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Protein

RNA-binding protein 39

Gene

Rbm39

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1. May be involved in pre-mRNA splicing process.1 Publication

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: MGI
  • transcription coactivator activity Source: MGI

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • RNA splicing Source: UniProtKB-KW
  • transcription, DNA-templated Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 39
Alternative name(s):
Coactivator of activating protein 1 and estrogen receptors
Short name:
Coactivator of AP-1 and ERs
RNA-binding motif protein 39
RNA-binding region-containing protein 2
Transcription coactivator CAPER
Gene namesi
Name:Rbm39
Synonyms:Caper, Rnpc2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:2157953. Rbm39.

Subcellular locationi

GO - Cellular componenti

  • microtubule cytoskeleton Source: MGI
  • microtubule organizing center Source: MGI
  • nucleoplasm Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000818152 – 530RNA-binding protein 39Add BLAST529

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei95PhosphotyrosineBy similarity1
Modified residuei97PhosphoserineBy similarity1
Modified residuei100PhosphoserineBy similarity1
Modified residuei117PhosphoserineCombined sources1
Modified residuei121PhosphoserineBy similarity1
Modified residuei136PhosphoserineCombined sources1
Modified residuei146PhosphothreonineBy similarity1
Modified residuei334PhosphoserineCombined sources1
Modified residuei337PhosphoserineCombined sources1
Modified residuei341PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ8VH51.
PeptideAtlasiQ8VH51.
PRIDEiQ8VH51.

PTM databases

iPTMnetiQ8VH51.
PhosphoSitePlusiQ8VH51.

Expressioni

Gene expression databases

BgeeiENSMUSG00000027620.
CleanExiMM_RBM39.
ExpressionAtlasiQ8VH51. baseline and differential.
GenevisibleiQ8VH51. MM.

Interactioni

Subunit structurei

Interacts with RSRC1 (via Arg/Ser-rich domain). Interacts with SF3B1 (By similarity). Interacts with NCOA6.By similarity1 Publication

Protein-protein interaction databases

BioGridi228442. 10 interactors.
IntActiQ8VH51. 5 interactors.
MINTiMINT-1751237.
STRINGi10090.ENSMUSP00000105216.

Structurei

Secondary structure

1530
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi424 – 431Combined sources8
Turni434 – 436Combined sources3
Beta strandi439 – 441Combined sources3
Helixi442 – 454Combined sources13
Turni455 – 458Combined sources4
Beta strandi461 – 465Combined sources5
Beta strandi474 – 477Combined sources4
Helixi481 – 491Combined sources11
Beta strandi502 – 506Combined sources5
Helixi508 – 514Combined sources7
Helixi516 – 518Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LQ5NMR-A418-530[»]
3S6EX-ray0.95A/B418-530[»]
4J5OX-ray1.11A/B418-530[»]
4RU2X-ray2.20A/C/E/G/I/K/M/O/Q418-530[»]
5CXTX-ray2.20A/C/E/G/I/K/M/O/Q418-530[»]
ProteinModelPortaliQ8VH51.
SMRiQ8VH51.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8VH51.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini153 – 230RRM 1PROSITE-ProRule annotationAdd BLAST78
Domaini250 – 328RRM 2PROSITE-ProRule annotationAdd BLAST79
Domaini445 – 508RRM 3PROSITE-ProRule annotationAdd BLAST64

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni291 – 406Interaction with JUN1 PublicationAdd BLAST116
Regioni291 – 355Activating domainAdd BLAST65
Regioni355 – 406Interaction with ESR1 and ESR21 PublicationAdd BLAST52
Regioni406 – 530Interaction with NCOA61 PublicationAdd BLAST125

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi41 – 90Arg/Ser-rich (RS domain)Add BLAST50
Compositional biasi409 – 416Poly-Ala8

Sequence similaritiesi

Belongs to the splicing factor SR family.Curated
Contains 3 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0147. Eukaryota.
ENOG410XP20. LUCA.
GeneTreeiENSGT00860000133811.
HOGENOMiHOG000236253.
HOVERGENiHBG057646.
InParanoidiQ8VH51.
KOiK13091.
OMAiTHRENEE.
OrthoDBiEOG091G0BQ9.
TreeFamiTF320448.

Family and domain databases

Gene3Di3.30.70.330. 3 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR029123. RBM39_linker.
IPR006509. RBM39_SF.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
[Graphical view]
PfamiPF15519. RBM39linker. 1 hit.
PF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
SM00361. RRM_1. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 4 hits.
TIGRFAMsiTIGR01622. SF-CC1. 1 hit.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Experimental confirmation may be lacking for some isoforms.
Isoform 1 (identifier: Q8VH51-1) [UniParc]FASTAAdd to basket
Also known as: HCC1.4

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MADDIDIEAM LEAPYKKDEN KLNSANGHEE RSKKRKKSKS RSRSHERKRS
60 70 80 90 100
KSKERKRSRD RERKKSKSRE RKRSRSKERR RSRSRSRDRR FRGRYRSPYS
110 120 130 140 150
GPKFNSAIRG KIGLPHSIKL SRRRSRSKSP FRKDKSPVRE PIDNLTPEER
160 170 180 190 200
DARTVFCMQL AARIRPRDLE EFFSTVGKVR DVRMISDRNS RRSKGIAYVE
210 220 230 240 250
FVDVSSVPLA IGLTGQRVLG VPIIVQASQA EKNRAAAMAN NLQKGSAGPM
260 270 280 290 300
RLYVGSLHFN ITEDMLRGIF EPFGRIESIQ LMMDSETGRS KGYGFITFSD
310 320 330 340 350
SECAKKALEQ LNGFELAGRP MKVGHVTERT DASSASSFLD SDELERTGID
360 370 380 390 400
LGTTGRLQLM ARLAEGTGLQ IPPAAQQALQ MSGSLAFGAV AEFSFVIDLQ
410 420 430 440 450
TRLSQQTEAS ALAAAASVQP LATQCFQLSN MFNPQTEEEV GWDTEIKDDV
460 470 480 490 500
IEECNKHGGV IHIYVDKNSA QGNVYVKCPS IAAAIAAVNA LHGRWFAGKM
510 520 530
ITAAYVPLPT YHNLFPDSMT ATQLLVPSRR
Length:530
Mass (Da):59,407
Last modified:July 27, 2011 - v2
Checksum:i0CC6103096B7A040
GO
Isoform 2 (identifier: Q8VH51-2) [UniParc]FASTAAdd to basket
Also known as: HCC1.3

The sequence of this isoform differs from the canonical sequence as follows:
     392-397: Missing.

Show »
Length:524
Mass (Da):58,684
Checksum:i2843A619B193697B
GO
Isoform 3 (identifier: Q8VH51-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-157: Missing.
     392-397: Missing.

Show »
Length:367
Mass (Da):39,818
Checksum:i18FCCA033F62CDA3
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti194K → R in AAL32373 (PubMed:11704680).Curated1
Sequence conflicti208P → R in AAL32373 (PubMed:11704680).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0058211 – 157Missing in isoform 3. 1 PublicationAdd BLAST157
Alternative sequenceiVSP_005822392 – 397Missing in isoform 2 and isoform 3. 2 Publications6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY061882 mRNA. Translation: AAL32373.1.
AK147076 mRNA. Translation: BAE27657.1.
BX649640, AL929404 Genomic DNA. Translation: CAM13496.1.
AL929404, BX649640 Genomic DNA. Translation: CAM26749.1.
CH466551 Genomic DNA. Translation: EDL06184.1.
BC004000 mRNA. Translation: AAH04000.1.
BC030493 mRNA. Translation: AAH30493.1.
BC086645 mRNA. Translation: AAH86645.1.
CCDSiCCDS16964.1. [Q8VH51-1]
CCDS71168.1. [Q8VH51-2]
RefSeqiNP_001278043.1. NM_001291114.1. [Q8VH51-2]
NP_001278044.1. NM_001291115.1. [Q8VH51-2]
NP_573505.2. NM_133242.3. [Q8VH51-1]
XP_011237628.1. XM_011239326.2. [Q8VH51-3]
XP_011237629.1. XM_011239327.2. [Q8VH51-3]
XP_017171483.1. XM_017315994.1. [Q8VH51-3]
XP_017171487.1. XM_017315998.1. [Q8VH51-3]
XP_017171494.1. XM_017316005.1. [Q8VH51-3]
XP_017171497.1. XM_017316008.1. [Q8VH51-3]
UniGeneiMm.392436.
Mm.436917.
Mm.436932.

Genome annotation databases

EnsembliENSMUST00000029149; ENSMUSP00000029149; ENSMUSG00000027620. [Q8VH51-2]
ENSMUST00000109587; ENSMUSP00000105216; ENSMUSG00000027620. [Q8VH51-1]
ENSMUST00000146297; ENSMUSP00000119298; ENSMUSG00000027620. [Q8VH51-2]
GeneIDi170791.
KEGGimmu:170791.
UCSCiuc008nmr.3. mouse. [Q8VH51-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY061882 mRNA. Translation: AAL32373.1.
AK147076 mRNA. Translation: BAE27657.1.
BX649640, AL929404 Genomic DNA. Translation: CAM13496.1.
AL929404, BX649640 Genomic DNA. Translation: CAM26749.1.
CH466551 Genomic DNA. Translation: EDL06184.1.
BC004000 mRNA. Translation: AAH04000.1.
BC030493 mRNA. Translation: AAH30493.1.
BC086645 mRNA. Translation: AAH86645.1.
CCDSiCCDS16964.1. [Q8VH51-1]
CCDS71168.1. [Q8VH51-2]
RefSeqiNP_001278043.1. NM_001291114.1. [Q8VH51-2]
NP_001278044.1. NM_001291115.1. [Q8VH51-2]
NP_573505.2. NM_133242.3. [Q8VH51-1]
XP_011237628.1. XM_011239326.2. [Q8VH51-3]
XP_011237629.1. XM_011239327.2. [Q8VH51-3]
XP_017171483.1. XM_017315994.1. [Q8VH51-3]
XP_017171487.1. XM_017315998.1. [Q8VH51-3]
XP_017171494.1. XM_017316005.1. [Q8VH51-3]
XP_017171497.1. XM_017316008.1. [Q8VH51-3]
UniGeneiMm.392436.
Mm.436917.
Mm.436932.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LQ5NMR-A418-530[»]
3S6EX-ray0.95A/B418-530[»]
4J5OX-ray1.11A/B418-530[»]
4RU2X-ray2.20A/C/E/G/I/K/M/O/Q418-530[»]
5CXTX-ray2.20A/C/E/G/I/K/M/O/Q418-530[»]
ProteinModelPortaliQ8VH51.
SMRiQ8VH51.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi228442. 10 interactors.
IntActiQ8VH51. 5 interactors.
MINTiMINT-1751237.
STRINGi10090.ENSMUSP00000105216.

PTM databases

iPTMnetiQ8VH51.
PhosphoSitePlusiQ8VH51.

Proteomic databases

PaxDbiQ8VH51.
PeptideAtlasiQ8VH51.
PRIDEiQ8VH51.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000029149; ENSMUSP00000029149; ENSMUSG00000027620. [Q8VH51-2]
ENSMUST00000109587; ENSMUSP00000105216; ENSMUSG00000027620. [Q8VH51-1]
ENSMUST00000146297; ENSMUSP00000119298; ENSMUSG00000027620. [Q8VH51-2]
GeneIDi170791.
KEGGimmu:170791.
UCSCiuc008nmr.3. mouse. [Q8VH51-1]

Organism-specific databases

CTDi9584.
MGIiMGI:2157953. Rbm39.

Phylogenomic databases

eggNOGiKOG0147. Eukaryota.
ENOG410XP20. LUCA.
GeneTreeiENSGT00860000133811.
HOGENOMiHOG000236253.
HOVERGENiHBG057646.
InParanoidiQ8VH51.
KOiK13091.
OMAiTHRENEE.
OrthoDBiEOG091G0BQ9.
TreeFamiTF320448.

Miscellaneous databases

ChiTaRSiRbm39. mouse.
EvolutionaryTraceiQ8VH51.
PROiQ8VH51.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000027620.
CleanExiMM_RBM39.
ExpressionAtlasiQ8VH51. baseline and differential.
GenevisibleiQ8VH51. MM.

Family and domain databases

Gene3Di3.30.70.330. 3 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR029123. RBM39_linker.
IPR006509. RBM39_SF.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
[Graphical view]
PfamiPF15519. RBM39linker. 1 hit.
PF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
SM00361. RRM_1. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 4 hits.
TIGRFAMsiTIGR01622. SF-CC1. 1 hit.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBM39_MOUSE
AccessioniPrimary (citable) accession number: Q8VH51
Secondary accession number(s): Q5RJI0, Q99KV0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2003
Last sequence update: July 27, 2011
Last modified: November 30, 2016
This is version 147 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.