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LINC01630 long intergenic non-protein coding RNA 1630 [ Homo sapiens (human) ]

Gene ID: 100287225, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01630provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1630provided by HGNC
Primary source
HGNC:HGNC:52295
See related
Ensembl:ENSG00000227115 AllianceGenome:HGNC:52295
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Low expression observed in reference dataset See more
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Genomic context

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See LINC01630 in Genome Data Viewer
Location:
18q21.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (51392042..51562469)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (51593780..51765428)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (48918412..49088839)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 125 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:48722055-48722676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9468 Neighboring gene mex-3 RNA binding family member C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9469 Neighboring gene RNA, U1 small nuclear 46, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:48943905-48944452 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:48947785-48948559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13331 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:48952779-48953978 Neighboring gene neuroepithelial cell transforming 1 pseudogene Neighboring gene SS18 like 2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13333 Neighboring gene small nucleolar RNA U13 Neighboring gene ribosomal L24 domain containing 1 pseudogene 9 Neighboring gene uncharacterized LOC105372120 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:49180808-49181646

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. Misregulation of the dependence receptor DCC and its upstream lincRNA, LOC100287225, in colorectal cancer. Kazemzadeh M, et al. Tumori, 2017 Jan 21. PMID 26429648
  2. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

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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Clone Names

  • FLJ37617

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_040074.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) defines the longer locus extent.
    Source sequence(s)
    AC011260, AC109315

  2. NR_040075.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has the same first exon as variant 1, and represents a novel second exon and 3' end.
    Source sequence(s)
    AC109315
    Related
    ENST00000578152.5

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
    51392042..51562469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    51593780..51765428
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases