Citrus Sinensis ID: 007386

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-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-----

MAFFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKLVESSDKTKEHESLRKVKAVNSDPSCGERTKNKNFDDVSNDSSYSQLSSDEIIDSFYTREAKQI

cccccccEEEEccccccccccccEEEEEEccHHHHHHHcccccHHHHHcccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHccccccccccccHHHHHHHHHHHHHHccccEEEEEcccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccEEEEEHHHHHHHHHHHHccccccccHHHHHHHHHHHcccEEEEHHHHHccHHHHHHHccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccccEEEccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHHHcccccEEEEEEEccEEEEEEccHHHHHHHHHHHHHccccccccccccHHHHHHcccccccccHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcc

ccccccEEEEEEccccccccccccEEEEEHHHHHHHHHccccHHHHHHcccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHcccccccccccccccccHHHHHHHHHHHHHccccEEEEEEccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccEEccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccEEcHHHHHHHccHHHHcccccHHHHHHHHHHHcccccccHHcccccccccccccEEccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHcHHcccccEEccccEcccccccccccccccccccccccEEEEEEccccccHHHHHHHHHHHcccccEEEEEEEcccEEEEEEcccHHHHHHHHHHccHHHHccHHHHHHHHHHHcccccEEccccccHHHHHccccccccHHHHHHHHcccccHHHHHHHcccccccccccccccccccccccccccccHHHHccccccccccHHHHHHHHHHHHHccc

maffgrhnffifqrqelpldgaAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNstyedesldswHSLKEIRdthlfnipdILFAERMKDRLSEWLGGllrnrdegsevqpsfndskQQFETIFFkmrpaislngftSHQLLLIQLVVRKHFKDLAYLRVsgenscsqNVIVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYskffgplpltAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLcpqialgsksthlalqpsvkvevevddirssnwnsgvkheagydAFMTGCVFAQAcshlgidfkqqsssenlaHNEKLREHVNLLYLSWtngeiinlstgnrtseslasnkrknhypkiLFECIVIvwgfpshlkawdIRECiskvygptsvisVYHVDETAVFVQFSRAEMVSKFLDlkgsldrnndpisvLHPLAKLleggntcaASYETYKEICSSTVSKVLFADQAKAVGIKWktklvessdktkeheslrkvkavnsdpscgertknknfddvsndssysqlssdeIIDSFYTREAKQI

MAFFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLrvsgenscsqnVIVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGsksthlalqpsVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYLSWTNGEIINLstgnrtseslasnkrknhyPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFAdqakavgikwktklvessdktkeheslrkvkavnsdpscgertknknfddvsndssysqlssdeiidSFYTREAKQI

**FFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLS******************SLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLR******************FETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYIE*********************MSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSIL************KAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFK************KLREHVNLLYLSWTNGEIINLST**************NHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKLV**************************************************************

MAFFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKAL**V***************************DILFAERMKDRLSEWLGGLLRN************D***********MRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQN***************************MSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK**TSLSKAFSVLCPQIAL****T*LALQPSVKVEVEVDDIR*******VKHEAGYDAFMTGCVFAQACSHLGIDFKQQ*****LAHNEKLREHVNLLYLSWTNGEIINLSTGN****************KILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS****ND**SVLHPLAKLLEGGNTCAASYETYKEICSSTV*****ADQAKAVGIKW****************************************************DEIIDSFYTR*****

MAFFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRD**********DSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQ**********SKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKL***************VKAVNSDPSCGERTKNKNFDDVSNDSSYSQLSSDEIIDSFYTREAKQI

*AFFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESL************HLFNIPDILFAERMKDRLSEWLGGLLRNR*****VQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKLVESSD***********************************SSYSQLSSDEIIDSFYTREAKQ*

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		605	2.2.26 [Sep-21-2011]
Q9LG26		689	Poly(A)-specific ribonucl	yes	no	0.867	0.761	0.579	1e-178
Q8W4C3		618	Poly(A)-specific ribonucl	no	no	0.765	0.749	0.248	3e-30
Q90ZA1		631	Poly(A)-specific ribonucl	N/A	no	0.651	0.624	0.261	7e-26
Q7ZU92		660	Poly(A)-specific ribonucl	yes	no	0.661	0.606	0.245	8e-23
P69341		638	Poly(A)-specific ribonucl	yes	no	0.659	0.625	0.233	2e-21
Q5RC51		639	Poly(A)-specific ribonucl	yes	no	0.657	0.622	0.230	2e-20
O95453		639	Poly(A)-specific ribonucl	yes	no	0.657	0.622	0.230	2e-20
Q8VDG3		624	Poly(A)-specific ribonucl	yes	no	0.647	0.628	0.235	6e-17
Q5R6R6		520	Poly(A)-specific ribonucl	no	no	0.477	0.555	0.254	6e-17
Q8NA58		520	Poly(A)-specific ribonucl	no	no	0.477	0.555	0.251	4e-16

>sp\|Q9LG26\|PARN_ARATH Poly(A)-specific ribonuclease PARN OS=Arabidopsis thaliana GN=PARN PE=1 SV=2	Back alignment and function desciption

 Score =  627 bits (1616), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 310/535 (57%), Positives = 403/535 (75%), Gaps = 10/535 (1%)

Query: 7   HNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHV 66
           HNFF+F RQEL  D  A+EFLCQTTSMDFLAKYQFDFN CIHEG+SYLSR +E++A K +
Sbjct: 124 HNFFVFPRQELTFDPPAHEFLCQTTSMDFLAKYQFDFNTCIHEGISYLSRREEEEASKRL 183

Query: 67  NSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSF 126
              + ++ +DS    +E++   L  + D+LFA RM+  L+EW  GLL   +  SE     
Sbjct: 184 KMLHGEDGIDSSGETEELK---LVRLADVLFAARMEKLLNEWRSGLLHGGNASSEFPRIS 240

Query: 127 NDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186
           N S Q  ET+F  MRPA+SL GFTSHQL ++  V+RKHF DL Y+  + ++S S++++VY
Sbjct: 241 NGSNQSMETVFHHMRPALSLKGFTSHQLRVLNSVLRKHFGDLVYIHSNDKSSSSRDIVVY 300

Query: 187 IESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYS 246
            +S+SDK+ LMKE KDE+K  AE  I+++IGFR VIDLL+SEKKLIVGHNCFLDIAH+YS
Sbjct: 301 TDSDSDKENLMKEAKDERKRLAERKIQSAIGFRQVIDLLASEKKLIVGHNCFLDIAHVYS 360

Query: 247 KFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306
           KF GPLP TAE+F++S+N +FP+I+DTKILLN N +L QRMKKSSTSLS AFS LCPQI 
Sbjct: 361 KFVGPLPSTAEKFVASINSHFPYIVDTKILLNVNPMLHQRMKKSSTSLSSAFSSLCPQIE 420

Query: 307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQ 366
             S+S+   LQ  V ++VE+D++R SNWN+G KHEAGYDAFMTGC+FAQAC+HLG DFKQ
Sbjct: 421 FSSRSSDSFLQQRVNIDVEIDNVRCSNWNAGGKHEAGYDAFMTGCIFAQACNHLGFDFKQ 480

Query: 367 QSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIV 426
            S  ++ A NEKL +++N LYLSWT G+II+L TG+  +++   +K K       +E IV
Sbjct: 481 HSQLDDFAQNEKLEKYINRLYLSWTRGDIIDLRTGHSNADNWRVSKFK-------YENIV 533

Query: 427 IVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDR 486
           ++W FP  LKA  I+ECI K +G  SV SVYHVD++AVFV F  +E+V  FL LK  L+ 
Sbjct: 534 LIWNFPRKLKARGIKECICKAFGSASVTSVYHVDDSAVFVLFKNSELVWDFLALKRQLES 593

Query: 487 NNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTK 541
           ++ P+SVLHPL+K+LEGGNT AA YE YKEICSS VS+V+F+DQA+ VG+K +T+
Sbjct: 594 SDGPVSVLHPLSKILEGGNTGAADYEAYKEICSSHVSEVMFSDQAETVGVKSRTR 648

3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs. Essential for early development, possibly by participating in silencing certain maternal mRNAs translationally. May have a pivotal role in stress response.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 4

>sp\|Q8W4C3\|PARNL_ARATH Poly(A)-specific ribonuclease PARN-like OS=Arabidopsis thaliana GN=At3g25430 PE=2 SV=1	Back alignment and function description

>sp\|Q90ZA1\|PARN_XENLA Poly(A)-specific ribonuclease PARN OS=Xenopus laevis GN=parn PE=1 SV=1	Back alignment and function description

>sp\|Q7ZU92\|PARN_DANRE Poly(A)-specific ribonuclease PARN OS=Danio rerio GN=parn PE=1 SV=2	Back alignment and function description

>sp\|P69341\|PARN_BOVIN Poly(A)-specific ribonuclease PARN OS=Bos taurus GN=PARN PE=1 SV=2	Back alignment and function description

>sp\|Q5RC51\|PARN_PONAB Poly(A)-specific ribonuclease PARN OS=Pongo abelii GN=PARN PE=2 SV=1	Back alignment and function description

>sp\|O95453\|PARN_HUMAN Poly(A)-specific ribonuclease PARN OS=Homo sapiens GN=PARN PE=1 SV=1	Back alignment and function description

>sp\|Q8VDG3\|PARN_MOUSE Poly(A)-specific ribonuclease PARN OS=Mus musculus GN=Parn PE=1 SV=1	Back alignment and function description

>sp\|Q5R6R6\|PNDC1_PONAB Poly(A)-specific ribonuclease PARN-like domain-containing protein 1 OS=Pongo abelii GN=PNLDC1 PE=2 SV=1	Back alignment and function description

>sp\|Q8NA58\|PNDC1_HUMAN Poly(A)-specific ribonuclease PARN-like domain-containing protein 1 OS=Homo sapiens GN=PNLDC1 PE=2 SV=2	Back alignment and function description

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		605
225461941		734	PREDICTED: poly(A)-specific ribonuclease	0.981	0.809	0.651	0.0
296089929		715	unnamed protein product [Vitis vinifera]	0.960	0.812	0.653	0.0
147799285		720	hypothetical protein VITISV_007764 [Viti	0.958	0.805	0.622	0.0
224061228		675	predicted protein [Populus trichocarpa]	0.877	0.786	0.680	0.0
255563538		699	conserved hypothetical protein [Ricinus	0.950	0.822	0.627	0.0
356524370		718	PREDICTED: poly(A)-specific ribonuclease	0.981	0.827	0.587	0.0
356569615		714	PREDICTED: poly(A)-specific ribonuclease	0.976	0.827	0.595	0.0
449461041		700	PREDICTED: poly(A)-specific ribonuclease	0.900	0.778	0.581	0.0
297847952		689	Poly(A)-specific ribonuclease [Arabidops	0.905	0.795	0.573	1e-179
240254280		689	Poly(A)-specific ribonuclease PARN [Arab	0.867	0.761	0.579	1e-177

>gi\|225461941\|ref\|XP_002266069.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  816 bits (2107), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/602 (65%), Positives = 488/602 (81%), Gaps = 8/602 (1%)

Query: 7   HNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHV 66
           HNF++F RQELP+DG +YEFLCQTTS+DFLAKYQFDFNACI+EG+SYLSREQE++ L+ +
Sbjct: 126 HNFYVFPRQELPVDGPSYEFLCQTTSIDFLAKYQFDFNACIYEGISYLSREQENEMLRCL 185

Query: 67  NSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSF 126
           NS  +DE    W ++KE+RDT L ++ D+LF+ERMK+R +EW   LL++R  GS+   + 
Sbjct: 186 NSECDDEMSLLWRNMKEVRDTPLVSVADVLFSERMKNRFNEWRKELLQDRKGGSQFLETS 245

Query: 127 NDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186
           ND KQQF+TIFFKMRPA+ LNGFT+HQL LIQLV++KHFKDL Y+R SG+ S S+ +IVY
Sbjct: 246 NDMKQQFQTIFFKMRPALILNGFTAHQLRLIQLVIKKHFKDLVYIRSSGDGSYSE-LIVY 304

Query: 187 IESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYS 246
           I+S++DK +LMKEVKD  + +AEM IK ++GFRHVIDLLSSE+KLIVGHNC LDIAHIY+
Sbjct: 305 IDSDNDKNLLMKEVKDGLRREAEMKIKTAVGFRHVIDLLSSEQKLIVGHNCLLDIAHIYN 364

Query: 247 KFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306
           KFFGPLPLTAE+F+SS++KYFP++IDTKILLN+N++L+  MK  STSLSKAF+ LCPQIA
Sbjct: 365 KFFGPLPLTAEDFVSSIHKYFPYMIDTKILLNTNNVLKHLMKNGSTSLSKAFASLCPQIA 424

Query: 307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQ 366
             SK++ LA QP V+VEV+VDD+RSSNWNSG KHEAGYDAFMTGCVFAQACS+LGIDFK+
Sbjct: 425 SSSKNSGLAFQPWVEVEVQVDDMRSSNWNSGAKHEAGYDAFMTGCVFAQACSNLGIDFKK 484

Query: 367 QSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIV 426
            SSS NLAHN+ L++HVN LY SW NG+II+L TGNR + +      K  YPKILF  IV
Sbjct: 485 HSSSANLAHNKNLQKHVNHLYFSWVNGDIIDLGTGNRIAATTVCYNLKRRYPKILFSNIV 544

Query: 427 IVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDR 486
           IVWGFPS L +  IRECISK +GP SV ++YH+DETAVFVQFS+ E+V+ FL LK +L+ 
Sbjct: 545 IVWGFPSQLSSKKIRECISKAFGPISVTTIYHLDETAVFVQFSKPELVADFLVLKETLET 604

Query: 487 NNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKLVESS 546
             DPISVLHPL+ LLEGGNTCAASYETYKEICSS +SKV+FADQAKAVGIKWKTKL+ES 
Sbjct: 605 IQDPISVLHPLSVLLEGGNTCAASYETYKEICSSPISKVMFADQAKAVGIKWKTKLIESK 664

Query: 547 D--KTKEHESLRKVKAVN---SDPSCGERTKNKNFDDVSNDSSYSQLSSDEIIDSFYTRE 601
           +  KT+E ES  K        SDP+  +++K +  +DV ++ S  ++S  EIIDS Y  +
Sbjct: 665 EKVKTQEDESFSKENGATDAASDPA--DKSKTRKIEDVIDNLSDDRISGSEIIDSLYAAQ 722

Query: 602 AK 603
            K
Sbjct: 723 TK 724

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|296089929\|emb\|CBI39748.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147799285\|emb\|CAN76999.1\| hypothetical protein VITISV_007764 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224061228\|ref\|XP_002300380.1\| predicted protein [Populus trichocarpa] gi\|222847638\|gb\|EEE85185.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255563538\|ref\|XP_002522771.1\| conserved hypothetical protein [Ricinus communis] gi\|223538009\|gb\|EEF39622.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|356524370\|ref\|XP_003530802.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Glycine max]	Back alignment and taxonomy information

>gi\|356569615\|ref\|XP_003552994.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Glycine max]	Back alignment and taxonomy information

>gi\|449461041\|ref\|XP_004148252.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Cucumis sativus] gi\|449524565\|ref\|XP_004169292.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297847952\|ref\|XP_002891857.1\| Poly(A)-specific ribonuclease [Arabidopsis lyrata subsp. lyrata] gi\|297337699\|gb\|EFH68116.1\| Poly(A)-specific ribonuclease [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|240254280|ref|NP_175983.5| Poly(A)-specific ribonuclease PARN [Arabidopsis thaliana] gi|60390594|sp|Q9LG26.2|PARN_ARATH RecName: Full=Poly(A)-specific ribonuclease PARN; AltName: Full=Polyadenylate-specific ribonuclease; Short=AtPARN; AltName: Full=Protein ABA hypersensitive germination 2 gi|65736526|dbj|BAD98514.1| poly(A)-specific ribonuclease [Arabidopsis thaliana] gi|332195190|gb|AEE33311.1| Poly(A)-specific ribonuclease PARN [Arabidopsis thaliana]

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		605
TAIR\|locus:2012100		689	AHG2 "ABA-HYPERSENSITIVE GERMI	0.890	0.782	0.572	6.6e-168
TAIR\|locus:2094533		618	AT3G25430 [Arabidopsis thalian	0.471	0.461	0.284	1.1e-27
ZFIN\|ZDB-GENE-040426-880		660	parn "poly(A)-specific ribonuc	0.406	0.372	0.269	1.3e-21
UNIPROTKB\|F1NEI8		631	F1NEI8 "Uncharacterized protei	0.310	0.297	0.273	1.3e-20
UNIPROTKB\|P69341		638	PARN "Poly(A)-specific ribonuc	0.370	0.351	0.276	3.3e-19
UNIPROTKB\|E2QZA0		496	PARN "Uncharacterized protein"	0.370	0.451	0.267	3.5e-19
UNIPROTKB\|F6XU41		638	PARN "Uncharacterized protein"	0.368	0.349	0.271	4.7e-19
RGD\|1565449		624	Parn "poly(A)-specific ribonuc	0.327	0.317	0.287	8e-19
UNIPROTKB\|O95453		639	PARN "Poly(A)-specific ribonuc	0.370	0.350	0.272	1.6e-18
UNIPROTKB\|E1BVT8		529	PNLDC1 "Uncharacterized protei	0.358	0.410	0.264	1.7e-18

TAIR\|locus:2012100 AHG2 "ABA-HYPERSENSITIVE GERMINATION 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1633 (579.9 bits), Expect = 6.6e-168, P = 6.6e-168
 Identities = 315/550 (57%), Positives = 410/550 (74%)

Query:     7 HNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHV 66
             HNFF+F RQEL  D  A+EFLCQTTSMDFLAKYQFDFN CIHEG+SYLSR +E++A K +
Sbjct:   124 HNFFVFPRQELTFDPPAHEFLCQTTSMDFLAKYQFDFNTCIHEGISYLSRREEEEASKRL 183

Query:    67 NSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSF 126
                + ++ +DS    +E++   L  + D+LFA RM+  L+EW  GLL   +  SE     
Sbjct:   184 KMLHGEDGIDSSGETEELK---LVRLADVLFAARMEKLLNEWRSGLLHGGNASSEFPRIS 240

Query:   127 NDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186
             N S Q  ET+F  MRPA+SL GFTSHQL ++  V+RKHF DL Y+  + ++S S++++VY
Sbjct:   241 NGSNQSMETVFHHMRPALSLKGFTSHQLRVLNSVLRKHFGDLVYIHSNDKSSSSRDIVVY 300

Query:   187 IESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYS 246
              +S+SDK+ LMKE KDE+K  AE  I+++IGFR VIDLL+SEKKLIVGHNCFLDIAH+YS
Sbjct:   301 TDSDSDKENLMKEAKDERKRLAERKIQSAIGFRQVIDLLASEKKLIVGHNCFLDIAHVYS 360

Query:   247 KFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306
             KF GPLP TAE+F++S+N +FP+I+DTKILLN N +L QRMKKSSTSLS AFS LCPQI 
Sbjct:   361 KFVGPLPSTAEKFVASINSHFPYIVDTKILLNVNPMLHQRMKKSSTSLSSAFSSLCPQIE 420

Query:   307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQ 366
               S+S+   LQ  V ++VE+D++R SNWN+G KHEAGYDAFMTGC+FAQAC+HLG DFKQ
Sbjct:   421 FSSRSSDSFLQQRVNIDVEIDNVRCSNWNAGGKHEAGYDAFMTGCIFAQACNHLGFDFKQ 480

Query:   367 QSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIV 426
              S  ++ A NEKL +++N LYLSWT G+II+L TG+    S A N R +   K  +E IV
Sbjct:   481 HSQLDDFAQNEKLEKYINRLYLSWTRGDIIDLRTGH----SNADNWRVS---KFKYENIV 533

Query:   427 IVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDR 486
             ++W FP  LKA  I+ECI K +G  SV SVYHVD++AVFV F  +E+V  FL LK  L+ 
Sbjct:   534 LIWNFPRKLKARGIKECICKAFGSASVTSVYHVDDSAVFVLFKNSELVWDFLALKRQLES 593

Query:   487 NNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKL-VES 545
             ++ P+SVLHPL+K+LEGGNT AA YE YKEICSS VS+V+F+DQA+ VG+K +T+   + 
Sbjct:   594 SDGPVSVLHPLSKILEGGNTGAADYEAYKEICSSHVSEVMFSDQAETVGVKSRTRPNAQC 653

Query:   546 SDKTKEHESL 555
               +T+E  ++
Sbjct:   654 ETETREENTV 663

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0009451 "RNA modification" evidence=ISS

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0009651 "response to salt stress" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0009751 "response to salicylic acid stimulus" evidence=IMP

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

TAIR\|locus:2094533 AT3G25430 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-880 parn "poly(A)-specific ribonuclease (deadenylation nuclease)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NEI8 F1NEI8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|P69341 PARN "Poly(A)-specific ribonuclease PARN" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QZA0 PARN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F6XU41 PARN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

RGD\|1565449 Parn "poly(A)-specific ribonuclease" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|O95453 PARN "Poly(A)-specific ribonuclease PARN" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BVT8 PNLDC1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LG26	PARN_ARATH	3, ., 1, ., 1, 3, ., 4	0.5794	0.8677	0.7619	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.13.4	0.914
3rd Layer	3.1.13	0.921

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		605
pfam04857		235	pfam04857, CAF1, CAF1 family ribonuclease	2e-15
pfam04857		235	pfam04857, CAF1, CAF1 family ribonuclease	7e-04

>gnl\|CDD\|147159 pfam04857, CAF1, CAF1 family ribonuclease	Back alignment and domain information

 Score = 75.4 bits (186), Expect = 2e-15
 Identities = 32/161 (19%), Positives = 54/161 (33%), Gaps = 40/161 (24%)

Query: 203 EQKIDAEMSIKASIGFRHVIDLLSS-------EKKLIVGHNCFLDIAHIYSKFFG-PLPL 254
           +Q  D     +  I +    +LL S            V  +   D  ++     G PLP 
Sbjct: 107 KQGFDFNKHRREGIPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPE 166

Query: 255 TAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHL 314
           T ++F+  + + FP + DTK L        +    S+  L                   L
Sbjct: 167 TLDDFLELLRELFPRVYDTKYL---AKFCFELDGGSNGGL-----------------QEL 206

Query: 315 ALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQ 355
           A         ++  +       G  H+AG D+ +T  VF +
Sbjct: 207 A---------DLLGVNRR---VGRLHQAGSDSLLTALVFFK 235

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution. Length = 235

>gnl\|CDD\|147159 pfam04857, CAF1, CAF1 family ribonuclease	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		605
PF04857		262	CAF1: CAF1 family ribonuclease; InterPro: IPR00694	100.0
KOG1990		564	consensus Poly(A)-specific exoribonuclease PARN [R	99.8
KOG0304		239	consensus mRNA deadenylase subunit [RNA processing	99.73
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	99.58
COG5228		299	POP2 mRNA deadenylase subunit [RNA processing and	99.27
cd02637		65	R3H_PARN R3H domain of Poly(A)-specific ribonuclea	98.03
PF10309		62	DUF2414: Protein of unknown function (DUF2414); In	97.12
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	96.96
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	96.92
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	96.91
PRK09145		202	DNA polymerase III subunit epsilon; Validated	96.69
PRK07740		244	hypothetical protein; Provisional	96.69
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	96.62
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	96.61
PRK06195		309	DNA polymerase III subunit epsilon; Validated	96.53
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	96.52
PRK05168		211	ribonuclease T; Provisional	96.4
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	96.26
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	96.05
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	95.97
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	95.78
PRK06310		250	DNA polymerase III subunit epsilon; Validated	95.68
PRK06722		281	exonuclease; Provisional	95.59
PRK09146		239	DNA polymerase III subunit epsilon; Validated	95.41
PRK06807		313	DNA polymerase III subunit epsilon; Validated	95.31
PRK07748		207	sporulation inhibitor KapD; Provisional	95.31
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	95.23
PRK07983		219	exodeoxyribonuclease X; Provisional	95.22
cd06127		159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	94.88
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	94.75
PRK06309		232	DNA polymerase III subunit epsilon; Validated	94.45
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	94.39
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	94.09
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	94.05
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	93.95
KOG4483		528	consensus Uncharacterized conserved protein [Funct	93.93
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	93.86
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	93.72
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	93.71
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	93.44
PRK00448		1437	polC DNA polymerase III PolC; Validated	92.75
smart00362		72	RRM_2 RNA recognition motif.	92.7
PRK07247		195	DNA polymerase III subunit epsilon; Validated	92.45
PRK07883		557	hypothetical protein; Validated	91.81
PF00929		164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	90.75
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	90.63
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	90.27
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	90.23
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	89.65
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	89.42
PRK09182		294	DNA polymerase III subunit epsilon; Validated	89.17
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	88.83
smart00360		71	RRM RNA recognition motif.	88.28
cd06138		183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	87.54
PRK05601		377	DNA polymerase III subunit epsilon; Validated	86.73
PTZ00315		582	2'-phosphotransferase; Provisional	86.36
COG0847		243	DnaQ DNA polymerase III, epsilon subunit and relat	86.13
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	85.92
cd06396		81	PB1_NBR1 The PB1 domain is an essential part of NB	85.58
PF01424		63	R3H: R3H domain; InterPro: IPR001374 The R3H motif	85.06
cd06407		82	PB1_NLP A PB1 domain is present in NIN like protei	84.85
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	83.32
PRK11779		476	sbcB exonuclease I; Provisional	80.99
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	80.24
cd02325		59	R3H R3H domain. The name of the R3H domain comes f	80.04

>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation	Back alignment and domain information

Probab=100.00  E-value=3.1e-41  Score=345.92  Aligned_cols=127  Identities=43%  Similarity=0.600  Sum_probs=88.5

Q ss_pred             hccHHHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCCh
Q 007386          215 SIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSL  294 (605)
Q Consensus       215 ~iGfr~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL  294 (605)
                      .+||+.|++.+.+++||||||||++|++|||++|+||||++++||++.++.+||.|||||||++.++       ...++|
T Consensus       135 ~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~-------~~~~~L  207 (262)
T PF04857_consen  135 LLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECP-------GKSTSL  207 (262)
T ss_dssp             HHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT-------TS-SSH
T ss_pred             hHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcc-------ccccCH
Confidence            4788888899999999999999999999999999999999999999999999999999999998765       247899


Q ss_pred             HHHHHhhhhhcccCCcccccccCCCceeeeeecccccc-CCCCCcccchhhhHHHHHHHHHH
Q 007386          295 SKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSS-NWNSGVKHEAGYDAFMTGCVFAQ  355 (605)
Q Consensus       295 ~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~-~~~~~~~HEAGyDA~mTG~vF~k  355 (605)
                      +.+++.+...-.....     ..+....  ........ .......|||||||||||+||++
T Consensus       208 ~~l~~~l~~~~~~~~~-----~~~~~~~--~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~  262 (262)
T PF04857_consen  208 QELAEELGIRRNPSSI-----SSPEGFP--SYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK  262 (262)
T ss_dssp             HHHHHHTTSTT----E-----EE-TTS---------------SS-TTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcccccc-----ccccccc--cccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence            9998776422100000     0000000  00100000 11334599999999999999986

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]	Back alignment and domain information

>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]	Back alignment and domain information

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]	Back alignment and domain information

>cd02637 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function	Back alignment and domain information

>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family	Back alignment and domain information

>PRK07942 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>PRK05711 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>PRK09145 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07740 hypothetical protein; Provisional	Back alignment and domain information

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T	Back alignment and domain information

>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins	Back alignment and domain information

>PRK06195 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial	Back alignment and domain information

>PRK05168 ribonuclease T; Provisional	Back alignment and domain information

>PRK06063 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	Back alignment and domain information

>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases	Back alignment and domain information

>PRK06310 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK06722 exonuclease; Provisional	Back alignment and domain information

>PRK09146 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK06807 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07748 sporulation inhibitor KapD; Provisional	Back alignment and domain information

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

>PRK07983 exodeoxyribonuclease X; Provisional	Back alignment and domain information

>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family	Back alignment and domain information

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

>PRK06309 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PRK08517 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type	Back alignment and domain information

>PRK00448 polC DNA polymerase III PolC; Validated	Back alignment and domain information

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>PRK07247 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07883 hypothetical protein; Validated	Back alignment and domain information

>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III	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

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

>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins	Back alignment and domain information

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation	Back alignment and domain information

>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>PRK09182 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins	Back alignment and domain information

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins	Back alignment and domain information

>PRK05601 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PTZ00315 2'-phosphotransferase; Provisional	Back alignment and domain information

>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]	Back alignment and domain information

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

>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62	Back alignment and domain information

>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids	Back alignment and domain information

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)	Back alignment and domain information

>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides	Back alignment and domain information

>PRK11779 sbcB exonuclease I; Provisional	Back alignment and domain information

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

>cd02325 R3H R3H domain	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		605
2a1r_A		430	Crystal Structure Of Parn Nuclease Domain Length =		1e-19
3d45_A		507	Crystal Structure Of Mouse Parn In Complex With M7g		2e-18

>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain Length = 430

Back alignment and structure

Iteration: 1

Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 86/359 (23%), Positives = 156/359 (43%), Gaps = 54/359 (15%) Query: 8 NFFIFQRQELPLDGAA--YEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKH 65 NF++F + P + ++ +F+CQ++S+DFLA FDFN G+ YL++E+E + + Sbjct: 89 NFYVFPK---PFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLREQ 145 Query: 66 VNSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMK--DRLSEWLGGLLRNRDEGSEVQ 123 + E S + + P + ++ K D++ E + LL++ + + Sbjct: 146 YD---EKRSQANGAGALSYVSPNTSKCPVTIPEDQKKFIDQVVEKIEDLLQSEENKN--- 199 Query: 124 PSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNV 183 + P GF + L+ Q + K+ K + + E V Sbjct: 200 --------------LDLEPC---TGF--QRKLIYQTLSWKYPKGIHVETLETEKKERYIV 240 Query: 184 IVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAH 243 I ++ E K+ ++ EQ+ + ++GF VI +++ KL++GHN LD+ H Sbjct: 241 ISKVDEEERKRREQQKHAKEQE-----ELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMH 295 Query: 244 IYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCP 303 +F+ PLP EF FP ++DTK++ + ++ F + Sbjct: 296 TVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMAS----------------TQPFKDIIN 339 Query: 304 QIALGSKSTHLALQPSVKVEVE-VDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 +L L P +VE + S + S HEAGYDA++TG F ++LG Sbjct: 340 NTSLAELEKRLKETPFNPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLG 398

PyMOL of 2a1r

>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg Length = 507

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		605
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	1e-57
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	2e-57
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-15
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	1e-09
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	2e-07
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	2e-05

>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Length = 430	Back alignment and structure

 Score =  199 bits (505), Expect = 1e-57
 Identities = 80/387 (20%), Positives = 152/387 (39%), Gaps = 53/387 (13%)

Query: 7   HNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHV 66
            NF++F +          +F+CQ++S+DFLA   FDFN     G+ YL++E+E +  +  
Sbjct: 88  FNFYVFPK-PFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLREQY 146

Query: 67  NSTYEDESLDSWHSLKEIRDT---HLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQ 123
           +      +     S      +            F +++ +++ + L              
Sbjct: 147 DEKRSQANGAGALSYVSPNTSKCPVTIPEDQKKFIDQVVEKIEDLLQS------------ 194

Query: 124 PSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNV 183
                          +    + L   T  Q  LI   +   +    ++         + +
Sbjct: 195 ---------------EENKNLDLEPCTGFQRKLIYQTLSWKYPKGIHVETLETEKKERYI 239

Query: 184 IVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAH 243
           ++    E ++K   ++   +++ +    +  ++GF  VI  +++  KL++GHN  LD+ H
Sbjct: 240 VISKVDEEERKRREQQKHAKEQEE----LNDAVGFSRVIHAIANSGKLVIGHNMLLDVMH 295

Query: 244 IYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCP 303
              +F+ PLP    EF       FP ++DTK++    S    +   ++TSL++       
Sbjct: 296 TVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMA---STQPFKDIINNTSLAELEK---- 348

Query: 304 QIALGSKSTHLALQPSVKVEVEVD-DIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGI 362
                     L   P    +VE      S +  S   HEAGYDA++TG  F    ++LG 
Sbjct: 349 ---------RLKETPFNPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLG- 398

Query: 363 DFKQQSSSENLAHNEKLREHVNLLYLS 389
            F         A ++ +    N L+L 
Sbjct: 399 SFLSPPKIHVSARSKLIEPFFNKLFLM 425

PyMOL of 2a1r

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Length = 507	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Length = 289	Back alignment and structure

>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Length = 333	Back alignment and structure

>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Length = 252	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		605
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	100.0
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	100.0
4gmj_B		285	CCR4-NOT transcription complex subunit 7; mRNA dec	99.94
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	99.94
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	99.93
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	99.93
1whv_A		100	Poly(A)-specific ribonuclease; RNA recognition mot	99.46
3ctr_A		101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	99.33
1ug8_A		87	Poly(A)-specific ribonuclease; R3H domain, poly(A)	99.0
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	96.59
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	96.2
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	96.08
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	95.96
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	95.84
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	95.57
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	95.48
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	95.47
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	95.34
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	95.15
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	95.14
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	95.1
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	95.07
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	95.05
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	95.05
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	94.99
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	94.97
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	94.95
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	94.91
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	94.85
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	94.73
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	94.7
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	94.68
2lkz_A		95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	94.68
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	94.65
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	94.59
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	94.58
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	94.56
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	94.56
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	94.5
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	94.41
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	94.29
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	94.24
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	94.22
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	94.2
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	94.19
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	94.18
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	94.14
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	94.13
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	94.13
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	94.09
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	94.08
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	94.07
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	94.05
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	94.04
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	94.03
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	94.01
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	93.98
3p5t_L		90	Cleavage and polyadenylation specificity factor S;	93.98
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	93.97
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	93.97
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	93.94
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	93.93
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	93.91
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	93.89
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	93.84
3md1_A		83	Nuclear and cytoplasmic polyadenylated RNA-bindin	93.81
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	93.8
2ad9_A		119	Polypyrimidine tract-binding protein 1; RBD, RRM,	93.8
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	93.79
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	93.79
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	93.77
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	93.75
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	93.73
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	93.7
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	93.69
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	93.69
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	93.68
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	93.64
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	93.62
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	93.61
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	93.51
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	93.48
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	93.46
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	93.43
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	93.42
2div_A		99	TRNA selenocysteine associated protein; structural	93.41
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	93.4
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	93.38
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	93.36
2lxi_A		91	RNA-binding protein 10; NMR {Homo sapiens}	93.33
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	93.3
2cq1_A		101	PTB-like protein L; RRM domain, structural genomic	93.26
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	93.2
1x5t_A		96	Splicing factor 3B subunit 4; structure genomics,	93.17
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	93.13
1sjq_A		105	Polypyrimidine tract-binding protein 1; babbab mot	93.03
1x4e_A		85	RNA binding motif, single-stranded interacting pro	93.01
2cqh_A		93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	93.0
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	92.96
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	92.95
2la6_A		99	RNA-binding protein FUS; structural genomics, nort	92.95
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	92.88
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	92.85
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	92.84
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	92.83
4fxv_A		99	ELAV-like protein 1; RNA recognition motif, putati	92.81
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	92.75
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	92.7
1x5o_A		114	RNA binding motif, single-stranded interacting pro	92.7
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	92.66
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	92.64
2dh8_A		105	DAZ-associated protein 1; RRM domain, structural g	92.63
2dis_A		109	Unnamed protein product; structural genomics, RRM	92.62
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	92.61
3n9u_C		156	Cleavage and polyadenylation specificity factor S;	92.57
2hzc_A		87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	92.47
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	92.4
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	92.32
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	92.29
1x4d_A		102	Matrin 3; structural genomics, RRM domain, NPPSFA,	92.14
1x4f_A		112	Matrin 3; structural genomics, RRM domain, NPPSFA,	92.08
1wi8_A		104	EIF-4B, eukaryotic translation initiation factor 4	92.06
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	91.98
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	91.95
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	91.94
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	91.73
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	91.65
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	91.62
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	91.61
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	91.57
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	91.49
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	91.45
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	91.42
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	91.39
2cq4_A		114	RNA binding motif protein 23; RRM domain, structur	91.33
3q2s_C		229	Cleavage and polyadenylation specificity factor S;	91.24
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	91.15
1wel_A		124	RNA-binding protein 12; structural genomics, NPPSF	91.14
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	91.11
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	90.99
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	90.98
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	90.9
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	90.86
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	90.86
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	90.85
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	90.82
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	90.78
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	90.7
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	90.68
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	90.38
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	90.38
2dgw_A		91	Probable RNA-binding protein 19; RRM domain, struc	90.3
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	90.27
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	90.25
2gbz_A		194	Oligoribonuclease; ORN, deddh, structural genomics	90.23
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	90.18
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	90.12
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	89.98
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	89.68
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	89.37
2lmi_A		107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	89.14
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	88.94
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	88.84
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	88.72
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	88.54
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	88.51
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	88.51
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	88.43
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	88.43
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	88.33
1x5p_A		97	Negative elongation factor E; structure genomics,	88.24
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	88.14
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	88.11
2jvr_A		111	Nucleolar protein 3; RNA recognition motif, nucleu	87.97
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	87.62
2cq2_A		114	Hypothetical protein LOC91801; RRM domain, structu	87.57
2diu_A		96	KIAA0430 protein; structural genomics, RRM domain,	87.55
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	87.52
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	87.51
1wez_A		102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	87.5
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	87.06
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	87.04
2db1_A		118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	86.99
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	86.98
2dha_A		123	FLJ20171 protein; RRM domain, structural genomics,	86.68
1wg5_A		104	Heterogeneous nuclear ribonucleoprotein H; structu	86.64
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	86.64
1owx_A		121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	86.54
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	86.35
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	86.1
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	86.07
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	85.89
1sjr_A		164	Polypyrimidine tract-binding protein 1; extended b	85.8
1fj7_A		101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	85.27
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	85.26
2cpy_A		114	RNA-binding protein 12; RRM domain, structural gen	84.65
2bz2_A		121	Negative elongation factor E; NELF E, RNA recognit	84.23
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	84.09
2qxf_A		482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	83.7
2e5i_A		124	Heterogeneous nuclear ribonucleoprotein L-like; RR	83.34
2hgl_A		136	HNRPF protein, heterogeneous nuclear ribonucleopro	83.22
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	83.1
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	82.84
2m2b_A		131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	82.24
2dnn_A		109	RNA-binding protein 12; RRM domain, RBD, structura	81.8
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	81.0
3zzy_A		130	Polypyrimidine tract-binding protein 1; protein bi	80.36
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	80.31

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}	Back alignment and structure

Probab=100.00  E-value=2.4e-81  Score=693.51  Aligned_cols=411  Identities=23%  Similarity=0.369  Sum_probs=253.9

Q ss_pred             CcccceeeeeeecCCCCCCCCCCeeEEEecchHHHHHHcCCCccchhhcCCCcCCHHHHHHHHHHhhhhccccccccccc
Q 007386            1 MAFFGRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESLDSWHS   80 (605)
Q Consensus         1 ~~~~rpyNFylFPr~~~~~~~~dr~F~cQaSSL~FLa~~gFDFNk~i~~GIpYLsr~eE~~~~~~l~~~~~~~~~~~~~~   80 (605)
                      .|.++|||||+||++. +...+|++|+||++||+||++||||||+|+++|||||+++||+.+++++.+++......    
T Consensus        84 ~~~~~~fNf~~fp~~~-~~~~~d~~~~~~~~Si~fL~~~GfDFnk~~~~GI~yl~~~ee~~~~~~~~~~~~~~~~~----  158 (507)
T 3d45_A           84 KHVTKSFNFYVFPKPF-SRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRSQANGA----  158 (507)
T ss_dssp             CEEEEEEEEEBCCCCC-SSSSCCCEEEEEHHHHHHHHTTTCCHHHHHTTCBCBCCHHHHHHHHHHSCC------------
T ss_pred             ceeEEeEEEEecCccc-cccCcccceeecHHHHHHHHHcCCChhhHHhcCCCCCChHHHHHHHHHHHhhhhhhhcc----
Confidence            3789999999999963 33467999999999999999999999999999999999999999999988765532210    


Q ss_pred             cccccccCCCCCcchHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCCcchhhhHHHhhccccccccCCCCHHHHHHHHHH
Q 007386           81 LKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLV  160 (605)
Q Consensus        81 ~~~~~d~~l~~~~D~~F~e~v~~~I~eWl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~l~L~~~~s~qrrLV~q~  160 (605)
                      ..+..+....+.+|..|+++++++|++|++...    .                       +.+.|++||+|||+||||+
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~I~~wl~~~~----~-----------------------~~l~i~~~n~~~r~Lv~q~  211 (507)
T 3d45_A          159 GALAKCPVTIPEDQKKFIDQVIEKIEDFLQSEE----K-----------------------RSLELDPCTGFQRKLIYQT  211 (507)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccCCcccCCHHHHHHHHHHHHHHHHHHhcCC----C-----------------------CccccCCCcHHHHHHHHHH
Confidence            001111112345778899999999999996421    0                       1356889999999999999


Q ss_pred             HHHhCCCeEEEEeccCCCCceeEEEEEcchhhHHHHHHHHHHHHHHHHHhhhhhhccHHHHHHHHhcCCCeEEechhhhH
Q 007386          161 VRKHFKDLAYLRVSGENSCSQNVIVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLD  240 (605)
Q Consensus       161 lr~~fp~lv~v~~~~~~~~~~~~vv~~~~~ee~~~l~ke~~ee~~~~~e~~l~~~iGfr~v~~~l~~s~kpiVgHN~~~D  240 (605)
                      |+++||+++++++....+..+.++|.+..++++.    ..++++..++++++.+++|||+|+++|++++||||||||++|
T Consensus       212 l~~~fp~~v~~~~~~~~~~~~~i~v~~~~~e~~~----~~~~~~~~~~~~~~~~~~Gfr~v~~~L~~~~kpiVgHN~l~D  287 (507)
T 3d45_A          212 LSWKYPKGIHVETLETDKKERHIVISKVDEEERK----RREQEKYTKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLD  287 (507)
T ss_dssp             --------------------------------------------CCSTHHHHHHHSBTHHHHHHHHHHCCEEEESSCHHH
T ss_pred             HHHhCCCceEeeeccCCCcceeEEEEeCCHHHHH----HHHHHHHHHHHHHHHhhhhHHHHHHHHHhCCCeEEEechHHH
Confidence            9999999998876432332333444444444432    233344445567899999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcccCCcccccccCCCc
Q 007386          241 IAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSV  320 (605)
Q Consensus       241 l~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v  320 (605)
                      |||||++|+||||++++|||+.+|.+||.|||||||++..+ ++...  .+++|+++++.|...         .+..|.|
T Consensus       288 l~~l~~~F~~pLP~~~~eFk~~i~~lFP~i~DTK~la~~~~-~~~~~--~~~~L~~l~~~l~~~---------~~~~p~i  355 (507)
T 3d45_A          288 VMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQP-FKDII--NNTSLAELEKRLKET---------PFDPPKV  355 (507)
T ss_dssp             HHHHHHHHTCSCCSSHHHHHHHHHHHCSCEEEHHHHTTSTT-HHHHC--CCCCHHHHHHHTTST---------TCCCCCE
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHhCCceeEhHhhhhcCc-ccccc--CCCCHHHHHHHHhcc---------CCCCCeE
Confidence            99999999999999999999999999999999999998653 44443  489999999886421         1223443


Q ss_pred             eeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCCCcccCCchhhhhhhhhhccccccccccCC-CccccccC
Q 007386          321 KVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYLSWT-NGEIINLS  399 (605)
Q Consensus       321 ~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg~~~~~~~~~~~l~~~~~l~~~~N~L~~~~~-~~~~idL~  399 (605)
                      .  + .++..++....++.|||||||||||+||++|+++||. +...+....++.+..+++|.|+|+++++ +.++|||.
T Consensus       356 ~--~-~~~~~~y~~~~~~~HeAGyDA~mTg~~F~kl~~~l~~-~~~~~~~~~~~~~~~l~~~~N~l~l~~~~d~~~i~l~  431 (507)
T 3d45_A          356 E--S-AEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGS-LLSPPKMCVSARSKLIEPFFNKLFLMRVMDIPYLNLE  431 (507)
T ss_dssp             E--E-CTTSCCCC----CCCCHHHHHHHHHHHHHHHHHHHCC----------CCSCSSSGGGTTEECCCSBSSCCSEESS
T ss_pred             E--e-cccccccccCCCCcccHHHHHHHHHHHHHHHHHHHhh-ccCCcccccccchhHHHhhheeeeeeccCCCceeeCC
Confidence            2  2 1222334455789999999999999999999999985 2222222234456689999999999985 56789999


Q ss_pred             CCCCCCccccccccccCCCcccccceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHH
Q 007386          400 TGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLD  479 (605)
Q Consensus       400 ~~~~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~  479 (605)
                      |.++.+++                ++||+|+||++|+++||.+||+ +||..   +|+|||||||||+|+++++|+++|+
T Consensus       432 g~d~~~~R----------------~~vl~v~f~~~~~~~~i~~~fs-~fg~v---~V~widdt~a~V~~~~~~~a~~~l~  491 (507)
T 3d45_A          432 GPDLQPKR----------------DHVLHVTFPKEWKTSDLYQLFS-AFGNI---QISWIDDTSAFVSLSQPEQVQIAVN  491 (507)
T ss_dssp             SCCCCCCG----------------GGEEEEECCTTCCHHHHHHHGG-GGCCC---EEEECSSSEEEEECSCHHHHHHHHH
T ss_pred             CCCCCCCc----------------CcEEEEeCCCCCCHHHHHHHHH-hcCCE---EEEEEcCCeEEEEECCHHHHHHHHH
Confidence            86654432                3599999999999999999995 89954   6799999999999999999999999


Q ss_pred             Hhcc
Q 007386          480 LKGS  483 (605)
Q Consensus       480 ~~~~  483 (605)
                      +++.
T Consensus       492 ~~~~  495 (507)
T 3d45_A          492 TSKY  495 (507)
T ss_dssp             HHTT
T ss_pred             HHHh
Confidence            8875

PyMOL of 3d45

>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A	Back alignment and structure

>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens}	Back alignment and structure

>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A	Back alignment and structure

>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9	Back alignment and structure

>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9	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

>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

>1ug8_A Poly(A)-specific ribonuclease; R3H domain, poly(A)-specific 3'-exoribonuclease, PARN, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.68.7.1	Back alignment and structure

>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A*	Back alignment and structure

>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens}	Back alignment and structure

>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8}	Back alignment and structure

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A	Back alignment and structure

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

>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens}	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

>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5	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

>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

>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

>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

>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

>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

>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

>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B*	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

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

>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

>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A	Back alignment and structure

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}	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

>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

>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

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

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

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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; 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

>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

>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

>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

>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

>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

>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

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; 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

>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

>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

>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

>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

>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

>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

>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

>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

>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {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

>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

>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

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

>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

>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5	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

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

>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

>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

>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

>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

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; 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

>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

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}	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

>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

>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

>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

>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

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, 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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

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

>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A	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

>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

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A	Back alignment and structure

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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

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

>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

>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

>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

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_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

>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV}	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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA 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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_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

>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

>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

>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

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

>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

>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

>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

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		605
d1uoca_		286	c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (	3e-15
d2d5ra1		252	c.55.3.9 (A:11-262) CCR4-NOT transcription complex	4e-11

>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 286	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: Pop2 RNase D domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 74.2 bits (182), Expect = 3e-15
 Identities = 25/193 (12%), Positives = 51/193 (26%), Gaps = 40/193 (20%)

Query: 203 EQKIDAEMSIKASIGFRHVIDLLSS-------EKKLIVGHNCFLDIAHIYSKFFG-PLPL 254
           +  I+ E      I       LL             I  H  + D+  + +      +P 
Sbjct: 120 KSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAY-DLGFLINILMNDSMPN 178

Query: 255 TAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHL 314
             E+F   V++Y P+  D  ++            K+      +      Q +L + +  L
Sbjct: 179 NKEDFEWWVHQYMPNFYDLNLVYKIIQEF-----KNPQLQQSSQQQQQQQYSLTTLADEL 233

Query: 315 ALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLA 374
            L                     +    G  + +    F Q        F   +      
Sbjct: 234 GLPR-----------------FSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTD----- 271

Query: 375 HNEKLREHVNLLY 387
                 ++  ++Y
Sbjct: 272 ----FAKYQGVIY 280

PyMOL of d1uoca_

>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 252	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		605
d2d5ra1		252	CCR4-NOT transcription complex subunit 7, CAF1 {Hu	99.97
d1uoca_		286	Pop2 RNase D domain {Baker's yeast (Saccharomyces	99.96
d1whva_		100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	99.55
d1ug8a_		87	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	98.91
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	96.37
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	95.99
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	95.96
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	95.63
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	95.44
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	95.42
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	95.32
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	95.3
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	95.22
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	95.21
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	94.93
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	94.89
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	94.8
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	94.71
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	94.68
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	94.66
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	94.57
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	94.45
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	94.43
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	94.22
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	94.2
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	94.19
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	94.16
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	94.08
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	94.01
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	93.96
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	93.82
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	93.69
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	93.68
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	93.65
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	93.63
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	93.63
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	93.54
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	93.52
d2cqha1		80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	93.52
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	93.44
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	93.41
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	93.38
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	93.36
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	93.31
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	93.17
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	93.0
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	92.84
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	92.82
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	92.73
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	92.7
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	92.67
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	92.66
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	92.58
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	92.53
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.51
d1wwha1		81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	92.47
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	92.46
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	92.38
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	92.19
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	92.14
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	92.09
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	92.0
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	91.99
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	91.96
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	91.84
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	91.59
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	91.5
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	91.41
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	91.33
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	91.24
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	91.18
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	90.91
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	90.76
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	90.64
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	90.44
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	90.37
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	90.2
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	90.02
d1owxa_		113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	89.98
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	89.61
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	89.42
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	89.23
d2cq2a1		101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	88.55
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	88.29
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	88.19
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	87.97
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	87.77
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	87.42
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	84.23
d1w0ha_		200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	83.96
d1u2fa_		90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	82.55

>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: CCR4-NOT transcription complex subunit 7, CAF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=8.2e-33  Score=278.17  Aligned_cols=110  Identities=23%  Similarity=0.287  Sum_probs=89.1

Q ss_pred             CeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcccC
Q 007386          230 KLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALG  308 (605)
Q Consensus       230 kpiVgHN~~~Dl~~l~~~F~-~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~~  308 (605)
                      ++||+|||++|++||+++|. +|||++++||++.+|.+||.|||||||++.++.+       .++|+.+.+.|.      
T Consensus       141 ~~wv~f~g~yD~~yl~k~l~~~~LP~~~~eF~~~v~~~FP~vyDtK~l~~~~~~~-------~~~L~~la~~L~------  207 (252)
T d2d5ra1         141 VKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNL-------KGGLQEVAEQLE------  207 (252)
T ss_dssp             CEEEESSCHHHHHHHHHHHHTSCCCSSHHHHHHHHHHHCSCEEEHHHHGGGCTTC-------CSSHHHHHHHHT------
T ss_pred             CcEEEecchhHHHHHHHHHcCCCCCCCHHHHHHHHHHHCchHhhHHHHHhhccCC-------CchHHHHHHHcC------
Confidence            57999999999999999996 4999999999999999999999999999887643       456887754431      


Q ss_pred             CcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCCCcccCCchhhhhhhhhhccccccccc
Q 007386          309 SKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYL  388 (605)
Q Consensus       309 ~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg~~~~~~~~~~~l~~~~~l~~~~N~L~~  388 (605)
                                       +.       +.|+.|||||||||||.||++|++.+.-.   .         .....|.|+||+
T Consensus       208 -----------------v~-------~~g~~H~AG~DsllT~~~F~~l~~~~~~~---~---------~~~~~~~g~i~G  251 (252)
T d2d5ra1         208 -----------------LE-------RIGPQHQAGSDSLLTGMAFFKMREMFFED---H---------IDDAKYCGHLYG  251 (252)
T ss_dssp             -----------------CC-------CCSSTTSHHHHHHHHHHHHHHHHHHTSCS---S---------CCHHHHTTBCTT
T ss_pred             -----------------CC-------CCCCCcchhHHHHHHHHHHHHHHHHHhcC---C---------CcHHHhCCcccC
Confidence                             11       34788999999999999999999988421   1         123457888775

PyMOL of d2d5ra1

>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ug8a_ d.68.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]}	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

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

>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]}	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

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {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

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {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

>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

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {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

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {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

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

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}	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

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

>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]}	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

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

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	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

>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

>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

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

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

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {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

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

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	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

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	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

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {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

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

>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

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {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

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {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

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {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

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {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

>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

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

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

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {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

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

>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

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {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

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {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

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {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

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {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

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]}	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

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

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	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

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {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

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {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

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {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

>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

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {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

>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]}	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