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    TCEA1 transcription elongation factor A1 [ Homo sapiens (human) ]

    Gene ID: 6917, updated on 5-May-2024

    Summary

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    Official Symbol
    TCEA1provided by HGNC
    Official Full Name
    transcription elongation factor A1provided by HGNC
    Primary source
    HGNC:HGNC:11612
    See related
    Ensembl:ENSG00000187735 MIM:601425; AllianceGenome:HGNC:11612
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SII; TCEA; TF2S; GTF2S; TFIIS
    Summary
    Predicted to enable DNA binding activity; translation elongation factor activity; and zinc ion binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within erythrocyte differentiation and positive regulation of transcription, DNA-templated. Located in nucleolus and nucleoplasm. Part of transcription factor TFIID complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 66.3), lymph node (RPKM 39.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    8q11.23
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (53966556..54022448, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (54343951..54399849, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (54879116..54935008, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene regulator of G protein signaling 20 Neighboring gene RPS27A pseudogene 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27366 Neighboring gene RNA, U6 small nuclear 1331, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:54856969-54858168 Neighboring gene ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54934747-54935540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54935541-54936332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54942814-54943544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54943545-54944276 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:54958280-54958473 Neighboring gene lysophospholipase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:54997169-54998116 Neighboring gene CRIPTO pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27371 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19199 Neighboring gene MPRA-validated peak7022 silencer Neighboring gene mitochondrial ribosomal protein L15

    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. Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability. Zatreanu D, et al. Mol Cell, 2019 Oct 3. PMID 31519522, Free PMC Article
    2. RNA interference against transcription elongation factor SII does not support its role in transcription-coupled nucleotide excision repair. Mackinnon-Roy C, et al. Mutat Res, 2011 Jan 10. PMID 21070792
    3. Transcription factor IIS impacts UV-inhibited transcription. Jensen A, et al. DNA Repair (Amst), 2010 Nov 10. PMID 20729154
    4. Transcription elongation factor SII (TCEA) maps to human chromosome 3p22 --> p21.3. DiMarco SP, et al. Genomics, 1996 Aug 15. PMID 8812434
    5. Elongation factor SII contacts the 3'-end of RNA in the RNA polymerase II elongation complex. Powell W, et al. J Biol Chem, 1996 Sep 13. PMID 8798387, Free PMC Article

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A ubiquitous disordered protein interaction module orchestrates transcription elongation.
      Title: A ubiquitous disordered protein interaction module orchestrates transcription elongation.
    2. A mutant form of TFIIS increased RNAPII pausing and backtracking results in R-loop formation and genome instability.
      Title: Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability.
    3. RNF20, presumably via H2Bub, selectively represses oncogenic genes by interfering with chromatin recruitment of TFIIS, a factor capable of relieving stalled RNA polymerase II. RNF20 inhibits the interaction between TFIIS and the PAF1 complex.
      Title: RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression.
    4. a role for TFIIS in transcription recovery and re-establishment of the balance between hypo- and hyper-phosphorylated RNAPII after DNA damage repair
      Title: Transcription factor IIS impacts UV-inhibited transcription.
    5. Results indicate that TFIIS is not limiting for the repair of transcription-blocking DNA lesions and thus the present work does not support a role for TFIIS in TC-NER.
      Title: RNA interference against transcription elongation factor SII does not support its role in transcription-coupled nucleotide excision repair.
    6. transcription factor IIF, hepatitis delta antigen, and stimulatory factor II control human RNA polymerase II (RNAP II) pausing and transcript cleavage
      Title: Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II.
    7. TFIIS has a role in suppression of transient pausing, which is the most important contribution of TFIIS to elongation from a stall position
      Title: Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism.
    8. Results provide a model of the RNA polymerase II-transcription elongation factor TFIIS complex from X-ray diffraction data to 3.8 A resolution.
      Title: Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
    9. PLAG1 protein is overexpressed in epithelial, myoepithelial, and mesenchymal-like tumor cells in tumors with fusions to CHCHD7 and TCEA1.
      Title: CHCHD7-PLAG1 and TCEA1-PLAG1 gene fusions resulting from cryptic, intrachromosomal 8q rearrangements in pleomorphic salivary gland adenomas.
    10. Data shpw that SII is a major component of chromatin transcription and strongly synergizes with p300 (histone acetylation) at a step subsequent to preinitiation complex formation.
      Title: Synergistic functions of SII and p300 in productive activator-dependent transcription of chromatin templates.
    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

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat TFIIS synergizes with HIV-1 Tat during transactivation of the HIV-1 LTR promoter PubMed
    tat HIV-1 Tat directly interacts with SII (TFIIS) as demonstrated by Tat-affinity column purification PubMed

    Go to the HIV-1, Human Interaction Database

    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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in transcription elongation by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of transcription factor TFIID complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcription elongation factor A protein 1
    Names
    epididymis secretory sperm binding protein
    transcription elongation factor A (SII), 1
    transcription elongation factor S-II protein 1
    transcription elongation factor TFIIS.o
    transcription factor IIS

    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_006756.4 → NP_006747.1  transcription elongation factor A protein 1 isoform 1

      See identical proteins and their annotated locations for NP_006747.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      BQ016366, DA021678, DB091231, X62585
      Consensus CDS
      CCDS47858.1
      UniProtKB/Swiss-Prot
      A6NF25, A8K339, P23193, Q15563, Q6FG87
      UniProtKB/TrEMBL
      A0A384MTX4, B7Z4W0
      Related
      ENSP00000428426.2, ENST00000521604.7
      Conserved Domains (1) summary
      TIGR01385
      Location:4 → 301
      TFSII; transcription elongation factor S-II

    2. NM_201437.3 → NP_958845.1  transcription elongation factor A protein 1 isoform 2

      See identical proteins and their annotated locations for NP_958845.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK297957, BC072460, BQ016366, DA021678, DB091231, X62585
      Consensus CDS
      CCDS47857.1
      UniProtKB/TrEMBL
      B7Z4W0
      Related
      ENSP00000395483.2, ENST00000396401.7
      Conserved Domains (1) summary
      cl02637
      Location:4 → 280
      TFIIS_M; Transcription factor S-II (TFIIS), central domain

    RNA

    1. NR_109901.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC072460, BQ016366, BX538034, DA021678, DB091231, X62585
      Related
      ENST00000521086.6

    2. NR_109902.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks several internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AK297729, BQ016366, DA021678, DB091231, X62585

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      53966556..54022448 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006716467.2 → XP_006716530.1  transcription elongation factor A protein 1 isoform X2

      See identical proteins and their annotated locations for XP_006716530.1

      UniProtKB/TrEMBL
      B7Z4W0
      Conserved Domains (1) summary
      TIGR01385
      Location:1 → 254
      TFSII; transcription elongation factor S-II

    2. XM_011517578.2 → XP_011515880.1  transcription elongation factor A protein 1 isoform X1

      UniProtKB/TrEMBL
      B7Z4W0
      Conserved Domains (1) summary
      cl02637
      Location:1 → 266
      TFIIS_M; Transcription factor S-II (TFIIS), central domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      54343951..54399849 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361111.1 → XP_054217086.1  transcription elongation factor A protein 1 isoform X2

    2. XM_054361110.1 → XP_054217085.1  transcription elongation factor A protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P23193.2 GenPept UniProtKB/Swiss-Prot:P23193

    Gene LinkOut

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

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