TCEAL3

Summary

TCEAL3 (transcription elongation factor A like 3, HGNC:28247) is a protein-coding gene on chromosome Xq22.2, encoding Transcription elongation factor A protein-like 3 (Q969E4). May be involved in transcriptional regulation.

This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family contain TFA domains and may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform.

Source: NCBI Gene 85012 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_032926

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28247
Approved symbol	TCEAL3
Name	transcription elongation factor A like 3
Location	Xq22.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC15737, WEX8
Ensembl gene	ENSG00000196507
Ensembl biotype	protein_coding
OMIM	301153
Entrez	85012

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 23 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000243286, ENST00000372627, ENST00000372628, ENST00000477014, ENST00000872581, ENST00000872582, ENST00000872583, ENST00000872584, ENST00000872585, ENST00000872586, ENST00000872587, ENST00000872588, ENST00000872589, ENST00000872590, ENST00000872591, ENST00000872592, ENST00000872593, ENST00000872594, ENST00000938709, ENST00000938710, ENST00000938711, ENST00000938712, ENST00000938713, ENST00000954593

RefSeq mRNA: 2 — MANE Select: NM_032926 NM_001006933, NM_032926

CCDS: CCDS14511

Canonical transcript exons

ENST00000372627 — 3 exons

Exon	Start	End
ENSE00001253332	103608604	103608673
ENSE00001253340	103607963	103608058
ENSE00001816487	103609038	103609927

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 98.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 42.3684 / max 1444.4415, expressed in 1716 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197032	40.3973	1713
197033	1.2596	635
197034	0.7115	336

Top tissues by expression

259 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
medial globus pallidus	UBERON:0002477	98.99	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.89	gold quality
globus pallidus	UBERON:0001875	98.79	gold quality
mucosa of stomach	UBERON:0001199	98.70	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.60	gold quality
hypothalamus	UBERON:0001898	98.58	gold quality
middle temporal gyrus	UBERON:0002771	98.52	gold quality
cerebellar vermis	UBERON:0004720	98.50	gold quality
spinal cord	UBERON:0002240	98.49	gold quality
substantia nigra pars compacta	UBERON:0001965	98.45	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.42	gold quality
substantia nigra	UBERON:0002038	98.36	gold quality
left uterine tube	UBERON:0001303	98.34	gold quality
right ovary	UBERON:0002118	98.34	gold quality
lateral globus pallidus	UBERON:0002476	98.34	gold quality
midbrain	UBERON:0001891	98.31	gold quality
inferior vagus X ganglion	UBERON:0005363	98.24	gold quality
thoracic aorta	UBERON:0001515	98.20	gold quality
pons	UBERON:0000988	98.18	gold quality
right coronary artery	UBERON:0001625	98.18	gold quality
ascending aorta	UBERON:0001496	98.16	gold quality
ventral tegmental area	UBERON:0002691	98.16	gold quality
left ovary	UBERON:0002119	98.13	gold quality
medulla oblongata	UBERON:0001896	98.07	gold quality
superior vestibular nucleus	UBERON:0007227	98.07	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.04	gold quality
body of uterus	UBERON:0009853	98.04	gold quality
descending thoracic aorta	UBERON:0002345	98.00	gold quality
parotid gland	UBERON:0001831	97.98	gold quality
amygdala	UBERON:0001876	97.98	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-10287	yes	48.07
E-GEOD-135922	yes	25.57
E-ANND-3	yes	17.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting TCEAL3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-5581-3P	98.55	70.31	1161
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-4513	95.04	67.06	727
HSA-MIR-6855-3P	95.04	66.57	725
HSA-MIR-6753-5P	94.70	64.08	470

Literature-anchored findings (GeneRIF, showing 1)

• Characterizes TCEAL1, another member of the human TCEAL gene family. (PMID:10051408)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tceal6	ENSMUSG00000031409
mus_musculus	Tceal3	ENSMUSG00000044550
mus_musculus	Tceal5	ENSMUSG00000054034
rattus_norvegicus	Tceal5	ENSRNOG00000046280
rattus_norvegicus	Tceal6	ENSRNOG00000046390
rattus_norvegicus	Tceal3	ENSRNOG00000049020

Paralogs (8): TCEAL4 (ENSG00000133142), TCEAL1 (ENSG00000172465), TCEAL8 (ENSG00000180964), TCEAL7 (ENSG00000182916), TCEAL2 (ENSG00000184905), TCEAL9 (ENSG00000185222), TCEAL5 (ENSG00000204065), TCEAL6 (ENSG00000204071)

Protein

Protein identifiers

Transcription elongation factor A protein-like 3 — Q969E4 (reviewed: Q969E4)

Alternative names: Transcription elongation factor S-II protein-like 3

All UniProt accessions (1): Q969E4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the TFS-II family. TFA subfamily.

RefSeq proteins (2): NP_001006934, NP_116315* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (11 total): compositionally biased region 6, modified residue 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969E4-F1	58.86	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 30, 65

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, RNGTGGGC_UNKNOWN, GOZGIT_ESR1_TARGETS_DN, MARTINEZ_RB1_TARGETS_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, USF_01, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, TCANNTGAY_SREBP1_01, HAMAI_APOPTOSIS_VIA_TRAIL_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHICAS_RB1_TARGETS_SENESCENT, chrXq22, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, SRC_UP.V1_UP, MIR5581_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

626 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEAL3	BEX5	Q5H9J7	682
TCEAL3	BEX1	Q9HBH7	641
TCEAL3	TCEAL1	Q15170	607
TCEAL3	TCEAL8	Q8IYN2	521
TCEAL3	BEX2	Q9BXY8	517
TCEAL3	BEX3	Q00994	498
TCEAL3	RAB40A	Q8WXH6	466
TCEAL3	TCEAL7	Q9BRU2	449
TCEAL3	OR8D1	Q8WZ84	433
TCEAL3	TCEAL9	Q9UHQ7	415
TCEAL3	RAB40C	Q96S21	392
TCEAL3	RD3L	P0DJH9	392
TCEAL3	RAB40B	Q12829	385
TCEAL3	MORF4L2	Q15014	379
TCEAL3	RAB9B	Q9NP90	344

IntAct

3 interactions, top by confidence:

A	B	Type	Score
TCEAL5	C3orf38	psi-mi:“MI:0914”(association)	0.350
ETS1	TCEAL3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): TCEAL3 (Reconstituted Complex), TCEAL3 (Affinity Capture-MS), TCEAL3 (Co-fractionation), UBA2 (Co-fractionation), TCEAL3 (Affinity Capture-MS), TCEAL3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1L429, A6NDE8, A6NER3, A6NGK3, O41801, O55777, O60829, O75459, O76087, P03204, P04611, P06937, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, P18804, P22421, P86478, P86479, P86480, P86481, P86496, Q13066, Q13069, Q13070, Q2T9P9, Q3KST0, Q4V321, Q4V326, Q5JRK9, Q5JUK9, Q6AY45, Q6I7R5, Q6IPX3, Q6NT46, Q7Z2X7, Q8AIH8, Q8CCT4

Diamond homologs: Q5H9L2, Q5R6B4, Q6IPX3, Q8CCT4, Q8R0A5, Q969E4, Q96EI5, Q9H3H9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

24 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

621 predictions. Top by Δscore:

Variant	Effect	Δscore
X:103608672:AG:A	donor_loss	1.0000
X:103608673:GGTC:G	donor_loss	1.0000
X:103608595:T:TA	acceptor_gain	0.9900
X:103608600:GCAGG:G	acceptor_loss	0.9900
X:103608601:CAGGT:C	acceptor_loss	0.9900
X:103608602:A:AG	acceptor_gain	0.9900
X:103608602:AGG:A	acceptor_loss	0.9900
X:103608603:G:GG	acceptor_gain	0.9900
X:103608645:G:GT	donor_gain	0.9900
X:103609023:A:AG	acceptor_gain	0.9900
X:103609024:T:G	acceptor_gain	0.9900
X:103609029:A:AG	acceptor_gain	0.9900
X:103609030:T:G	acceptor_gain	0.9900
X:103609032:CCCCA:C	acceptor_loss	0.9900
X:103609033:CCCAG:C	acceptor_loss	0.9900
X:103609034:CCA:C	acceptor_loss	0.9900
X:103609035:CAGGA:C	acceptor_loss	0.9900
X:103609036:A:AG	acceptor_gain	0.9900
X:103609036:AG:A	acceptor_gain	0.9900
X:103609036:AGG:A	acceptor_loss	0.9900
X:103609037:G:GC	acceptor_loss	0.9900
X:103609037:G:GG	acceptor_gain	0.9900
X:103609037:GG:G	acceptor_gain	0.9900
X:103609037:GGACA:G	acceptor_gain	0.9900
X:103628789:GAGAG:G	donor_gain	0.9900
X:103628791:GAG:G	donor_gain	0.9900
X:103628792:AGGTG:A	donor_loss	0.9900
X:103628794:G:GA	donor_loss	0.9900
X:103628795:T:A	donor_loss	0.9900
X:103629552:A:T	donor_gain	0.9900

AlphaMissense

1325 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:103609397:A:C	K111N	0.976
X:103609397:A:T	K111N	0.976
X:103609403:A:C	K113N	0.970
X:103609403:A:T	K113N	0.970
X:103609391:A:C	K109N	0.968
X:103609391:A:T	K109N	0.968
X:103609400:A:C	R112S	0.967
X:103609400:A:T	R112S	0.967
X:103609402:A:T	K113I	0.964
X:103609390:A:T	K109I	0.949
X:103609402:A:C	K113T	0.943
X:103609396:A:T	K111I	0.932
X:103609401:A:G	K113E	0.919
X:103609396:A:C	K111T	0.916
X:103609412:G:C	R116S	0.912
X:103609412:G:T	R116S	0.912
X:103609384:C:A	P107H	0.905
X:103609390:A:C	K109T	0.905
X:103609401:A:C	K113Q	0.901
X:103609610:G:C	R182S	0.900
X:103609610:G:T	R182S	0.900
X:103609529:A:C	K155N	0.899
X:103609529:A:T	K155N	0.899
X:103609619:G:C	R185S	0.898
X:103609619:G:T	R185S	0.898
X:103609389:A:G	K109E	0.894
X:103609399:G:C	R112T	0.894
X:103609389:A:C	K109Q	0.891
X:103609399:G:T	R112I	0.886
X:103609548:T:C	F162L	0.886

dbSNP variants (sampled 300 via entrez): RS1000217403 (X:103606100 A>G), RS1001408916 (X:103606646 T>C), RS1002526248 (X:103608639 A>C), RS1003079255 (X:103609118 A>G), RS1005537597 (X:103606711 A>T), RS1011849022 (X:103608042 G>C), RS1012145769 (X:103608567 T>C), RS1012684464 (X:103608708 C>T), RS1013308917 (X:103606032 C>G), RS1013777770 (X:103606605 A>G,T), RS1015001555 (X:103607096 A>G), RS1016401045 (X:103608709 A>AG), RS1017456192 (X:103606755 G>A), RS1017572200 (X:103610179 C>T), RS1018510378 (X:103607163 T>C)

Disease associations

OMIM: gene MIM:301153 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
Valproic Acid	increases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
GSK-J4	decreases expression	1
sulforaphane	decreases expression	1
sodium arsenite	affects cotreatment, decreases expression	1
potassium chromate(VI)	decreases expression	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases expression	1
jinfukang	increases expression	1
Temozolomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases methylation	1
Doxorubicin	increases expression	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Hydrogen Peroxide	affects expression	1
Ozone	decreases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, decreases expression, increases abundance	1
Potassium Dichromate	increases expression	1
Dihydrotestosterone	increases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Tretinoin	affects cotreatment, decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.