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

Gene ID: 84536, updated on 10-Oct-2023

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, Apr 2022]
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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Location:
21q22.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44933284..44939913, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43294033..43300661, complement)
105.20220307 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
  • 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)

Genotypes

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_2023_10

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

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Chemical Information
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Research Materials
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