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RBM15B RNA binding motif protein 15B [ Homo sapiens (human) ]

Gene ID: 29890, updated on 5-May-2024

Summary

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Official Symbol
RBM15Bprovided by HGNC
Official Full Name
RNA binding motif protein 15Bprovided by HGNC
Primary source
HGNC:HGNC:24303
See related
Ensembl:ENSG00000259956 MIM:612602; AllianceGenome:HGNC:24303
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
OTT3; HsOTT3; HUMAGCGB
Summary
Members of the SPEN (Split-end) family of proteins, including RBM15B, have repressor function in several signaling pathways and may bind to RNA through interaction with spliceosome components (Hiriart et al., 2005 [PubMed 16129689]).[supplied by OMIM, Feb 2009]
Orthologs
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Genomic context

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Location:
3p21.2
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (51391285..51397908)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (51421702..51428325)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (51428716..51435339)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 3 Neighboring gene NANOG hESC enhancer GRCh37_chr3:50928312-50928861 Neighboring gene Sharpr-MPRA regulatory region 894 Neighboring gene ST13, Hsp70 interacting protein pseudogene 14 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14407 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:51263456-51264655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:51377300-51378184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:51430225-51430730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:51430731-51431238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14412 Neighboring gene DDB1 and CUL4 associated factor 1 Neighboring gene mesencephalic astrocyte derived neurotrophic factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14414 Neighboring gene uncharacterized LOC105377085 Neighboring gene Sharpr-MPRA regulatory region 10823 Neighboring gene Sharpr-MPRA regulatory region 62 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19920 Neighboring gene NANOG hESC enhancer GRCh37_chr3:51578193-51578834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:51581873-51582372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:51589128-51590066 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:51617110-51617895 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:51627487-51627690 Neighboring gene RAD54 like 2 Neighboring gene RNA, U6atac small nuclear 29, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. N(6)-Methyladenosine regulator RBM15B acts as an independent prognostic biomarker and its clinical significance in uveal melanoma. Wang T, et al. Front Immunol, 2022. PMID 36003405, Free PMC Article
  2. BAP1 expression is prognostic in breast and uveal melanoma but not colon cancer and is highly positively correlated with RBM15B and USP19. Shahriyari L, et al. PLoS One, 2019. PMID 30716094, Free PMC Article
  3. Kaposi's sarcoma-associated herpesvirus ORF57 interacts with cellular RNA export cofactors RBM15 and OTT3 to promote expression of viral ORF59. Majerciak V, et al. J Virol, 2011 Feb. PMID 21106733, Free PMC Article
  4. Interaction of the Epstein-Barr virus mRNA export factor EB2 with human Spen proteins SHARP, OTT1, and a novel member of the family, OTT3, links Spen proteins with splicing regulation and mRNA export. Hiriart E, et al. J Biol Chem, 2005 Nov 4. PMID 16129689
  5. m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Patil DP, et al. Nature, 2016 Sep 15. PMID 27602518, Free PMC Article

See all (58) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. N(6)-Methyladenosine regulator RBM15B acts as an independent prognostic biomarker and its clinical significance in uveal melanoma.
    Title: N(6)-Methyladenosine regulator RBM15B acts as an independent prognostic biomarker and its clinical significance in uveal melanoma.
  2. BAP1 is highly positively correlated with RBM15B and USP19 expression in invasive breast carcinoma, UM, and colon adenocarcinoma
    Title: BAP1 expression is prognostic in breast and uveal melanoma but not colon cancer and is highly positively correlated with RBM15B and USP19.
  3. HHV-8 ORF57 interacts with RBM15 and OTT3 to promote expression of viral intronless genes.
    Title: Kaposi's sarcoma-associated herpesvirus ORF57 interacts with cellular RNA export cofactors RBM15 and OTT3 to promote expression of viral ORF59.
  4. The RNA-binding motif protein 15B (RBM15B/OTT3) acts as cofactor of the nuclear export receptor NXF1.
    Title: The RNA-binding motif protein 15B (RBM15B/OTT3) acts as cofactor of the nuclear export receptor NXF1.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag NXF1 upregulates the OTT3-mediated Gag expression from pNLgag-RTE, suggesting cooperation between OTT3 and NXF1 PubMed
integrase gag-pol Analysis of HIV-1 proviral integration sites in antiretroviral treatment patients indicates that RBM15B gene favors HIV-1 integration for expansion and persistence of infected cells, suggesting HIV-1 IN interacts with RBM15B PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables mRNA 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 methylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in dosage compensation by inactivation of X chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA export from nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in nucleocytoplasmic transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of alternative mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of RNA N6-methyladenosine methyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
NOT located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
putative RNA-binding protein 15B
Names
chromosome 3p21.1 gene sequence
huOTT3
one twenty two protein 3

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_013286.5 → NP_037418.3  putative RNA-binding protein 15B

    See identical proteins and their annotated locations for NP_037418.3

    Status: VALIDATED

    Source sequence(s)
    AC092037, BM980577
    Consensus CDS
    CCDS33764.1
    UniProtKB/Swiss-Prot
    A4QPG7, Q6QE19, Q8NDT2, Q9BV96
    Related
    ENSP00000454545.1, ENST00000563281.2
    Conserved Domains (5) summary
    cd12554
    Location:137 → 218
    RRM1_RBM15B; RNA recognition motif 1 in putative RNA binding motif protein 15B (RBM15B) from vertebrate
    cd12556
    Location:329 → 413
    RRM2_RBM15B; RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate
    cd12558
    Location:416 → 491
    RRM3_RBM15B; RNA recognition motif 3 in putative RNA-binding protein 15B (RBM15B) from vertebrate
    pfam07744
    Location:712 → 887
    SPOC; SPOC domain
    cl25887
    Location:529 → 639
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    51391285..51397908
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    51421702..51428325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NDT2.3 GenPept UniProtKB/Swiss-Prot:Q8NDT2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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