TCEAL5

Summary

TCEAL5 (transcription elongation factor A like 5, HGNC:22282) is a protein-coding gene on chromosome Xq22.1, encoding Transcription elongation factor A protein-like 5 (Q5H9L2). May be involved in transcriptional regulation.

This gene, which is located on the X chromosome, encodes a protein which contains a BEX (brain expressed X-liked like family) domain. This domain is found in proteins encoded by the TCEAL elongation factor (transcription elongation factor A (SII)-like) gene family also located on the X chromosome. The coding region for this gene is located entirely in the terminal exon.

Source: NCBI Gene 340543 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total
• MANE Select transcript: NM_001012979

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22282
Approved symbol	TCEAL5
Name	transcription elongation factor A like 5
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	WEX4
Ensembl gene	ENSG00000204065
Ensembl biotype	protein_coding
OMIM	301155
Entrez	340543

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000372680, ENST00000909247, ENST00000909248, ENST00000909249, ENST00000911483, ENST00000911484, ENST00000911485, ENST00000911486, ENST00000911487, ENST00000911488

RefSeq mRNA: 1 — MANE Select: NM_001012979 NM_001012979

CCDS: CCDS35356

Canonical transcript exons

ENST00000372680 — 3 exons

Exon	Start	End
ENSE00001458378	103273691	103274590
ENSE00001458379	103275275	103275342
ENSE00001458380	103276673	103276750

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 97.54.

FANTOM5 (CAGE): breadth broad, TPM avg 10.6800 / max 4119.4873, expressed in 291 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199986	6.7252	263
199987	1.9777	235
199988	1.5577	224
199985	0.3980	87
199989	0.0213	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
superior frontal gyrus	UBERON:0002661	97.54	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.97	gold quality
cerebellar cortex	UBERON:0002129	96.92	gold quality
cerebellum	UBERON:0002037	96.89	gold quality
cerebellar hemisphere	UBERON:0002245	96.89	gold quality
nucleus accumbens	UBERON:0001882	96.87	gold quality
right frontal lobe	UBERON:0002810	96.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.73	gold quality
hypothalamus	UBERON:0001898	96.72	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.72	gold quality
frontal cortex	UBERON:0001870	96.65	gold quality
primary visual cortex	UBERON:0002436	96.53	gold quality
anterior cingulate cortex	UBERON:0009835	96.47	gold quality
prefrontal cortex	UBERON:0000451	96.46	gold quality
cerebral cortex	UBERON:0000956	96.41	gold quality
putamen	UBERON:0001874	96.18	gold quality
brain	UBERON:0000955	96.07	gold quality
caudate nucleus	UBERON:0001873	96.00	gold quality
amygdala	UBERON:0001876	95.88	gold quality
temporal lobe	UBERON:0001871	95.85	gold quality
adenohypophysis	UBERON:0002196	95.79	gold quality
Ammon’s horn	UBERON:0001954	95.58	gold quality
right testis	UBERON:0004534	95.57	gold quality
pituitary gland	UBERON:0000007	95.43	gold quality
left testis	UBERON:0004533	95.09	gold quality
testis	UBERON:0000473	95.06	gold quality
cortical plate	UBERON:0005343	94.34	gold quality
substantia nigra	UBERON:0002038	93.66	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.32	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.18	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	36.65
E-GEOD-84465	yes	6.88
E-ANND-3	no	2.97
E-GEOD-83139	no	2.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting TCEAL5, 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-6835-3P	99.93	70.49	2904
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-133A-5P	99.28	69.13	941
HSA-MIR-4717-3P	99.06	66.34	1072
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-5581-3P	98.55	70.31	1161
HSA-MIR-4490	98.51	68.47	943
HSA-MIR-138-5P	98.43	70.49	1292
HSA-MIR-1262	98.17	66.52	757
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-6736-5P	98.17	66.43	760
HSA-MIR-93-3P	98.15	66.65	1309
HSA-MIR-6131	97.22	66.72	960
HSA-MIR-6872-3P	97.08	66.99	750
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-1236-5P	96.62	66.38	856
HSA-MIR-152-5P	96.42	66.59	960
HSA-MIR-4509	96.19	65.80	900

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), TCEAL3 (ENSG00000196507), TCEAL6 (ENSG00000204071)

Protein

Protein identifiers

Transcription elongation factor A protein-like 5 — Q5H9L2 (reviewed: Q5H9L2)

Alternative names: Transcription elongation factor S-II protein-like 5

All UniProt accessions (1): Q5H9L2

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 (1): NP_001012997* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (10 total): compositionally biased region 8, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H9L2-F1	58.48	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): GSE13522_WT_VS_IFNG_KO_SKIN_DN, CHEN_METABOLIC_SYNDROM_NETWORK, chrXq22, YANG_BCL3_TARGETS_UP, MIR6835_3P, MIR3919, MIR5589_3P, MIR5581_3P, MIR3692_5P, MIR133A_5P, MIR152_5P, MANNO_MIDBRAIN_NEUROTYPES_HDA, MANNO_MIDBRAIN_NEUROTYPES_HDA2, MANNO_MIDBRAIN_NEUROTYPES_HGABA, MANNO_MIDBRAIN_NEUROTYPES_HOMTN

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEAL5	TCEAL8	Q8IYN2	678
TCEAL5	BEX1	Q9HBH7	644
TCEAL5	BEX5	Q5H9J7	588
TCEAL5	TCEAL7	Q9BRU2	578
TCEAL5	TCEAL9	Q9UHQ7	545
TCEAL5	TCEAL1	Q15170	537
TCEAL5	BEX2	Q9BXY8	520
TCEAL5	BEX3	Q00994	467
TCEAL5	RAB40C	Q96S21	394
TCEAL5	RAB40A	Q8WXH6	392
TCEAL5	RAB40B	Q12829	390
TCEAL5	CHAMP1	Q96JM3	339
TCEAL5	MEA1	Q16626	329
TCEAL5	FAM162B	Q5T6X4	323
TCEAL5	ARMCX4	Q5H9R4	322

IntAct

9 interactions, top by confidence:

A	B	Type	Score
BCL2L1	BCL2L11	psi-mi:“MI:0914”(association)	0.870
NR4A2	TCEAL5	psi-mi:“MI:0915”(physical association)	0.520
ZNF74	GAPDHS	psi-mi:“MI:0914”(association)	0.350
TCEAL5	C3orf38	psi-mi:“MI:0914”(association)	0.350
TCEAL5	NR4A2	psi-mi:“MI:0915”(physical association)	0.000
DEDD	TCEAL5	psi-mi:“MI:0915”(physical association)	0.000
HNF1A	TCEAL5	psi-mi:“MI:0915”(physical association)	0.000
PRKAR1A	TCEAL5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): KLHL8 (Affinity Capture-MS), C3orf38 (Affinity Capture-MS), TCEAL3 (Affinity Capture-MS), USP7 (Affinity Capture-MS), TCEAL5 (Affinity Capture-MS), TCEAL5 (Cross-Linking-MS (XL-MS)), TCEAL5 (Cross-Linking-MS (XL-MS)), TCEAL5 (Cross-Linking-MS (XL-MS)), TCEAL5 (Cross-Linking-MS (XL-MS)), TCEAL3 (Cross-Linking-MS (XL-MS)), TCEAL5 (Reconstituted Complex)

ESM2 similar proteins: A0A8I5ZN27, A2TJV2, A4FU49, A8MU46, E1AZ71, E9Q9K5, O54963, P10636, P10637, P19332, P36225, P82179, Q13127, Q28139, Q28181, Q29026, Q2EI20, Q4R729, Q5FVI4, Q5H9L2, Q5S6V2, Q5SRN2, Q5STT6, Q5TGJ6, Q5YCV9, Q5YCW0, Q5YCW1, Q62313, Q62314, Q63803, Q640N3, Q6IPX3, Q6P6B1, Q7Z6I6, Q811Q2, Q8BHB9, Q8CCT4, Q8K0S2, Q8N111, Q8R0A5

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

627 predictions. Top by Δscore:

Variant	Effect	Δscore
X:103274586:CTTTC:C	acceptor_gain	1.0000
X:103274591:C:CA	acceptor_loss	1.0000
X:103274591:C:CC	acceptor_gain	1.0000
X:103275272:GACCT:G	donor_loss	1.0000
X:103275273:A:T	donor_loss	1.0000
X:103275274:C:A	donor_loss	1.0000
X:103275297:T:TA	donor_gain	1.0000
X:103275343:C:CA	acceptor_loss	1.0000
X:103275343:C:CC	acceptor_gain	1.0000
X:103275344:T:C	acceptor_loss	1.0000
X:103274587:TTTC:T	acceptor_gain	0.9900
X:103274588:TTC:T	acceptor_gain	0.9900
X:103274589:TC:T	acceptor_gain	0.9900
X:103274590:CC:C	acceptor_gain	0.9900
X:103274599:C:CT	acceptor_gain	0.9900
X:103274600:A:T	acceptor_gain	0.9900
X:103275339:AGAC:A	acceptor_gain	0.9900
X:103275340:GAC:G	acceptor_gain	0.9900
X:103275341:AC:A	acceptor_gain	0.9900
X:103275342:CC:C	acceptor_gain	0.9900
X:103275346:C:CT	acceptor_gain	0.9900
X:103275347:A:T	acceptor_gain	0.9900
X:103276668:CCGA:C	donor_loss	0.9900
X:103276670:GA:G	donor_loss	0.9900
X:103276671:AC:A	donor_loss	0.9900
X:103276672:C:CT	donor_loss	0.9900
X:103274591:C:T	acceptor_gain	0.9800
X:103275274:CCT:C	donor_gain	0.9800
X:103275276:TGC:T	donor_gain	0.9800
X:103275338:AAGAC:A	acceptor_gain	0.9800

AlphaMissense

1370 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:103274213:T:A	K117N	0.973
X:103274213:T:G	K117N	0.973
X:103274207:T:A	K119N	0.964
X:103274207:T:G	K119N	0.964
X:103274219:T:A	K115N	0.962
X:103274219:T:G	K115N	0.962
X:103274210:T:A	R118S	0.960
X:103274210:T:G	R118S	0.960
X:103274208:T:A	K119I	0.951
X:103274220:T:A	K115I	0.939
X:103274208:T:G	K119T	0.931
X:103274214:T:A	K117I	0.929
X:103274205:G:A	T120I	0.909
X:103274209:T:C	K119E	0.907
X:103274214:T:G	K117T	0.907
X:103274000:C:A	R188S	0.905
X:103274000:C:G	R188S	0.905
X:103274220:T:G	K115T	0.897
X:103274198:C:A	R122S	0.895
X:103274198:C:G	R122S	0.895
X:103274226:G:T	P113H	0.894
X:103274221:T:C	K115E	0.883
X:103274081:T:A	K161N	0.878
X:103274081:T:G	K161N	0.878
X:103274060:A:C	F168L	0.877
X:103274060:A:T	F168L	0.877
X:103274062:A:G	F168L	0.877
X:103273991:C:A	R191S	0.876
X:103273991:C:G	R191S	0.876
X:103274211:C:G	R118T	0.872

dbSNP variants (sampled 300 via entrez): RS1000146119 (X:103274871 A>G), RS1002614609 (X:103277747 T>A,C), RS1003618018 (X:103275571 G>A), RS1003808938 (X:103276344 G>A), RS1005868285 (X:103278162 C>A,G), RS1006081186 (X:103276568 A>G), RS1007067212 (X:103277577 C>T), RS1007183260 (X:103277044 A>T), RS1007553831 (X:103277977 C>T), RS1007581645 (X:103277434 T>C), RS1007915203 (X:103275327 C>T), RS1010599534 (X:103276025 C>T), RS1011165566 (X:103277323 C>T), RS1011366923 (X:103276942 G>A), RS1011863410 (X:103278251 G>T)

Disease associations

OMIM: gene MIM:301155 | 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
bisphenol A	increases methylation	1
Benzo(a)pyrene	decreases methylation, affects methylation	1
Potassium Dichromate	increases expression	1

Clinical trials (associated diseases)

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