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LOC121627940 Sharpr-MPRA regulatory region 8125 [ Homo sapiens (human) ]

Gene ID: 121627940, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627940
Gene description
Sharpr-MPRA regulatory region 8125
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 Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (33848261..33848555)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (34305607..34305902)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (34244249..34244543)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene LARGE xylosyl- and glucuronyltransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34118270-34118798 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34134617-34135136 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34134097-34134616 Neighboring gene small nucleolar RNA, H/ACA box 50B Neighboring gene LARGE antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34175765-34176266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:34178675-34179175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13646 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:34231147-34231704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18886 Neighboring gene Sharpr-MPRA regulatory region 672 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34245227-34245862 Neighboring gene H3K27ac hESC enhancers GRCh37_chr22:34249333-34249834 and GRCh37_chr22:34249835-34250334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34265535-34266035 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34265034-34265534 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34263445-34263944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:34271643-34272142 Neighboring gene Sharpr-MPRA regulatory region 329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:34294924-34295536 Neighboring gene Sharpr-MPRA regulatory region 1840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13650 Neighboring gene LARGE1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18888 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:34411551-34412114 Neighboring gene long intergenic non-protein coding RNA 1643 Neighboring gene uncharacterized LL22NC03-13G6.2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:34556235-34556992 Neighboring gene NANOG hESC enhancer GRCh37_chr22:34590594-34591168

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 13647

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_075131.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    33848261..33848555
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    34305607..34305902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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