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    LINC01547 long intergenic non-protein coding RNA 1547 [ Homo sapiens (human) ]

    Gene ID: 84536, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LINC01547provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 1547provided by HGNC
    Primary source
    HGNC:HGNC:15707
    See related
    Ensembl:ENSG00000183250 AllianceGenome:HGNC:15707
    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
    PRED54; C21orf67; C21orf69
    Summary
    Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 2.2), spleen (RPKM 1.8) and 25 other tissues See more
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    Genomic context

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    See LINC01547 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44933284..44939913, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43294033..43300661, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46353199..46359828, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene integrin subunit beta 2 Neighboring gene uncharacterized LOC107987303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46329075-46329574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46333656-46334156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46337409-46338321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13395 Neighboring gene ITGB2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46345923-46346812 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:46347045-46348244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46351267-46352146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13396 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:46359630-46360194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46369323-46369908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46369909-46370494 Neighboring gene SLX9 ribosome biogenesis factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46371986-46372936 Neighboring gene FAM207A intron CAGE-defined mid-level expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46389870-46390685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46390686-46391500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46398896-46399794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46399795-46400691 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46406949-46407903 Neighboring gene long intergenic non-protein coding RNA 163 Neighboring gene long intergenic non-protein coding RNA 165

    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 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. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. Reymond A, et al. Genomics, 2001 Nov. PMID 11707072
    2. Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins. Hu YH, et al. BMC Genomics, 2006 Jun 16. PMID 16780588, Free PMC Article
    3. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Luo J, et al. Cell, 2009 May 29. PMID 19490893, Free PMC Article
    4. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
    5. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Clone Names

    • MGC120186, MGC120187, MGC120188, MGC120189, MGC149386, MGC149387

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in endoplasmic reticulum HDA PubMed 

    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_027128.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL844908, BI829356, BI907880, BM674075

    2. NR_027129.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes an alternate exon near the 5' end and has an alternate 3' splice pattern, compared to variant 1.
      Source sequence(s)
      AF380178, BI907880
      Related
      ENST00000330551.3

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      44933284..44939913 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      43294033..43300661 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_058188.1: Suppressed sequence

      Description
      NM_058188.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.

    2. NM_058189.1: Suppressed sequence

      Description
      NM_058189.1: This RefSeq was permanently suppressed because it is primarily UTR sequence.

    3. NM_182900.1: Suppressed sequence

      Description
      NM_182900.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P58512.1 GenPept UniProtKB/Swiss-Prot:P58512

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials