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LOC121853020 Sharpr-MPRA regulatory region 12386 [ Homo sapiens (human) ]

Gene ID: 121853020, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853020
Gene description
Sharpr-MPRA regulatory region 12386
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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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 (63197117..63197411)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65002440..65002734)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61828469..61828763)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904952 Neighboring gene MPRA-validated peak4310 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61799372-61800146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61803896-61804472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61804473-61805047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61805624-61806198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61809099-61810059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13147 Neighboring gene microRNA 124-3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61818311-61818811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61830673-61831272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61831273-61831874 Neighboring gene YTH N6-methyladenosine RNA binding protein F1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61857740-61858694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61862252-61863021 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:61863095-61864294 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:61865058-61865253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61866073-61866674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61870596-61871096 Neighboring gene uncharacterized LOC124904950 Neighboring gene baculoviral IAP repeat containing 7 Neighboring gene microRNA 3196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61879175-61880007 Neighboring gene sodium/potassium transporting ATPase interacting 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61880008-61880839

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_076128.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63197117..63197411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65002440..65002734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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