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

    Gene ID: 6434, updated on 28-Oct-2024

    Summary

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    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

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    See TRA2B in Genome Data Viewer
    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_000003.12Genomic Context describing neighboring genes Neighboring gene insulin like growth factor 2 mRNA binding protein 2 Neighboring gene uncharacterized LOC124906313 Neighboring gene Sharpr-MPRA regulatory region 9603 Neighboring gene Sharpr-MPRA regulatory region 5696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185487094-185487594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185487595-185488095 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185491440-185492292 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:185496875-185497772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185497860-185498360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185501879-185502772 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185504559-185505450 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185507237-185508130 Neighboring gene microRNA 548aq Neighboring gene VISTA enhancer hs1976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185516757-185517258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185517259-185517758 Neighboring gene NANOG hESC enhancer GRCh37_chr3:185520396-185520897 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:185525354-185525896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:185540833-185541696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14977 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185542636-185542866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14978 Neighboring gene Sharpr-MPRA regulatory region 6530 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185623478-185623669 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185655136-185655863 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185667767-185668709 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185666824-185667766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185670624-185671147 Neighboring gene Sharpr-MPRA regulatory region 2251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185701333-185701854 Neighboring gene NmrA like redox sensor 2, pseudogene Neighboring gene uncharacterized LOC124909470 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185795356-185795551 Neighboring gene ETS variant transcription factor 5 Neighboring gene ETV5 antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Human transformer-2-beta gene (SFRS10): complete nucleotide sequence, chromosomal localization, and generation of a tissue-specific isoform. Nayler O, et al. Genomics, 1998 Oct 15. PMID 9790768
    2. Prognostic value of transformer 2β expression in prostate cancer. Diao Y, et al. Int J Clin Exp Pathol, 2015. PMID 26261585, Free PMC Article
    3. Clustered variants in the 5' coding region of TRA2B cause a distinctive neurodevelopmental syndrome. Ramond F, et al. Genet Med, 2023 Apr. PMID 36549593
    4. Significance of nuclear hTra2-beta1 expression in cervical cancer. Gabriel B, et al. Acta Obstet Gynecol Scand, 2009. PMID 19037821
    5. Exclusion of Htra2-beta1, an up-regulator of full-length SMN2 transcript, as a modifying gene for spinal muscular atrophy. Helmken C, et al. Hum Genet, 2000 Dec. PMID 11153908

    See all (211) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    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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    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686F18120

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA 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 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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    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_029862.1 RefSeqGene

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

    mRNA and Protein(s)

    1. 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

    2. 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

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      185914558..185938014 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448717.1 → XP_047304673.1  transformer-2 protein homolog beta isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      188730348..188753803 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347538.1 → XP_054203513.1  transformer-2 protein homolog beta isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P62995.1 GenPept UniProtKB/Swiss-Prot:P62995

    Gene LinkOut

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

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