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LOC121627894 Sharpr-MPRA regulatory region 11342 [ Homo sapiens (human) ]

Gene ID: 121627894, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627894
Gene description
Sharpr-MPRA regulatory region 11342
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (16241924..16242218)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (16291207..16291501)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (16222569..16222863)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904874 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:16187279-16187780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:16187781-16188280 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:16208020-16208897 Neighboring gene peptidylprolyl isomerase A pseudogene 17 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:16240179-16240692 Neighboring gene kinesin family member 16B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17561 Neighboring gene Sharpr-MPRA regulatory region 7814 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12682 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:16417298-16418497 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:16456599-16456834 Neighboring gene Sharpr-MPRA regulatory region 3089 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59877 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:16553850-16554371 Neighboring gene uncharacterized LOC124904875

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_075085.1 

    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
    16241924..16242218
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    16291207..16291501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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