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GAPLINC gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNA [ Homo sapiens (human) ]

Gene ID: 100505592, updated on 10-Oct-2023

Summary

Official Symbol
GAPLINCprovided by HGNC
Official Full Name
gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNAprovided by HGNC
Primary source
HGNC:HGNC:51308
See related
Ensembl:ENSG00000266835 AllianceGenome:HGNC:51308
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
LINC01540
Expression
Biased expression in placenta (RPKM 2.1), lung (RPKM 1.0) and 7 other tissues See more
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Genomic context

See GAPLINC in Genome Data Viewer
Location:
18p11.31
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (3466250..3478978)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (3625722..3638452)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (3466248..3478976)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3425706-3426206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3426207-3426707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:3433772-3434272 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:3434707-3434917 Neighboring gene uncharacterized LOC124904237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9254 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3448381-3449002 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3449003-3449622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:3452109-3452730 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3452731-3453350 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:3451487-3452108 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:3455215-3455834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:3457616-3458176 Neighboring gene uncharacterized LOC105371965 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:3466751-3467438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:3469136-3469926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13048 Neighboring gene TGFB induced factor homeobox 1 Neighboring gene Sharpr-MPRA regulatory region 485 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:3554877-3555427 Neighboring gene small nucleolar RNA U13 Neighboring gene DLG associated protein 1 Neighboring gene RNA, 7SL, cytoplasmic 39, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog

General gene information

Other Names

  • RP11-838N2.4
  • TCONS_00026238
  • gastric adenocarcinoma predictive long intergenic noncoding RNA
  • lncRNA-uc002kmd.1
  • long intergenic non-protein coding RNA 1540

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_110428.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site and is shorter than variant 1.
    Source sequence(s)
    BM782281, BX107736
  2. NR_110429.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is the longer transcript.
    Source sequence(s)
    AJ707365, AP001025
    Related
    ENST00000581442.5

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    3466250..3478978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    3625722..3638452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)