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    TAF1C TATA-box binding protein associated factor, RNA polymerase I subunit C [ Homo sapiens (human) ]

    Gene ID: 9013, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TAF1Cprovided by HGNC
    Official Full Name
    TATA-box binding protein associated factor, RNA polymerase I subunit Cprovided by HGNC
    Primary source
    HGNC:HGNC:11534
    See related
    Ensembl:ENSG00000103168 MIM:604905; AllianceGenome:HGNC:11534
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SL1; TAFI95; TAFI110; MGC:39976
    Summary
    Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs) specific for RNA polymerase I. This complex, known as SL1, binds to the core promoter of ribosomal RNA genes to position the polymerase properly and acts as a channel for regulatory signals. This gene encodes the largest SL1-specific TAF. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2011]
    Expression
    Ubiquitous expression in spleen (RPKM 19.0), ovary (RPKM 12.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TAF1C in Genome Data Viewer
    Location:
    16q24.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84177855..84187057, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90243928..90253130, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84211461..84220663, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene polo like kinase 1 pseudogene Neighboring gene hydroxysteroid dehydrogenase like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84169151-84169748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84170943-84171538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7780 Neighboring gene dynein axonemal assembly factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84220503-84221003 Neighboring gene Sharpr-MPRA regulatory region 3417 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84227912-84229111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84229267-84229889 Neighboring gene splicing factor proline/glutamine-rich Neighboring gene adenosine deaminase domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84247937-84248438 Neighboring gene potassium voltage-gated channel modifier subfamily G member 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Frameshift mutations of TAF1C gene, a core component for transcription by RNA polymerase I, and its regional heterogeneity in gastric and colorectal cancers. Oh HR, et al. Pathology, 2015 Feb. PMID 25551296
    2. Association of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) with T2DM. Abdulwahab RA, et al. Gene, 2019 Jul 20. PMID 31039436
    3. Homozygous TAF1C variants are associated with a novel childhood-onset neurological phenotype. Knuutinen O, et al. Clin Genet, 2020 Nov. PMID 32779182
    4. Individual common variants exert weak effects on the risk for autism spectrum disorders. Anney R, et al. Hum Mol Genet, 2012 Nov 1. PMID 22843504, Free PMC Article
    5. TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter. Friedrich JK, et al. J Biol Chem, 2005 Aug 19. PMID 15970593, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Homozygous TAF1C variants are associated with a novel childhood-onset neurological phenotype.
      Title: Homozygous TAF1C variants are associated with a novel childhood-onset neurological phenotype.
    2. Observed significantly higher TAF1C expression in patients with type 2 diabetes mellitus (T2DM), suggesting a role for increased protein synthesis in T2DM.
      Title: Association of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) with T2DM.
    3. hCdc14B promotes reactivation of rDNA transcription by dephosphorylating TAFI110. SIRT1 becomes transiently enriched in nucleoli at the onset of mitosis. SIRT1 deacetylates TAFI68 destabilizing SL1 binding to the rDNA promoter
      Title: Cooperative Action of Cdk1/cyclin B and SIRT1 Is Required for Mitotic Repression of rRNA Synthesis.
    4. Our results indicate that TAF1C gene harboured not only somatic frameshift mutations but also the mutational ITH, which together might play a role in tumourigenesis of gastric and colorectal cancer.
      Title: Frameshift mutations of TAF1C gene, a core component for transcription by RNA polymerase I, and its regional heterogeneity in gastric and colorectal cancers.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: A genome-wide scan for common alleles affecting risk for autism.
    7. PTEN represses RNA Pol I transcription through a novel mechanism that involves disruption of the SL1 complex
      Title: PTEN represses RNA Polymerase I transcription by disrupting the SL1 complex.
    8. SL1 directs preinitiation complex formation, functioning in core promoter binding, RNA polymerase I recruitment, and UBF stabilization.
      Title: TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Individual common variants exert weak effects on the risk for autism spectrum disorderspi.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase I core promoter sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase I core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase I general transcription initiation factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA polymerase I preinitiation complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase I TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in transcription initiation at RNA polymerase I promoter NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase transcription factor SL1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in fibrillar center IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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 C
    Names
    RNA polymerase I-specific TBP-associated factor 110 kDa
    SL1, 110kD subunit
    TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD
    TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa
    TATA box-binding protein-associated factor 1C
    TATA-box binding protein associated factor, RNA polymerase I, C
    TBP-associated factor 1C
    transcription factor SL1
    transcription initiation factor SL1/TIF-IB subunit C

    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_001243156.2 → NP_001230085.2  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal segment in the CDS, compared to variant 1. The resulting isoform (3) is shorter by lacking of an internal segment, compared to isoform 1.
      Source sequence(s)
      AC009123
      Consensus CDS
      CCDS58489.1
      Related
      ENSP00000455933.1, ENST00000566732.6

    2. NM_001243157.2 → NP_001230086.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 4

      See identical proteins and their annotated locations for NP_001230086.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two internal exons and an internal segment, and has a downstream AUG start codon, compared to variant 1. The resulting isoform (4) is much shorter at the N-terminus, compared to isoform 1. Variants 4 and 5 encode the same isoform 4.
      Source sequence(s)
      AC009123
      Consensus CDS
      CCDS58488.1
      UniProtKB/Swiss-Prot
      Q15572
      Related
      ENSP00000437900.2, ENST00000541676.5

    3. NM_001243158.2 → NP_001230087.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 4

      See identical proteins and their annotated locations for NP_001230087.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two internal segments and four consecutive exons, and has a downstream AUG start codon, compared to variant 1. The resulting isoform (4) has a much shorter N-terminus, compared to isoform 1. Variants 4 and 5 encode the same isoform 4.
      Source sequence(s)
      AC009123, AK299347, AK315982, CA397963
      Consensus CDS
      CCDS58488.1
      UniProtKB/Swiss-Prot
      Q15572
      Related
      ENSP00000455247.1, ENST00000570117.5

    4. NM_001243159.2 → NP_001230088.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks two internal segments but has a downstream additional segment, and has a downstream AUG start codon, compared to variant 1. The resulting isoform 5 is much shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC009123
      UniProtKB/TrEMBL
      B3KUE8
      Related
      ENST00000564208.5

    5. NM_001243160.2 → NP_001230089.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in several regions and has a downstream AUG start codon, compared to variant 1. The resulting isoform (6) is much shorter at the N-terminus and lacks an internal amino acid 'G', compared to isoform 1.
      Source sequence(s)
      AC009123
      UniProtKB/TrEMBL
      B3KUE8

    6. NM_005679.4 → NP_005670.4  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC009123
      Consensus CDS
      CCDS32496.1
      UniProtKB/Swiss-Prot
      B7Z5K5, B7Z5S4, B7Z908, B7Z9L7, Q15572, Q59F67, Q8N6V3
      Related
      ENSP00000455265.1, ENST00000567759.5

    7. NM_139353.3 → NP_647610.3  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has alternate splice sites in three regions, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, lacks an internal segment and an internal amino acid 'G', compared to isoform 1.
      Source sequence(s)
      AC009123
      Consensus CDS
      CCDS45535.1
      Related
      ENSP00000345305.6, ENST00000341690.10

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      84177855..84187057 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023847.2 → XP_016879336.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X6

    2. XM_005256227.4 → XP_005256284.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X5

      See identical proteins and their annotated locations for XP_005256284.1

    3. XM_017023845.2 → XP_016879334.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X4

      UniProtKB/Swiss-Prot
      Q15572

    4. XM_005256226.4 → XP_005256283.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X2

      See identical proteins and their annotated locations for XP_005256283.1

      UniProtKB/Swiss-Prot
      B7Z5K5, B7Z5S4, B7Z908, B7Z9L7, Q15572, Q59F67, Q8N6V3

    5. XM_006721326.4 → XP_006721389.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X3

    6. XM_006721325.4 → XP_006721388.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      90243928..90253130 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314308.1 → XP_054170283.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X6

    2. XM_054314307.1 → XP_054170282.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X5

    3. XM_054314306.1 → XP_054170281.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X4

    4. XM_054314304.1 → XP_054170279.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X2

    5. XM_054314305.1 → XP_054170280.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X3

    6. XM_054314303.1 → XP_054170278.1  TATA box-binding protein-associated factor RNA polymerase I subunit C isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15572.2 GenPept UniProtKB/Swiss-Prot:Q15572

    Gene LinkOut

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

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