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LINC01258 long intergenic non-protein coding RNA 1258 [ Homo sapiens (human) ]

Gene ID: 101928776, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01258provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1258provided by HGNC
Primary source
HGNC:HGNC:49898
See related
Ensembl:ENSG00000249534 AllianceGenome:HGNC:49898
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 LINC01258 in Genome Data Viewer
Location:
4p14
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (38420662..38523180, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (38389704..38492227, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (38422283..38524801, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374409 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:38282548-38282707 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21431 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:38319550-38320050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:38320051-38320551 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:38359157-38359381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21432 Neighboring gene long intergenic non-protein coding RNA 2513 Neighboring gene Sharpr-MPRA regulatory region 4229 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:38426307-38426839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:38478457-38478956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21436 Neighboring gene long intergenic non-protein coding RNA 1259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21439 Neighboring gene long intergenic non-protein coding RNA 2278 Neighboring gene KLF3-I enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38623749-38624601 Neighboring gene KLF3 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79844 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79852 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79860 Neighboring gene KLF3-II enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15359 Neighboring gene KLF3 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15362 Neighboring gene KLF transcription factor 3

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. 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
  2. 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

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_110951.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC106893, AK057434
    Related
    ENST00000512517.1

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    38420662..38523180 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    38389704..38492227 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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