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TRA2B transformer 2 beta homolog [ Homo sapiens (human) ]

Gene ID: 6434, updated on 12-Oct-2019

Summary

Official Symbol
TRA2Bprovided by HGNC
Official Full Name
transformer 2 beta homologprovided by HGNC
Primary source
HGNC:HGNC:10781
See related
Ensembl:ENSG00000136527 MIM:602719
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
SFRS10; SRFS10; TRAN2B; PPP1R156; TRA2-BETA; Htra2-beta
Summary
This gene encodes a nuclear protein which functions as sequence-specific serine/arginine splicing factor which plays a role in mRNA processing, splicing patterns, and gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in bone marrow (RPKM 41.9), lymph node (RPKM 15.3) and 25 other tissues See more
Orthologs

Genomic context

See TRA2B in Genome Data Viewer
Location:
3q27.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (185914558..185938027, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (185632356..185655924, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene insulin like growth factor 2 mRNA binding protein 2 Neighboring gene microRNA 548aq Neighboring gene VISTA enhancer hs1976 Neighboring gene NmrA like redox sensor 2, pseudogene Neighboring gene ETS variant transcription factor 5

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 Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Multiply spliced HIV-1 RNA is increased by TRA2B overexpression resulting in blocking of HIV-1 genomic RNA export PubMed
HIV-1 RNA splice site usage is altered by the overexpression of TRA2B (in 293T cells) and different isoforms of TRA2A exhibit different altered splice site usage patterns PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 Env protein expression is inhibited by the overexpression of TRA2A (in 293T cells), both full length isoform and truncated N-terminal isoform PubMed
Pr55(Gag) gag HIV-1 Gag protein expression is inhibited by the overexpression of TRA2A (in 293T cells), both full length isoform and truncated N-terminal isoform PubMed
Tat tat TRA2B (transformer 2 beta homolog) inhibits HIV-1 Tat-mediated transactivation activity in HEK293 cells PubMed
Vpr vpr The splicing factors TRA2-alpha and TRA2-beta bind to the exonic splicing enhancer ESEvpr for the activation of exon 3 inclusion, vpr mRNA splicing, and Vpr protein expression PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • 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...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686F18120

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
pre-mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
nuclear inner membrane IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
transformer-2 protein homolog beta
Names
TRA-2 beta
protein phosphatase 1, regulatory subunit 156
splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)
transformer-2 protein homolog B

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_029862.1 RefSeqGene

    Range
    5123..28579
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243879.2NP_001230808.1  transformer-2 protein homolog beta isoform 2

    See identical proteins and their annotated locations for NP_001230808.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region and uses a downstream start codon, compared to variant 1. Isoform 2 has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC009247, AK301118, DA164444, U61267
    Consensus CDS
    CCDS58872.1
    UniProtKB/Swiss-Prot
    P62995
    Related
    ENSP00000371626.4, ENST00000382191.4
    Conserved Domains (1) summary
    cd12641
    Location:997
    RRM_TRA2B; RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins
  2. NM_004593.3NP_004584.1  transformer-2 protein homolog beta isoform 1

    See identical proteins and their annotated locations for NP_004584.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC009247, BC000160, DA164444, U61267
    Consensus CDS
    CCDS33905.1
    UniProtKB/Swiss-Prot
    P62995
    Related
    ENSP00000416959.2, ENST00000453386.7
    Conserved Domains (1) summary
    cl17169
    Location:109197
    RRM_SF; RNA recognition motif (RRM) superfamily

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    185914558..185938027 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247703.2XP_005247760.1  transformer-2 protein homolog beta isoform X1

    See identical proteins and their annotated locations for XP_005247760.1

    UniProtKB/Swiss-Prot
    P62995
    Conserved Domains (1) summary
    cd12641
    Location:997
    RRM_TRA2B; RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins
  2. XM_024453706.1XP_024309474.1  transformer-2 protein homolog beta isoform X1

    Conserved Domains (1) summary
    cd12641
    Location:997
    RRM_TRA2B; RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins
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