U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 75316, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    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 AllianceGenome:MGI:1922566
    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
    Summary
    Predicted to enable identical protein binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in cytosol; microtubule cytoskeleton; and nucleolus. Predicted to be part of RNA polymerase transcription factor SL1 complex. Predicted to be active in nucleoplasm. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and sensory organ. Orthologous to human TAF1D (TATA-box binding protein associated factor, RNA polymerase I subunit D). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in CNS E11.5 (RPKM 12.6), limb E14.5 (RPKM 10.4) and 23 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Taf1d in Genome Data Viewer
    Location:
    9 A2; 9 4.78 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (15217485..15228293)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (15305953..15316997)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 51702 Neighboring gene V-set and transmembrane domain containing 5 Neighboring gene STARR-seq mESC enhancer starr_23372 Neighboring gene mediator complex subunit 17 Neighboring gene RIKEN cDNA 4931406C07 gene Neighboring gene STARR-positive B cell enhancer ABC_E6715 Neighboring gene microRNA 7650 Neighboring gene predicted gene, 24455 Neighboring gene predicted gene, 24299 Neighboring gene predicted gene, 25791 Neighboring gene predicted gene, 22620 Neighboring gene predicted gene, 24357 Neighboring gene small nucleolar RNA SNORA32 Neighboring gene predicted gene, 22579 Neighboring gene centrosomal protein 295 Neighboring gene small Cajal body-specific RNA 9 Neighboring gene predicted gene, 24339

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Global Hypertranscription in the Mouse Embryonic Germline. Percharde M, et al. Cell Rep, 2017 Jun 6. PMID 28591571, Free PMC Article
    2. Reconstitution of human rRNA gene transcription in mouse cells by a complete SL1 complex. Murano K, et al. J Cell Sci, 2014 Aug 1. PMID 24928901
    3. Relationship of quantitative reverse transcription polymerase chain reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome identifies mouse preimplantation embryo reference genes†. Tscherner AK, et al. Biol Reprod, 2023 Nov 15. PMID 37669129, Free PMC Article
    4. Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each. Dogar AM, et al. PLoS One, 2018. PMID 30418981, Free PMC Article
    5. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC117821

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase transcription factor SL1 complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriolar satellite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitotic spindle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    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_027261.3 → NP_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/TrEMBL
      Q8K176
      Related
      ENSMUSP00000129141.2, ENSMUST00000164079.9
      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      TAF1D; TATA box-binding protein-associated factor 1D

    2. NM_029248.2 → NP_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
      Q149X7, Q8C7I5, Q9CZG0, Q9D4V4, Q9D5U6
      Related
      ENSMUSP00000034415.6, ENSMUST00000034415.6
      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      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
      ENSMUST00000213763.2

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      15217485..15228293
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036155366.1 → XP_036011259.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      TAF1D; TATA box-binding protein-associated factor 1D

    2. XM_036155369.1 → XP_036011262.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      TAF1D; TATA box-binding protein-associated factor 1D

    3. XM_036155367.1 → XP_036011260.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      TAF1D; TATA box-binding protein-associated factor 1D

    4. XM_011242620.3 → XP_011240922.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X3

      See identical proteins and their annotated locations for XP_011240922.1

      UniProtKB/Swiss-Prot
      Q149X7, Q8C7I5, Q9CZG0, Q9D4V4, Q9D5U6
      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      TAF1D; TATA box-binding protein-associated factor 1D

    5. XM_036155368.1 → XP_036011261.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      Conserved Domains (1) summary
      pfam15333
      Location:31 → 243
      TAF1D; TATA box-binding protein-associated factor 1D

    RNA

    1. XR_870541.3 RNA Sequence

    2. XR_870543.3 RNA Sequence

    3. XR_870542.3 RNA Sequence

    4. XR_379141.5 RNA Sequence

    5. XR_004935589.1 RNA Sequence

    6. XR_004935588.1 RNA Sequence

    7. XR_004935591.1 RNA Sequence

    8. XR_004935590.1 RNA Sequence

    9. XR_003948044.2 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.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D4V4.2 GenPept UniProtKB/Swiss-Prot:Q9D4V4

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous