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LOC112997551 Sharpr-MPRA regulatory region 12583 [ Homo sapiens (human) ]

Gene ID: 112997551, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997551
Gene description
Sharpr-MPRA regulatory region 12583
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). It also displayed weak repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Aug 2018]
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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 (10588897..10589191)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (10527758..10528052)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (10589009..10589303)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10503261-10504155 Neighboring gene long intergenic non-protein coding RNA 2212 Neighboring gene long intergenic non-protein coding RNA 2213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10532633-10533600 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10551849-10552646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10564245-10565139 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10565140-10566033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10566137-10566638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22363 Neighboring gene ankyrin repeat domain 33B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22364 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:10595324-10596523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22371 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10631614-10632356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22377 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10637082-10637814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10656245-10657193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10673987-10674687 Neighboring gene intersectin 1 (SH3 domain protein) pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10681857-10682357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10699642-10700465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10702999-10703721 Neighboring gene death associated protein Neighboring gene ReSE screen-validated silencer GRCh37_chr5:10726428-10726591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10727463-10727962 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:10731097-10731598 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:10731599-10732098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15930 Neighboring gene DAP divergent transcript

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_061547.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    10588897..10589191
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    10527758..10528052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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