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LINC01269 long intergenic non-protein coding RNA 1269 [ Homo sapiens (human) ]

Gene ID: 103695436, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01269provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1269provided by HGNC
Primary source
HGNC:HGNC:50325
See related
Ensembl:ENSG00000258689 AllianceGenome:HGNC:50325
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HNSCAT1; PARLncRNA-1
Expression
Biased expression in esophagus (RPKM 3.7), gall bladder (RPKM 0.7) and 1 other tissue See more
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Genomic context

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See LINC01269 in Genome Data Viewer
Location:
14q24.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (70698698..70712153)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (64904696..64918153)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (71165415..71178870)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 77, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8655 Neighboring gene TTC9 divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:71102515-71103714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5889 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:71120238-71120824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8658 Neighboring gene tetratricopeptide repeat domain 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:71133100-71133600 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:71133601-71134101 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:71164525-71165724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8661 Neighboring gene mitogen-activated protein kinase kinase kinase 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:71208701-71209202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5891 Neighboring gene MAP3K9 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 11364/13366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5892 Neighboring gene uncharacterized LOC124903341

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The Long Noncoding Transcript HNSCAT1 Activates KRT80 and Triggers Therapeutic Efficacy in Head and Neck Squamous Cell Carcinoma. Zhao Y, et al. Oxid Med Cell Longev, 2022. PMID 35965679, Free PMC Article
  2. Large-Scale Profiling on lncRNAs in Human Platelets: Correlation with Platelet Reactivity. Sun Y, et al. Cells, 2022 Jul 21. PMID 35883699, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

GeneRIFs: Gene References Into Functions

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

General gene information

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Other Names

  • head and neck squamous carcinoma associated transcript 1
  • platelet activation-related lncRNA 1

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_125769.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC004816
    Related
    ENST00000553682.1

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    70698698..70712153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    64904696..64918153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases