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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-Nov-2024

Summary

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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, Nov 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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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

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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. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
  5. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

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

Pathways from PubChem

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General gene information

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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

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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)

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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_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

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