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LOC124252642 Sharpr-MPRA regulatory region 13386 [ Homo sapiens (human) ]

Gene ID: 124252642, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124252642
Gene description
Sharpr-MPRA regulatory region 13386
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (38087972..38088266)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (38111900..38112194)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (38087969..38088263)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene RNA, U7 small nuclear 124 pseudogene Neighboring gene SH2 domain containing adaptor protein B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37951849-37952348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37997675-37998176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28408 Neighboring gene Sharpr-MPRA regulatory region 5136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38008584-38009525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38010092-38010724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19915 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38016883-38017646 Neighboring gene Sharpr-MPRA regulatory region 2787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38021463-38021972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38026045-38026553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38026554-38027063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38027064-38027572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38027573-38028081 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:38028793-38028962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38030139-38030638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38032069-38032570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38037811-38038416 Neighboring gene VISTA enhancer hs2062 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:38047203-38048402 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:38048927-38049920 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:38058891-38060090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38067661-38068464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19917 Neighboring gene uncharacterized LOC105376039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28411 Neighboring gene U8 small nucleolar RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28412 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:38170544-38171743 Neighboring gene small nucleolar RNA U13

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 active region 28409

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_078820.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    38087972..38088266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    38111900..38112194
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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