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LOC112590821 Sharpr-MPRA regulatory region 865 [ Homo sapiens (human) ]

Gene ID: 112590821, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112590821
Gene description
Sharpr-MPRA regulatory region 865
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). [provided by RefSeq, Jun 2018]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (8165709..8166003)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (7696758..7697052)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (8225769..8226063)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ERRFI1 divergent transcript Neighboring gene MPRA-validated peak44 silencer Neighboring gene ribosomal protein L7a pseudogene 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8127937-8128436 Neighboring gene VISTA enhancer hs1833 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:8154529-8155728 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:8156741-8157940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8175654-8176154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 100 Neighboring gene uncharacterized LOC107984915 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:8227009-8227682 Neighboring gene RPL7AP18-LOC102724539 intergenic ENCODE-defined enhancer Neighboring gene eukaryotic translation initiation factor 2 subunit gamma pseudogene Neighboring gene RNA, U1 small nuclear 7, 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_060611.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    8165709..8166003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    7696758..7697052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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