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LINC01250 long intergenic non-protein coding RNA 1250 [ Homo sapiens (human) ]

Gene ID: 101927554, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01250provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1250provided by HGNC
Primary source
HGNC:HGNC:49844
See related
Ensembl:ENSG00000234423 AllianceGenome:HGNC:49844
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 LINC01250 in Genome Data Viewer
Location:
2p25.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (2895048..3126026, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (2905851..3140139, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (2898820..3129798, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15220 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:2775469-2775986 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2791409-2792013 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2792014-2792618 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2792619-2793223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2796071-2796790 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2796791-2797509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2841318-2841951 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:2845889-2846419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2854499-2855406 Neighboring gene uncharacterized LOC124905968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11106 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:2952587-2953786 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58239 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:3034172-3035371 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3038327-3038874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3066843-3067343 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3105730-3106514 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3108292-3108999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3112467-3113140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3118175-3118676 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3131179-3131343 Neighboring gene uncharacterized LOC107985840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3172751-3173696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3182069-3182826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3183585-3184342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3184343-3185098 Neighboring gene Sharpr-MPRA regulatory region 8446 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:3202367-3202905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3204190-3204746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15224 Neighboring gene MPRA-validated peak3584 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:3237853-3239052 Neighboring gene Sharpr-MPRA regulatory region 3808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15226 Neighboring gene EARP complex and GARP complex interacting protein 1 Neighboring gene VISTA enhancer hs1385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3284251-3284751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3289510-3290088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3290089-3290666 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3310431-3310601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3323251-3323862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3326607-3327134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3327135-3327662 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3358809-3358982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15228

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. White matter integrity as an intermediate phenotype: exploratory genome-wide association analysis in individuals at high risk of bipolar disorder. Sprooten E, et al. Psychiatry Res, 2013 Apr 30. PMID 23218918
  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
White matter integrity as an intermediate phenotype: exploratory genome-wide association analysis in individuals at high risk of bipolar disorder.
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_110228.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC011995, AC019118, AC074264
    Related
    ENST00000457478.1

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    2895048..3126026 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    2905851..3140139 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases