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LOC121009644 Sharpr-MPRA regulatory region 1149 [ Homo sapiens (human) ]

Gene ID: 121009644, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009644
Gene description
Sharpr-MPRA regulatory region 1149
Gene type
biological region
Feature type(s)
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (13850412..13850706)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (13851042..13851336)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (13891909..13892203)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100293612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13696034-13696534 Neighboring gene Sharpr-MPRA regulatory region 4110 Neighboring gene long intergenic non-protein coding RNA 620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13716597-13717098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13723071-13723616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13738746-13739365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13739985-13740604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13742088-13742588 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13769563-13770149 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:13770150-13770736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13814826-13815326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13822297-13822796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13828435-13829175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13829176-13829915 Neighboring gene tRNA suppressor (anticodon CTA) 2-1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13834054-13834694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13875041-13875541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13876230-13876730 Neighboring gene Wnt family member 7A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13894067-13894571 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:13895244-13896443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13920041-13920542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13921045-13921546 Neighboring gene uncharacterized LOC105376957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19494 Neighboring gene Sharpr-MPRA regulatory region 1925 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64801 Neighboring gene vomeronasal 1 receptor 20 pseudogene

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-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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)

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_074041.1 

    Range
    101..395
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    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    13850412..13850706
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    13851042..13851336
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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