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... See more...

Aliases for LINC00312 Gene

Subcategory (RNA class) for LINC00312 Gene

lncRNA

Aliases for LINC00312 Gene

External Ids for LINC00312 Gene

Previous HGNC Symbols for LINC00312 Gene

  • LOH3CR2A
  • NCRNA00312

Previous GeneCards Identifiers for LINC00312 Gene

  • GC03P008613

Summaries for LINC00312 Gene

Entrez Gene Summary for LINC00312 Gene

  • 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]

GeneCards Summary for LINC00312 Gene

LINC00312 (Long Intergenic Non-Protein Coding RNA 312) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with LINC00312 include Nasopharyngeal Carcinoma and Thyroid Carcinoma.

Additional gene information for LINC00312 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LINC00312 Gene

Genomics for LINC00312 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LINC00312 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J008571 Enhancer 0.5 Ensembl dbSUPER 258.6 -0.4 -380 2 SPI1 ZNF16 LINC00312 HSALNG0023974 SETD5 LMCD1-AS1 LMCD1 RAD18 CAV3 piR-58960
GH03J008573 Enhancer 0.9 Ensembl ENCODE dbSUPER 8.4 +4.0 3979 5 MAFF ZNF316 FOSL1 ZBTB40 MAFK MAFG BHLHE40 ATF3 FOS CEBPB lnc-SSUH2-8 LINC00312 HSALNG0023974 ENSG00000224884 LMCD1-AS1 LOC107986009 LMCD1 CAV3
GH03J008558 Enhancer 1 Ensembl ENCODE dbSUPER 6.6 -10.8 -10792 4.8 ARNT VEZF1 TAL1 FOSL1 HDAC2 STAT5A TCF12 SCRT1 MTA2 TEAD4 LMCD1-AS1 LMCD1 LINC00312 piR-58960 HSALNG0023964 CAV3
GH03J008538 Enhancer 0.9 Ensembl ENCODE dbSUPER 5.7 -31.8 -31833 2.9 MAFF ZNF316 MAFG ATF4 BHLHE40 MAFK CEBPB FOS NR2F2 EMSY LMCD1-AS1 LINC00312 HSALNG0023964 LMCD1 CAV3
GH03J008581 Enhancer 0.3 dbSUPER 7.8 +10.2 10189 1.9 ZNF316 MAFK LINC00312 lnc-SSUH2-8 ENSG00000224884 LOC107986009 LMCD1-AS1 LMCD1 CAV3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINC00312 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for LINC00312 Gene

Latest Assembly
chr3:8,571,781-8,574,668
(GRCh38/hg38)
Size:
2,888 bases
Orientation:
Plus strand

Previous Assembly
chr3:8,613,468-8,616,354
(GRCh37/hg19 by Entrez Gene)
Size:
2,887 bases
Orientation:
Plus strand

Genomic View for LINC00312 Gene

Genes around LINC00312 on UCSC Golden Path with GeneCards custom track
LINC00312 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
LINC00312 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINC00312 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINC00312 Gene

Proteins for LINC00312 Gene

  • Protein details for LINC00312 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y6C7-L3R2A_HUMAN
    Recommended name:
    Putative uncharacterized protein encoded by LINC00312
    Protein Accession:
    Q9Y6C7

    Protein attributes for LINC00312 Gene

    Size:
    94 amino acids
    Molecular mass:
    11024 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LINC00312 Gene

Post-translational modifications for LINC00312 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINC00312 Gene

Domains & Families for LINC00312 Gene

Gene Families for LINC00312 Gene

Protein Domains for LINC00312 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for LINC00312 Gene

GenScript: Design optimal peptide antigens:
  • Loss of heterozygosity 3 chromosomal region 2 gene A protein (L3R2A_HUMAN)
genes like me logo Genes that share domains with LINC00312: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LINC00312 Gene

Function for LINC00312 Gene

Phenotypes From GWAS Catalog for LINC00312 Gene

Phenotypes for LINC00312 Gene

genes like me logo Genes that share phenotypes with LINC00312: view

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LINC00312 Gene

Localization for LINC00312 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LINC00312 gene
Compartment Confidence
extracellular 1
cytoskeleton 1
nucleus 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for LINC00312 Gene

Pathways & Interactions for LINC00312 Gene

PathCards logo

SuperPathways for LINC00312 Gene

No Data Available

Interacting Proteins for LINC00312 Gene

Gene Ontology (GO) - Biological Process for LINC00312 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LINC00312 Gene

Drugs & Compounds for LINC00312 Gene

No Compound Related Data Available

Transcripts for LINC00312 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for LINC00312 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS00008B8B78_9606 lncRNA 2887 3

RefSeq: NR_024065,

LNCipedia: LINC00312:3,

NONCODE: NONHSAT087716.2,

URS0000EC0212_9606 lncRNA 2888 1

LncBook: HSALNT0289326,

URS0001BF73C8_9606 lncRNA 2887 1

LncBook: HSALNT0289326,

URS00008B916B_9606 lncRNA 2113 1

LNCipedia: LINC00312:2,

URS0000003CB3_9606 lncRNA 2094 1

LNCipedia: LINC00312:1,

LINC00312 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for LINC00312 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :

CRISPR products for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LINC00312

Alternative Splicing Database (ASD) splice patterns (SP) for LINC00312 Gene

No ASD Table

Relevant External Links for LINC00312 Gene

GeneLoc Exon Structure for
LINC00312

Expression for LINC00312 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LINC00312 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LINC00312

SOURCE GeneReport for Unigene cluster for LINC00312 Gene:

Hs.433151
genes like me logo Genes that share expression patterns with LINC00312: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LINC00312 Gene

Orthologs for LINC00312 Gene

No data available for Orthologs and Evolution for LINC00312 Gene

Paralogs for LINC00312 Gene

No data available for Paralogs for LINC00312 Gene

Variants for LINC00312 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LINC00312 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LINC00312 Gene

Variant ID Type Subtype PubMed ID
esv3595218 CNV loss 21293372
nsv1011096 CNV loss 25217958

Additional Variant Information for LINC00312 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINC00312

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for LINC00312 Gene

Disorders for LINC00312 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LINC00312 Gene - From: LNC, COP, and GCD

Disorder Aliases PubMed IDs
nasopharyngeal carcinoma
  • npca
thyroid carcinoma
  • thyroid cancer
bladder cancer
  • bladder cancer, somatic
lung cancer
  • lung cancer, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LINC00312

genes like me logo Genes that share disorders with LINC00312: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LINC00312 Gene

Publications for LINC00312 Gene

  1. Effects of NPC-associated gene NAG7 on cell cycle and apoptosis in nasopharyngeal carcinoma cells. (PMID: 12452030) Tan C … Li GY (Ai zheng = Aizheng = Chinese journal of cancer 2002) 2 3 23 74
  2. 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. (PMID: 23529758) Zhang W … Li G (Journal of molecular histology 2013) 2 3 74
  3. Expression of tumor related genes NGX6, NAG-7, BRD7 in gastric and colorectal cancer. (PMID: 12918109) Zhang XM … Li J (World journal of gastroenterology 2003) 2 3 23
  4. Long non-coding RNA 00312 regulated by HOXA5 inhibits tumour proliferation and promotes apoptosis in Non-small cell lung cancer. (PMID: 28338293) Zhu Q … Song Y (Journal of cellular and molecular medicine 2017) 3 74
  5. Identification of long non-coding RNA 00312 and 00673 in human NSCLC tissues. (PMID: 28849087) Tan Q … Tu J (Molecular medicine reports 2017) 3 74

Products for LINC00312 Gene

Sources for LINC00312 Gene