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

    Gene ID: 29896, updated on 27-Nov-2024

    Summary

    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
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    Genomic context

    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

    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?

    HIV-1 interactions

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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.

    mRNA and Protein(s)

    1. NM_001282757.2NP_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:1796
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins
    2. NM_001282758.2NP_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:1796
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins
    3. NM_001282759.2NP_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:1796
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins
    4. NM_001362759.2NP_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:112134
      RRM_SF; RNA recognition motif (RRM) superfamily
    5. NM_001362760.2NP_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:1796
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins
    6. NM_001362761.2NP_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:1796
      RRM_TRA2; RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins
    7. NM_013293.5NP_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:118197
      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_047420285.1XP_047276241.1  transformer-2 protein homolog alpha isoform X1

    2. XM_047420284.1XP_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_054358028.1XP_054214003.1  transformer-2 protein homolog alpha isoform X1

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

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