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LOC112935959 Sharpr-MPRA regulatory region 9383 [ Homo sapiens (human) ]

Gene ID: 112935959, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935959
Gene description
Sharpr-MPRA regulatory region 9383
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 K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Aug 2018]
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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 (73192078..73192372)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (73233586..73233880)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (73241229..73241523)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:73160026-73160587 Neighboring gene RNA, U2 small nuclear 64, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:73213631-73214237 Neighboring gene GPATCH11 pseudogene 1 Neighboring gene RNA, U6 small nuclear 1270, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73343679-73344179 Neighboring gene PDZ domain containing ring finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20099 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:73533722-73534255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20102 Neighboring gene uncharacterized LOC101927296

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_061474.1 

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

    Range
    73192078..73192372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    73233586..73233880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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