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LOC112694714 Sharpr-MPRA regulatory region 6747 [ Homo sapiens (human) ]

Gene ID: 112694714, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694714
Gene description
Sharpr-MPRA regulatory region 6747
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43959269..43959563)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45692435..45692729)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42587909..42588203)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904908 Neighboring gene long intergenic non-protein coding RNA 1728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42543229-42543946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42543947-42544664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42564724-42565224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42565225-42565725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42571264-42571764 Neighboring gene TOX high mobility group box family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17918 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:42583279-42584478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42584612-42585246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42634840-42635340 Neighboring gene RNA, 7SL, cytoplasmic 443, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42696545-42697061 Neighboring gene Sharpr-MPRA regulatory region 7745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42739928-42740441 Neighboring gene Sharpr-MPRA regulatory region 3924 Neighboring gene junctophilin 2 Neighboring gene uncharacterized LOC124904909 Neighboring gene JPH2 intron CAGE-defined T cell enhancer

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_060744.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    43959269..43959563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    45692435..45692729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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