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LOC112935921 Sharpr-MPRA regulatory region 6697 [ Homo sapiens (human) ]

Gene ID: 112935921, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935921
Gene description
Sharpr-MPRA regulatory region 6697
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 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2018]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (194205740..194206034)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (196902466..196902760)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (193923529..193923823)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 215, pseudogene Neighboring gene uncharacterized LOC107986172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193878773-193879704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193893180-193894093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15018 Neighboring gene long intergenic non-protein coding RNA 2036 Neighboring gene VISTA enhancer hs1543 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:193932031-193932834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193949267-193949768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193949769-193950268 Neighboring gene long intergenic non-protein coding RNA 2037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15019 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:193988835-193989766 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:193994438-193995637 Neighboring gene long intergenic non-protein coding RNA 2048

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_061436.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    194205740..194206034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    196902466..196902760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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