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LOC108281149 ODF3B-KLHDC7B intergenic CAGE-defined mid-level expression enhancer [ Homo sapiens (human) ]

Gene ID: 108281149, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281149
Gene description
ODF3B-KLHDC7B intergenic CAGE-defined mid-level 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 intergenic region between the ODF3B (outer dense fiber of sperm tails 3B) and KLHDC7B (kelch domain containing 7B) genes. It was defined as a mid-level expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). A subregion was validated as a functional enhancer by reporter assays in both HeLa and HepG2 cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
22q13.33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50539410..50540028)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (51049978..51050596)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50977909..50978457)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13986 Neighboring gene synthesis of cytochrome C oxidase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50965237-50965808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19324 Neighboring gene thymidine phosphorylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13989 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50969361-50969866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13993 Neighboring gene ciliary microtubule associated protein 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19326 Neighboring gene uncharacterized LOC102724608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19329 Neighboring gene Sharpr-MPRA regulatory region 5393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19330 Neighboring gene KLHDC7B divergent transcript Neighboring gene Sharpr-MPRA regulatory region 13947 Neighboring gene kelch domain containing 7B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13996

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. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829
  2. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 19327
  • ODF3B-KLHDC7B interval mid 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_051109.2 

    Range
    101..719
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    50539410..50540028
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    51049978..51050596
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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