQPQSALPSLVSKRPRTDYDVPSGHELSSYYTRDDDRGALRGMRDTDSLGASYDRYLRSAQISSYSGGQSARHMSGGMPSRPVDDPRIVGIGGMDPGPSAKDRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLLF

**************************************************************************************************************************************LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLL*

*ADGYWR***************************************************SLGASYDRYL****************************************************************STLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLLF

MADGYWRYSDARQPQSALPSLVSKRPRTDYDVPSGHELSSYYTRDDDRGALRGMRDTDSLGASYDRYLRSAQI******************RPVDDPRIVGIGGMDPGPSAKDRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLLF

*****W**SD******AL*****KRPRTDYDVPSGHELSSYYTRDDDRGALRGMRDTDSLGASYDRYLRSAQISSYSGGQSARHMSGGMPSRPVDDPRIVGIGGMDPGPSAKDRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLLF

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MADGYWRYSDARQPQSALPSLVSKRPRTDYDVPSGHELSSYYTRDDDRGALRGMRDTDSLGASYDRYLRSAQISSYSGGQSARHMSGGMPSRPVDDPRIVGIGGMDPGPSAKDRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVSMIFLLF

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		179
255549562		232	nucleic acid binding protein, putative [	0.944	0.728	0.807	9e-71
427199356		233	RNA-binding protein with multiple splici	0.955	0.733	0.779	1e-70
224118350		233	predicted protein [Populus trichocarpa]	0.949	0.729	0.745	7e-64
302143942		230	unnamed protein product [Vitis vinifera]	0.944	0.734	0.684	6e-61
359490723		229	PREDICTED: uncharacterized protein LOC10	0.938	0.733	0.678	8e-59
224135091		220	predicted protein [Populus trichocarpa]	0.882	0.718	0.715	4e-58
449456997		232	PREDICTED: uncharacterized protein LOC10	0.944	0.728	0.625	3e-55
363807818		230	uncharacterized protein LOC100786188 [Gl	0.944	0.734	0.625	2e-53
363818125		230	uncharacterized protein LOC100800440 [Gl	0.944	0.734	0.619	7e-53
388505956		232	unknown [Lotus japonicus]	0.938	0.724	0.616	8e-52

>gi\|255549562\|ref\|XP_002515833.1\| nucleic acid binding protein, putative [Ricinus communis] gi\|223545062\|gb\|EEF46575.1\| nucleic acid binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  271 bits (693), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 138/171 (80%), Positives = 151/171 (88%), Gaps = 2/171 (1%)

Query: 1   MADGYWRYSDARQPQSA-LPSLVSKRPRTDYDVPSGHELSSYYTRDDDRGALRGMRDTDS 59
           MAD YWRYSDARQPQ   +P+LV KR R+DYDV SGHEL +YYTRDDDRGALR +RDTDS
Sbjct: 1   MADAYWRYSDARQPQQQPIPTLVGKRSRSDYDVTSGHELPNYYTRDDDRGALRAIRDTDS 60

Query: 60  LGASYDRYLRSAQISSYSGGQSARHMSGGMPSRPVDDPRIVGIGGMDPGPSAKDRALGLG 119
           +GASYDRYLRSA ISSYSGGQSAR +SG +P+R  DDPRI+GIGG+DPGP+ KDR LGLG
Sbjct: 61  IGASYDRYLRSAPISSYSGGQSARPISG-VPNRVADDPRIMGIGGLDPGPTVKDRTLGLG 119

Query: 120 GGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESR 170
            GR E  LPPDA+STLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESR
Sbjct: 120 SGRPETSLPPDATSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESR 170

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|427199356\|gb\|AFY26894.1\| RNA-binding protein with multiple splicing [Morella rubra]	Back alignment and taxonomy information

>gi\|224118350\|ref\|XP_002317797.1\| predicted protein [Populus trichocarpa] gi\|222858470\|gb\|EEE96017.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|302143942\|emb\|CBI23047.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359490723\|ref\|XP_002275189.2\| PREDICTED: uncharacterized protein LOC100265772 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224135091\|ref\|XP_002321981.1\| predicted protein [Populus trichocarpa] gi\|222868977\|gb\|EEF06108.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449456997\|ref\|XP_004146235.1\| PREDICTED: uncharacterized protein LOC101218789 [Cucumis sativus] gi\|449529543\|ref\|XP_004171759.1\| PREDICTED: uncharacterized protein LOC101224897 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|363807818\|ref\|NP_001241926.1\| uncharacterized protein LOC100786188 [Glycine max] gi\|255640386\|gb\|ACU20480.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|363818125\|ref\|NP_001242627.1\| uncharacterized protein LOC100800440 [Glycine max] gi\|255644702\|gb\|ACU22853.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|388505956\|gb\|AFK41044.1\| unknown [Lotus japonicus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		179
TAIR\|locus:2025232		233	AT1G76940 [Arabidopsis thalian	0.888	0.682	0.467	1.6e-29
TAIR\|locus:2014937		421	AT1G21320 [Arabidopsis thalian	0.810	0.344	0.456	5.6e-29
RGD\|1561067		110	Rbpms "RNA binding protein wit	0.195	0.318	0.513	0.00062

TAIR\|locus:2025232 AT1G76940 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 87/186 (46%), Positives = 113/186 (60%)

Query:     1 MADGYWRYSDARQPQSALPSLVSKRPRTDYDVPS-----GHELSSYYTRDDDRGALRGMR 55
             MADGYW  +  RQ Q   P    KRPR+D++ PS     GH    YY RD+D      + 
Sbjct:     1 MADGYW--NQQRQ-QHHPPGGPMKRPRSDFEAPSSTMTIGHG-GGYYPRDEDLD----VP 52

Query:    56 DTDSLGASYDRYLRSAQIS---SYSGGQSARHMSGGMPS-RPVDD--PRIVGIGGMDPGP 109
             DT ++G++YDRYL+S Q     S S G+S     GG  + + +DD   R  G+  +D GP
Sbjct:    53 DTRTIGSAYDRYLQSVQSGEGGSVSMGRSGGGGGGGGGNVQTIDDFMLRRGGVLPLDHGP 112

Query:   110 SAKDRALGLGG----GRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLV 165
             +     +G       GR    LP DAS+TL+VEGLPS+CSRREVAHIFRPFVGY+EVRLV
Sbjct:   113 NG--HTIGFDPPEPVGRRN--LPSDASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLV 168

Query:   166 SKESRH 171
             +K+S+H
Sbjct:   169 TKDSKH 174

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR\|locus:2014937 AT1G21320 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

RGD\|1561067 Rbpms "RNA binding protein with multiple splicing" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		179
cd12420		79	cd12420, RRM_RBPMS_like, RNA recognition motif in	5e-17
cd12247		72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	5e-08
cd12683		76	cd12683, RRM_RBPMS2, RNA recognition motif in vert	5e-04
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-04
cd12682		76	cd12682, RRM_RBPMS, RNA recognition motif in verte	9e-04
smart00360		73	smart00360, RRM, RNA recognition motif	0.002
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	0.002

>gnl\|CDD\|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins	Back alignment and domain information

 Score = 71.5 bits (176), Expect = 5e-17
 Identities = 26/50 (52%), Positives = 32/50 (64%), Gaps = 3/50 (6%)

Query: 133 STLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHVS---MIFLLF 179
            TLFV GLPSD   RE+AH+FRPF GY+  RLV KE +      + F+ F
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDF 50

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

>gnl\|CDD\|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family	Back alignment and domain information

>gnl\|CDD\|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2)	Back alignment and domain information

>gnl\|CDD\|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily	Back alignment and domain information

>gnl\|CDD\|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing (RBP-MS)	Back alignment and domain information

>gnl\|CDD\|214636 smart00360, RRM, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|215696 pfam00076, RRM_1, RNA recognition motif	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		179
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.92
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	98.42
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	97.96
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	97.77
KOG1457		284	consensus RNA binding protein (contains RRM repeat	97.61
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.58
KOG1457		284	consensus RNA binding protein (contains RRM repeat	97.52
smart00362		72	RRM_2 RNA recognition motif.	97.5
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	97.42
COG0724		306	RNA-binding proteins (RRM domain) [General functio	97.38
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	97.35
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	97.16
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.11
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	96.94
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	96.83
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	96.82
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	96.7
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	96.56
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	96.48
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	96.42
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	96.39
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	96.27
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	96.24
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	95.96
smart00360		71	RRM RNA recognition motif.	95.64
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	95.61
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	95.17
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	94.69
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	94.48
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	93.31
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	92.41
KOG0122		270	consensus Translation initiation factor 3, subunit	91.53
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	90.91
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	90.81
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	90.55
KOG1855		484	consensus Predicted RNA-binding protein [General f	90.27
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	89.75
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	88.97
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	88.74
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	88.48
KOG1548		382	consensus Transcription elongation factor TAT-SF1	87.93
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	87.49
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	87.02
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	86.75
KOG0533		243	consensus RRM motif-containing protein [RNA proces	85.88
KOG4660		549	consensus Protein Mei2, essential for commitment t	85.42
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	85.35
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	83.46
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	83.25
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	82.9
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	80.6

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

Probab=98.92  E-value=1.7e-09  Score=92.79  Aligned_cols=81  Identities=21%  Similarity=0.337  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCcccc-cCCCCCCCCCCCCcccc----------------------------CCCCCC----CCCCCCCCCe
Q 030341           88 GMPSRPVDDPRIVG-IGGMDPGPSAKDRALGL----------------------------GGGRSE----VPLPPDASST  134 (179)
Q Consensus        88 g~~~~~~~d~~~~~-~~~~d~~~~~~~~~~~~----------------------------~~~~p~----~~lPpdpn~i  134 (179)
                      -|.|.++.|..|+. +..-++|...+-++.-.                            ...+|.    ...||  |+|
T Consensus        71 ~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~pp--n~i  148 (221)
T KOG4206|consen   71 ALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPP--NNI  148 (221)
T ss_pred             HhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCC--ceE
Confidence            68999999999987 56667776654221100                            011122    22455  999


Q ss_pred             EEecCCCCcccHHHHHhhcCCCCCcceEEeeeccCC
Q 030341          135 LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESR  170 (179)
Q Consensus       135 LFVqNLP~d~T~~eL~~LF~qFpGFkEVRLVp~r~~  170 (179)
                      ||++|||.+++.++|+.||.||+||||||+|+.++.
T Consensus       149 lf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~  184 (221)
T KOG4206|consen  149 LFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSG  184 (221)
T ss_pred             EEEecCCcchhHHHHHHHHhhCcccceeEeccCCCc
Confidence            999999999999999999999999999999998764

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PF00076 RRM_1: RNA recognition motif	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>PLN03134 glycine-rich RNA-binding protein 4; Provisional	Back alignment and domain information

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>PF14259 RRM_6: RNA recognition motif (a	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>cd00590 RRM RRM (RNA recognition motif), 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	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]	Back alignment and domain information

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]	Back alignment and domain information

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]	Back alignment and domain information

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		179
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	98.47
2cq1_A		101	PTB-like protein L; RRM domain, structural genomic	98.46
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.45
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	98.39
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	98.38
1wi8_A		104	EIF-4B, eukaryotic translation initiation factor 4	98.37
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.37
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	98.36
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	98.35
2ad9_A		119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.32
1x4d_A		102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.32
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	98.32
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	98.3
1x4e_A		85	RNA binding motif, single-stranded interacting pro	98.3
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	98.29
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.28
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	98.28
2la6_A		99	RNA-binding protein FUS; structural genomics, nort	98.28
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	98.27
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.27
1wg5_A		104	Heterogeneous nuclear ribonucleoprotein H; structu	98.24
1sjq_A		105	Polypyrimidine tract-binding protein 1; babbab mot	98.24
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.23
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.23
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	98.23
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	98.23
2lxi_A		91	RNA-binding protein 10; NMR {Homo sapiens}	98.22
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	98.22
2dgw_A		91	Probable RNA-binding protein 19; RRM domain, struc	98.2
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	98.2
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	98.2
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	98.2
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	98.2
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.18
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	98.17
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.16
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	98.15
1x4f_A		112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.15
1wez_A		102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.15
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	98.15
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	98.14
2lkz_A		95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.14
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.13
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	98.12
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	98.12
2m2b_A		131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.12
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	98.12
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.11
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.11
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	98.11
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.11
2lmi_A		107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.11
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	98.1
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.09
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	98.09
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	98.09
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.09
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.09
2div_A		99	TRNA selenocysteine associated protein; structural	98.09
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.09
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.08
2cpy_A		114	RNA-binding protein 12; RRM domain, structural gen	98.08
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	98.08
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	98.07
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.07
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	98.06
2dh8_A		105	DAZ-associated protein 1; RRM domain, structural g	98.06
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.06
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	98.06
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.06
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	98.06
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.05
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	98.05
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.05
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.04
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	98.04
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	98.03
4fxv_A		99	ELAV-like protein 1; RNA recognition motif, putati	98.03
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	98.03
1x5t_A		96	Splicing factor 3B subunit 4; structure genomics,	98.03
2cq4_A		114	RNA binding motif protein 23; RRM domain, structur	98.02
2hgn_A		139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.02
2hgm_A		126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.01
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.01
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	98.0
2db1_A		118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.0
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	98.0
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	98.0
1x5o_A		114	RNA binding motif, single-stranded interacting pro	98.0
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	97.99
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	97.98
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	97.98
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	97.98
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	97.98
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	97.97
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	97.97
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	97.97
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	97.97
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	97.96
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	97.96
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	97.94
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.93
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	97.93
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	97.93
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	97.93
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	97.92
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	97.92
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	97.92
3zzy_A		130	Polypyrimidine tract-binding protein 1; protein bi	97.92
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	97.92
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	97.91
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	97.91
2dnn_A		109	RNA-binding protein 12; RRM domain, RBD, structura	97.9
2dha_A		123	FLJ20171 protein; RRM domain, structural genomics,	97.9
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	97.88
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	97.88
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	97.87
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	97.87
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	97.87
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	97.87
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	97.87
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	97.87
3p5t_L		90	Cleavage and polyadenylation specificity factor S;	97.86
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	97.86
1wel_A		124	RNA-binding protein 12; structural genomics, NPPSF	97.86
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	97.86
2dis_A		109	Unnamed protein product; structural genomics, RRM	97.86
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	97.85
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	97.82
2hgl_A		136	HNRPF protein, heterogeneous nuclear ribonucleopro	97.82
3md1_A		83	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.82
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	97.8
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	97.8
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	97.8
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	97.79
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	97.79
2e5i_A		124	Heterogeneous nuclear ribonucleoprotein L-like; RR	97.78
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	97.77
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	97.77
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	97.77
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	97.76
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	97.74
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	97.74
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	97.74
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	97.72
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	97.68
2cqh_A		93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	97.67
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	97.66
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	97.66
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.65
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	97.65
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	97.64
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	97.62
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	97.62
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	97.6
2hzc_A		87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	97.6
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	97.58
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	97.58
3n9u_C		156	Cleavage and polyadenylation specificity factor S;	97.57
2lcw_A		116	RNA-binding protein FUS; RRM, nucleic acid binding	96.7
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	97.55
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	97.55
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	97.54
2jvr_A		111	Nucleolar protein 3; RNA recognition motif, nucleu	97.52
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	97.5
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	97.5
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	97.48
3q2s_C		229	Cleavage and polyadenylation specificity factor S;	97.46
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	97.45
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.43
1x5p_A		97	Negative elongation factor E; structure genomics,	97.43
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	97.42
1sjr_A		164	Polypyrimidine tract-binding protein 1; extended b	97.41
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	97.34
2bz2_A		121	Negative elongation factor E; NELF E, RNA recognit	97.34
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	97.32
1fj7_A		101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	97.28
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	97.24
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	96.98
2cq2_A		114	Hypothetical protein LOC91801; RRM domain, structu	96.97
3u1l_A		240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.95
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	96.89
2diu_A		96	KIAA0430 protein; structural genomics, RRM domain,	96.69
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	96.48
1owx_A		121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	96.37
2wbr_A		89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	96.13
3tht_A		345	Alkylated DNA repair protein ALKB homolog 8; struc	95.97
2dit_A		112	HIV TAT specific factor 1 variant; structural geno	95.79
2d9o_A		100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	95.06
2pe8_A		105	Splicing factor 45; RRM, protein binding; 2.00A {H	94.36
1whv_A		100	Poly(A)-specific ribonuclease; RNA recognition mot	93.97
2j8a_A		136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	93.16
3v4m_A		105	Splicing factor U2AF 65 kDa subunit; canonical RNA	89.02
3ctr_A		101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	87.44
2dhx_A		104	Poly (ADP-ribose) polymerase family, member 10 var	85.87
3ue2_A		118	Poly(U)-binding-splicing factor PUF60; RNA recogni	85.32
1uw4_A		91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	82.55

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

Probab=98.47  E-value=1.7e-07  Score=65.83  Aligned_cols=44  Identities=27%  Similarity=0.533  Sum_probs=38.1

Q ss_pred             CCCCCCCCCeEEecCCCCcccHHHHHhhcCCCCCcceEEeeeccC
Q 030341          125 VPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKES  169 (179)
Q Consensus       125 ~~lPpdpn~iLFVqNLP~d~T~~eL~~LF~qFpGFkEVRLVp~r~  169 (179)
                      .+.|+.++++|||.|||.++|+++|..+|.+| |.++|+++..+.
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~-gi~~v~i~~~~~   51 (103)
T 2dng_A            8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKD   51 (103)
T ss_dssp             CCCCSSSCEEEEEESCCTTCCHHHHHHHTTTS-CEEEEEEEECSS
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhC-CceEEEEeecCC
Confidence            34445568999999999999999999999999 799999997653

PyMOL of 2dng

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}	Back alignment and structure

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B	Back alignment and structure

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}	Back alignment and structure

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A	Back alignment and structure

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}	Back alignment and structure

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A	Back alignment and structure

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A	Back alignment and structure

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}	Back alignment and structure

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A	Back alignment and structure

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A	Back alignment and structure

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}	Back alignment and structure

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A	Back alignment and structure

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}	Back alignment and structure

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A	Back alignment and structure

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B	Back alignment and structure

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}	Back alignment and structure

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A	Back alignment and structure

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}	Back alignment and structure

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}	Back alignment and structure

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}	Back alignment and structure

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}	Back alignment and structure

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*	Back alignment and structure

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}	Back alignment and structure

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}	Back alignment and structure

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A	Back alignment and structure

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A	Back alignment and structure

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*	Back alignment and structure

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A	Back alignment and structure

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}	Back alignment and structure

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}	Back alignment and structure

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A	Back alignment and structure

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A	Back alignment and structure

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*	Back alignment and structure

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}	Back alignment and structure

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}	Back alignment and structure

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A	Back alignment and structure

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}	Back alignment and structure

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A	Back alignment and structure

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}	Back alignment and structure

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A	Back alignment and structure

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}	Back alignment and structure

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}	Back alignment and structure

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X	Back alignment and structure

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}	Back alignment and structure

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A	Back alignment and structure

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...	Back alignment and structure

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A	Back alignment and structure

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A	Back alignment and structure

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A	Back alignment and structure

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A	Back alignment and structure

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A	Back alignment and structure

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A	Back alignment and structure

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1	Back alignment and structure

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A	Back alignment and structure

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A	Back alignment and structure

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0	Back alignment and structure

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}	Back alignment and structure

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A	Back alignment and structure

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A	Back alignment and structure

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A	Back alignment and structure

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A	Back alignment and structure

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}	Back alignment and structure

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}	Back alignment and structure

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*	Back alignment and structure

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1	Back alignment and structure

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A	Back alignment and structure

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}	Back alignment and structure

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}	Back alignment and structure

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A	Back alignment and structure

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A	Back alignment and structure

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A	Back alignment and structure

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}	Back alignment and structure

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1	Back alignment and structure

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A	Back alignment and structure

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A	Back alignment and structure

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B	Back alignment and structure

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A	Back alignment and structure

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A	Back alignment and structure

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A	Back alignment and structure

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B	Back alignment and structure

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A	Back alignment and structure

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A	Back alignment and structure

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}	Back alignment and structure

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*	Back alignment and structure

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A	Back alignment and structure

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*	Back alignment and structure

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}	Back alignment and structure

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A	Back alignment and structure

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}	Back alignment and structure

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A	Back alignment and structure

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		179
d2f9da1		114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-04
d2cpha1		94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-04
d1x4ga1		96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-04
d2cqca1		83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	0.001
d2adca2		88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	0.002

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 5e-04
 Identities = 9/35 (25%), Positives = 18/35 (51%)

Query: 127 LPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKE 161
           LPP+ +  L++  LP   +  E+  IF  +   ++
Sbjct: 2   LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ 36

PyMOL of d2f9da1

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83	Back information, alignment and structure

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		179
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	98.81
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.58
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	98.45
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	98.43
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.36
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.35
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.34
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.3
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.3
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.29
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.25
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.23
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.23
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.21
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.21
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.2
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	98.17
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.17
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.14
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.14
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.14
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.13
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	98.12
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	98.11
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.11
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.1
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.08
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.08
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.08
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.08
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.07
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.06
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	98.05
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.04
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.04
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.0
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.0
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	97.98
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	97.97
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	97.96
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	97.96
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	97.95
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	97.94
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.94
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	97.92
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	97.92
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	97.9
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.9
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	97.89
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	97.89
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.89
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	97.89
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	97.89
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	97.87
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	97.85
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	97.84
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.84
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	97.83
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	97.81
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.77
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	97.76
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	97.75
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	97.74
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	97.72
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.71
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	97.71
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	97.67
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	97.67
d2cqha1		80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	97.63
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	97.6
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	97.6
d2cq2a1		101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	97.58
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	97.55
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	97.53
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	97.5
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	97.49
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	97.47
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.4
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.22
d1owxa_		113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.21
d1weya_		104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	96.76
d1u2fa_		90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.66
d2dita1		99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	89.82
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_		104	U2	88.52
d1wwha1		81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	88.34
d1o0pa_		104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	83.16

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=98.81  E-value=1.9e-09  Score=73.46  Aligned_cols=41  Identities=37%  Similarity=0.733  Sum_probs=37.6

Q ss_pred             CCCCCCCCCeEEecCCCCcccHHHHHhhcCCCCCcceEEeeec
Q 030341          125 VPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSK  167 (179)
Q Consensus       125 ~~lPpdpn~iLFVqNLP~d~T~~eL~~LF~qFpGFkEVRLVp~  167 (179)
                      ...||  |+||||.|||.++|+++|..+|++|.+.++|++++.
T Consensus         3 ~~~pP--~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~   43 (83)
T d2b0ga1           3 TEQPP--NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN   43 (83)
T ss_dssp             CCCSC--CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT
T ss_pred             CCCCC--CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc
Confidence            45566  999999999999999999999999999999999864

PyMOL of d2b0ga1

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}	Back information, alignment and structure

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure