TCEAL4

Summary

TCEAL4 (transcription elongation factor A like 4, HGNC:26121) is a protein-coding gene on chromosome Xq22.2, encoding Transcription elongation factor A protein-like 4 (Q96EI5). May be involved in transcriptional regulation.

This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. This family is comprised of nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. Alternatively splicing results in multiple transcript variants. There is a pseudogene for this gene on chromosome 13.

Source: NCBI Gene 79921 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001006935

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26121
Approved symbol	TCEAL4
Name	transcription elongation factor A like 4
Location	Xq22.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21174, WEX7
Ensembl gene	ENSG00000133142
Ensembl biotype	protein_coding
OMIM	301154
Entrez	79921

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 35 protein_coding, 1 retained_intron

ENST00000372629, ENST00000415568, ENST00000425011, ENST00000434216, ENST00000459722, ENST00000468024, ENST00000469586, ENST00000472484, ENST00000472745, ENST00000481555, ENST00000490644, ENST00000494801, ENST00000898934, ENST00000898935, ENST00000898936, ENST00000898937, ENST00000898938, ENST00000898939, ENST00000898940, ENST00000898941, ENST00000898942, ENST00000898943, ENST00000898944, ENST00000898945, ENST00000898946, ENST00000932240, ENST00000932241, ENST00000932242, ENST00000932243, ENST00000932244, ENST00000960659, ENST00000960660, ENST00000960661, ENST00000960662, ENST00000960663, ENST00000960664

RefSeq mRNA: 7 — MANE Select: NM_001006935 NM_001006935, NM_001006937, NM_001300901, NM_001305840, NM_001305841, NM_001305842, NM_024863

CCDS: CCDS14510, CCDS76004

Canonical transcript exons

ENST00000472484 — 3 exons

Exon	Start	End
ENSE00001596982	103586219	103586291
ENSE00001828442	103585515	103585624
ENSE00001898643	103586649	103587729

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 99.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 134.8905 / max 4613.3030, expressed in 1739 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197026	126.5306	1738
197028	2.3865	879
197029	2.3150	939
209764	1.2699	462
197030	0.7234	398
197027	0.7153	315
209765	0.5724	269
197031	0.3773	152

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right ovary	UBERON:0002118	99.61	gold quality
left ovary	UBERON:0002119	99.60	gold quality
body of uterus	UBERON:0009853	99.53	gold quality
seminal vesicle	UBERON:0000998	99.52	gold quality
mucosa of stomach	UBERON:0001199	99.48	gold quality
left uterine tube	UBERON:0001303	99.47	gold quality
myometrium	UBERON:0001296	99.44	gold quality
right coronary artery	UBERON:0001625	99.42	gold quality
endocervix	UBERON:0000458	99.41	gold quality
choroid plexus epithelium	UBERON:0003911	99.37	gold quality
thoracic aorta	UBERON:0001515	99.27	gold quality
ascending aorta	UBERON:0001496	99.25	gold quality
saphenous vein	UBERON:0007318	99.25	gold quality
germinal epithelium of ovary	UBERON:0001304	99.24	gold quality
descending thoracic aorta	UBERON:0002345	99.23	gold quality
tendon of biceps brachii	UBERON:0008188	99.22	gold quality
left coronary artery	UBERON:0001626	99.21	gold quality
lower esophagus muscularis layer	UBERON:0035833	99.19	gold quality
coronary artery	UBERON:0001621	99.18	gold quality
lower esophagus	UBERON:0013473	99.18	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	99.16	gold quality
urethra	UBERON:0000057	99.13	gold quality
sural nerve	UBERON:0015488	99.10	gold quality
corpus epididymis	UBERON:0004359	99.09	gold quality
aorta	UBERON:0000947	99.06	gold quality
cauda epididymis	UBERON:0004360	99.05	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	99.02	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.00	gold quality
right lung	UBERON:0002167	98.99	gold quality
tibial nerve	UBERON:0001323	98.97	gold quality

Single-cell (SCXA)

Detected in 17 experiment(s), a significant marker in 14.

Experiment	Marker?	Max mean expression
E-MTAB-10287	yes	2172.81
E-GEOD-134144	yes	1408.21
E-MTAB-6701	yes	134.65
E-HCAD-1	yes	74.68
E-HCAD-4	yes	63.10
E-CURD-112	yes	32.30
E-MTAB-6678	yes	28.78
E-GEOD-135922	yes	28.05
E-HCAD-5	yes	18.52
E-CURD-46	yes	8.65
E-HCAD-11	yes	8.52
E-HCAD-9	yes	6.87
E-MTAB-10042	yes	5.63
E-MTAB-8381	no	1444.78
E-GEOD-124858	no	220.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting TCEAL4, 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-4795-3P	100.00	74.62	4024
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-3133	99.81	70.92	3506

Literature-anchored findings (GeneRIF, showing 1)

• Expression of TCEAL4 was down-regulated in all anaplastic thyroid carcinomas studied. Loss of TCEAL4 expression might be associated with development of ATC from pre-existing diffferentiated TC. (PMID:17076909)

Cross-species orthologs

0 orthologs

Paralogs (8): TCEAL1 (ENSG00000172465), TCEAL8 (ENSG00000180964), TCEAL7 (ENSG00000182916), TCEAL2 (ENSG00000184905), TCEAL9 (ENSG00000185222), TCEAL3 (ENSG00000196507), TCEAL5 (ENSG00000204065), TCEAL6 (ENSG00000204071)

Protein

Protein identifiers

Transcription elongation factor A protein-like 4 — Q96EI5 (reviewed: Q96EI5)

Alternative names: Transcription elongation factor S-II protein-like 4

All UniProt accessions (7): A0A384NKK0, D6RCE9, D6RD44, D6RHZ1, D6RIH3, Q96EI5, J3KQY4

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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96EI5-1	1	yes
Q96EI5-2	2

RefSeq proteins (7): NP_001006936, NP_001006938, NP_001287830, NP_001292769, NP_001292770, NP_001292771, NP_079139 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (10 total): modified residue 4, sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EI5-F1	61.46	0.07

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 (4): 1, 6, 88, 102

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): MODULE_66, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, TIEN_INTESTINE_PROBIOTICS_24HR_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, MODULE_11, RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN, MODULE_12, HAMAI_APOPTOSIS_VIA_TRAIL_UP, PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN, MODULE_100, MODULE_49, CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP, KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP, KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP, chrXq22

GO Biological Process (1): translational elongation (GO:0006414)

GO Molecular Function (2): translation elongation factor activity (GO:0003746), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
translation	1
macromolecule biosynthetic process	1
translational elongation	1
translation factor activity	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

790 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEAL4	DHX40	Q8IX18	637
TCEAL4	TCEAL1	Q15170	603
TCEAL4	ZNF628	Q5EBL2	559
TCEAL4	BEX3	Q00994	467
TCEAL4	TCEAL8	Q8IYN2	464
TCEAL4	FGD1	P98174	461
TCEAL4	MIS18BP1	Q6P0N0	450
TCEAL4	TCEAL7	Q9BRU2	449
TCEAL4	TSACC	Q96A04	449
TCEAL4	PPIL4	Q8WUA2	447
TCEAL4	BEX5	Q5H9J7	433
TCEAL4	LYSMD1	Q96S90	419
TCEAL4	ARMH4	Q86TY3	394
TCEAL4	RAB40A	Q8WXH6	392
TCEAL4	PHLDB3	Q6NSJ2	379

IntAct

16 interactions, top by confidence:

A	B	Type	Score
TCEAL4	PEX1	psi-mi:“MI:0915”(physical association)	0.560
TCEAL4	WFS1	psi-mi:“MI:0915”(physical association)	0.560
TCEAL4	USP11	psi-mi:“MI:0914”(association)	0.530
TCEAL4	USP11	psi-mi:“MI:0914”(association)	0.350
USP11	CNOT8	psi-mi:“MI:0914”(association)	0.350
USP7	STIL	psi-mi:“MI:0914”(association)	0.350
USP11	PRRC2B	psi-mi:“MI:0914”(association)	0.350
TCEAL1	PDCD5	psi-mi:“MI:0914”(association)	0.350
MIF	BLTP3B	psi-mi:“MI:0914”(association)	0.350
TCEAL2	MYL9	psi-mi:“MI:0914”(association)	0.350
SV2B	C15orf61	psi-mi:“MI:0914”(association)	0.350

BioGRID (65): IFRD1 (Affinity Capture-MS), TRIM27 (Affinity Capture-MS), HLTF (Affinity Capture-MS), USP7 (Affinity Capture-MS), USP11 (Affinity Capture-MS), RB1CC1 (Affinity Capture-MS), USP15 (Affinity Capture-MS), SPTLC1 (Affinity Capture-MS), ATXN2L (Affinity Capture-MS), VPS41 (Affinity Capture-MS), SLC35F6 (Affinity Capture-MS), CAMSAP3 (Affinity Capture-MS), TCEAL4 (Affinity Capture-MS), TCEAL4 (Affinity Capture-MS), ACTL8 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQG5, A0A1D9BZF0, B3EWZ0, B3EWZ1, B4F777, D3YZV8, O01949, O46383, O75459, P04922, P08116, P13665, P31568, P31569, P32447, P49451, P62521, P82970, Q01033, Q01042, Q02752, Q0ZNK1, Q14093, Q28139, Q2GIB5, Q54RM7, Q5H9L2, Q5MIT9, Q5MJ10, Q5R6B4, Q5SRN2, Q6AXX0, Q6BYE5, Q6CI62, Q6IPX3, Q6SJ82, Q7M3V1, Q7YT37, Q8BGC0, Q8CCT4

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

429 predictions. Top by Δscore:

Variant	Effect	Δscore
X:103586302:G:GG	donor_gain	1.0000
X:103586634:A:AG	acceptor_gain	1.0000
X:103585672:G:GT	donor_gain	0.9900
X:103586214:TGCA:T	acceptor_loss	0.9900
X:103586215:GCA:G	acceptor_loss	0.9900
X:103586216:CA:C	acceptor_loss	0.9900
X:103586263:G:GT	donor_gain	0.9900
X:103586289:CAGGT:C	donor_loss	0.9900
X:103586290:AG:A	donor_loss	0.9900
X:103586291:GG:G	donor_loss	0.9900
X:103586292:GTCC:G	donor_loss	0.9900
X:103586293:T:G	donor_loss	0.9900
X:103586299:A:T	donor_gain	0.9900
X:103586333:GGT:G	donor_gain	0.9900
X:103586635:C:G	acceptor_gain	0.9900
X:103586640:A:AG	acceptor_gain	0.9900
X:103586641:T:G	acceptor_gain	0.9900
X:103586643:CCCCA:C	acceptor_loss	0.9900
X:103586644:CCCAG:C	acceptor_loss	0.9900
X:103586645:CCA:C	acceptor_loss	0.9900
X:103586646:CAG:C	acceptor_loss	0.9900
X:103585682:GG:G	donor_gain	0.9800
X:103585683:GG:G	donor_gain	0.9800
X:103585937:G:GT	donor_gain	0.9800
X:103586210:T:TA	acceptor_gain	0.9800
X:103586217:A:AG	acceptor_gain	0.9800
X:103586218:G:GG	acceptor_gain	0.9800
X:103585620:TCCAG:T	donor_loss	0.9700
X:103585621:CCAGG:C	donor_loss	0.9700
X:103585622:CAGG:C	donor_loss	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000402403 (X:103576961 T>C), RS1000847812 (X:103586213 C>T), RS1000900159 (X:103586522 T>C), RS1001004830 (X:103581900 T>C), RS1001164580 (X:103578137 T>C), RS1001216797 (X:103578859 T>C), RS1001575459 (X:103583122 C>T), RS1001919202 (X:103580734 T>C), RS1002222452 (X:103576108 G>T), RS1002699729 (X:103577718 G>A), RS1002836384 (X:103580775 A>G), RS1002887374 (X:103581353 A>G), RS1003590364 (X:103578450 T>C,G), RS1004315593 (X:103587928 A>G), RS1004704551 (X:103576152 T>C)

Disease associations

OMIM: gene MIM:301154 | disease phenotypes: MIM:164500

GenCC curated gene-disease

Mondo (1): spinocerebellar ataxia 7 (MONDO:0016163)

Orphanet (2): Autosomal dominant cerebellar ataxia type II (Orphanet:208508), Spinocerebellar ataxia type 7 (Orphanet:94147)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009391_550	Metabolite levels	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010496	hippuric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
cobaltous chloride	decreases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
potassium chromate(VI)	decreases expression	1
coumarin	decreases phosphorylation	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
pyrachlostrobin	decreases expression	1
picoxystrobin	decreases expression	1
Temozolomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Antimycin A	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Dexamethasone	increases expression	1
Doxorubicin	increases expression	1
Methyl Methanesulfonate	increases expression	1
Potassium Dichromate	increases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Valproic Acid	affects expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
beta-Naphthoflavone	decreases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03701399	PHASE3	ACTIVE_NOT_RECRUITING	Troriluzole in Adult Participants With Spinocerebellar Ataxia
NCT04301284	PHASE2	WITHDRAWN	Study of CAD-1883 for Spinocerebellar Ataxia
NCT03660917	PHASE2/PHASE3	RECRUITING	Riluzole in Patients With Spinocerebellar Ataxia Type 7
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT04288128	Not specified	COMPLETED	Integrated Functional Evaluation of the Cerebellum
NCT05826171	Not specified	ACTIVE_NOT_RECRUITING	Priming Motor Learning Through Exercise in People With Spinocerebellar Ataxia