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LINC00554 long intergenic non-protein coding RNA 554 [ Homo sapiens (human) ]

Gene ID: 100861542, updated on 10-Oct-2023

Summary

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Official Symbol
LINC00554provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 554provided by HGNC
Primary source
HGNC:HGNC:43697
See related
Ensembl:ENSG00000260738 AllianceGenome:HGNC:43697
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
lncZic2
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Genomic context

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Location:
13q32.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99994899..99997909, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (99205810..99208818, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (100647153..100650163, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene Zic family member 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100626468-100627010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100627011-100627551 Neighboring gene OCT4 hESC enhancer GRCh37_chr13:100631077-100631586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5475 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:100635796-100636995 Neighboring gene Zic family member 2 polyalanine repeat instability region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100642562-100643511 Neighboring gene Zic family member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100649774-100650719 Neighboring gene NADH:ubiquinone oxidoreductase subunit A12 pseudogene 1 Neighboring gene uncharacterized LOC124903200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100706176-100706676 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:100710682-100711207

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Withdrawal:The long noncoding RNA lncZic2 drives the self-renewal of liver tumor-initiating cells via the protein kinase C substrates MARCKS and MARCKSL1. Chen Z, et al. J Biol Chem, 2018 May 25. PMID 29588366, Free PMC Article
  2. Genome-wide meta-analysis of myopia and hyperopia provides evidence for replication of 11 loci. Simpson CL, et al. PLoS One, 2014. PMID 25233373, Free PMC Article
  3. 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

EBI GWAS Catalog

Description
Genome-wide meta-analysis of myopia and hyperopia provides evidence for replication of 11 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)

Genotypes

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_047483.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL355338
    Related
    ENST00000564841.1

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    99994899..99997909 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    99205810..99208818 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases