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LINC01488 long intergenic non-protein coding RNA 1488 [ Homo sapiens (human) ]

Gene ID: 101928292, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01488provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1488provided by HGNC
Primary source
HGNC:HGNC:51144
See related
MIM:617696; AllianceGenome:HGNC:51144
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
BRCAT8; CUPID1
Expression
Restricted expression toward liver (RPKM 3.0) See more
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Genomic context

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Location:
11q13.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (69481663..69493210)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (69498779..69510326)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (69300329..69308311)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902703 Neighboring gene long intergenic non-protein coding RNA 2952 Neighboring gene GATA motif-containing MPRA enhancer 291 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69270026-69270770 Neighboring gene NANOG hESC enhancer GRCh37_chr11:69276040-69276608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69278453-69279186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69289663-69290348 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:69290349-69291033 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:69291034-69291718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69291719-69292403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69295265-69296231 Neighboring gene long intergenic non-protein coding RNA 2747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69299754-69300291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69300292-69300830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69304402-69305070 Neighboring gene VISTA enhancer hs1920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69314370-69314904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69316310-69316810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69324803-69325431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69325432-69326060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69328322-69328822 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69335476-69336233 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69336234-69336990 Neighboring gene MPRA-validated peak1326 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69350505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69351691-69352192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69352193-69352692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69353440-69354100 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69354185 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69367118 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69370584 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69371642 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69375393 Neighboring gene Sharpr-MPRA regulatory region 10534 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:69388143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69390821-69391383 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:69407786-69408985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69415650-69416150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69416151-69416651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69430076-69430934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69452808-69453748 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:69453749-69454687 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:69456195-69456897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69458416-69459160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69462137-69462880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69463625-69464368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69469698-69470635 Neighboring gene uncharacterized LOC124902704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69472515-69473242 Neighboring gene cyclin D1

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. A Novel Long Non-Coding RNA-01488 Suppressed Metastasis and Tumorigenesis by Inducing miRNAs That Reduce Vimentin Expression and Ubiquitination of Cyclin E. Lin SL, et al. Cells, 2020 Jun 20. PMID 32575745, Free PMC Article
  2. Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage. Betts JA, et al. Am J Hum Genet, 2017 Aug 3. PMID 28777932, Free PMC Article
  3. A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. Ahsan H, et al. Cancer Epidemiol Biomarkers Prev, 2014 Apr. PMID 24493630, Free PMC Article

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
A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age.
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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Other Names

  • CCND1-upstream intergenic DNA repair 1
  • breast cancer-associated transcript 8

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_120542.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AP000439

  2. NR_120543.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 3' region, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AP000439

  3. NR_120544.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' region, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AP000439

  4. NR_120545.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two alternate exons in the 5' region, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AP000439

  5. NR_185868.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  6. NR_185869.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  7. NR_185870.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  8. NR_185871.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  9. NR_185872.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  10. NR_185873.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  11. NR_185875.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  12. NR_185876.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

  13. NR_185878.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000439

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    69481663..69493210
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    69498779..69510326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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