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    LINC01619 long intergenic non-protein coding RNA 1619 [ Homo sapiens (human) ]

    Gene ID: 256021, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC01619provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 1619provided by HGNC
    Primary source
    HGNC:HGNC:27409
    See related
    Ensembl:ENSG00000257242 AllianceGenome:HGNC:27409
    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
    C12orf79
    Expression
    Biased expression in bone marrow (RPKM 7.3), lymph node (RPKM 0.9) and 6 other tissues See more
    Orthologs
    all
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    Genomic context

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    See LINC01619 in Genome Data Viewer
    Location:
    12q21.33
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (91984976..92142831, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (91962471..92120393, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (92378752..92536607, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2404 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:92296093-92297292 Neighboring gene uncharacterized LOC105369901 Neighboring gene MPRA-validated peak1883 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr12:92356292-92356496 Neighboring gene NANOG hESC enhancer GRCh37_chr12:92415340-92415873 Neighboring gene Sharpr-MPRA regulatory region 2068 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:92471461-92472660 Neighboring gene Sharpr-MPRA regulatory region 10753 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:92501486-92502024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6722 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92538603-92539139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6726 Neighboring gene BTG1 divergent transcript Neighboring gene ribosomal protein L21 pseudogene 106 Neighboring gene BTG anti-proliferation factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6727 Neighboring gene long intergenic non-protein coding RNA 2391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6729 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92718856-92719356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92719357-92719857 Neighboring gene NANOG hESC enhancer GRCh37_chr12:92725117-92725618 Neighboring gene uncharacterized LOC105369902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6731

    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. Long Noncoding RNA LINC01619 Regulates MicroRNA-27a/Forkhead Box Protein O1 and Endoplasmic Reticulum Stress-Mediated Podocyte Injury in Diabetic Nephropathy. Bai X, et al. Antioxid Redox Signal, 2018 Aug 1. PMID 29334763
    2. Biological insights from 108 schizophrenia-associated genetic loci. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Nature, 2014 Jul 24. PMID 25056061, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. study demonstrates that LINC01619 functions as a competing endogenous RNA and regulates miR-27a/FOXO1-mediated ER stress and podocyte injury in diabetic nephropathy
      Title: Long Noncoding RNA LINC01619 Regulates MicroRNA-27a/Forkhead Box Protein O1 and Endoplasmic Reticulum Stress-Mediated Podocyte Injury in Diabetic Nephropathy.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    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)

    General gene information

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    Markers

    Homology

    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_046159.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate 5' exon and an additional internal exon, and uses an alternate splice site in another internal exon, compared to variant 1.
      Source sequence(s)
      BC029844, CA438667
      Related
      ENST00000551843.5

    2. NR_046160.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an additional internal exon and uses an alternate splice site in another internal exon, compared to variant 1.
      Source sequence(s)
      BC029844, BC118985, CA438667, DB121637

    3. NR_132339.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AK055439, BC029844, CA438667, DB121637
      Related
      ENST00000549802.5

    4. NR_132340.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1.
      Source sequence(s)
      BC029844, BC107595, CA438667, DB121637

    5. NR_132341.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites in an internal exon, compared to variant 1.
      Source sequence(s)
      BC029844, BC122534, CA438667, DB121637

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      91984976..92142831 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      91962471..92120393 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001256373.1: Suppressed sequence

      Description
      NM_001256373.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.

    2. NM_001256374.1: Suppressed sequence

      Description
      NM_001256374.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.

    3. NM_001256375.1: Suppressed sequence

      Description
      NM_001256375.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version

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