TCEAL9

Summary

TCEAL9 (transcription elongation factor A like 9, HGNC:30084) is a protein-coding gene on chromosome Xq22.2, encoding Transcription elongation factor A protein-like 9 (Q9UHQ7). May be involved in transcriptional regulation.

The globular WW domain is composed of 38 to 40 semiconserved amino acids shared by proteins of diverse functions including structural, regulatory, and signaling proteins. The domain is involved in mediating protein-protein interactions through the binding of polyproline ligands. This gene encodes a WW domain binding protein. This gene also encodes a domain with similarity to the transcription elongation factor A, SII-related family. Alternative splicing results in multiple transcript variants encoding a single isoform.

Source: NCBI Gene 51186 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 6 total — 1 pathogenic
• MANE Select transcript: NM_016303

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30084
Approved symbol	TCEAL9
Name	transcription elongation factor A like 9
Location	Xq22.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp313K1940, WEX6
Ensembl gene	ENSG00000185222
Ensembl biotype	protein_coding
OMIM	301158
Entrez	51186

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000372656, ENST00000372661, ENST00000646896, ENST00000908653, ENST00000908654, ENST00000908655, ENST00000928953, ENST00000928954, ENST00000928955, ENST00000928956, ENST00000928957, ENST00000928958, ENST00000928959, ENST00000928960, ENST00000928961, ENST00000928962

RefSeq mRNA: 4 — MANE Select: NM_016303 NM_001006612, NM_001006613, NM_001006614, NM_016303

CCDS: CCDS14507

Canonical transcript exons

ENST00000372661 — 3 exons

Exon	Start	End
ENSE00001318428	103357083	103357161
ENSE00001458330	103357615	103358462
ENSE00003815269	103356506	103356606

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 99.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 169.2757 / max 6761.7916, expressed in 1676 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197013	169.2757	1676

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ovary	UBERON:0002119	99.17	gold quality
adrenal tissue	UBERON:0018303	99.10	gold quality
right adrenal gland	UBERON:0001233	99.05	gold quality
right adrenal gland cortex	UBERON:0035827	99.02	gold quality
right ovary	UBERON:0002118	98.98	gold quality
left adrenal gland	UBERON:0001234	98.97	gold quality
adrenal cortex	UBERON:0001235	98.96	gold quality
left adrenal gland cortex	UBERON:0035825	98.93	gold quality
adrenal gland	UBERON:0002369	98.91	gold quality
stromal cell of endometrium	CL:0002255	98.87	gold quality
germinal epithelium of ovary	UBERON:0001304	98.78	gold quality
corpus epididymis	UBERON:0004359	98.77	gold quality
pericardium	UBERON:0002407	98.72	gold quality
placenta	UBERON:0001987	98.67	gold quality
descending thoracic aorta	UBERON:0002345	98.42	gold quality
caput epididymis	UBERON:0004358	98.40	gold quality
choroid plexus epithelium	UBERON:0003911	98.36	gold quality
seminal vesicle	UBERON:0000998	98.31	gold quality
vena cava	UBERON:0004087	98.21	gold quality
islet of Langerhans	UBERON:0000006	98.18	gold quality
thoracic aorta	UBERON:0001515	98.15	gold quality
ascending aorta	UBERON:0001496	98.14	gold quality
calcaneal tendon	UBERON:0003701	98.13	gold quality
left lobe of thyroid gland	UBERON:0001120	98.08	gold quality
mucosa of stomach	UBERON:0001199	98.06	gold quality
ovary	UBERON:0000992	97.99	gold quality
adenohypophysis	UBERON:0002196	97.91	gold quality
smooth muscle tissue	UBERON:0001135	97.85	gold quality
thyroid gland	UBERON:0002046	97.84	gold quality
cauda epididymis	UBERON:0004360	97.82	gold quality

Single-cell (SCXA)

Detected in 14 experiment(s), a significant marker in 13.

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	132.82
E-GEOD-75688	yes	82.07
E-HCAD-1	yes	78.38
E-HCAD-10	yes	44.44
E-GEOD-134144	yes	43.76
E-MTAB-8410	yes	34.22
E-HCAD-5	yes	32.54
E-HCAD-9	yes	15.77
E-CURD-46	yes	13.86
E-CURD-112	yes	7.89
E-GEOD-130148	yes	7.35
E-MTAB-10553	yes	5.11
E-GEOD-125970	no	3.17
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

50 targeting TCEAL9, 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-98-3P	100.00	74.08	3907
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-2053	99.57	69.15	1635
HSA-MIR-143-3P	99.49	69.05	1457

Literature-anchored findings (GeneRIF, showing 2)

• WW domain binding protein 5 can modulate MDR through the Hippo pathway under the regulation of miR-335. WW domain binding protein 5 may be a prognostic predictor and a potential target for interfering with MDR in SCLC. (PMID:27336605)
• High WBP5 expression correlates with elevation of HOX genes levels and is associated with inferior survival in patients with acute myeloid leukaemia. (PMID:32103106)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tceal9	ENSMUSG00000042712
rattus_norvegicus	Tceal9	ENSRNOG00000034198

Paralogs (8): TCEAL4 (ENSG00000133142), TCEAL1 (ENSG00000172465), TCEAL8 (ENSG00000180964), TCEAL7 (ENSG00000182916), TCEAL2 (ENSG00000184905), TCEAL3 (ENSG00000196507), TCEAL5 (ENSG00000204065), TCEAL6 (ENSG00000204071)

Protein

Protein identifiers

Transcription elongation factor A protein-like 9 — Q9UHQ7 (reviewed: Q9UHQ7)

Alternative names: Transcription elongation factor S-II protein-like 9, WW domain-binding protein 5

All UniProt accessions (1): Q9UHQ7

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 (4): NP_001006613, NP_001006614, NP_001006615, NP_057387* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UHQ7-F1	67.51	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 213 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10, FISCHER_G1_S_CELL_CYCLE, SP3_Q3, STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CREBP1_Q2, GGGTGGRR_PAX4_03, HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP, GOLDRATH_ANTIGEN_RESPONSE, EVI1_05, BORLAK_LIVER_CANCER_EGF_UP, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, KOYAMA_SEMA3B_TARGETS_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2

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

380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEAL9	BEX3	Q00994	594
TCEAL9	TCEAL5	Q5H9L2	545
TCEAL9	COPS9	Q8WXC6	517
TCEAL9	BEX2	Q9BXY8	454
TCEAL9	BEX1	Q9HBH7	452
TCEAL9	H3BUI4	H3BUI4	447
TCEAL9	TCEAL3	Q969E4	415
TCEAL9	DCAF12L2	Q5VW00	372
TCEAL9	C1orf226	A1L170	360
TCEAL9	FMNL3	Q8IVF7	352
TCEAL9	FAM53C	Q9NYF3	323
TCEAL9	REX1BD	Q96EN9	315
TCEAL9	NSRP1	Q9H0G5	308
TCEAL9	E7EQY1	E7EQY1	300
TCEAL9	TPGS2	Q68CL5	298

IntAct

23 interactions, top by confidence:

A	B	Type	Score
ARMC8	HTRA2	psi-mi:“MI:0914”(association)	0.750
GID8	HTRA2	psi-mi:“MI:0914”(association)	0.610
INSL6	POTEF	psi-mi:“MI:0914”(association)	0.530
KRBA1	TRIM27	psi-mi:“MI:0914”(association)	0.530
TCEAL9	RANBP10	psi-mi:“MI:0914”(association)	0.530
RMND5A	HTRA2	psi-mi:“MI:0914”(association)	0.350
KRBA1	TOMM40	psi-mi:“MI:0914”(association)	0.350
GDF15	CCDC85C	psi-mi:“MI:0914”(association)	0.350
TBC1D2	HMMR	psi-mi:“MI:0914”(association)	0.350
TCEAL9	DIRAS1	psi-mi:“MI:0914”(association)	0.350
PLEKHA6	KCTD9	psi-mi:“MI:0914”(association)	0.350
GOLGA2	UPK2	psi-mi:“MI:0914”(association)	0.350
TCEAL9	TGM5	psi-mi:“MI:0914”(association)	0.350
TCEAL9		psi-mi:“MI:0915”(physical association)	0.000
TCEAL9	RPL31	psi-mi:“MI:0915”(physical association)	0.000
TCEAL9	USP11	psi-mi:“MI:0915”(physical association)	0.000
TCEAL9	PIP	psi-mi:“MI:0915”(physical association)	0.000
TCEAL9	KDELR1	psi-mi:“MI:0915”(physical association)	0.000
SOD2	TCEAL9	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (47): WBP5 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), USP11 (Affinity Capture-MS), SDCCAG3 (Affinity Capture-MS), KDELR1 (Affinity Capture-MS), RPL31 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), WBP5 (Proximity Label-MS), WBP5 (Far Western), DIRAS1 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS)

ESM2 similar proteins: A2RD68, A2RN34, A7SPE8, A9CB93, B2IS88, B5XMI5, B8YB65, B9DV47, C0H3Y7, O01949, O29015, P03720, P0C745, P0C746, P0C747, P0CAZ8, P0DL22, P0DOZ5, P0DP00, P17684, P21596, P21597, P33177, P39101, P42625, P80349, P80577, P80730, P81528, P81673, P81834, P83989, P84972, Q02WP2, Q08628, Q1JAJ5, Q1JFN8, Q1JKP7, Q48S19, Q4JAJ6

Diamond homologs: A1YEW9, A2D4U8, A2D5N1, A2D671, A2T6K9, Q15170, Q2KIJ9, Q3T020, Q5PPP3, Q6I7R5, Q8IYN2, Q921P9, Q9CZY2, Q9DD24, Q9UHQ7, A3KGA4, D3ZT37, Q9BRU2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
145995	GRCh38/hg38 Xp22.33-q28(chrX:20297-156026127)x1	Pathogenic

SpliceAI

219 predictions. Top by Δscore:

Variant	Effect	Δscore
X:103357614:GAA:G	acceptor_gain	1.0000
X:103356604:CAG:C	donor_loss	0.9900
X:103356605:AGG:A	donor_loss	0.9900
X:103356607:GTT:G	donor_loss	0.9900
X:103356608:T:G	donor_loss	0.9900
X:103357613:A:AG	acceptor_gain	0.9900
X:103357614:G:GG	acceptor_gain	0.9900
X:103357614:GA:G	acceptor_gain	0.9900
X:103357614:GAAGT:G	acceptor_gain	0.9900
X:103356577:G:GT	donor_gain	0.9800
X:103357081:A:AG	acceptor_gain	0.9800
X:103357082:G:GG	acceptor_gain	0.9800
X:103357611:CTAG:C	acceptor_loss	0.9800
X:103357614:G:A	acceptor_loss	0.9800
X:103357082:GTTT:G	acceptor_gain	0.9700
X:103357160:AG:A	donor_loss	0.9700
X:103357162:GTAG:G	donor_loss	0.9700
X:103357163:T:G	donor_loss	0.9700
X:103357605:T:TA	acceptor_gain	0.9700
X:103357612:TAGAA:T	acceptor_gain	0.9500
X:103357080:CAGT:C	acceptor_loss	0.9400
X:103357081:A:AC	acceptor_loss	0.9400
X:103357082:G:GA	acceptor_loss	0.9400
X:103357613:AGAAG:A	acceptor_gain	0.9400
X:103356619:G:GG	donor_gain	0.9300
X:103357162:G:GG	donor_gain	0.9300
X:103357617:GTC:G	acceptor_gain	0.9300
X:103357082:GTT:G	acceptor_gain	0.9200
X:103357082:GTTTA:G	acceptor_gain	0.9200
X:103357160:AGGT:A	donor_gain	0.9200

AlphaMissense

708 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:103357936:A:C	R84S	0.946
X:103357936:A:T	R84S	0.946
X:103357850:T:C	F56L	0.932
X:103357852:T:A	F56L	0.932
X:103357852:T:G	F56L	0.932
X:103357960:G:C	W92C	0.913
X:103357960:G:T	W92C	0.913
X:103357927:G:C	R81S	0.911
X:103357927:G:T	R81S	0.911
X:103357942:A:C	K86N	0.901
X:103357942:A:T	K86N	0.901
X:103357817:T:C	F45L	0.893
X:103357819:T:A	F45L	0.893
X:103357819:T:G	F45L	0.893
X:103357944:T:C	L87P	0.893
X:103357935:G:T	R84I	0.884
X:103357938:A:T	N85I	0.878
X:103357830:T:C	L49P	0.876
X:103357958:T:A	W92R	0.872
X:103357958:T:C	W92R	0.872
X:103357941:A:T	K86I	0.869
X:103357963:G:C	K93N	0.866
X:103357963:G:T	K93N	0.866
X:103357851:T:C	F56S	0.863
X:103357935:G:C	R84T	0.860
X:103357954:G:A	M90I	0.850
X:103357954:G:C	M90I	0.850
X:103357954:G:T	M90I	0.850
X:103357830:T:A	L49Q	0.846
X:103357854:A:T	K57I	0.846

dbSNP variants (sampled 300 via entrez): RS1000540790 (X:103355954 A>C), RS1001009911 (X:103355511 T>G), RS1001527220 (X:103356505 T>C), RS1001558591 (X:103356720 G>A), RS1001910070 (X:103354907 T>C), RS1002932822 (X:103358352 G>A), RS1003544149 (X:103355242 A>C), RS1004908683 (X:103356129 C>T), RS1005516859 (X:103356465 A>T), RS1005558135 (X:103355973 GA>G,GAA), RS1005693673 (X:103355278 A>G), RS1009008225 (X:103358172 A>G), RS1009737969 (X:103355429 A>G), RS1010120335 (X:103355142 A>C), RS1011797331 (X:103358064 A>G,T)

Disease associations

OMIM: gene MIM:301158 | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
perfluorooctane sulfonic acid	decreases expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Cyclosporine	increases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	decreases expression	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
azoxystrobin	increases expression	1
chloropicrin	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
picoxystrobin	increases expression	1
MT19c compound	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Vorinostat	increases expression	1
Gemcitabine	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Antimycin A	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cadmium	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B3J4	Abcam HEK293T TCEAL9 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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