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LOC121627897 Sharpr-MPRA regulatory region 7426 [ Homo sapiens (human) ]

Gene ID: 121627897, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627897
Gene description
Sharpr-MPRA regulatory region 7426
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 non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without 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 (20360445..20360739)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (20418973..20419267)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (20341089..20341383)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 61 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:20247710-20248210 Neighboring gene CFAP61 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12710 Neighboring gene RNA, 7SL, cytoplasmic 690, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:20347841-20348611 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:20373434-20374633 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:20375973-20376516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:20375428-20375972 Neighboring gene Sharpr-MPRA regulatory region 956 Neighboring gene NANOG hESC enhancer GRCh37_chr20:20391221-20391855 Neighboring gene Ral GTPase activating protein catalytic subunit alpha 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17608 Neighboring gene INSM transcriptional repressor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17611 Neighboring gene VISTA enhancer hs688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17614 Neighboring gene eukaryotic translation initiation factor 4E family member 2 pseudogene 1

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_075088.1 

    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
    20360445..20360739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    20418973..20419267
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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