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    LINC00513 long intergenic non-protein coding RNA 513 [ Homo sapiens (human) ]

    Gene ID: 100506860, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC00513provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 513provided by HGNC
    Primary source
    HGNC:HGNC:43566
    See related
    Ensembl:ENSG00000233559 AllianceGenome:HGNC:43566
    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
    Biased expression in colon (RPKM 1.7), kidney (RPKM 0.7) and 10 other tissues See more
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    Genomic context

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    See LINC00513 in Genome Data Viewer
    Location:
    7q32.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (130913464..130921946)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (132230974..132239461)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (130598223..130606705)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130571236-130572435 Neighboring gene Sharpr-MPRA regulatory region 2521 Neighboring gene long intergenic non-protein coding RNA, p53 induced transcript Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:130588151-130589350 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr7:130595421-130595954 and GRCh37_chr7:130595955-130596488 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:130597482-130598681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18651 Neighboring gene microRNA 29b-1 Neighboring gene microRNA 29a Neighboring gene ReSE screen-validated silencer GRCh37_chr7:130635654-130635822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26659 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130644756-130645955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26664 Neighboring gene Sharpr-MPRA regulatory region 13565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26667 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130729465 Neighboring gene Sharpr-MPRA regulatory region 6658 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130743720 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130743868 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 7:130744026 and 7:130744055 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130746088 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130750088 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130751957 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130751320 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130754812 Neighboring gene RNA, U6 small nuclear 1010, pseudogene Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130757740 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130758576 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130763709 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:130775512-130776367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:130792685-130793536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18657 Neighboring gene MKLN1 intron CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18660 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130848608-130849807 Neighboring gene muskelin 1 Neighboring gene MPRA-validated peak6722 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130872973-130874172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:130875573-130876331 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130880490 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130888388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26673 Neighboring gene MPRA-validated peak6724 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26675 Neighboring gene ribosomal protein L27 pseudogene 11

    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. Identification of LncRNA Linc00513 Containing Lupus-Associated Genetic Variants as a Novel Regulator of Interferon Signaling Pathway. Xue Z, et al. Front Immunol, 2018. PMID 30619325, Free PMC Article
    2. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Liu SJ, et al. Science, 2017 Jan 6. PMID 27980086, Free PMC Article
    3. Transcriptome analysis of human gastric cancer. Oh JH, et al. Mamm Genome, 2005 Dec. PMID 16341674

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study data identify rs205764 and rs547311 functional promoter variants of linc00513 that contribute to increased level of linc00513 and confer susceptibility to systemic lupus erythematosus.
      Title: Identification of LncRNA Linc00513 Containing Lupus-Associated Genetic Variants as a Novel Regulator of Interferon Signaling Pathway.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    General gene information

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    Markers

    Clone Names

    • AC016831.7

    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_109780.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC016831, AW138292, BM763100
      Related
      ENST00000846181.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      130913464..130921946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      132230974..132239461
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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