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LOC113002586 Sharpr-MPRA regulatory region 13881 [ Homo sapiens (human) ]

Gene ID: 113002586, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113002586
Gene description
Sharpr-MPRA regulatory region 13881
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 21:Repr, strong Polycomb repression), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
5p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (6350396..6350690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (6279164..6279458)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (6350509..6350803)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene high mobility group box 3 pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 2145 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:6315844-6316069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:6343159-6343659 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:6367530-6367697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22330 Neighboring gene mediator complex subunit 10 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:6408294-6409493 Neighboring gene uncharacterized LOC124900933

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_061597.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    6350396..6350690
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791776.1 Reference GRCh38.p14 PATCHES

    Range
    52570..52864
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    6279164..6279458
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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