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LOC108281184 CALCOCO1-CISTR intergenic nontranscribed DNase I hypersensitive site-defined enhancer [ Homo sapiens (human) ]

Gene ID: 108281184, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281184
Gene description
CALCOCO1-CISTR intergenic nontranscribed DNase I hypersensitive site-defined enhancer
Gene type
biological region
Feature type(s)
regulatory: DNase_I_hypersensitive_site, enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic element is located in the intergenic region between the CALCOCO1 (calcium binding and coiled-coil domain 1) and CISTR (chondrogenesis-associated transcript) genes. It was defined as a nontranscribed region with regulatory potential based on the presence of a DNase I hypersensitive site (DHS), with an absence of capped transcripts by cap analysis of gene expression (CAGE) in HeLa cells. It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
12q13.13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53743489..53744035)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53709243..53709789)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54137273..54137819)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATP synthase membrane subunit c locus 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6427 Neighboring gene Sharpr-MPRA regulatory region 7415 Neighboring gene calcium binding and coiled-coil domain 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:54118812-54120011 Neighboring gene uncharacterized LOC105369774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54133003-54133792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54141521-54142049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54142050-54142577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54144138-54144726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4518 Neighboring gene chondrogenesis-associated transcript Neighboring gene uncharacterized LOC105378250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6429

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • CALCOCO1-CISTR interval no CAGE DHS FANTOM5 enhancer

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.

Genomic

  1. NG_051144.1 

    Range
    101..647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53743489..53744035
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53709243..53709789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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