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Protein

RNA-binding protein 39

Gene

RBM39

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

Miscellaneous

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

GO - Molecular functioni

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • RNA processing Source: ProtInc
  • RNA splicing Source: UniProtKB-KW

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):
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

EuPathDBiHostDB:ENSG00000131051.21
HGNCiHGNC:15923 RBM39
MIMi604739 gene
neXtProtiNX_Q14498

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

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
Cross-linki111Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei117PhosphoserineCombined sources1
Cross-linki119Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei121PhosphoserineCombined sources1
Modified residuei136PhosphoserineCombined sources1
Modified residuei146PhosphothreonineCombined sources1
Cross-linki244Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei334PhosphoserineCombined sources1
Modified residuei337PhosphoserineCombined sources1
Modified residuei341PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ14498
MaxQBiQ14498
PaxDbiQ14498
PeptideAtlasiQ14498
PRIDEiQ14498
ProteomicsDBi60005
60006 [Q14498-2]
60007 [Q14498-3]

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 Expressed in 197 organ(s), highest expression level in intestine
CleanExiHS_RBM39
ExpressionAtlasiQ14498 baseline and differential
GenevisibleiQ14498 HS

Organism-specific databases

HPAiHPA001591

Interactioni

Subunit structurei

Interacts with NCOA6 and JUN. Interacts with ESR1 and ESR2, in the presence of estradiol (E2) (By similarity). Interacts with RSRC1 (via Arg/Ser-rich domain) (PubMed:15798186). Interacts with SF3B1 (PubMed:24795046). Interacts with ZNF106 (via N-terminus) (By similarity).By similarity2 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi114952, 158 interactors
CORUMiQ14498
DIPiDIP-32928N
IntActiQ14498, 86 interactors
MINTiQ14498
STRINGi9606.ENSP00000253363

Structurei

Secondary structure

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

3D structure databases

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0147 Eukaryota
ENOG410XP20 LUCA
GeneTreeiENSGT00930000150902
HOGENOMiHOG000236253
HOVERGENiHBG057646
InParanoidiQ14498
KOiK13091
OMAiPIMVQHT
OrthoDBiEOG091G0BQ9
PhylomeDBiQ14498
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

This entry has 3 described isoforms and 14 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 14 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
G3XAC6G3XAC6_HUMAN
RNA-binding protein 39
RBM39 RNPC2, hCG_38221
423Annotation score:
Q5QP23Q5QP23_HUMAN
RNA-binding protein 39
RBM39
231Annotation score:
H0Y4X3H0Y4X3_HUMAN
RNA-binding protein 39
RBM39
336Annotation score:
A0A0U1RQH7A0A0U1RQH7_HUMAN
RNA-binding protein 39
RBM39
245Annotation score:
Q5QP22Q5QP22_HUMAN
RNA-binding protein 39
RBM39
193Annotation score:
A0A0U1RQW2A0A0U1RQW2_HUMAN
RNA-binding protein 39
RBM39
163Annotation score:
F2Z2Z5F2Z2Z5_HUMAN
RNA-binding protein 39
RBM39
47Annotation score:
A8MYG5A8MYG5_HUMAN
RNA-binding protein 39
RBM39
95Annotation score:
F8WF24F8WF24_HUMAN
RNA-binding protein 39
RBM39
39Annotation score:
H0Y6I9H0Y6I9_HUMAN
RNA-binding protein 39
RBM39
86Annotation score:
There are more potential isoformsShow all

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0152282A → V. Corresponds to variant dbSNP:rs1803701Ensembl.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 No translation available.
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

Similar proteinsi

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 No translation available.
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, 158 interactors
CORUMiQ14498
DIPiDIP-32928N
IntActiQ14498, 86 interactors
MINTiQ14498
STRINGi9606.ENSP00000253363

PTM databases

iPTMnetiQ14498
PhosphoSitePlusiQ14498
SwissPalmiQ14498

Polymorphism and mutation databases

BioMutaiRBM39
DMDMi28201880

Proteomic databases

EPDiQ14498
MaxQBiQ14498
PaxDbiQ14498
PeptideAtlasiQ14498
PRIDEiQ14498
ProteomicsDBi60005
60006 [Q14498-2]
60007 [Q14498-3]

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
EuPathDBiHostDB:ENSG00000131051.21
GeneCardsiRBM39
HGNCiHGNC:15923 RBM39
HPAiHPA001591
MIMi604739 gene
neXtProtiNX_Q14498
OpenTargetsiENSG00000131051
PharmGKBiPA34450
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0147 Eukaryota
ENOG410XP20 LUCA
GeneTreeiENSGT00930000150902
HOGENOMiHOG000236253
HOVERGENiHBG057646
InParanoidiQ14498
KOiK13091
OMAiPIMVQHT
OrthoDBiEOG091G0BQ9
PhylomeDBiQ14498
TreeFamiTF320448

Miscellaneous databases

ChiTaRSiRBM39 human
EvolutionaryTraceiQ14498
GeneWikiiRBM39
GenomeRNAii9584
PROiPR:Q14498
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000131051 Expressed in 197 organ(s), highest expression level in intestine
CleanExiHS_RBM39
ExpressionAtlasiQ14498 baseline and differential
GenevisibleiQ14498 HS

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_HUMAN
AccessioniPrimary (citable) accession number: Q14498
Secondary accession number(s): A2RRD3
, A5D8W2, B0BLV3, E1P5S0, E1P5S1, Q14499
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 2003
Last sequence update: February 1, 2003
Last modified: November 7, 2018
This is version 200 of the entry and version 2 of the sequence. See 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

Keywords - Technical termi

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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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