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LOC122056772 Sharpr-MPRA regulatory region 11658 [ Homo sapiens (human) ]

Gene ID: 122056772, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056772
Gene description
Sharpr-MPRA regulatory region 11658
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive DNase matched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (15837254..15837548)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (15278525..15278819)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16163749..16164043)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ubiquinol-cytochrome c reductase hinge protein like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16161483-16162468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 314 Neighboring gene ribosomal protein S16 pseudogene 1 Neighboring gene SPEN antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 249 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16173332-16173844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16173845-16174356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 317 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16175780-16176374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16191755-16192255 Neighboring gene spen family transcriptional repressor Neighboring gene NFE2L2 motif-containing MPRA enhancer 216 Neighboring gene MPRA-validated peak83 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene MPRA-validated peak84 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16261375-16261876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:16268619-16269818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16276391-16277178 Neighboring gene uncharacterized LOC124903855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 254 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:16278891-16280090 Neighboring gene zinc finger and BTB domain containing 17 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:16287659-16288532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 256

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_076228.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    15837254..15837548
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    15278525..15278819
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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