TUBE1

Summary

TUBE1 (tubulin epsilon 1, HGNC:20775) is a protein-coding gene on chromosome 6q21, encoding Tubulin epsilon chain (Q9UJT0). It is a selective cancer dependency (DepMap: 56.5% of cell lines).

This gene encodes a member of the tubulin superfamily. This protein localizes to the centriolar sub-distal appendages that are associated with the older of the two centrioles after centrosome duplication. This protein plays a central role in organization of the microtubules during centriole duplication. A pseudogene of this gene is found on chromosome 5.

Source: NCBI Gene 51175 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 66 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 56.5% of screened cell lines
• MANE Select transcript: NM_016262

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20775
Approved symbol	TUBE1
Name	tubulin epsilon 1
Location	6q21
Locus type	gene with protein product
Status	Approved
Aliases	dJ142L7.2, FLJ22589, TUBE
Ensembl gene	ENSG00000074935
Ensembl biotype	protein_coding
OMIM	607345
Entrez	51175

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 5 retained_intron, 5 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000368657, ENST00000368662, ENST00000441191, ENST00000603621, ENST00000603651, ENST00000603722, ENST00000604689, ENST00000604743, ENST00000604814, ENST00000604967, ENST00000605457, ENST00000856770, ENST00000856771, ENST00000937354, ENST00000956039

RefSeq mRNA: 1 — MANE Select: NM_016262 NM_016262

CCDS: CCDS5100

Canonical transcript exons

ENST00000368662 — 12 exons

Exon	Start	End
ENSE00001447692	112087410	112087482
ENSE00001956692	112070663	112071570
ENSE00003523823	112072758	112072898
ENSE00003537359	112084189	112084246
ENSE00003549928	112086556	112086608
ENSE00003562346	112075937	112076112
ENSE00003606979	112074710	112074850
ENSE00003646398	112071902	112072076
ENSE00003657301	112079633	112079754
ENSE00003679572	112076322	112076509
ENSE00003679984	112087233	112087306
ENSE00003683668	112081092	112081207

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 95.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.8164 / max 206.8422, expressed in 1796 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
75150	20.4204	1794
75151	0.3960	176

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	95.50	gold quality
cerebellar hemisphere	UBERON:0002245	95.35	gold quality
cerebellar cortex	UBERON:0002129	95.28	gold quality
oocyte	CL:0000023	95.06	gold quality
cerebellum	UBERON:0002037	94.58	gold quality
secondary oocyte	CL:0000655	93.84	gold quality
epithelial cell of pancreas	CL:0000083	93.78	gold quality
calcaneal tendon	UBERON:0003701	93.52	gold quality
body of uterus	UBERON:0009853	93.32	gold quality
right lobe of liver	UBERON:0001114	92.75	gold quality
cardiac muscle of right atrium	UBERON:0003379	91.96	gold quality
right atrium auricular region	UBERON:0006631	91.70	gold quality
cardiac atrium	UBERON:0002081	91.58	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.55	gold quality
right ovary	UBERON:0002118	91.53	gold quality
left ovary	UBERON:0002119	91.51	gold quality
apex of heart	UBERON:0002098	91.44	gold quality
liver	UBERON:0002107	91.27	gold quality
endocervix	UBERON:0000458	90.89	gold quality
heart left ventricle	UBERON:0002084	90.78	gold quality
spinal cord	UBERON:0002240	90.66	gold quality
body of pancreas	UBERON:0001150	90.58	gold quality
adrenal tissue	UBERON:0018303	90.56	gold quality
cardiac ventricle	UBERON:0002082	90.52	gold quality
heart	UBERON:0000948	90.41	gold quality
left ventricle myocardium	UBERON:0006566	90.27	gold quality
right uterine tube	UBERON:0001302	90.16	gold quality
tibial nerve	UBERON:0001323	90.13	gold quality
adenohypophysis	UBERON:0002196	90.02	gold quality
ovary	UBERON:0000992	89.91	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.40
E-GEOD-111727	no	240.62
E-GEOD-75367	no	184.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting TUBE1, 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-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-545-3P	99.95	70.74	2783
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-518A-5P	99.70	69.01	2209

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 56.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• EB1 recognizes the nucleotide state of tubulin in the microtubule lattice (PMID:19851462)
• Here, the authors report that centrioles in delta-tubulin and epsilon-tubulin null mutant human cells lack triplet microtubules and fail to undergo centriole maturation. (PMID:28906251)
• Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. (PMID:34355505)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tube1	ENSDARG00000096620
mus_musculus	Tube1	ENSMUSG00000019845
rattus_norvegicus	Tube1	ENSRNOG00000000598

Paralogs (23): TUBG2 (ENSG00000037042), TUBA3D (ENSG00000075886), TUBB1 (ENSG00000101162), TUBB4A (ENSG00000104833), TUBD1 (ENSG00000108423), TUBA1B (ENSG00000123416), TUBA4A (ENSG00000127824), TUBG1 (ENSG00000131462), TUBB2A (ENSG00000137267), TUBB2B (ENSG00000137285), TUBA3E (ENSG00000152086), TUBA1A (ENSG00000167552), TUBA1C (ENSG00000167553), TUBB8B (ENSG00000173213), TUBB6 (ENSG00000176014), TUBAL3 (ENSG00000178462), TUBA8 (ENSG00000183785), TUBB4B (ENSG00000188229), TUBB (ENSG00000196230), TUBA3C (ENSG00000198033), TUBA4B (ENSG00000243910), TUBB3 (ENSG00000258947), TUBB8 (ENSG00000261456)

Protein

Protein identifiers

Tubulin epsilon chain — Q9UJT0 (reviewed: Q9UJT0)

Alternative names: Epsilon-tubulin

All UniProt accessions (4): Q9UJT0, A0A0B4J2B9, S4R3K3, S4R424

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Found in a complex with TEDC1, TEDC2, TUBE1 and TUBD1.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Similarity. Belongs to the tubulin family.

RefSeq proteins (1): NP_057346* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000217	Tubulin	Family
IPR003008	Tubulin_FtsZ_GTPase	Domain
IPR004057	Epsilon_tubulin	Family
IPR008280	Tub_FtsZ_C	Homologous_superfamily
IPR017975	Tubulin_CS	Conserved_site
IPR018316	Tubulin/FtsZ_2-layer-sand-dom	Domain
IPR023123	Tubulin_C	Homologous_superfamily
IPR036525	Tubulin/FtsZ_GTPase_sf	Homologous_superfamily

Pfam: PF00091, PF03953

UniProt features (4 total): sequence conflict 2, chain 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UJT0-F1	89.07	0.73

Functional residue map

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

Ligand- & substrate-binding residues (1): 148–154

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 130 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GSE45365_NK_CELL_VS_CD11B_DC_UP, MODULE_453, GOCC_MICROTUBULE_ORGANIZING_CENTER, KOYAMA_SEMA3B_TARGETS_UP, GOCC_CENTROSOME, GOBP_MITOTIC_CELL_CYCLE, PEART_HDAC_PROLIFERATION_CLUSTER_DN, RFX1_02, ZHENG_BOUND_BY_FOXP3, MARSON_BOUND_BY_E2F4_UNSTIMULATED, ZHENG_FOXP3_TARGETS_IN_THYMUS_DN, GARY_CD5_TARGETS_UP, GOCC_PERICENTRIOLAR_MATERIAL

GO Biological Process (4): microtubule cytoskeleton organization (GO:0000226), mitotic cell cycle (GO:0000278), centrosome cycle (GO:0007098), microtubule-based process (GO:0007017)

GO Molecular Function (3): structural constituent of cytoskeleton (GO:0005200), GTP binding (GO:0005525), nucleotide binding (GO:0000166)

GO Cellular Component (6): pericentriolar material (GO:0000242), cytoplasm (GO:0005737), microtubule (GO:0005874), centrosome (GO:0005813), cytoskeleton (GO:0005856), microtubule cytoskeleton (GO:0015630)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoskeleton organization	2
cytoskeleton	2
cellular anatomical structure	2
microtubule-based process	1
cell cycle	1
mitotic nuclear division	1
cell cycle process	1
microtubule organizing center organization	1
cellular process	1
structural molecule activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
centrosome	1
intracellular anatomical structure	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
centriole	1
microtubule organizing center	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

3231 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TUBE1	CNTRL	Q7Z7A1	819
TUBE1	NIN	Q8N4C6	788
TUBE1	CEP170	Q5SW79	738
TUBE1	ODF2	Q5BJF6	732
TUBE1	SASS6	Q6UVJ0	701
TUBE1	CC2D2A	Q9P2K1	577
TUBE1	PLK4	O00444	576
TUBE1	TUBD1	Q9UJT1	576
TUBE1	CEP128	Q6ZU80	564
TUBE1	NINL	Q9Y2I6	526
TUBE1	CEP192	Q8TEP8	526
TUBE1	CPAP	Q9HC77	507
TUBE1	CEP135	Q66GS9	501
TUBE1	STIL	Q15468	494
TUBE1	POC5	Q8NA72	489

IntAct

10 interactions, top by confidence:

A	B	Type	Score
TUBE1	TEDC2	psi-mi:“MI:0914”(association)	0.530
FGL1	DNM1L	psi-mi:“MI:0914”(association)	0.350
DEF8	DPYSL4	psi-mi:“MI:0914”(association)	0.350
NPM1	RPS3A	psi-mi:“MI:0914”(association)	0.350
P2RY10	POTEF	psi-mi:“MI:0914”(association)	0.350
GPR182	METTL15	psi-mi:“MI:0914”(association)	0.350
GPR45	VWA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (32): TUBE1 (Affinity Capture-MS), TUBD1 (Affinity Capture-MS), C16orf59 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), C14orf80 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), TUBD1 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), C16orf59 (Affinity Capture-MS), C14orf80 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS), TUBE1 (Affinity Capture-MS)

ESM2 similar proteins: A1A4J7, A2CEI4, A2RV06, B2RYI0, E7F654, E7FAW3, E9QAM5, F1Q7Z7, F1QNV4, O01939, O75064, O75153, O95248, P97564, Q08CY4, Q0P4Q0, Q0VA04, Q1L908, Q1LXZ7, Q2YDW2, Q32PH0, Q3T1I9, Q3U1Y4, Q4JF28, Q5U249, Q61586, Q6GPP1, Q6PD24, Q6TEN6, Q6ZNJ1, Q6ZPE2, Q6ZPG2, Q6ZQA0, Q6ZTN6, Q764M6, Q7T006, Q7TMQ7, Q7ZVS8, Q80U56, Q861Y6

Diamond homologs: P04688, P18695, P23257, P23258, P23330, P25295, P32348, P34785, P34786, P34787, P38557, P38558, P42271, P49741, P53377, P54403, P54404, P54405, P83887, P83888, P86221, P90548, Q0VCD2, Q32KM1, Q39582, Q41807, Q41808, Q41874, Q4R7T7, Q55AR3, Q6DIM3, Q75A43, Q7Z9Z2, Q8HZV4, Q8SRD2, Q8VCK3, Q9GKK5, Q9NRH3, Q9R1K7, Q9UJT0

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
“vincaleukoblastine sulfate”	“down-regulates activity”	TUBE1	“chemical inhibition”
TUBE1	up-regulates	Microtubule_polimerization
KATNAL2	“down-regulates quantity by destabilization”	TUBE1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	47
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
155160	GRCh38/hg38 6q16.3-22.31(chr6:100054889-120488154)x1	Pathogenic

SpliceAI

1749 predictions. Top by Δscore:

Variant	Effect	Δscore
6:112071900:A:AC	donor_gain	1.0000
6:112071900:A:AT	donor_loss	1.0000
6:112071900:AC:A	donor_gain	1.0000
6:112071901:C:CC	donor_gain	1.0000
6:112071901:CC:C	donor_gain	1.0000
6:112071901:CCT:C	donor_gain	1.0000
6:112072047:C:CT	acceptor_gain	1.0000
6:112072047:C:T	acceptor_gain	1.0000
6:112072072:TTAAT:T	acceptor_gain	1.0000
6:112072073:TAAT:T	acceptor_gain	1.0000
6:112072075:AT:A	acceptor_gain	1.0000
6:112072076:TC:T	acceptor_loss	1.0000
6:112072077:C:A	acceptor_loss	1.0000
6:112072077:C:CC	acceptor_gain	1.0000
6:112072078:T:G	acceptor_loss	1.0000
6:112072796:T:A	donor_gain	1.0000
6:112072894:CCAAT:C	acceptor_gain	1.0000
6:112072895:CAAT:C	acceptor_gain	1.0000
6:112072895:CAATC:C	acceptor_gain	1.0000
6:112072897:ATCT:A	acceptor_loss	1.0000
6:112072898:TCTG:T	acceptor_loss	1.0000
6:112072899:C:CC	acceptor_gain	1.0000
6:112072899:CT:C	acceptor_loss	1.0000
6:112074851:C:CC	acceptor_gain	1.0000
6:112075932:ATTAC:A	donor_loss	1.0000
6:112075933:TTAC:T	donor_loss	1.0000
6:112075934:TA:T	donor_loss	1.0000
6:112075935:ACCTC:A	donor_loss	1.0000
6:112075936:C:T	donor_loss	1.0000
6:112076320:A:AC	donor_gain	1.0000

AlphaMissense

3147 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:112087271:A:G	W21R	0.999
6:112087271:A:T	W21R	0.999
6:112076497:C:T	G154E	0.998
6:112081093:A:G	W109R	0.998
6:112081093:A:T	W109R	0.998
6:112072033:A:G	W380R	0.997
6:112072033:A:T	W380R	0.997
6:112074850:G:C	S271R	0.997
6:112074850:G:T	S271R	0.997
6:112075938:T:G	S271R	0.997
6:112081188:T:A	E77V	0.997
6:112081207:C:G	A71P	0.997
6:112087269:C:A	W21C	0.997
6:112087269:C:G	W21C	0.997
6:112087303:C:A	G10V	0.997
6:112087303:C:T	G10D	0.997
6:112072797:C:A	G352V	0.996
6:112072800:C:A	R351I	0.996
6:112074757:G:C	S302R	0.996
6:112074757:G:T	S302R	0.996
6:112074759:T:G	S302R	0.996
6:112074834:C:G	G277R	0.996
6:112074834:C:T	G277R	0.996
6:112074841:T:A	R274S	0.996
6:112074841:T:G	R274S	0.996
6:112074842:C:G	R274T	0.996
6:112076385:A:C	N191K	0.996
6:112076385:A:T	N191K	0.996
6:112076503:C:T	G152E	0.996
6:112079746:C:T	G112D	0.996

dbSNP variants (sampled 300 via entrez): RS1000085628 (6:112089430 T>G), RS1000431472 (6:112082923 G>A), RS1000802493 (6:112075710 T>C), RS1000919012 (6:112083320 A>C,T), RS1000968420 (6:112075214 G>A), RS1001653673 (6:112078549 T>C,G), RS1001874389 (6:112077213 C>T), RS1001883373 (6:112084457 A>G), RS1001936459 (6:112078887 C>T), RS1002140771 (6:112070181 C>G,T), RS1002334645 (6:112084137 T>C,G), RS1002390813 (6:112076850 G>A,T), RS1002540482 (6:112080536 T>C), RS1002808664 (6:112073321 T>A), RS1003119907 (6:112086937 T>C,G)

Disease associations

OMIM: gene MIM:607345 | 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

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	4
Aflatoxin B1	affects expression, decreases expression, decreases methylation	3
sodium arsenite	decreases expression, increases expression	2
Air Pollutants	increases abundance, increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression	2
Hydrogen Peroxide	affects expression, decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	affects expression	1
methylparaben	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
K 7174	increases expression	1
ICG 001	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
jinfukang	decreases expression	1
prothioconazole	increases expression	1
NSC668394	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Gemcitabine	increases expression	1
Ampicillin	decreases expression	1
Dimethyl Sulfoxide	increases expression	1

Clinical trials (associated diseases)

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