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    Taf1d TATA-box binding protein associated factor, RNA polymerase I subunit D [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363017, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Taf1dprovided by RGD
    Official Full Name
    TATA-box binding protein associated factor, RNA polymerase I subunit Dprovided by RGD
    Primary source
    RGD:1309627
    See related
    EnsemblRapid:ENSRNOG00000010921 AllianceGenome:RGD:1309627
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Josd3; RGD1309627
    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. Orthologous to human TAF1D (TATA-box binding protein associated factor, RNA polymerase I subunit D). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 232.1), Spleen (RPKM 180.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Taf1d in Genome Data Viewer
    Location:
    8q12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (20427894..20438046)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (12146511..12156647)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (13861242..13871508)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102552229 Neighboring gene similar to human chromosome 11 open reading frame 54 Neighboring gene small nucleolar RNA SNORA40 Neighboring gene small nucleolar RNA SNORA8 Neighboring gene small nucleolar RNA SNORA32 Neighboring gene small nucleolar RNA, H/ACA box 18 Neighboring gene small nucleolar RNA, C/D box 5 Neighboring gene small nucleolar RNA, H/ACA box 25B Neighboring gene small nucleolar RNA, H/ACA box 1B Neighboring gene small nucleolar RNA, C/D box 6 Neighboring gene centrosomal protein 295 Neighboring gene small nucleolar RNA U2-30 Neighboring gene small nucleolar RNA U2-19

    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. TFIIB-related factors in RNA polymerase I transcription. Knutson BA, et al. Biochim Biophys Acta, 2013 Mar-Apr. PMID 22960599, Free PMC Article
    2. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Schneider DA. Gene, 2012 Feb 10. PMID 21893173, Free PMC Article
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. 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

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriolar satellite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitotic spindle IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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, 41kDa
    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_001393862.1 → NP_001380791.1  TATA box-binding protein-associated factor RNA polymerase I subunit D

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0
      Related
      ENSRNOP00000068730.3, ENSRNOT00000078161.3
      Conserved Domains (1) summary
      pfam15333
      Location:32 → 240
      TAF1D; TATA box-binding protein-associated factor 1D

    RNA

    1. NR_172024.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    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_086026.1 Reference GRCr8

      Range
      20427894..20438046
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063265684.1 → XP_063121754.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      UniProtKB/TrEMBL
      A0A0G2JTJ0, A6JNC6
      Related
      ENSRNOP00000096126.2, ENSRNOT00000096680.2

    2. XM_063265686.1 → XP_063121756.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    3. XM_063265701.1 → XP_063121771.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    4. XM_063265695.1 → XP_063121765.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    5. XM_063265698.1 → XP_063121768.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    6. XM_063265702.1 → XP_063121772.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    7. XM_063265697.1 → XP_063121767.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    8. XM_063265691.1 → XP_063121761.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    9. XM_063265699.1 → XP_063121769.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    10. XM_063265704.1 → XP_063121774.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    11. XM_063265688.1 → XP_063121758.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    12. XM_063265696.1 → XP_063121766.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    13. XM_063265705.1 → XP_063121775.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    14. XM_063265700.1 → XP_063121770.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    15. XM_063265690.1 → XP_063121760.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    16. XM_063265692.1 → XP_063121762.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    17. XM_063265693.1 → XP_063121763.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    18. XM_063265689.1 → XP_063121759.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    19. XM_063265706.1 → XP_063121776.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    20. XM_063265694.1 → XP_063121764.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0

    21. XM_063265685.1 → XP_063121755.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X1

      UniProtKB/TrEMBL
      A0A0G2JTJ0, A6JNC6
      Related
      ENSRNOP00000014605.6, ENSRNOT00000014605.8

    22. XM_063265687.1 → XP_063121757.1  TATA box-binding protein-associated factor RNA polymerase I subunit D isoform X2

      UniProtKB/Swiss-Prot
      Q5M948
      UniProtKB/TrEMBL
      A0A8I6ANJ9, A6JNC0
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5M948.1 GenPept UniProtKB/Swiss-Prot:Q5M948

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