TCEA1 Gene

HGNC Family	General transcription factors (GTF)
Name	transcription elongation factor A (SII), 1
Description	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 DNA-templated transcription. Located in nucleolus and nucleoplasm. Part of transcription factor TFIID complex. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nTCEA1, which encodes the transcription elongation factor TFIIS, plays a central role in enabling RNA polymerase II (RNAPII) to resume productive elongation. Structural studies have revealed that TCEA1 protrudes into RNAPII’s active site where its invariant acidic residues help coordinate a metal ion and water molecule to catalyze RNA cleavage. Kinetic analyses further show that by promoting transcript cleavage, TCEA1 facilitates the recovery from stalled transcription complexes and suppresses prolonged pausing, thereby maintaining an efficient cycle of nucleotide addition and forward translocation."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its catalytic role, TCEA1 is critical for maintaining transcriptional fidelity and genomic stability. By preventing excessive RNAPII stalling and backtracking, TCEA1 limits the formation of deleterious R-loops and transcription–replication conflicts that can lead to DNA double-strand breaks and micronuclei. Studies using mutant forms of TFIIS indicate that impairment of TCEA1 function exacerbates RNAPII arrest and contributes to genome instability, while its proper recruitment is necessary to navigate challenges imposed by highly compact chromatin and other regulatory factors."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its enzymatic activity, TCEA1 interacts with a network of transcription regulatory complexes to fine‐tune gene expression. Its N-terminal domains engage with native unstructured motifs in other elongation factors and coactivators, thereby coordinating complex assembly and modulating RNAPII elongation dynamics. Moreover, TCEA1’s chromatin recruitment is subject to regulatory inhibition—such as by RNF20—to repress the transcription of pro-oncogenic genes, and it can participate in promoter swapping events that lead to oncogene activation. Although downregulation of TCEA1 can impair transcription recovery following DNA damage, its depletion does not necessarily compromise transcription-coupled nucleotide excision repair, underscoring a context-dependent role in the cellular response to genotoxic stress."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "7", "end_ref": "11"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Hubert Kettenberger, Karim-Jean Armache, Patrick Cramer "}, {"type": "b", "children": [{"type": "t", "text": "Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/s0092-8674(03)00598-1"}], "href": "https://doi.org/10.1016/s0092-8674(03"}, {"type": "t", "text": "00598-1) PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12914699"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12914699"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Chunfen Zhang, Honggao Yan, Zachary F Burton "}, {"type": "b", "children": [{"type": "t", "text": "Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M307590200"}], "href": "https://doi.org/10.1074/jbc.M307590200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14506279"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14506279"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Chunfen Zhang, Zachary F Burton "}, {"type": "b", "children": [{"type": "t", "text": "Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Biol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jmb.2004.07.070"}], "href": "https://doi.org/10.1016/j.jmb.2004.07.070"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15351637"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15351637"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Efrat Shema, Jaehoon Kim, Robert G Roeder, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2011.03.011"}], "href": "https://doi.org/10.1016/j.molcel.2011.03.011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21596312"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21596312"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Diana Zatreanu, Zhong Han, Richard Mitter, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2019.07.037"}], "href": "https://doi.org/10.1016/j.molcel.2019.07.037"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31519522"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31519522"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Renée C Duardo, Jessica Marinello, Marco Russo, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Human DNA topoisomerase I poisoning causes R loop-mediated genome instability attenuated by transcription factor IIS."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Adv (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/sciadv.adm8196"}], "href": "https://doi.org/10.1126/sciadv.adm8196"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38787953"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38787953"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Mohamed Guermah, Vikas B Palhan, Alan J Tackett, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Synergistic functions of SII and p300 in productive activator-dependent transcription of chromatin templates."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2006.01.055"}], "href": "https://doi.org/10.1016/j.cell.2006.01.055"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16630816"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16630816"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Julia Asp, Fredrik Persson, Maria Kost-Alimova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CHCHD7-PLAG1 and TCEA1-PLAG1 gene fusions resulting from cryptic, intrachromosomal 8q rearrangements in pleomorphic salivary gland adenomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Chromosomes Cancer (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/gcc.20346"}], "href": "https://doi.org/10.1002/gcc.20346"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16736500"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16736500"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Anne Jensen, Leon H F Mullenders "}, {"type": "b", "children": [{"type": "t", "text": "Transcription factor IIS impacts UV-inhibited transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "DNA Repair (Amst) (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.dnarep.2010.08.002"}], "href": "https://doi.org/10.1016/j.dnarep.2010.08.002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20729154"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20729154"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Christine Mackinnon-Roy, Lawton J Stubbert, Bruce C McKay "}, {"type": "b", "children": [{"type": "t", "text": "RNA interference against transcription elongation factor SII does not support its role in transcription-coupled nucleotide excision repair."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mutat Res (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.mrfmmm.2010.10.010"}], "href": "https://doi.org/10.1016/j.mrfmmm.2010.10.010"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21070792"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21070792"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Katerina Cermakova, Jonas Demeulemeester, Vanda Lux, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A ubiquitous disordered protein interaction module orchestrates transcription elongation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.abe2913"}], "href": "https://doi.org/10.1126/science.abe2913"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34822292"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34822292"}]}]}]}
Synonyms	SII, GTF2S, TCEA, TF2S
Proteins	TCEA1_HUMAN
NCBI Gene ID	6917
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

TCEA1 has 6,748 functional associations with biological entities spanning 8 categories (molecular profile, organism, functional term, phrase or reference, chemical, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 116 datasets.

Click the + buttons to view associations for TCEA1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

TCEA1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by TCEA1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of TCEA1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of TCEA1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of TCEA1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of TCEA1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of TCEA1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of TCEA1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of TCEA1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Mutation Profiles	cell lines with TCEA1 gene mutations from the CCLE Cell Line Gene Mutation Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with TCEA1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with TCEA1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of TCEA1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of TCEA1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of TCEA1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing TCEA1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing TCEA1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing TCEA1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing TCEA1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with TCEA1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with TCEA1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of TCEA1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with TCEA1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with TCEA1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with TCEA1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with TCEA1 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of TCEA1 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by TCEA1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with TCEA1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with TCEA1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with TCEA1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with TCEA1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at TCEA1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of TCEA1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of TCEA1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing TCEA1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with TCEA1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with TCEA1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of TCEA1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with TCEA1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing TCEA1 from the GeneSigDB Published Gene Signatures dataset.