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LINC01553 long intergenic non-protein coding RNA 1553 [ Homo sapiens (human) ]

Gene ID: 283025, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01553provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1553provided by HGNC
Primary source
HGNC:HGNC:23524
See related
Ensembl:ENSG00000235931 AllianceGenome:HGNC:23524
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
C10orf40
Expression
Restricted expression toward testis (RPKM 4.1) See more
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Genomic context

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See LINC01553 in Genome Data Viewer
Location:
10q21.2
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (59958217..59960913, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (60812962..60815651, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (61717975..61720671, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:61521925-61522472 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:61529872-61530061 Neighboring gene NANOG hESC enhancer GRCh37_chr10:61549690-61550191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:61562933-61563434 Neighboring gene Sharpr-MPRA regulatory region 6982 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:61607379-61608319 Neighboring gene myoregulin Neighboring gene Sharpr-MPRA regulatory region 3861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3390 Neighboring gene coiled-coil domain containing 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2385 Neighboring gene Sharpr-MPRA regulatory region 3982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2386 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:61667949-61668742 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:61763136-61763882 Neighboring gene NANOG hESC enhancer GRCh37_chr10:61788258-61788759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3394 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:61889195-61889380 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:61889679-61890254 Neighboring gene ankyrin 3 Neighboring gene NANOG hESC enhancer GRCh37_chr10:62018096-62018597 Neighboring gene Sharpr-MPRA regulatory region 14495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2388 Neighboring gene uncharacterized LOC124902430 Neighboring gene ADP ribosylation factor like GTPase 4A pseudogene 1

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. The involvement of Parkin-dependent mitophagy in the anti-cancer activity of Ginsenoside. Sun X, et al. J Ginseng Res, 2022 Mar. PMID 35509820, Free PMC Article
  2. 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

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

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_024340.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC023904
    Related
    ENST00000444900.1

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    59958217..59960913 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    60812962..60815651 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001017982.1: Suppressed sequence

    Description
    NM_001017982.1: 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
A4QN01.1 GenPept UniProtKB/Swiss-Prot:A4QN01

Gene LinkOut

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

Other Literature Sources
Chemical Information
Molecular Biology Databases
Research Materials