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

Gene ID: 9013, updated on 11-Apr-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
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Genomic context

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Location:
16q24.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84177855..84187057, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90243928..90253130, complement)
105.20220307 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
  • 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. Homozygous TAF1C variants are associated with a novel childhood-onset neurological phenotype. Knuutinen O, et al. Clin Genet, 2020 Nov. PMID 32779182
  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. 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
  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 (52) 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_2023_10

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

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