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LOC112997586 Sharpr-MPRA regulatory region 1936 [ Homo sapiens (human) ]

Gene ID: 112997586, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997586
Gene description
Sharpr-MPRA regulatory region 1936
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112997586 in Genome Data Viewer
Location:
5p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (2993395..2993689)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (2908260..2908554)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (2993509..2993803)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107983966 Neighboring gene uncharacterized LOC107984098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3029100-3029600 Neighboring gene uncharacterized LOC105374621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:3079616-3080276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:3099596-3100470 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:3100471-3101344 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:3101345-3102218 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:3103093-3103967 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:3127153-3127350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3133320-3133820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3133821-3134321 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:3176917-3178116 Neighboring gene long intergenic non-protein coding RNA 1377

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_061585.1 

    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
    2993395..2993689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    2908260..2908554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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