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

Gene ID: 9584, updated on 10-Oct-2024

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; AllianceGenome:HGNC:15923
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
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Genomic context

See RBM39 in Genome Data Viewer
Location:
20q11.22
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35701347..35742260, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37422322..37463242, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34289269..34330182, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NFS1 cysteine desulfurase Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34286841-34287500 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34287501-34288160 Neighboring gene reactive oxygen species modulator 1 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17795 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34330085-34330770 Neighboring gene ribosome production factor 2 homolog pseudogene 1 Neighboring gene MPRA-validated peak4202 silencer Neighboring gene uncharacterized LOC124904972

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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 Functions

What'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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ44170, DKFZp781C0423

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RS domain binding IEA
Inferred from Electronic Annotation
more info
 
enables U1 snRNP binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in RNA processing TAS
Traceable Author Statement
more info
PubMed 
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
 
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in nuclear speck IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
part_of 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)

NEW Try the new Transcript table

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_029955.2 RefSeqGene

    Range
    5000..45913
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242599.2NP_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, AL357374, BC141835, C75555, DC346351
    Consensus CDS
    CCDS56186.1
    UniProtKB/TrEMBL
    B4DRA0
    Related
    ENSP00000436747.2, ENST00000528062.7
    Conserved Domains (1) summary
    TIGR01622
    Location:46496
    SF-CC1; splicing factor, CC1-like family
  2. NM_001242600.2NP_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, AL357374, BC131543, BC141835, C75555, DC346351
    UniProtKB/TrEMBL
    B4DRA0
    Conserved Domains (1) summary
    TIGR01622
    Location:46490
    SF-CC1; splicing factor, CC1-like family
  3. NM_001323422.2NP_001310351.1  RNA-binding protein 39 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555
    UniProtKB/TrEMBL
    B4E1M7
    Conserved Domains (1) summary
    TIGR01622
    Location:46486
    SF-CC1; splicing factor, CC1-like family
  4. NM_001323423.2NP_001310352.1  RNA-binding protein 39 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    UniProtKB/TrEMBL
    Q6MZY7, Q7Z3L0
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  5. NM_001323424.2NP_001310353.1  RNA-binding protein 39 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    UniProtKB/TrEMBL
    B4E1M7
    Conserved Domains (1) summary
    TIGR01622
    Location:46517
    SF-CC1; splicing factor, CC1-like family
  6. NM_004902.4NP_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)
    AL357374, BC141835, C75555, DC346351
    Consensus CDS
    CCDS13265.1
    UniProtKB/TrEMBL
    B4E1M7
    Related
    ENSP00000354437.6, ENST00000361162.10
    Conserved Domains (1) summary
    TIGR01622
    Location:46512
    SF-CC1; splicing factor, CC1-like family
  7. NM_184234.3NP_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)
    AL357374, BC141835, C75555, DC346351
    Consensus CDS
    CCDS13266.1
    UniProtKB/Swiss-Prot
    A2RRD3, A5D8W2, B0BLV3, E1P5S0, E1P5S1, Q14498, Q14499
    UniProtKB/TrEMBL
    A0A384NQ03, B4E1M7
    Related
    ENSP00000253363.6, ENST00000253363.11
    Conserved Domains (1) summary
    TIGR01622
    Location:46518
    SF-CC1; splicing factor, CC1-like family

RNA

  1. NR_040722.2 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
  2. NR_040723.2 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
    Related
    ENST00000639702.1
  3. NR_040724.2 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)
    AL357374, BC141835, BX640714, C75555, DC346351
  4. NR_136587.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL357374, DA189970

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    35701347..35742260 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028138.3XP_016883627.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    B4DRA0
  2. XM_047440604.1XP_047296560.1  RNA-binding protein 39 isoform X4

  3. XM_006723891.5XP_006723954.1  RNA-binding protein 39 isoform X4

    See identical proteins and their annotated locations for XP_006723954.1

    UniProtKB/TrEMBL
    Q6MZY7, Q7Z3L0
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  4. XM_047440605.1XP_047296561.1  RNA-binding protein 39 isoform X4

  5. XM_024452023.2XP_024307791.1  RNA-binding protein 39 isoform X5

    UniProtKB/TrEMBL
    Q6MZY7, Q6N037, Q7Z3L0
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  6. XM_047440602.1XP_047296558.1  RNA-binding protein 39 isoform X2

    Related
    ENSP00000344581.6, ENST00000338163.10
  7. XM_047440603.1XP_047296559.1  RNA-binding protein 39 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    37422322..37463242 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324247.1XP_054180222.1  RNA-binding protein 39 isoform X1

  2. XM_054324250.1XP_054180225.1  RNA-binding protein 39 isoform X4

  3. XM_054324252.1XP_054180227.1  RNA-binding protein 39 isoform X4

  4. XM_054324251.1XP_054180226.1  RNA-binding protein 39 isoform X4

  5. XM_054324253.1XP_054180228.1  RNA-binding protein 39 isoform X5

    UniProtKB/TrEMBL
    Q6N037
  6. XM_054324248.1XP_054180223.1  RNA-binding protein 39 isoform X2

  7. XM_054324249.1XP_054180224.1  RNA-binding protein 39 isoform X3

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.