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    Htatsf1 HIV-1 Tat specific factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317612, updated on 10-Jul-2024

    Summary

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    Official Symbol
    Htatsf1provided by RGD
    Official Full Name
    HIV-1 Tat specific factor 1provided by RGD
    Primary source
    RGD:1563377
    See related
    EnsemblRapid:ENSRNOG00000027761 AllianceGenome:RGD:1563377
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1563377
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be part of U2 snRNP and U2-type spliceosomal complex. Orthologous to human HTATSF1 (HIV-1 Tat specific factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 106.6), Muscle (RPKM 104.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Htatsf1 in Genome Data Viewer
    Location:
    Xq36
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (139972742..139986923)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (134935426..134949607)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (159514053..159528281)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene adhesion G protein-coupled receptor G4 Neighboring gene bombesin receptor subtype 3 Neighboring gene high mobility group nucleosomal binding domain 4, pseudogene 5 Neighboring gene vestigial-like family member 1 Neighboring gene heat shock protein 90 alpha family class B member 1, pseudogene 15

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin-protein adaptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly-ADP-D-ribose modification-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in U2-type prespliceosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of U2 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    17S U2 SnRNP complex component HTATSF1
    Names
    HIV TAT specific factor 1
    HIV Tat-specific factor 1

    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_001108259.1 → NP_001101729.1  17S U2 SnRNP complex component HTATSF1

      See identical proteins and their annotated locations for NP_001101729.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474106
      UniProtKB/TrEMBL
      A6KSQ2, D4A997
      Related
      ENSRNOP00000061583.2, ENSRNOT00000065636.5
      Conserved Domains (3) summary
      COG0724
      Location:84 → 218
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12281
      Location:132 → 222
      RRM1_TatSF1_like; RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins
      cd12282
      Location:263 → 353
      RRM2_TatSF1_like; RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      139972742..139986923
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063280104.1 → XP_063136174.1  17S U2 SnRNP complex component HTATSF1 isoform X1

      UniProtKB/TrEMBL
      A6KSQ2, D4A997
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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