TCEAL7

Summary

TCEAL7 (transcription elongation factor A like 7, HGNC:28336) is a protein-coding gene on chromosome Xq22.2, encoding Transcription elongation factor A protein-like 7 (Q9BRU2). Plays a role in the negative regulation of NF-kappa-B signaling at the basal level by modulating transcriptional activity of NF-kappa-B on its target gene promoters.

Involved in negative regulation of DNA-templated transcription and negative regulation of NF-kappaB transcription factor activity. Located in nucleoplasm.

Source: NCBI Gene 56849 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_152278

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28336
Approved symbol	TCEAL7
Name	transcription elongation factor A like 7
Location	Xq22.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC23947, WEX5
Ensembl gene	ENSG00000182916
Ensembl biotype	protein_coding
OMIM	300771
Entrez	56849

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000332431, ENST00000372666, ENST00000861133, ENST00000861134, ENST00000861135, ENST00000932017, ENST00000932018, ENST00000932019, ENST00000932020, ENST00000932021, ENST00000932022, ENST00000960918

RefSeq mRNA: 2 — MANE Select: NM_152278 NM_001348258, NM_152278

CCDS: CCDS14506

Canonical transcript exons

ENST00000332431 — 3 exons

Exon	Start	End
ENSE00001291638	103330239	103330304
ENSE00001305966	103330923	103331040
ENSE00001325535	103331377	103332326

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 98.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.9294 / max 759.8381, expressed in 973 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197011	34.9294	973

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 46	UBERON:0006483	98.29	gold quality
hypothalamus	UBERON:0001898	98.21	gold quality
pons	UBERON:0000988	98.12	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.11	gold quality
prefrontal cortex	UBERON:0000451	98.10	gold quality
spinal cord	UBERON:0002240	97.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.80	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.70	gold quality
substantia nigra	UBERON:0002038	97.28	gold quality
frontal cortex	UBERON:0001870	97.24	gold quality
superior vestibular nucleus	UBERON:0007227	97.17	gold quality
anterior cingulate cortex	UBERON:0009835	97.08	gold quality
midbrain	UBERON:0001891	97.00	gold quality
neocortex	UBERON:0001950	96.97	gold quality
cerebral cortex	UBERON:0000956	96.85	gold quality
amygdala	UBERON:0001876	96.85	gold quality
cerebellar cortex	UBERON:0002129	96.84	gold quality
cerebellar hemisphere	UBERON:0002245	96.83	gold quality
corpus callosum	UBERON:0002336	96.79	gold quality
right frontal lobe	UBERON:0002810	96.70	gold quality
cerebellum	UBERON:0002037	96.61	gold quality
Ammon’s horn	UBERON:0001954	96.58	gold quality
subthalamic nucleus	UBERON:0001906	96.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.39	gold quality
brain	UBERON:0000955	96.27	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.24	gold quality
postcentral gyrus	UBERON:0002581	96.21	gold quality
forebrain	UBERON:0001890	96.20	gold quality
dorsal plus ventral thalamus	UBERON:0001897	96.19	gold quality
medulla oblongata	UBERON:0001896	96.05	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	13.16
E-ANND-3	yes	7.96
E-HCAD-5	no	8.08

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MAX, MYC, NFKB

miRNA regulators (miRDB)

51 targeting TCEAL7, 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-8485	100.00	77.57	4731
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-196A-3P	99.19	67.34	1204
HSA-MIR-4796-3P	99.08	68.38	1681

Literature-anchored findings (GeneRIF, showing 9)

• TCEAL7 is a cell death regulatory protein that is frequently inactivated in ovarian cancers, and may function as a tumor suppressor. (PMID:15870691)
• A role for candidate tumor-suppressor gene TCEAL7 in the regulation of c-Myc activity, cyclin D1 levels and cellular transformation is reported. (PMID:18806825)
• TCEAL7 polymorphisms may play a role in the development of invasive serous ovarian cancers. (PMID:19419758)
• TCEAL7 in the negative regulation of NF-kappaB signaling at the basal level by modulating transcriptional activity of NF-kappaB on its target gene promoters in ovarian cells. (PMID:19966855)
• alteration of TCEAL7 expression levels in recombination-based alternative lengthening of telomeres and telomerase-positive cells affects hTERT expression (PMID:20454512)
• Our study suggests that TCEAL7 might serve as a candidate tumor suppressor and a potential prognostic biomarker in gastric carcinogenesis. (PMID:23372750)
• Findings show that TCEAL7 expression is down-regulated in non-small cell lung cancer (NSCLC) like in other human cancers. This down-regulation was also associated with CCND1 over-expression in lung tumors. (PMID:31321645)
• These results suggest that miR-301a promotes radiation resistance by repressing anti-oncogene TCEAL7 expression and then activity of the Wnt/beta-catenin-signaling pathway. (PMID:31402274)
• Long non-coding RNA HAND2-AS1 inhibits gastric cancer progression by suppressing TCEAL7 expression via targeting miR-769-5p. (PMID:32952069)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tceal7	ENSMUSG00000079428
rattus_norvegicus	Tceal7	ENSRNOG00000037645

Paralogs (8): TCEAL4 (ENSG00000133142), TCEAL1 (ENSG00000172465), TCEAL8 (ENSG00000180964), TCEAL2 (ENSG00000184905), TCEAL9 (ENSG00000185222), TCEAL3 (ENSG00000196507), TCEAL5 (ENSG00000204065), TCEAL6 (ENSG00000204071)

Protein

Protein identifiers

Transcription elongation factor A protein-like 7 — Q9BRU2 (reviewed: Q9BRU2)

Alternative names: Transcription elongation factor S-II protein-like 7

All UniProt accessions (1): Q9BRU2

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the negative regulation of NF-kappa-B signaling at the basal level by modulating transcriptional activity of NF-kappa-B on its target gene promoters. Associates with cyclin D1 promoter containing Myc E-box sequence and transcriptionally represses cyclin D1 expression. Regulates telomerase reverse transcriptase expression and telomerase activity in both ALT (alternative lengthening of telomeres)and telomerase-positive cell lines.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in normal and fetal brain tissues, and weakly expressed in uterus and ovary. Down-regulated in epithelial ovarian, cervical, prostate, breast, brain and lung cancer cell lines and in brain and ovarian tumors.

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

RefSeq proteins (2): NP_001335187, NP_689491* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (4 total): chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRU2-F1	71.23	0.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, BEIER_GLIOMA_STEM_CELL_DN, MYOD_01, GOBP_NEGATIVE_REGULATION_OF_NF_KAPPAB_TRANSCRIPTION_FACTOR_ACTIVITY, OCT1_03, WONG_ENDMETRIUM_CANCER_DN, GOBP_NEGATIVE_REGULATION_OF_MOLECULAR_FUNCTION, AFP1_Q6, GFI1_01, USF_02, FREAC7_01

GO Biological Process (2): obsolete negative regulation of NF-kappaB transcription factor activity (GO:0032088), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

404 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEAL7	TCEAL1	Q15170	948
TCEAL7	BEX3	Q00994	896
TCEAL7	TCEAL5	Q5H9L2	578
TCEAL7	TCEAL3	Q969E4	449
TCEAL7	TCEAL4	Q96EI5	449
TCEAL7	BEX4	Q9NWD9	433
TCEAL7	BEX5	Q5H9J7	402
TCEAL7	TCEAL2	Q9H3H9	399
TCEAL7	BEX2	Q9BXY8	356
TCEAL7	BEX1	Q9HBH7	355
TCEAL7	CCDC126	Q96EE4	307
TCEAL7	TCEANC2	Q96MN5	302
TCEAL7	ARMCX1	Q9P291	274
TCEAL7	RAB9B	Q9NP90	269
TCEAL7	KLHL40	Q2TBA0	252

IntAct

4 interactions, top by confidence:

A	B	Type	Score
TCEAL7	LACTB	psi-mi:“MI:0915”(physical association)	0.400
TCEAL7	CSNK2B	psi-mi:“MI:0915”(physical association)	0.370
TCEAL7	DHX16	psi-mi:“MI:0914”(association)	0.350

BioGRID (23): TCEAL7 (Proximity Label-MS), PRRC2A (Affinity Capture-MS), ZAK (Affinity Capture-MS), ZC3H13 (Affinity Capture-MS), GTF2F2 (Affinity Capture-MS), DHX16 (Affinity Capture-MS), ARGLU1 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), ESF1 (Affinity Capture-MS), TCEB3 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RP9 (Affinity Capture-MS), NEK2 (Affinity Capture-MS), NEMF (Affinity Capture-MS), UTP18 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVZ2, A1ANL2, A3KGA4, A6X972, A8FCS8, B0C118, B2IUW7, B3DZB3, B4U2P9, B8DCF0, C0H3Q9, C0HJJ3, C1L1X9, C4L552, C6BYN6, D3ZT37, O13916, O34800, O59835, O68946, P0ADX5, P0ADX6, P11191, P13313, P13328, P22385, P25337, P41321, P42320, P56618, P67356, P67357, P71080, Q07927, Q09375, Q0TBK7, Q138N7, Q1R4Z6, Q24475, Q37928

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

362 predictions. Top by Δscore:

Variant	Effect	Δscore
X:103331376:GA:G	acceptor_gain	1.0000
X:103330295:G:T	donor_gain	0.9900
X:103330918:T:TA	acceptor_gain	0.9900
X:103330924:T:A	acceptor_gain	0.9900
X:103330972:T:TA	acceptor_gain	0.9900
X:103331364:A:AG	acceptor_gain	0.9900
X:103331365:T:G	acceptor_gain	0.9900
X:103331375:A:AG	acceptor_gain	0.9900
X:103331376:G:GG	acceptor_gain	0.9900
X:103331376:G:GT	acceptor_loss	0.9900
X:103331376:GAGTT:G	acceptor_gain	0.9900
X:103330299:G:GT	donor_gain	0.9800
X:103331376:GAGT:G	acceptor_gain	0.9800
X:103331374:TAGAG:T	acceptor_gain	0.9700
X:103330301:AGAGG:A	donor_loss	0.9600
X:103330303:AG:A	donor_loss	0.9600
X:103330304:G:GT	donor_loss	0.9600
X:103330305:GTAA:G	donor_loss	0.9600
X:103330919:G:A	acceptor_gain	0.9600
X:103330302:GAG:G	donor_gain	0.9500
X:103330973:G:A	acceptor_gain	0.9500
X:103331375:AGAG:A	acceptor_gain	0.9500
X:103331376:G:C	acceptor_gain	0.9500
X:103330921:AGCT:A	acceptor_gain	0.9400
X:103330922:GCTG:G	acceptor_gain	0.9400
X:103331374:TAG:T	acceptor_gain	0.9400
X:103331375:AGA:A	acceptor_gain	0.9400
X:103330295:G:GT	donor_gain	0.9300
X:103330968:T:A	acceptor_gain	0.9300
X:103331036:CACAG:C	donor_loss	0.9300

AlphaMissense

675 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:103331545:T:C	F48L	0.953
X:103331547:T:A	F48L	0.953
X:103331547:T:G	F48L	0.953
X:103331643:A:C	R80S	0.917
X:103331643:A:T	R80S	0.917
X:103331550:A:C	K49N	0.895
X:103331550:A:T	K49N	0.895
X:103331546:T:C	F48S	0.888
X:103331639:T:C	L79P	0.873
X:103331630:T:C	I76T	0.861
X:103331525:T:A	L41Q	0.846
X:103331650:T:C	F83L	0.846
X:103331652:T:A	F83L	0.846
X:103331652:T:G	F83L	0.846
X:103331642:G:T	R80I	0.842
X:103331549:A:T	K49I	0.835
X:103331517:A:C	R38S	0.819
X:103331517:A:T	R38S	0.819
X:103331642:G:C	R80T	0.814
X:103331525:T:C	L41P	0.810
X:103331513:T:C	F37S	0.808
X:103331512:T:C	F37L	0.805
X:103331514:T:A	F37L	0.805
X:103331514:T:G	F37L	0.805
X:103331651:T:C	F83S	0.774
X:103331546:T:G	F48C	0.765
X:103331525:T:G	L41R	0.749
X:103331528:T:C	L42P	0.747
X:103331639:T:A	L79Q	0.731
X:103331554:G:C	D51H	0.730

dbSNP variants (sampled 300 via entrez): RS1000309013 (X:103329419 C>T), RS1003275773 (X:103331991 T>C), RS1004289731 (X:103329158 C>T), RS1004360232 (X:103328350 C>A), RS1007830725 (X:103332463 A>G), RS1007874775 (X:103332602 C>T), RS1008038767 (X:103330841 A>G), RS1008175998 (X:103330329 T>C), RS1010645492 (X:103332409 G>C), RS1011450513 (X:103332132 A>C,G), RS1012158066 (X:103331918 A>G), RS1013785636 (X:103329674 G>T), RS1014885928 (X:103331065 CTG>C), RS1015764815 (X:103328780 T>C), RS1015856330 (X:103328381 T>C)

Disease associations

OMIM: gene MIM:300771 | 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

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
Particulate Matter	decreases expression, increases abundance, increases expression	3
Air Pollutants	decreases expression, increases abundance, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
methylmercuric chloride	increases expression	1
bisphenol A	increases expression	1
lead acetate	affects cotreatment, increases expression	1
sodium arsenate	increases abundance, increases expression	1
trichostatin A	affects cotreatment, decreases expression	1
arsenite	increases methylation	1
sodium arsenite	affects cotreatment, increases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, decreases expression, affects cotreatment	1
dorsomorphin	decreases expression, affects cotreatment, increases expression	1
MRK 003	decreases expression	1
Temozolomide	decreases expression	1
Arsenic	increases abundance, increases expression	1
Clorgyline	increases expression	1
Cytarabine	increases expression	1
Nickel	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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