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LOC121627933 Sharpr-MPRA regulatory region 15419 [ Homo sapiens (human) ]

Gene ID: 121627933, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627933
Gene description
Sharpr-MPRA regulatory region 15419
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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). 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 (23315622..23315916)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (23738479..23738773)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (23657809..23658103)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene BCR activator of RhoGEF and GTPase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:23611303-23611973 Neighboring gene BCR-ABL p195 breakpoint cluster region Neighboring gene F-box and WD repeat domain containing 4 pseudogene 1 Neighboring gene BCR-ABL p200 breakpoint cluster region Neighboring gene ReSE screen-validated silencer GRCh37_chr22:23621943-23622250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13538 Neighboring gene uncharacterized LOC107985554 Neighboring gene BCR-ABL major-breakpoint cluster region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18755 Neighboring gene BCR-ABL p225 breakpoint cluster region Neighboring gene BCR-ABL micro-breakpoint cluster region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:23656171-23656672 Neighboring gene POM121 transmembrane nucleoporin like 11, pseudogene Neighboring gene ribosomal protein S10 pseudogene 30 Neighboring gene long intergenic non-protein coding RNA 2556

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 13539

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_075124.1 

    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
    23315622..23315916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    23738479..23738773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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