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Protein

RNA-binding protein 39

Gene

Rbm39

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

  • RNA binding Source: UniProtKB-KW
  • transcription coactivator activity Source: MGI

GO - Biological processi

Keywordsi

Molecular functionActivator, RNA-binding
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:2157953 Rbm39

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
Cross-linki111Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei117PhosphoserineCombined sources1
Cross-linki119Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei121PhosphoserineBy similarity1
Modified residuei136PhosphoserineCombined sources1
Modified residuei146PhosphothreonineBy similarity1
Cross-linki244Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei334PhosphoserineCombined sources1
Modified residuei337PhosphoserineCombined sources1
Modified residuei341PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ8VH51
PeptideAtlasiQ8VH51
PRIDEiQ8VH51

PTM databases

iPTMnetiQ8VH51
PhosphoSitePlusiQ8VH51

Expressioni

Gene expression databases

BgeeiENSMUSG00000027620 Expressed in 299 organ(s), highest expression level in skin of back
CleanExiMM_RBM39
ExpressionAtlasiQ8VH51 baseline and differential
GenevisibleiQ8VH51 MM

Interactioni

Subunit structurei

Interacts with NCOA6 and JUN (PubMed:11704680). Interacts with ESR1 and ESR2, in the presence of estradiol (E2) (PubMed:11704680). Interacts with RSRC1 (via Arg/Ser-rich domain) (By similarity). Interacts with SF3B1 (By similarity). Interacts with ZNF106 (via N-terminus) (PubMed:27418600).By similarity2 Publications

Protein-protein interaction databases

BioGridi228442, 11 interactors
IntActiQ8VH51, 5 interactors
MINTiQ8VH51
STRINGi10090.ENSMUSP00000105216

Structurei

Secondary structure

1530
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0147 Eukaryota
ENOG410XP20 LUCA
GeneTreeiENSGT00930000150902
HOGENOMiHOG000236253
HOVERGENiHBG057646
InParanoidiQ8VH51
KOiK13091
OMAiPIMVQHT
OrthoDBiEOG091G0BQ9
TreeFamiTF320448

Family and domain databases

Gene3Di3.30.70.330, 3 hits
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR029123 RBM39_linker
IPR006509 RBM39_SF
IPR000504 RRM_dom
IPR003954 RRM_dom_euk
PfamiView protein in Pfam
PF15519 RBM39linker, 1 hit
PF00076 RRM_1, 2 hits
SMARTiView protein in SMART
SM00360 RRM, 3 hits
SM00361 RRM_1, 2 hits
SUPFAMiSSF54928 SSF54928, 2 hits
TIGRFAMsiTIGR01622 SF-CC1, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 2 hits

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.

This entry has 3 described isoforms and 9 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 9 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B7ZD61B7ZD61_MOUSE
RNA-binding protein 39
Rbm39
273Annotation score:
E9Q8F0E9Q8F0_MOUSE
RNA-binding protein 39
Rbm39
415Annotation score:
F7AA45F7AA45_MOUSE
RNA-binding protein 39
Rbm39
311Annotation score:
B7ZD63B7ZD63_MOUSE
RNA-binding protein 39
Rbm39
156Annotation score:
B7ZD64B7ZD64_MOUSE
RNA-binding protein 39
Rbm39
38Annotation score:
E9Q999E9Q999_MOUSE
RNA-binding protein 39
Rbm39
47Annotation score:
D6RJ85D6RJ85_MOUSE
RNA-binding protein 39
Rbm39
62Annotation score:
E9PZF9E9PZF9_MOUSE
RNA-binding protein 39
Rbm39
39Annotation score:
D6RCZ8D6RCZ8_MOUSE
RNA-binding protein 39
Rbm39
40Annotation score:

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
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

Similar proteinsi

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
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, 11 interactors
IntActiQ8VH51, 5 interactors
MINTiQ8VH51
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
GeneTreeiENSGT00930000150902
HOGENOMiHOG000236253
HOVERGENiHBG057646
InParanoidiQ8VH51
KOiK13091
OMAiPIMVQHT
OrthoDBiEOG091G0BQ9
TreeFamiTF320448

Miscellaneous databases

ChiTaRSiRbm39 mouse
EvolutionaryTraceiQ8VH51
PROiPR:Q8VH51
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000027620 Expressed in 299 organ(s), highest expression level in skin of back
CleanExiMM_RBM39
ExpressionAtlasiQ8VH51 baseline and differential
GenevisibleiQ8VH51 MM

Family and domain databases

Gene3Di3.30.70.330, 3 hits
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR029123 RBM39_linker
IPR006509 RBM39_SF
IPR000504 RRM_dom
IPR003954 RRM_dom_euk
PfamiView protein in Pfam
PF15519 RBM39linker, 1 hit
PF00076 RRM_1, 2 hits
SMARTiView protein in SMART
SM00360 RRM, 3 hits
SM00361 RRM_1, 2 hits
SUPFAMiSSF54928 SSF54928, 2 hits
TIGRFAMsiTIGR01622 SF-CC1, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiRBM39_MOUSE
AccessioniPrimary (citable) accession number: Q8VH51
Secondary accession number(s): Q5RJI0, Q99KV0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 2003
Last sequence update: July 27, 2011
Last modified: November 7, 2018
This is version 163 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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