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LOC121740713 Sharpr-MPRA regulatory region 13991 [ Homo sapiens (human) ]

Gene ID: 121740713, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740713
Gene description
Sharpr-MPRA regulatory region 13991
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Another subregion was validated as an enhancer by Sharpr-MPRA (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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (26512033..26512986)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (26788610..26789563)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (26369549..26369843)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27127 Neighboring gene DNAJB6 pseudogene 2 Neighboring gene vegetative cell wall protein gp1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:26346103-26346626 Neighboring gene PNMA family member 2 Neighboring gene dihydropyrimidinase like 2 Neighboring gene proteasome activator subunit 2 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:26433901-26434598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:26434599-26435296 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:26435598-26436492 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:26436493-26437387 Neighboring gene uncharacterized LOC124901916 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:26448723-26449328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19045

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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K4me1 hESC enhancer GRCh37_chr8:26369630-26370502

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_075775.2 

    Range
    101..1054
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    26512033..26512986
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    26788610..26789563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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