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LOC108228199 HOXC11-HOXC10 intergenic CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108228199, updated on 17-Sep-2024

Summary

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Gene symbol
LOC108228199
Gene description
HOXC11-HOXC10 intergenic CAGE-defined high expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
regulatory: 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 HOXC (homeobox C) gene cluster, in the intergenic region between the HOXC11 and HOXC10 genes. It was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
Orthologs
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Genomic context

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See LOC108228199 in Genome Data Viewer
Location:
12q13.3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53978916..53979430)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53944426..53944940)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54372700..54373214)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369775 Neighboring gene homeobox C12 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:54355207-54355431 Neighboring gene HOX transcript antisense RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54360165-54361069 Neighboring gene NUP98-HOXC11 recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54368136-54368730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6430 Neighboring gene homeobox C11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54379714-54380594 Neighboring gene HOXC cluster antisense RNA 3 Neighboring gene homeobox C10 Neighboring gene microRNA 196a-2

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

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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Homology

Other Names

  • HOXC11-HOXC10 interval high CAGE 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_050969.1 

    Range
    101..615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53978916..53979430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53944426..53944940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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