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

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; AllianceGenome:HGNC:10781
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: mouse all
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Genomic context

Location:: 3q27.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (185914558..185938014, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (188730348..188753803, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (185632346..185655802, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Autoregulated splicing of TRA2beta programs T cell fate in response to antigen-receptor stimulation.
Title: Autoregulated splicing of TRA2β programs T cell fate in response to antigen-receptor stimulation.
Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation.
Title: Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation.
Clustered variants in the 5' coding region of TRA2B cause a distinctive neurodevelopmental syndrome.
Title: Clustered variants in the 5' coding region of TRA2B cause a distinctive neurodevelopmental syndrome.
Tra2beta Enhances Cell Proliferation by Inducing the Expression of Transcription Factor SP1 in Cervical Cancer.
Title: Tra2β Enhances Cell Proliferation by Inducing the Expression of Transcription Factor SP1 in Cervical Cancer.
MicroRNA-330-3p represses the proliferation and invasion of laryngeal squamous cell carcinoma through downregulation of Tra2beta-mediated Akt signaling.
Title: MicroRNA-330-3p represses the proliferation and invasion of laryngeal squamous cell carcinoma through downregulation of Tra2β-mediated Akt signaling.
Tra2beta protects against the degeneration of chondrocytes by inhibiting chondrocyte apoptosis via activating the PI3K/Akt signaling pathway.
Title: Tra2β protects against the degeneration of chondrocytes by inhibiting chondrocyte apoptosis via activating the PI3K/Akt signaling pathway.
Bone marrow mesenchymal stem cell-derived exosomal miR-206 inhibits osteosarcoma progression by targeting TRA2B.
Title: Bone marrow mesenchymal stem cell-derived exosomal miR-206 inhibits osteosarcoma progression by targeting TRA2B.
HnRNPA1 interacts with G-quadruplex in the TRA2B promoter and stimulates its transcription in human colon cancer cells.
Title: HnRNPA1 interacts with G-quadruplex in the TRA2B promoter and stimulates its transcription in human colon cancer cells.
Findings demonstrate that Tra2b is upregulated in non-small cell lung cancer (NSCLC) and is associated with poor prognosis. Furthermore, Tra2b was identified as a direct target of miR-335. These results indicate that the interaction between miR-335 and Tra2b may play a vital role in the pathogenesis of NSCLC.
Title: miR-335 inhibited cell proliferation of lung cancer cells by target Tra2β.
It seems that a new signaling axis, SIRT1-SFRS10-LPIN1 axis, acting in the pathogenesis of alcoholic fatty liver disease exists.
Title: Roles of silent information regulator 1-serine/arginine-rich splicing factor 10-lipin 1 axis in the pathogenesis of alcohol fatty liver disease.

Submit: New GeneRIF Correction See all GeneRIFs (33)

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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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 synthesis is enhanced (slightly) by endogeneous levels of TRA2B; shRNA knockdown of TRA2B reduces Env synthesis slightly (~2 fold) in the HeLa rtTA HIVdletamls cell line (contains stably integrated, doxycycline (Dox) inducible HIV-1 provirus)	PubMed
	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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

WI-14755 (e-PCR)
- UniSTS:24215

SHGC-77608 (e-PCR)
- UniSTS:47262

MARC_5257-5258:991939526:5 (e-PCR)
- UniSTS:231145

MARC_5257-5258:996690205:1 (e-PCR)
- UniSTS:231145

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables pre-mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing, via transesterification reactions	TAS Traceable Author Statement more info	PubMed
involved_in cellular response to glucose stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebral cortex regionalization	IEA Inferred from Electronic Annotation more info
involved_in embryonic brain development	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info
involved_in regulation of RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nuclear inner membrane	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info
part_of spliceosomal complex	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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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)

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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.

Genomic

NG_029862.1 RefSeqGene

Range

5123..28579

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243879.2 → NP_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:11 → 97

RRM_TRA2B; RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins
NM_004593.3 → NP_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

B4DVK2, D3DNU3, O15449, P62995, Q15815, Q64283

Related

ENSP00000416959.2, ENST00000453386.7

Conserved Domains (1) summary

cd12363
Location:117 → 196

RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins