Seroatlas · Human Serome Atlas

RBM39

RNA-binding protein 39

Also known as: CAPER, CAPERalpha, CC1.3, fSAP59, HCC1, RBM39_HUMAN, RNPC2

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q14498
Gene
RBM39
Ensembl
ENSG00000131051
Chromosome
20
Canonical length
530 aa
Protein class
Plasma proteins, Predicted intracellular proteins
Subcellular location
Nucleoplasm,Nuclear speckles,Microtubules,Centriolar satellite

OverviewNCBI Gene

This gene encodes a member of the U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to play a role in both steroid hormone receptor-mediated transcription and alternative splicing, and it is also a transcriptional coregulator of the viral oncoprotein v-Rel. Multiple transcript variants have been observed for this gene. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Aug 2011]

Canonical amino-acid sequenceUniProt

530 residues, UniProt reviewed canonical sequence.

>Q14498|RBM39
     1  MADDIDIEAM LEAPYKKDEN KLSSANGHEE RSKKRKKSKS RSRSHERKRS KSKERKRSRD
    61  RERKKSKSRE RKRSRSKERR RSRSRSRDRR FRGRYRSPYS GPKFNSAIRG KIGLPHSIKL
   121  SRRRSRSKSP FRKDKSPVRE PIDNLTPEER DARTVFCMQL AARIRPRDLE EFFSTVGKVR
   181  DVRMISDRNS RRSKGIAYVE FVDVSSVPLA IGLTGQRVLG VPIIVQASQA EKNRAAAMAN
   241  NLQKGSAGPM RLYVGSLHFN ITEDMLRGIF EPFGRIESIQ LMMDSETGRS KGYGFITFSD
   301  SECAKKALEQ LNGFELAGRP MKVGHVTERT DASSASSFLD SDELERTGID LGTTGRLQLM
   361  ARLAEGTGLQ IPPAAQQALQ MSGSLAFGAV AEFSFVIDLQ TRLSQQTEAS ALAAAASVQP
   421  LATQCFQLSN MFNPQTEEEV GWDTEIKDDV IEECNKHGGV IHIYVDKNSA QGNVYVKCPS
   481  IAAAIAAVNA LHGRWFAGKM ITAAYVPLPT YHNLFPDSMT ATQLLVPSRR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against RBM39 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.48
Highest tissue expression
162 nTPM

Expression across tissuesHPA

Tissue

  • bone marrow: 162 nTPM
  • thymus: 48 nTPM
  • retina: 46 nTPM
  • ovary: 45 nTPM
  • urinary bladder: 43 nTPM
  • skeletal muscle: 41 nTPM

Single-cell type

  • neutrophils: 1,198 nCPM
  • syncytiotrophoblasts: 803 nCPM
  • megakaryocyte-erythroid progenitors: 729 nCPM
  • nk-cells: 728 nCPM
  • mast cells: 715 nCPM
  • endometrial glandular cells: 697 nCPM

Immune cell

  • neutrophil: 430 nTPM
  • basophil: 252 nTPM
  • eosinophil: 198 nTPM
  • plasmacytoid DC: 161 nTPM
  • naive B-cell: 141 nTPM
  • memory B-cell: 132 nTPM

Brain region

  • cerebellum: 93 nTPM
  • cerebral cortex: 81 nTPM
  • white matter: 78 nTPM
  • hypothalamus: 75 nTPM
  • medulla oblongata: 75 nTPM
  • midbrain: 75 nTPM

ReferencesPubMed · IEDB

Publications for RBM39 from three distinct lines of evidence, kept separate because they answer different questions: whether antibodies are directed at the protein, whether a B-cell epitope has been mapped on it, and whether a T-cell epitope has. Each is labelled with its source.

Reference: AutoantibodyPubMed

3 publications

Sources: PubMed — antigen-level antibody evidence from a custom retrieval. Records matching a controlled set of autoantibody terms (the MeSH descriptors Autoantibodies and Autoantigens, with title and abstract term variants) were obtained through NCBI E-utilities, and their titles and abstracts parsed for constructions that direct an antibody at a named protein rather than for co-occurrence. Captured names were resolved against UniProt nomenclature and each antigen adjudicated individually against the source text. Bibliographic records from PubMed and MeSH, U.S. National Library of Medicine; citation metrics from NIH iCite (Hutchins et al., PLoS Biology 2016). Titles link to PubMed; abstracts are not reproduced here. The NLM does not endorse this analysis.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.21
gnomAD pLI
1
gnomAD missense Z
4.26
DepMap mean gene effect
-2.2
DepMap dependency class
pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 12% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of RBM39 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads RBM39 as an antibody target. Whether an autoantibody or antibody against RBM39 could matter depends on whether native RBM39 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

RBM39 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label RBM39 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/RBM39. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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