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LINC00312 long intergenic non-protein coding RNA 312 [ Homo sapiens (human) ]

Gene ID: 29931, updated on 10-Oct-2023

Summary

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Official Symbol
LINC00312provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 312provided by HGNC
Primary source
HGNC:HGNC:6662
See related
MIM:610485; AllianceGenome:HGNC:6662
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NAG7; ERR10; NAG-7; ERR-10; LMCD1DN; LOH3CR2A; NCRNA00312
Summary
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. [provided by RefSeq, Mar 2017]
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Genomic context

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See LINC00312 in Genome Data Viewer
Location:
3p25.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (8571782..8574668)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (8563123..8566009)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (8613468..8616354)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8061875-8062376 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:8082288-8083487 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8155298-8155871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:8270919-8271420 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:8271421-8271920 Neighboring gene LMCD1 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:8361398-8362597 Neighboring gene uncharacterized LOC107986010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8413440-8413972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8413973-8414503 Neighboring gene RNA, U4atac small nuclear 17, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8453270-8453770 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:8482473-8482990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:8497791-8498357 Neighboring gene Sharpr-MPRA regulatory region 2381 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8540163-8541096 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8541097-8542030 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:8577298-8578266 Neighboring gene uncharacterized LOC107986009 Neighboring gene LIM and cysteine rich domains 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8652364-8653245 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8653246-8654126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8664536-8665156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14028 Neighboring gene ssu-2 homolog Neighboring gene olfactory receptor family 7 subfamily E member 122 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Long non-coding RNA Linc00312 modulates the sensitivity of ovarian cancer to cisplatin via the Bcl-2/Caspase-3 signaling pathway. Zhang C, et al. Biosci Trends, 2018 Jul 17. PMID 29952351
  2. Identification of dysregulated long non-coding RNAs/microRNAs/mRNAs in TNM I stage lung adenocarcinoma. Tian Z, et al. Oncotarget, 2017 Aug 1. PMID 28881680, Free PMC Article
  3. Expression of LINC00312, a long intergenic non-coding RNA, is negatively correlated with tumor size but positively correlated with lymph node metastasis in nasopharyngeal carcinoma. Zhang W, et al. J Mol Histol, 2013 Oct. PMID 23529758
  4. Effects of NPC-associated gene NAG7 on cell cycle and apoptosis in nasopharyngeal carcinoma cells. Tan C, et al. Ai Zheng, 2002 May. PMID 12452030
  5. Proteomic analysis of differential protein expression in human nasopharyngeal carcinoma cells induced by NAG7 transfection. Tan C, et al. Proteomics, 2002 Mar. PMID 11921446

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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
    Title: LINC00312 represses proliferation and metastasis of colorectal cancer cells by regulation of miR-21.
  2. LINC00312 induced migration, invasion and VM of lung cancer cells by direct binding to the transcription factor Y-Box Binding Protein 1 (YBX1).
    Title: The long noncoding RNA LINC00312 induces lung adenocarcinoma migration and vasculogenic mimicry through directly binding YBX1.
  3. Expression of Linc00312 down-regulated significantly in chemo-resistant serous epithelial ovarian cancer tissues and in SKOV3/DDP cells.
    Title: Long non-coding RNA Linc00312 modulates the sensitivity of ovarian cancer to cisplatin via the Bcl-2/Caspase-3 signaling pathway.
  4. 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.
    Title: Identification of long non-coding RNA 00312 and 00673 in human NSCLC tissues.
  5. HOXA5 could bind in the promoter of linc00312 and up-regulated the expression of it.
    Title: Long non-coding RNA 00312 regulated by HOXA5 inhibits tumour proliferation and promotes apoptosis in Non-small cell lung cancer.
  6. LINC00312 inhibited bladder cancer cell invasion and metastasis through mediating miR-197-3p.
    Title: LINC00312 inhibits the migration and invasion of bladder cancer cells by targeting miR-197-3p.
  7. Expression of LINC00312 is negatively correlated with tumor size but positively correlated with lymph node metastasis in nasopharyngeal carcinoma.
    Title: Expression of LINC00312, a long intergenic non-coding RNA, is negatively correlated with tumor size but positively correlated with lymph node metastasis in nasopharyngeal carcinoma.
  8. 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.
    Title: NAG7 promotes human nasopharyngeal carcinoma invasion through inhibition of estrogen receptor alpha and up-regulation of JNK2/AP-1/MMP1 pathways.
  9. 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.
    Title: Expression of tumor related genes NGX6, NAG-7, BRD7 in gastric and colorectal cancer.
  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.
    Title: Effects of NPC-associated gene NAG7 on cell cycle and apoptosis in nasopharyngeal carcinoma cells.
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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • LMCD1 downstream neighbor
  • estrogen receptor repressor 10
  • loss of heterozygosity, 3, chromosomal region 2, gene A
  • nasopharyngeal carcinoma candidate 7

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_024065.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087859

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    8571782..8574668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    8563123..8566009
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_013343.1: Suppressed sequence

    Description
    NM_013343.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version

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