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Protein

RNA-binding protein 39

Gene

RBM39

Organism
Homo sapiens (Human)
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 (By similarity). May be involved in pre-mRNA splicing process.By similarity

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

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):
CAPER alpha
Hepatocellular carcinoma protein 1
RNA-binding motif protein 39
RNA-binding region-containing protein 2
Splicing factor HCC1
Gene namesi
Name:RBM39
Synonyms:HCC1, RNPC2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15923. RBM39.

Subcellular locationi

  • Nucleus speckle

  • Note: Concentrated in nuclear speckles. Colocalizes with the core spliceosomal snRNP proteins.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi9584.
OpenTargetsiENSG00000131051.
PharmGKBiPA34450.

Polymorphism and mutation databases

BioMutaiRBM39.
DMDMi28201880.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00000818142 – 530RNA-binding protein 39Add BLAST529

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1 Publication1
Modified residuei95PhosphotyrosineCombined sources1
Modified residuei97PhosphoserineCombined sources1
Modified residuei100PhosphoserineCombined sources1
Modified residuei117PhosphoserineCombined sources1
Modified residuei121PhosphoserineCombined sources1
Modified residuei136PhosphoserineCombined sources1
Modified residuei146PhosphothreonineCombined sources1
Modified residuei334PhosphoserineCombined sources1
Modified residuei337PhosphoserineCombined sources1
Modified residuei341PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ14498.
MaxQBiQ14498.
PaxDbiQ14498.
PeptideAtlasiQ14498.
PRIDEiQ14498.

PTM databases

iPTMnetiQ14498.
PhosphoSitePlusiQ14498.
SwissPalmiQ14498.

Expressioni

Tissue specificityi

Widely expressed. Highly expressed in pancreas, skeletal muscle, lung and brain. Expressed at intermediate level in kidney, liver and heart.

Gene expression databases

BgeeiENSG00000131051.
CleanExiHS_RBM39.
ExpressionAtlasiQ14498. baseline and differential.
GenevisibleiQ14498. HS.

Organism-specific databases

HPAiHPA001591.

Interactioni

Subunit structurei

Interacts with NCOA6 (By similarity). Interacts with RSRC1 (via Arg/Ser-rich domain). Interacts with SF3B1.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
AK8Q96MA63EBI-6654703,EBI-8466265
ARL6IP4Q66PJ3-33EBI-395290,EBI-10248982
BANPQ8N9N53EBI-6654703,EBI-744695
C11orf57Q6ZUT13EBI-395290,EBI-3920396
C11orf57Q6ZUT1-23EBI-395290,EBI-10180231
CLK2P497606EBI-395290,EBI-750020
FAM200AQ8TCP93EBI-6654703,EBI-2799179
GOLGA2Q083793EBI-6654703,EBI-618309
hCG_1744368A0A024RA763EBI-395290,EBI-10180729
HOMEZQ8IX15-33EBI-6654703,EBI-10172004
KIAA0907Q7Z7F03EBI-6654703,EBI-751942
KRTAP12-2P599913EBI-395290,EBI-10176379
MLXQ9UH923EBI-6654703,EBI-741109
PHC2Q8IXK03EBI-395290,EBI-713786
PPIGQ134273EBI-395290,EBI-396072
PRPF40AO75400-23EBI-395290,EBI-5280197
RELQ048643EBI-6654703,EBI-307352
SAP18O004224EBI-395290,EBI-1044156
SDCBPO005603EBI-395290,EBI-727004
SF3B4Q154273EBI-395290,EBI-348469
SP100P234973EBI-6654703,EBI-751145
SREK1IP1Q8N9Q23EBI-395290,EBI-10268630
SRPK1Q96SB42EBI-395290,EBI-539478
SRPK2P783629EBI-395290,EBI-593303
SRSF11Q055193EBI-6654703,EBI-1051785
THAP1Q9NVV95EBI-395290,EBI-741515
ZBTB22O152093EBI-6654703,EBI-723574
ZCCHC10Q8TBK64EBI-395290,EBI-597063

Protein-protein interaction databases

BioGridi114952. 149 interactors.
DIPiDIP-32928N.
IntActiQ14498. 78 interactors.
MINTiMINT-5004569.
STRINGi9606.ENSP00000253363.

Structurei

Secondary structure

1530
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi147 – 151Combined sources5
Beta strandi154 – 160Combined sources7
Helixi166 – 173Combined sources8
Turni174 – 176Combined sources3
Beta strandi179 – 184Combined sources6
Beta strandi189 – 192Combined sources4
Beta strandi195 – 203Combined sources9
Helixi206 – 211Combined sources6
Turni212 – 215Combined sources4
Beta strandi224 – 227Combined sources4
Beta strandi235 – 238Combined sources4
Beta strandi250 – 255Combined sources6
Helixi263 – 270Combined sources8
Turni271 – 273Combined sources3
Beta strandi276 – 283Combined sources8
Turni285 – 287Combined sources3
Beta strandi290 – 299Combined sources10
Helixi301 – 311Combined sources11
Beta strandi316 – 319Combined sources4
Beta strandi322 – 324Combined sources3
Beta strandi424 – 431Combined sources8
Turni434 – 436Combined 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 – 519Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JRSNMR-A235-331[»]
2MHNNMR-A144-234[»]
4OO6X-ray2.70B73-99[»]
4OZ0X-ray2.20A/B417-530[»]
4OZ1X-ray1.74A/B417-530[»]
4YUDX-ray1.28A144-234[»]
ProteinModelPortaliQ14498.
SMRiQ14498.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ14498.

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 JUNBy similarityAdd BLAST116
Regioni291 – 355Activating domainBy similarityAdd BLAST65
Regioni355 – 406Interaction with ESR1 and ESR2By similarityAdd BLAST52
Regioni406 – 530Interaction with NCOA6By similarityAdd 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.
InParanoidiQ14498.
KOiK13091.
OMAiTHRENEE.
OrthoDBiEOG091G0BQ9.
PhylomeDBiQ14498.
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

Isoform 1 (identifier: Q14498-1) [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 KLSSANGHEE 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):59,380
Last modified:February 1, 2003 - v2
Checksum:i0CC610356D4AA040
GO
Isoform 2 (identifier: Q14498-2) [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):58,657
Checksum:i1843A619B1950802
GO
Isoform 3 (identifier: Q14498-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     100-121: Missing.

Show »
Length:508
Mass (Da):57,090
Checksum:i646BBB6287AAFB09
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0152282A → V.Corresponds to variant rs1803701dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_043375100 – 121Missing in isoform 3. 2 PublicationsAdd BLAST22
Alternative sequenceiVSP_005820392 – 397Missing in isoform 2. 1 Publication6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10910 mRNA. Translation: AAA16346.1.
L10911 mRNA. Translation: AAA16347.1.
AK299678 mRNA. Translation: BAG61586.1.
AL357374 Genomic DNA. Translation: CAC11118.1.
AL357374 Genomic DNA. Translation: CAC11119.1.
CH471077 Genomic DNA. Translation: EAW76159.1.
CH471077 Genomic DNA. Translation: EAW76161.1.
CH471077 Genomic DNA. Translation: EAW76162.1.
CH471077 Genomic DNA. Translation: EAW76163.1.
BC131543 mRNA. Translation: AAI31544.1.
BC141835 mRNA. Translation: AAI41836.1.
BC158172 mRNA. Translation: AAI58173.1.
CCDSiCCDS13265.1. [Q14498-2]
CCDS13266.1. [Q14498-1]
CCDS56186.1. [Q14498-3]
PIRiI55595.
RefSeqiNP_001229528.1. NM_001242599.1. [Q14498-3]
NP_001229529.1. NM_001242600.1.
NP_004893.1. NM_004902.3. [Q14498-2]
NP_909122.1. NM_184234.2. [Q14498-1]
UniGeneiHs.282901.
Hs.731837.

Genome annotation databases

EnsembliENST00000253363; ENSP00000253363; ENSG00000131051. [Q14498-1]
ENST00000361162; ENSP00000354437; ENSG00000131051. [Q14498-2]
ENST00000528062; ENSP00000436747; ENSG00000131051. [Q14498-3]
GeneIDi9584.
KEGGihsa:9584.
UCSCiuc002xeb.4. human. [Q14498-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10910 mRNA. Translation: AAA16346.1.
L10911 mRNA. Translation: AAA16347.1.
AK299678 mRNA. Translation: BAG61586.1.
AL357374 Genomic DNA. Translation: CAC11118.1.
AL357374 Genomic DNA. Translation: CAC11119.1.
CH471077 Genomic DNA. Translation: EAW76159.1.
CH471077 Genomic DNA. Translation: EAW76161.1.
CH471077 Genomic DNA. Translation: EAW76162.1.
CH471077 Genomic DNA. Translation: EAW76163.1.
BC131543 mRNA. Translation: AAI31544.1.
BC141835 mRNA. Translation: AAI41836.1.
BC158172 mRNA. Translation: AAI58173.1.
CCDSiCCDS13265.1. [Q14498-2]
CCDS13266.1. [Q14498-1]
CCDS56186.1. [Q14498-3]
PIRiI55595.
RefSeqiNP_001229528.1. NM_001242599.1. [Q14498-3]
NP_001229529.1. NM_001242600.1.
NP_004893.1. NM_004902.3. [Q14498-2]
NP_909122.1. NM_184234.2. [Q14498-1]
UniGeneiHs.282901.
Hs.731837.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JRSNMR-A235-331[»]
2MHNNMR-A144-234[»]
4OO6X-ray2.70B73-99[»]
4OZ0X-ray2.20A/B417-530[»]
4OZ1X-ray1.74A/B417-530[»]
4YUDX-ray1.28A144-234[»]
ProteinModelPortaliQ14498.
SMRiQ14498.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114952. 149 interactors.
DIPiDIP-32928N.
IntActiQ14498. 78 interactors.
MINTiMINT-5004569.
STRINGi9606.ENSP00000253363.

PTM databases

iPTMnetiQ14498.
PhosphoSitePlusiQ14498.
SwissPalmiQ14498.

Polymorphism and mutation databases

BioMutaiRBM39.
DMDMi28201880.

Proteomic databases

EPDiQ14498.
MaxQBiQ14498.
PaxDbiQ14498.
PeptideAtlasiQ14498.
PRIDEiQ14498.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000253363; ENSP00000253363; ENSG00000131051. [Q14498-1]
ENST00000361162; ENSP00000354437; ENSG00000131051. [Q14498-2]
ENST00000528062; ENSP00000436747; ENSG00000131051. [Q14498-3]
GeneIDi9584.
KEGGihsa:9584.
UCSCiuc002xeb.4. human. [Q14498-1]

Organism-specific databases

CTDi9584.
DisGeNETi9584.
GeneCardsiRBM39.
HGNCiHGNC:15923. RBM39.
HPAiHPA001591.
MIMi604739. gene.
neXtProtiNX_Q14498.
OpenTargetsiENSG00000131051.
PharmGKBiPA34450.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0147. Eukaryota.
ENOG410XP20. LUCA.
GeneTreeiENSGT00860000133811.
HOGENOMiHOG000236253.
HOVERGENiHBG057646.
InParanoidiQ14498.
KOiK13091.
OMAiTHRENEE.
OrthoDBiEOG091G0BQ9.
PhylomeDBiQ14498.
TreeFamiTF320448.

Miscellaneous databases

ChiTaRSiRBM39. human.
EvolutionaryTraceiQ14498.
GeneWikiiRBM39.
GenomeRNAii9584.
PROiQ14498.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000131051.
CleanExiHS_RBM39.
ExpressionAtlasiQ14498. baseline and differential.
GenevisibleiQ14498. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: Q14498
Secondary accession number(s): A2RRD3
, A5D8W2, B0BLV3, E1P5S0, E1P5S1, Q14499
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2003
Last sequence update: February 1, 2003
Last modified: November 30, 2016
This is version 180 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Antibodies against RNPC2 are present in sera from a patient with hepatocellular carcinoma who developed several autoantibodies.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.