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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

PharmGKBiPA34450.

Polymorphism and mutation databases

BioMutaiRBM39.
DMDMi28201880.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources1 Publication
Chaini2 – 530529RNA-binding protein 39PRO_0000081814Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources1 Publication
Modified residuei95 – 951PhosphotyrosineCombined sources
Modified residuei97 – 971PhosphoserineCombined sources
Modified residuei100 – 1001PhosphoserineCombined sources
Modified residuei117 – 1171PhosphoserineCombined sources
Modified residuei121 – 1211PhosphoserineCombined sources
Modified residuei136 – 1361PhosphoserineCombined sources
Modified residuei146 – 1461PhosphothreonineCombined sources
Modified residuei334 – 3341PhosphoserineCombined sources
Modified residuei337 – 3371PhosphoserineCombined sources
Modified residuei341 – 3411PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ14498.
MaxQBiQ14498.
PaxDbiQ14498.
PeptideAtlasiQ14498.
PRIDEiQ14498.

PTM databases

iPTMnetiQ14498.
PhosphoSiteiQ14498.
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-6654703,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-395290,EBI-1051785
THAP1Q9NVV93EBI-395290,EBI-741515
ZBTB22O152093EBI-6654703,EBI-723574
ZCCHC10Q8TBK64EBI-395290,EBI-597063

Protein-protein interaction databases

BioGridi114952. 149 interactions.
DIPiDIP-32928N.
IntActiQ14498. 74 interactions.
MINTiMINT-5004569.
STRINGi9606.ENSP00000253363.

Structurei

Secondary structure

1
530
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi147 – 1515Combined sources
Beta strandi154 – 1607Combined sources
Helixi166 – 1738Combined sources
Turni174 – 1763Combined sources
Beta strandi179 – 1846Combined sources
Beta strandi189 – 1924Combined sources
Beta strandi195 – 2039Combined sources
Helixi206 – 2116Combined sources
Turni212 – 2154Combined sources
Beta strandi224 – 2274Combined sources
Beta strandi235 – 2384Combined sources
Beta strandi250 – 2556Combined sources
Helixi263 – 2708Combined sources
Turni271 – 2733Combined sources
Beta strandi276 – 2838Combined sources
Turni285 – 2873Combined sources
Beta strandi290 – 29910Combined sources
Helixi301 – 31111Combined sources
Beta strandi316 – 3194Combined sources
Beta strandi322 – 3243Combined sources
Beta strandi424 – 4318Combined sources
Turni434 – 4363Combined sources
Helixi442 – 45413Combined sources
Turni455 – 4584Combined sources
Beta strandi461 – 4655Combined sources
Beta strandi474 – 4774Combined sources
Helixi481 – 49111Combined sources
Beta strandi502 – 5065Combined sources
Helixi508 – 5147Combined sources
Helixi516 – 5194Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 137-331, 418-530.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ14498.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini153 – 23078RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini250 – 32879RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini445 – 50864RRM 3PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni291 – 406116Interaction with JUNBy similarityAdd
BLAST
Regioni291 – 35565Activating domainBy similarityAdd
BLAST
Regioni355 – 40652Interaction with ESR1 and ESR2By similarityAdd
BLAST
Regioni406 – 530125Interaction with NCOA6By similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi41 – 9050Arg/Ser-rich (RS domain)Add
BLAST
Compositional biasi409 – 4168Poly-Ala

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.
GeneTreeiENSGT00840000129750.
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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti2 – 21A → V.
Corresponds to variant rs1803701 [ dbSNP | Ensembl ].
VAR_015228

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei100 – 12122Missing in isoform 3. 2 PublicationsVSP_043375Add
BLAST
Alternative sequencei392 – 3976Missing in isoform 2. 1 PublicationVSP_005820

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
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. Positions 137-331, 418-530.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114952. 149 interactions.
DIPiDIP-32928N.
IntActiQ14498. 74 interactions.
MINTiMINT-5004569.
STRINGi9606.ENSP00000253363.

PTM databases

iPTMnetiQ14498.
PhosphoSiteiQ14498.
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.
GeneCardsiRBM39.
HGNCiHGNC:15923. RBM39.
HPAiHPA001591.
MIMi604739. gene.
neXtProtiNX_Q14498.
PharmGKBiPA34450.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0147. Eukaryota.
ENOG410XP20. LUCA.
GeneTreeiENSGT00840000129750.
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: September 7, 2016
This is version 177 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.