LINC00312

Summary

LINC00312 (long intergenic non-protein coding RNA 312, HGNC:6662) is a long non-coding RNA gene on chromosome 3p25.3.

This gene produces an intronless transcript that is thought to function as a tumor suppressor. This transcript is downregulated in nasopharyngeal carcinoma and is a negative regulator of estrogen receptor signaling. A common polymorphism in this transcript allows the production of a 94 aa open reading frame in some individuals, which may interact directly with estrogen receptor 1 (PMID:15474036). This open reading frame does not exist on the reference genome haplotype, which is hypothesized to function through a non-coding RNA product.

Source: NCBI Gene 29931 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total — 1 pathogenic

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6662
Approved symbol	LINC00312
Name	long intergenic non-protein coding RNA 312
Location	3p25.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	NAG7, NAG-7, ERR10, ERR-10, LMCD1DN
OMIM	610485
Entrez	29931
RNAcentral	URS00008B8B78 — lncRNA, 2887 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Top tissues by expression

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

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 10)

• NAG7 gene re-expression could inhibit overproliferation of NPC cell by delaying the progression of G1 into S in cell cycle and inducing cell apoptosis. (PMID:12452030)
• Expression levels of NAG-7, and BRD7 did not alter in gastric and colorectal cancers. NAG-7 and BRD7 genes may not play role in gastric and colorectal carcinogenesis. (PMID:12918109)
• NAG7 plays a potential role in promoting nasopharyngeal carcinoma invasion by regulation of ERalpha and the H-ras/p-c-Raf and JNK2/AP-1/MMP1 signaling pathways. (PMID:19591174)
• Expression of LINC00312 is negatively correlated with tumor size but positively correlated with lymph node metastasis in nasopharyngeal carcinoma. (PMID:23529758)
• LINC00312 inhibited bladder cancer cell invasion and metastasis through mediating miR-197-3p. (PMID:27631965)
• HOXA5 could bind in the promoter of linc00312 and up-regulated the expression of it. (PMID:28338293)
• lncRNA 00312 may serve an important role in the tumorigenesis and deterioration of human NSCLC. Moreover, linc00673 is upregulated in LAD but not in LSCC tissues, implying that it can be a potential candidate tissue specific lncRNA for NSCLC. (PMID:28849087)
• Expression of Linc00312 down-regulated significantly in chemo-resistant serous epithelial ovarian cancer tissues and in SKOV3/DDP cells. (PMID:29952351)
• our results elucidate the role of the LINC00312-miR-21-PTEN axis in colorectal cancer (CRC) cell proliferation and tumour progression and may lead to new lncRNA-based diagnostics or therapeutics for CRC (PMID:30134003)
• LINC00312 induced migration, invasion and VM of lung cancer cells by direct binding to the transcription factor Y-Box Binding Protein 1 (YBX1). (PMID:30470227)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Putative uncharacterized protein encoded by LINC00312 — Q9Y6C7 (reviewed: Q9Y6C7)

Alternative names: Loss of heterozygosity 3 chromosomal region 2 gene A protein

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6C7-F1	61.67	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

4 interactions, top by confidence:

A	B	Type	Score
LINC00312	ESR1	psi-mi:“MI:0915”(physical association)	0.590
LINC00312	ESR1	psi-mi:“MI:0407”(direct interaction)	0.590
ESR1	LINC00312	psi-mi:“MI:0915”(physical association)	0.590
LINC00312	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440

ESM2 similar proteins: A0A023PZA4, A0A1D0BRC1, B1ANH7, B8NYW8, G2TRL6, O13513, O13544, O13553, O13913, O56124, O60756, O94143, P0C854, P0DTG0, P14588, P15099, P16759, P16802, P16835, P17148, P20969, P24274, P38309, P38320, P40057, P47003, P47162, P53211, P53342, P75202, P93284, P93299, Q02826, Q02918, Q04019, Q05612, Q06235, Q07649, Q54NT8, Q6GZT2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

3 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
1807781	GRCh37/hg19 3p26.3-25.3(chr3:61892-9769457)x1	Pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001666445 (3:8572379 G>A), RS1001995561 (3:8571990 G>A), RS1003403018 (3:8573680 C>T), RS1004126775 (3:8572114 T>C), RS1004193132 (3:8570667 G>A,C), RS1004289739 (3:8570986 G>A), RS1005195830 (3:8572092 A>G), RS1005290713 (3:8572470 C>A,T), RS1006291517 (3:8573986 T>C), RS1006413643 (3:8570526 C>T), RS1008348819 (3:8570204 T>G), RS1008963300 (3:8572240 T>C), RS1010029559 (3:8571219 A>C), RS1010138918 (3:8573602 T>C), RS1010860031 (3:8574675 G>T)

Disease associations

OMIM: gene MIM:610485 | 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

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	increases expression, affects expression, affects cotreatment	2
Silicon Dioxide	decreases expression, increases expression	2
Valproic Acid	increases expression	2
bisphenol F	decreases expression, affects cotreatment	1
bisphenol A	decreases methylation	1
trichostatin A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
potassium chromate(VI)	decreases expression	1
15-acetyldeoxynivalenol	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Dasatinib	increases expression	1
Benzo(a)pyrene	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Cytarabine	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Melphalan	increases expression	1
Progesterone	increases expression	1
Tamoxifen	affects cotreatment, decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Triclosan	increases expression	1
Vanadates	increases expression	1
Vitamin E	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Medroxyprogesterone Acetate	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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