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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

TCEA3 Gene

protein-coding GIFtS: 49
GCID: GC01M023706

transcription elongation factor A (SII), 3

Explore 7 diseases affiliated with
TCEA3 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Transcription Elongation Factor A (SII), 3¹ ²		TFIIS²
TFIIS.H¹ ²		Rhabdomyosarcoma Antigen MU-RMS-40.22²
Transcription Elongation Factor S-II Protein 3² ³		Transcription Elongation Factor A Protein 3²
Transcription Elongation Factor TFIIS.H² ³		TFIISH³

External Ids:	HGNC: 11615¹	Entrez Gene: 6920²	Ensembl: ENSG00000204219⁷	OMIM: 604128⁵	UniProtKB: O75764³

Export aliases for TCEA3 gene to outside databases

Previous GC identifers: GC01M023264 GC01M022778 GC01M023176 GC01M023177 GC01M023453 GC01M023580 GC01M021959

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: TCEA3_HUMAN, O75764

Function: Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The

arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass

through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of

elongation from the new 3'-terminus

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000001.10 NC_018912.1 NT_004610.19

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the TCEA3 gene promoter:
SRF NRSF form 1 SRF (504 AA) RREB-1 NRSF form 2 Egr-4 C/EBPalpha CHOP-10 MZF-1 FOXC1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: TCEA3 promoter sequence

Search SABiosciences Chromatin IP Primers for TCEA3

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TCEA3

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36.12 Ensembl cytogenetic band: 1p36.12 HGNC cytogenetic band: 1p36.11

TCEA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TCEA3 gene location

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01M023706: view genomic region (about GC identifiers)

Start:	23,707,554 bp from pter	End:	23,751,261 bp from pter
Size:	43,708 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TCEA3_HUMAN, O75764 (See protein sequence)

Recommended Name: Transcription elongation factor A protein 3

Size: 348 amino acids; 38972 Da

Subcellular location: Nucleus (By similarity)

Secondary accessions: A8K2K7

Explore the universe of human proteins at neXtProt for TCEA3: NX_O75764

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_O75764

TCEA3 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_003187.1

ENSEMBL proteins:

ENSP00000406293 ENSP00000363729

Human Recombinant Protein Products for TCEA3:

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	Uscn Proteins for TCEA3

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IEA	--

TCEA3 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

TCEA3 for domains About GeneDecksing

5/7 InterPro domains/families (see all 7):

IPR003617 TFIIS/CRSP70_N_sub

IPR001222 Znf_TFIIS

IPR003618 TFIIS_cen_dom

IPR017923 TFIIS_N

IPR017890 TFS2M

Graphical View of Domain Structure for InterPro Entry O75764

ProtoNet protein and cluster: O75764

1 Blocks protein family: IPB003617 Transcription elongation factor S-II

UniProtKB/Swiss-Prot: TCEA3_HUMAN, O75764

Similarity: Belongs to the TFS-II family

Similarity: Contains 1 TFIIS central domain

Similarity: Contains 1 TFIIS N-terminal domain

Similarity: Contains 1 TFIIS-type zinc finger

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: TCEA3_HUMAN, O75764

Function: Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The

arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass

through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of

elongation from the new 3'-terminus

Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	IEA	--
GO:0008270	zinc ion binding	IEA	--

TCEA3 for ontologies About GeneDecksing

Animal Models:

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for TCEA3

miRNA Products:		OriGene 3'-UTR Clone: TCEA3 Browse MicroRNA Expression Plasmids
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		7 QIAGEN miScript miRNA Assays for microRNAs that regulate TCEA3:
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In Situ Assay
Products:

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Assembly of RNA Polymerase-II Initiation Complex

Transcription of mRNA

0.91

1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for TCEA3

Transcription of mRNA

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for TCEA3

STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

4 Interacting proteins for TCEA3 (ENSP00000406293⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
RPH3AL	ENSP00000319210⁴	STRING: ENSP00000319210
POLR2E	ENSP00000215587⁴	STRING: ENSP00000215587
POLR2F	ENSP00000403852⁴	STRING: ENSP00000403852
POLR2I	ENSP00000221859⁴	STRING: ENSP00000221859

About this table

Gene Ontology (GO): 3 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006351	transcription, DNA-dependent	IEA	--
GO:0006357	regulation of transcription from RNA polymerase II promoter	IEA	--
GO:0032784	regulation of DNA-dependent transcription, elongation	IEA	--

TCEA3 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

TCEA3 for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for TCEA3
2 Novoseek chemical compound relationships for TCEA3 gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
6-azauracil	86.3	2	12511561 (1), 15780939 (1)
zinc	24.1	7	1868060 (3), 9724522 (2), 9712887 (1)

Search CenterWatch for drugs/clinical trials and news about TCEA3

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for TCEA3 gene:

NM_003196.1

Unigene Cluster for TCEA3:

Transcription elongation factor A (SII), 3

Hs.446354 [show with all ESTs]

Unigene Representative Sequence: NM_003196

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000450454(uc009vqm.2 uc021oig.1 uc021oih.1 uc010ody.1)

ENST00000476978 ENST00000461794 ENST00000374602 ENST00000492271 ENST00000374601

miRNA Products:		OriGene 3'-UTR Clone: TCEA3 Browse OriGene MicroRNA Expression Plasmids
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		hsa-miR-515-5p hsa-miR-145 hsa-miR-516a-3p hsa-miR-516b* hsa-miR-450b-5p hsa-miR-766 hsa-miR-519e*
		SwitchGear 3'UTR luciferase reporter plasmid: TCEA3 3' UTR sequence

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		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TCEA3
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Additional cDNA sequence:

AJ223473.1 AK027024.1 AK290272.1 AK300707.1 AK310039.1 AY540752.1 BC041613.1

11 DOTS entries:

DT.448657 DT.432013 DT.92420864 DT.100780717 DT.91939517 DT.92420863 DT.91667417 DT.91880930

DT.91886475 DT.95072939 DT.95199690

24/121 AceView cDNA sequences (see all 121):

BQ006295 AW151718 AI669819 CA435035 AI572481 NM_003196 AA688241 T95597

AA970866 AI202589 AI308948 BG059665 AA888058 AI097019 AK027024 AA071471

AI193651 AI393002 AI861898 AJ223473 BE880226 CA449942 CF127872 BC041613

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

TCEA3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AACAAGGTGA

About this image

TCEA3 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Sox17-GFP genetically modified stem cells (Embryonic Stem Cell)

Early Embryo, Inner Cell Mass

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See TCEA3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for TCEA3

SOURCE GeneReport for Unigene cluster: Hs.446354

SABiosciences Custom PCR Arrays for TCEA3

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of eukaryotes.

Orthologs for TCEA3 gene from 8/29 species (see all 29) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	LOC100858897¹	transcription elongation factor A protein 3-like	65.82(n) 64.97(a)		100858897 XM_003642574.1 XP_003642622.1
lizard (Anolis carolinensis)	Reptilia	TCEA3⁶	--	73(a)	1 ↔ 1	GL343904.1(59829-71600)
African clawed frog (Xenopus laevis)	Amphibia	Xl.408²	Xenopus laevis mRNA for transcription elongation factor more	74.15(n)		AB040437.1
zebrafish (Danio rerio)	Actinopterygii	Dr.15634²	Transcribed sequence with moderate similarity to protein more	80.7(n)		BM342366.1
fruit fly (Drosophila melanogaster)	Insecta	TfIIS^{1 , 3}	RNA elongation from Pol II promoter transcription more³ RNA polymerase II elongation factor¹	62(a) (best of 2)³ 57.48(n)¹ 51.92(a)¹		34883¹ NM_057619.3¹ NP_476967.1¹
worm (Caenorhabditis elegans)	Secernentea	T24H10.1³	transcription factor S-II	37(a)		II(9099286-9100363) --
thale cress (Arabidopsis thaliana)	eudicotyledons	TFIIS¹	transcript elongation factor IIS	43.94(n) 33.77(a)		818438 NM_129413.3 NP_181390.1
rice (Oryza sativa)	Liliopsida	Os03g0815900¹	hypothetical protein	43.57(n) 30.7(a)		4334559 NM_001058222.1 NP_001051687.1

ENSEMBL Gene Tree for TCEA3 (if available)
TreeFam Gene Tree for TCEA3 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for TCEA3 gene

TCEA1² TCEANC² TCEA2²

2 SIMAP similar genes for TCEA3 using alignment to 2 protein entries: TCEA3_HUMAN (see all proteins):

TCEA1 TCEA2

TCEA3 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs651542^1,2	C,F,A,H	--	23707401(-)	`AGAACA/TGTTGA`	1	--	ds500¹		23		NS EA NA WA CSA	1546
rs186054402^1,2		--	23707429(+)	`GTGGGA/GGTGGG`	1	--	ds500¹		0	--	--	--	--
rs113375730^1,2		--	23707432(+)	`GGGGTG/CGGGTA`	1	--	ds500¹		2		CSA WA	120
rs651036^1,2	C,F,H	--	23707516(-)	`CAGACC/GTTTGC`	1	--	ds500¹		18		NA NS EA WA CSA	920
rs3192564^1,2	F	--	23707641(-)	`cgcttA/Gacccc`	1	--	ut3¹		1		MN	184
rs650102^1,2	C,F	--	23707692(-)	`GGTGGC/TTTATG`	1	--	ut3¹ ese³		12		MN NA WA CSA EA	556
rs138848408^1,2		--	23707798(+)	`ATGACC/TGATTA`	1	--	ut3¹		0	--	--	--	--
rs189723104^1,2		--	23707845(+)	`ATCCCA/GCTCAG`	1	--	ut3¹		0	--	--	--	--
rs78678072^1,2		--	23707860(+)	`AGTTCA/GGTATT`	1	--	ut3¹		1		WA	118
rs181329716^1,2		--	23707935(+)	`CCTCAC/TCTTGT`	1	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for TCEA3 (23707554 - 23751261 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for TCEA3
1 Indel: 60806

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TCEA3

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

TCEA3 for disorders           About GeneDecksing

OMIM gene information: 604128    OMIM disorders: --

7 diseases for TCEA3:    About MalaCards

rhabdomyosarcoma acute myeloid leukemia cockayne syndrome myeloid leukemia

conjunctivitis leukemia malaria

Human Genome Epidemiology (HuGE) Navigator: TCEA3 (3 documents)

Export disorders for TCEA3 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for TCEA3 gene, integrated from 9 sources (see all 45):
(articles sorted by number of sources associating them with TCEA3)

Utopia: connect your pdf to the dynamic
world of online information

Identification of novel genes encoding transcription elongation factor TFIIS (TCEA) in vertebrates: conservation of three distinct TFIIS isoforms in frog, mouse, and human. (PubMed id 9790746)^{1, 2, 3, 9} Labhart P. and Morgan G.T. (1998)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
The human PAF1 complex acts in chromatin transcriptio n elongation both independently and cooperatively with SII/TFIIS. (PubMed id 20178742)¹ Kim J....Roeder R.G. (2010)
Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)¹ Bailey S.D....Anand S. (2010)
Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)¹ Talmud P.J.... . (2009)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)² Gregory S.G.... Bentley D.R. (2006)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)² Ota T.... Sugano S. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
The HIV-1 Tat cellular coactivator Tat-SF1 is a general transcription elongation factor. (PubMed id 9765201)¹ Li X.-Y. and Green M.R. (1998)
HIV-1 Tat acts as a processivity factor in vitro in conjunction with cellular elongation factors. (PubMed id 1559613)¹ Kato H....Roeder R.G. (1992)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 6920	HGNC: 11615	AceView: TCEA3	Ensembl:ENSG00000204219	euGenes: HUgn6920
ECgene: TCEA3	H-InvDB: TCEA3

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for TCEA3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for TCEA3 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for TCEA3 gene:
Search GeneIP for patents involving TCEA3

GeneCards and IP:
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transcription elongation factor A (SII), 3

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transcription elongation factor A (SII), 3

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