BLACAT1

Summary

BLACAT1 (BLACAT1 overlapping LEMD1 locus, HGNC:48597) is a protein-coding gene on chromosome 1q32.1.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001397426

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48597
Approved symbol	BLACAT1
Name	BLACAT1 overlapping LEMD1 locus
Location	1q32.1
Locus type	gene with protein product
Status	Approved
Aliases	linc-UBC1, LINC00912, onco-lncRNA-30
Ensembl gene	ENSG00000281406
Ensembl biotype	protein_coding
OMIM	615480
Entrez	101669762

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 14 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000625854, ENST00000626538, ENST00000629113, ENST00000629624, ENST00000901442, ENST00000933960, ENST00000933961, ENST00000933962, ENST00000933963, ENST00000933964, ENST00000933965, ENST00000933966, ENST00000933967, ENST00000933968, ENST00000933969

RefSeq mRNA: 1 — MANE Select: NM_001397426 NM_001397426

CCDS: CCDS91151

Canonical transcript exons

ENST00000629624 — 2 exons

Exon	Start	End
ENSE00003773608	205434886	205441062
ENSE00003841541	205455917	205456045

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 79.58.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5328 / max 273.2724, expressed in 203 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
16995	1.4113	186
16993	0.1215	73

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	79.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.95	gold quality
cerebellar cortex	UBERON:0002129	75.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.63	gold quality
cerebellar hemisphere	UBERON:0002245	75.62	gold quality
cerebellum	UBERON:0002037	75.38	gold quality
ventricular zone	UBERON:0003053	74.34	gold quality
cortical plate	UBERON:0005343	72.57	gold quality
cerebellar vermis	UBERON:0004720	71.81	silver quality
corpus epididymis	UBERON:0004359	70.74	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	69.03	gold quality
lower esophagus mucosa	UBERON:0035834	67.81	gold quality
endothelial cell	CL:0000115	66.91	gold quality
left lobe of thyroid gland	UBERON:0001120	64.85	gold quality
right lobe of thyroid gland	UBERON:0001119	64.35	gold quality
thyroid gland	UBERON:0002046	63.99	gold quality
cauda epididymis	UBERON:0004360	62.64	gold quality
minor salivary gland	UBERON:0001830	61.44	gold quality
palpebral conjunctiva	UBERON:0001812	61.05	silver quality
pons	UBERON:0000988	59.40	silver quality
saliva-secreting gland	UBERON:0001044	59.38	gold quality
prefrontal cortex	UBERON:0000451	59.37	gold quality
nasal cavity epithelium	UBERON:0005384	59.15	gold quality
mouth mucosa	UBERON:0003729	59.06	gold quality
right uterine tube	UBERON:0001302	58.99	gold quality
esophagus mucosa	UBERON:0002469	58.94	gold quality
Brodmann (1909) area 23	UBERON:0013554	58.71	silver quality
primary visual cortex	UBERON:0002436	58.07	gold quality
nasal cavity mucosa	UBERON:0001826	57.31	gold quality
germinal epithelium of ovary	UBERON:0001304	56.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.76

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 25)

• Frequently overexpressed linc-UBC1 physically associates with PRC2 complex, and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer (PMID:23688781)
• Our study suggests that linc-UBC1 may represent a novel diagnostic, prognostic biomarker and a potential therapeutic target of gastric cancer (PMID:25755750)
• Mechanistic investigations demonstrated that BLACAT1 had a key role in G1/G0 arrest, and showed that BLACAT1 can repress p15 expression by binding to EZH2, thus contributing to the regulation of CRC cell cycle and proliferation. Our results suggest that BLACAT1, as a cell cycle regulator, may serve as a potential target for colon cancer prevention and treatment in human CRC (PMID:28277544)
• combining experiments of miR-144 and BLACAT1 indicated that miR-144 could reverse the function of BLACAT1 on nonsmall cell lung cancer (PMID:28885863)
• results indicate that linc-UBC1 is a novel oncogene in tumorigenesis and could promote the metastasis via EZH2 and E-cadherin in esophageal squamous cell carcinoma (PMID:29552776)
• our results conclude that BLACAT1 accelerates the oxaliplatin-resistance of gastric cancer via promoting ABCB1 protein expression by targeting miR-361, providing a novel insight for the chemoresistance of gastric cancer. (PMID:29710482)
• Study identified that BLACAT1 was upregulated in cisplatin (DDP)resistant nonsmall cell lung cancer (NSCLC) cells, and confirmed the interaction of lncRNA BLACAT1 and miR17. In addition, lncRNA BLACAT1 facilitated autophagy through the miR17/ATG7 signaling pathway, thus promoting chemoresistance of NSCLC cells. (PMID:30387831)
• LncRNA BLACAT1 contributes to the proliferation and migration of osteosarcoma cells by regulating STAT3 (PMID:30665678)
• the expression of BLACAT1 had no significant association with age (p = 0.92), gender (p = 0.55), and smoking (p = 0.62). CONCLUSION: High expression of lncRNA BLACAT1 may predict a poor prognosis in OS, TNM stage, tumor grade, and LNM. Its predictive roles were not significantly affected by age, gender, or smoking. Therefore, lncRNA BLACAT1 may serve as a promising predictor in cancer prognosis. (PMID:31061820)
• this study highlights the important roles of BLACAT1/miR-605-3p/VASP axis in glioma progression. (PMID:31093978)
• BLACAT1 is aberrantly upregulated in hepatocellular carcinoma (HCC) and its inhibition had tumor suppressing effects in human HCC, possibly through endogenously competing against has-miR-485-5p. (PMID:31174090)
• BLACAT1 is negatively associated with prognosis in patients with NSCLC and inhibits cell progression, metastasis and epithelial-mesenchymal transition through down-regulating Wnt/beta-catenin signaling pathway. (PMID:31364123)
• BLACAT1 knockdown enhanced radioresistance of head and neck squamous cell carcinoma cells via regulating PSEN1, exposing the probable target role of BLACAT1 in head and neck squamous cell carcinoma. This was the first time that the pivotal role of BLACAT1 was investigated in head and neck squamous cell carcinoma, which provided a novel therapeutic direction for head and neck squamous cell carcinoma patients. (PMID:31944856)
• Long non-coding RNA BLACAT1 inhibits prostate cancer cell proliferation through sponging miR-361. (PMID:31957820)
• LncRNA BLACAT1 Is Upregulated in Cervical Squamous Cell Carcinoma (CSCC) and Predicts Poor Survival. (PMID:32046460)
• Down-regulation of lncRNA BLACAT1 inhibits ovarian cancer progression by suppressing the Wnt/beta-catenin signaling pathway via regulating miR-519d-3p. (PMID:32095930)
• Linc-UBC1 stimulates the metastasis and progression of ovarian cancer via downregulating p53 level. (PMID:32096175)
• Expression and Diagnostic Value of lncRNA BLACAT1 in Peripheral Blood of Patients with Acute Myeloid Leukemia. (PMID:32255290)
• Transcription factor ZNF703 activates linc-UBC1 to stimulate the progression of glioma. (PMID:32271436)
• Effect of lncRNA-BLACAT1 on drug resistance of non-small cell lung cancer cells in DDP chemotherapy by regulating cyclin D1 expression. (PMID:33015788)
• LncRNA BLACAT1 Promotes Proliferation, Migration and Invasion of Prostate Cancer Cells via Regulating miR-29a-3p/DVL3 Axis. (PMID:33641528)
• Up-regulation of long non-coding RNA BLACAT1 predicts aggressive clinicopathologic characteristics and poor prognosis of glioma. (PMID:33725920)
• Yin Yang 1-stimulated long noncoding RNA bladder cancer-associated transcript 1 upregulation facilitates esophageal carcinoma progression via the microRNA-5590-3p/programmed cell death-ligand 1 pathway. (PMID:35435118)
• Role of BLACAT1 in IL-1beta-Induced Human Articular Chondrocyte Apoptosis and Extracellular Matrix Degradation via the miR-149-5p/ HMGCR Axis. (PMID:35657039)
• Urinary BLACAT1 as a non-invasive biomarker for bladder cancer. (PMID:36939965)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (1): A0A494BZU2

RefSeq proteins (1): NP_001384355* (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): ZBTB18_TARGET_GENES, SS18_SSX1_FUSION_UNIPROT_Q8IZH1_UNREVIEWED_TARGET_GENES, chr1q32, COLDREN_GEFITINIB_RESISTANCE_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

219 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:205441005:A:G	C8R	0.984
1:205441003:G:C	C8W	0.983
1:205440980:C:G	C16S	0.981
1:205440980:C:T	C16Y	0.981
1:205440981:A:T	C16S	0.981
1:205441016:A:G	F4S	0.981
1:205440979:G:C	C16W	0.980
1:205441009:G:C	F6L	0.979
1:205441009:G:T	F6L	0.979
1:205441011:A:G	F6L	0.979
1:205440981:A:G	C16R	0.978
1:205440982:G:C	F15L	0.978
1:205440982:G:T	F15L	0.978
1:205440984:A:G	F15L	0.978
1:205441015:G:C	F4L	0.978
1:205441015:G:T	F4L	0.978
1:205441017:A:G	F4L	0.978
1:205440999:A:G	C10R	0.977
1:205441004:C:T	C8Y	0.977
1:205440998:C:T	C10Y	0.976
1:205440997:A:C	C10W	0.975
1:205440983:A:G	F15S	0.973
1:205441010:A:G	F6S	0.971
1:205441000:G:C	F9L	0.966
1:205441000:G:T	F9L	0.966
1:205441002:A:G	F9L	0.966
1:205441016:A:C	F4C	0.959
1:205440998:C:G	C10S	0.950
1:205440999:A:T	C10S	0.950
1:205440976:T:A	K17N	0.949

dbSNP variants (sampled 300 via entrez): RS1000000971 (1:205444187 C>A,G), RS1000095534 (1:205444426 G>C,T), RS1000105702 (1:205444381 A>C), RS1000171642 (1:205442889 T>C), RS1000371276 (1:205449243 GA>G), RS1000404142 (1:205454626 G>A), RS1000835813 (1:205438231 G>A), RS1000852273 (1:205455858 G>A), RS1000911825 (1:205450008 C>T), RS1000983437 (1:205449830 T>C), RS1001567845 (1:205436936 G>A), RS1001595006 (1:205454813 C>A,T), RS1001673031 (1:205442711 C>T), RS1001766208 (1:205443112 G>C,T), RS1001857141 (1:205452395 C>T)

Disease associations

OMIM: gene MIM:615480 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008062_108	Blood urea nitrogen levels	6.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression	2
aristolochic acid I	increases expression	1
fluorene-9-bisphenol	increases expression	1
sotorasib	affects cotreatment, decreases expression	1
bisphenol A	decreases expression	1
trichostatin A	decreases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
monomethylarsonous acid	decreases expression	1
dimethylarsinous acid	decreases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Methapyrilene	decreases methylation	1
Phenylmercuric Acetate	decreases expression	1
Propofol	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
p-Chloromercuribenzoic Acid	decreases expression	1

Clinical trials (associated diseases)

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