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    Taf1d TATA-box binding protein associated factor, RNA polymerase I, D [ Mus musculus (house mouse) ]

    Gene ID: 75316, updated on 2-Oct-2018

    Summary

    Official Symbol
    Taf1dprovided by MGI
    Official Full Name
    TATA-box binding protein associated factor, RNA polymerase I, Dprovided by MGI
    Primary source
    MGI:MGI:1922566
    See related
    Ensembl:ENSMUSG00000031939 Vega:OTTMUSG00000062264
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Josd3; TAFI41; TAF(I)41; 2810003M17Rik; 4930553M18Rik; 5930426I11Rik
    Expression
    Broad expression in CNS E11.5 (RPKM 12.6), limb E14.5 (RPKM 10.4) and 23 other tissues See more
    Orthologs

    Genomic context

    See Taf1d in Genome Data Viewer
    Location:
    9; 9 A2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 9 NC_000075.6 (15306199..15316997)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (15110658..15121441)

    Chromosome 9 - NC_000075.6Genomic Context describing neighboring genes Neighboring gene V-set and transmembrane domain containing 5 Neighboring gene mediator complex subunit 17 Neighboring gene RIKEN cDNA 4931406C07 gene Neighboring gene predicted gene, 25500 Neighboring gene centrosomal protein 295 Neighboring gene small Cajal body-specific RNA 9 Neighboring gene predicted gene, 34973

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Related articles in PubMed

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Clone Names

    • MGC117821

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    biological_process ND
    No biological Data available
    more info
     
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    RNA polymerase transcription factor SL1 complex IEA
    Inferred from Electronic Annotation
    more info
     
    microtubule organizing center ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    TATA box-binding protein-associated factor RNA polymerase I subunit D
    Names
    Josephin domain containing 3
    TATA box binding protein (Tbp)-associated factor, RNA polymerase I, D
    TATA box-binding protein-associated factor 1D
    TBP-associated factor 1D
    transcription initiation factor SL1/TIF-IB subunit D

    NCBI Reference Sequences (RefSeq)

    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_027261.3NP_081537.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform 3

      See identical proteins and their annotated locations for NP_081537.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains a different segment in the 3' coding region, compared to variant 2. The resulting protein (isoform 3) has a shorter and distinct C-terminus when it is compared to isoform 2.
      Source sequence(s)
      AK012662, BU850945, CB523122
      Consensus CDS
      CCDS52726.1
      UniProtKB/Swiss-Prot
      Q9D4V4
      Related
      ENSMUSP00000129141.1, OTTMUSP00000078747, ENSMUST00000164079.8, OTTMUST00000151891
      Conserved Domains (1) summary
      pfam15333
      Location:31243
      TAF1D; TATA box-binding protein-associated factor 1D
    2. NM_029248.2NP_083524.2  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform 2

      See identical proteins and their annotated locations for NP_083524.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) encodes the longer protein (isoform 2).
      Source sequence(s)
      AK016109, AU044383, BC117070, BU850945
      Consensus CDS
      CCDS22836.1
      UniProtKB/Swiss-Prot
      Q9D4V4
      Related
      ENSMUSP00000034415.5, OTTMUSP00000078744, ENSMUST00000034415.5, OTTMUST00000151888
      Conserved Domains (1) summary
      pfam15333
      Location:31243
      TAF1D; TATA box-binding protein-associated factor 1D

    RNA

    1. NR_028401.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an alternate internal exon and contains additional 3' exons, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK014920, AK050165, BU850945
      Related
      ENSMUST00000213763.1, OTTMUST00000151924

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000075.6 Reference GRCm38.p4 C57BL/6J

      Range
      15306199..15316997
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011242620.2XP_011240922.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      See identical proteins and their annotated locations for XP_011240922.1

      UniProtKB/Swiss-Prot
      Q9D4V4
      Conserved Domains (1) summary
      pfam15333
      Location:31243
      TAF1D; TATA box-binding protein-associated factor 1D
    2. XM_006510663.2XP_006510726.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      See identical proteins and their annotated locations for XP_006510726.1

      UniProtKB/Swiss-Prot
      Q9D4V4
      Conserved Domains (1) summary
      pfam15333
      Location:31243
      TAF1D; TATA box-binding protein-associated factor 1D

    RNA

    1. XR_001779058.1 RNA Sequence

    2. XR_870543.2 RNA Sequence

    3. XR_870542.2 RNA Sequence

    4. XR_379141.3 RNA Sequence

    5. XR_870541.2 RNA Sequence

    6. XR_001779059.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_026541.1: Suppressed sequence

      Description
      NM_026541.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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