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    TRA2A transformer 2 alpha homolog [ Homo sapiens (human) ]

    Gene ID: 29896, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TRA2Aprovided by HGNC
    Official Full Name
    transformer 2 alpha homologprovided by HGNC
    Primary source
    HGNC:HGNC:16645
    See related
    Ensembl:ENSG00000164548 MIM:602718; AllianceGenome:HGNC:16645
    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
    AWMS1; HSU53209
    Summary
    This gene is a member of the transformer 2 homolog family and encodes a protein with several RRM (RNA recognition motif) domains. This phosphorylated nuclear protein binds to specific RNA sequences and plays a role in the regulation of pre-mRNA splicing. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]
    Expression
    Ubiquitous expression in bone marrow (RPKM 46.2), endometrium (RPKM 25.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRA2A in Genome Data Viewer
    Location:
    7p15.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (23504780..23531981, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (23644119..23671311, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (23544399..23571600, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene chromosome 5 open reading frame 13 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25731 Neighboring gene ribosomal protein S2 pseudogene 32 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:23570658-23571228 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:23571229-23571798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:23571837-23572338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:23572339-23572838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25737 Neighboring gene ATP binding cassette subfamily E member 1 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr7:23620581-23620772 Neighboring gene CDC like kinase 2, pseudogene 1

    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. TRA2A promotes proliferation, migration, invasion and epithelial mesenchymal transition of glioma cells. Tan Y, et al. Brain Res Bull, 2018 Oct. PMID 30367895
    2. Transformer 2 alpha homolog is a downstream gene of hypoxia-inducible factor 1 subunit alpha and is involved in the progression of pancreatic cancer. Cao W, et al. Bioengineered, 2022 May. PMID 35635094, Free PMC Article
    3. Expression of tumor-promoting Cyr61 is regulated by hTRA2-β1 and acidosis. Hirschfeld M, et al. Hum Mol Genet, 2011 Jun 15. PMID 21447598
    4. Integrative network analysis identifies cell-specific trans regulators of m6A. An S, et al. Nucleic Acids Res, 2020 Feb 28. PMID 31912146, Free PMC Article
    5. TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing. Liu T, et al. Mol Cancer Ther, 2017 Jul. PMID 28416606

    See all (126) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Transformer 2 alpha homolog is a downstream gene of hypoxia-inducible factor 1 subunit alpha and is involved in the progression of pancreatic cancer.
      Title: Transformer 2 alpha homolog is a downstream gene of hypoxia-inducible factor 1 subunit alpha and is involved in the progression of pancreatic cancer.
    2. TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment.
      Title: TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment.
    3. we knocked down three regulators respectively and found two of them (TRA2A and CAPRIN1) selectively promoted the methylations of the m6A sites co-localized with their binding targets on RNAs through physical interactions with the m6A writers. Knockdown of TRA2A increased the stabilities of the RNAs with TRA2A bound near the m6A sites and decreased the viability of cells
      Title: Integrative network analysis identifies cell-specific trans regulators of m6A.
    4. Overexpression of TRA2A in glioma SHG44 cell lines promoted the tumor cells proliferation, migration, invasion and epithelial mesenchymal transition (EMT), while, knockdown of TRA2A showed the opposite effect.
      Title: TRA2A promotes proliferation, migration, invasion and epithelial mesenchymal transition of glioma cells.
    5. our findings suggest that paclitaxel targets the TRA2A-RSRC2 splicing pathway, and deregulated TRA2A and RSRC2 expression may confer paclitaxel resistance. In addition, our study demonstrates that expression of TRA2A in conjunction with RSRC2 may provide valuable molecular biomarker evidence for triple-negative breast cancer (TNBC)clinical treatment decisions and patient outcome
      Title: TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing.
    6. Overexpression of either Tra2alpha or Tra2beta results in a marked reduction in HIV-1 Gag/ Env expression.
      Title: Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression.
    7. findings show the inclusion of both HIV-1 exon 3 and vpr mRNA processing is promoted by an exonic splicing enhancer (ESEvpr) localized between exonic splicing silencer ESSV and 5'ss D3; the ESEvpr sequence was found to be bound by members of the Tra2 protein family
      Title: Tra2-mediated recognition of HIV-1 5' splice site D3 as a key factor in the processing of vpr mRNA.
    8. Expression of tumor-promoting Cyr61 is regulated by hTRA2-beta1 and acidosis.
      Title: Expression of tumor-promoting Cyr61 is regulated by hTRA2-β1 and acidosis.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 RNA splice site usage is altered by the overexpression of TRA2A (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
    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

    Homology

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transformer-2 protein homolog alpha
    Names
    TRA-2 alpha
    TRA2-alpha
    Tra2alpha
    htra-2 alpha
    putative MAPK activating protein PM24
    transformer-2 alpha
    transformer-2 protein homolog A

    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_001282757.2 → NP_001269686.1  transformer-2 protein homolog alpha isoform 2

      See identical proteins and their annotated locations for NP_001269686.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an additional exon in the 5' region that results in translation initiation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AB097048, AK300565, BP376263, U53209
      Consensus CDS
      CCDS64609.1
      UniProtKB/Swiss-Prot
      Q13595
      UniProtKB/TrEMBL
      Q549U1
      Conserved Domains (1) summary
      cd12363
      Location:17 → 96
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

    2. NM_001282758.2 → NP_001269687.1  transformer-2 protein homolog alpha isoform 2

      See identical proteins and their annotated locations for NP_001269687.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an additional exon in the 5' region that results in translation initiation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AB097048, AK300741, U53209
      Consensus CDS
      CCDS64609.1
      UniProtKB/Swiss-Prot
      Q13595
      UniProtKB/TrEMBL
      Q549U1
      Related
      ENSP00000480822.1, ENST00000621813.4
      Conserved Domains (1) summary
      cd12363
      Location:17 → 96
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

    3. NM_001282759.2 → NP_001269688.1  transformer-2 protein homolog alpha isoform 3

      See identical proteins and their annotated locations for NP_001269688.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains two additional exons in the 5' region and uses an alternate in-frame acceptor splice site in the 3' coding region compared to variant 1. The former difference results in translation initiation from an in-frame downstream start codon, and an isoform (3) with a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AB097048, AK298815, AK300741
      Consensus CDS
      CCDS75569.1
      UniProtKB/Swiss-Prot
      Q13595
      UniProtKB/TrEMBL
      Q549U1
      Related
      ENSP00000376290.4, ENST00000392502.8
      Conserved Domains (1) summary
      cd12363
      Location:17 → 96
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

    4. NM_001362759.2 → NP_001349688.1  transformer-2 protein homolog alpha isoform 4

      Status: REVIEWED

      Source sequence(s)
      AB097048, AK300565, CN428527, HY021807, U53209
      Conserved Domains (1) summary
      cl17169
      Location:112 → 134
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. NM_001362760.2 → NP_001349689.1  transformer-2 protein homolog alpha isoform 2

      Status: REVIEWED

      Source sequence(s)
      AB097048, AK300565, AK311687, BG722500, U53209
      Consensus CDS
      CCDS64609.1
      Conserved Domains (1) summary
      cd12363
      Location:17 → 96
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

    6. NM_001362761.2 → NP_001349690.1  transformer-2 protein homolog alpha isoform 2

      Status: REVIEWED

      Source sequence(s)
      AB097048, AK300565, BP376263, DA361083, U53209
      Consensus CDS
      CCDS64609.1
      Conserved Domains (1) summary
      cd12363
      Location:17 → 96
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

    7. NM_013293.5 → NP_037425.1  transformer-2 protein homolog alpha isoform 1

      See identical proteins and their annotated locations for NP_037425.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB097048, BP376263, U53209
      Consensus CDS
      CCDS5383.1
      UniProtKB/Swiss-Prot
      B4DQI6, B4DUA9, E9PD75, Q13595
      UniProtKB/TrEMBL
      Q549U1
      Related
      ENSP00000297071.4, ENST00000297071.9
      Conserved Domains (1) summary
      cd12363
      Location:118 → 197
      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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      23504780..23531981 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420285.1 → XP_047276241.1  transformer-2 protein homolog alpha isoform X1

    2. XM_047420284.1 → XP_047276240.1  transformer-2 protein homolog alpha isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      23644119..23671311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358028.1 → XP_054214003.1  transformer-2 protein homolog alpha isoform X1

    2. XM_054358030.1 → XP_054214005.1  transformer-2 protein homolog alpha isoform X1

    3. XM_054358029.1 → XP_054214004.1  transformer-2 protein homolog alpha isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13595.1 GenPept UniProtKB/Swiss-Prot:Q13595

    Gene LinkOut

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

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