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RBM39 RNA binding motif protein 39 [ Homo sapiens (human) ]

Gene ID: 9584, updated on 9-Dec-2018

Summary

Official Symbol
RBM39provided by HGNC
Official Full Name
RNA binding motif protein 39provided by HGNC
Primary source
HGNC:HGNC:15923
See related
Ensembl:ENSG00000131051 MIM:604739
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HCC1; CAPER; RNPC2; FSAP59; CAPERalpha
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 103.4), lymph node (RPKM 47.1) and 25 other tissues See more
Orthologs

Genomic context

See RBM39 in Genome Data Viewer
Location:
20q11.22
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (35703609..35742336, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34291531..34330258, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene copine 1 Neighboring gene RNA binding motif protein 12 Neighboring gene NFS1 cysteine desulfurase Neighboring gene reactive oxygen species modulator 1 Neighboring gene ribosome production factor 2 homolog pseudogene 1 Neighboring gene PHD finger protein 20 Neighboring gene cytochrome c oxidase subunit 7B pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, RNA binding motif protein 39 (RBM39), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with RBM39 is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ44170, DKFZp781C0423

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA processing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing IEA
Inferred from Electronic Annotation
more info
 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 
microtubule organizing center IDA
Inferred from Direct Assay
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nuclear speck IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
RNA-binding protein 39
Names
CAPER alpha
RNA-binding region (RNP1, RRM) containing 2
coactivator of activating protein-1 and estrogen receptors
epididymis secretory sperm binding protein
functional spliceosome-associated protein 59
hepatocellular carcinoma protein 1
splicing factor HCC1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029955.1 RefSeqGene

    Range
    5001..43728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242599.1NP_001229528.1  RNA-binding protein 39 isoform c

    See identical proteins and their annotated locations for NP_001229528.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (c) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AK299678, BC141835, C75555, DC346351
    Consensus CDS
    CCDS56186.1
    UniProtKB/Swiss-Prot
    Q14498
    Related
    ENSP00000436747.2, ENST00000528062.7
    Conserved Domains (1) summary
    TIGR01622
    Location:46496
    SF-CC1; splicing factor, CC1-like family
  2. NM_001242600.1NP_001229529.1  RNA-binding protein 39 isoform d

    See identical proteins and their annotated locations for NP_001229529.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (d) lacks two internal segments, compared to isoform a.
    Source sequence(s)
    AK299165, BC131543, BC141835, C75555, DC346351
    UniProtKB/Swiss-Prot
    Q14498
    UniProtKB/TrEMBL
    B4DRA0
    Conserved Domains (1) summary
    TIGR01622
    Location:46490
    SF-CC1; splicing factor, CC1-like family
  3. NM_001323422.1NP_001310351.1  RNA-binding protein 39 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    Conserved Domains (1) summary
    TIGR01622
    Location:46486
    SF-CC1; splicing factor, CC1-like family
  4. NM_001323423.1NP_001310352.1  RNA-binding protein 39 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    UniProtKB/TrEMBL
    E1P5S2
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  5. NM_001323424.1NP_001310353.1  RNA-binding protein 39 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    Conserved Domains (1) summary
    TIGR01622
    Location:46517
    SF-CC1; splicing factor, CC1-like family
  6. NM_004902.3NP_004893.1  RNA-binding protein 39 isoform b

    See identical proteins and their annotated locations for NP_004893.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (b, also called CC1.3) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    BC141835, C75555, DC346351
    Consensus CDS
    CCDS13265.1
    UniProtKB/Swiss-Prot
    Q14498
    Related
    ENSP00000354437.6, ENST00000361162.10
    Conserved Domains (1) summary
    TIGR01622
    Location:46512
    SF-CC1; splicing factor, CC1-like family
  7. NM_184234.2NP_909122.1  RNA-binding protein 39 isoform a

    See identical proteins and their annotated locations for NP_909122.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a, also called CC1.4).
    Source sequence(s)
    BC141835, C75555, DC346351
    Consensus CDS
    CCDS13266.1
    UniProtKB/Swiss-Prot
    Q14498
    Related
    ENSP00000253363.6, ENST00000253363.10
    Conserved Domains (1) summary
    TIGR01622
    Location:46518
    SF-CC1; splicing factor, CC1-like family

RNA

  1. NR_040722.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL357374, BC141835, BX640812, C75555, DC346351
    Related
    ENST00000403542.6
  2. NR_040723.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) includes an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL357374, BC141835, BX537770, C75555, DC346351
  3. NR_040724.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) includes an additional exon in the 5' region, and uses an alternate splice site in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC141835, BX640714, C75555, DC346351
    Related
    ENST00000338163.10
  4. NR_136587.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL357374, CA419145, DA189970

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    35703609..35742336 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028146.2XP_016883635.1  RNA-binding protein 39 isoform X4

  2. XM_017028138.2XP_016883627.1  RNA-binding protein 39 isoform X1

  3. XM_017028147.1XP_016883636.1  RNA-binding protein 39 isoform X4

  4. XM_017028145.2XP_016883634.1  RNA-binding protein 39 isoform X3

    UniProtKB/TrEMBL
    Q6N037
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  5. XM_017028140.2XP_016883629.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    E1P5S2
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  6. XM_006723890.4XP_006723953.1  RNA-binding protein 39 isoform X2

    See identical proteins and their annotated locations for XP_006723953.1

    UniProtKB/TrEMBL
    E1P5S2
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  7. XM_011529111.3XP_011527413.1  RNA-binding protein 39 isoform X2

    See identical proteins and their annotated locations for XP_011527413.1

    UniProtKB/TrEMBL
    E1P5S2
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  8. XM_017028139.2XP_016883628.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    E1P5S2
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  9. XM_006723891.4XP_006723954.1  RNA-binding protein 39 isoform X2

    See identical proteins and their annotated locations for XP_006723954.1

    UniProtKB/TrEMBL
    E1P5S2
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  10. XM_024452022.1XP_024307790.1  RNA-binding protein 39 isoform X2

  11. XM_017028141.2XP_016883630.1  RNA-binding protein 39 isoform X3

    UniProtKB/TrEMBL
    Q6N037
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  12. XM_017028143.2XP_016883632.1  RNA-binding protein 39 isoform X3

    UniProtKB/TrEMBL
    Q6N037
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  13. XM_017028142.2XP_016883631.1  RNA-binding protein 39 isoform X3

    UniProtKB/TrEMBL
    Q6N037
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  14. XM_017028144.2XP_016883633.1  RNA-binding protein 39 isoform X3

    UniProtKB/TrEMBL
    Q6N037
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  15. XM_024452025.1XP_024307793.1  RNA-binding protein 39 isoform X3

    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  16. XM_024452023.1XP_024307791.1  RNA-binding protein 39 isoform X3

    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  17. XM_024452024.1XP_024307792.1  RNA-binding protein 39 isoform X3

    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family

RNA

  1. XR_001754439.2 RNA Sequence

    Related
    ENST00000444878.5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_184237.1: Suppressed sequence

    Description
    NM_184237.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_184241.1: Suppressed sequence

    Description
    NM_184241.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  3. NM_184244.1: Suppressed sequence

    Description
    NM_184244.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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