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LOC115804260 CRISPRi-validated cis-regulatory element chr2.403 [ Homo sapiens (human) ]

Gene ID: 115804260, updated on 12-Sep-2024

Summary

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Gene symbol
LOC115804260
Gene description
CRISPRi-validated cis-regulatory element chr2.403
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the HPCAL1 (hippocalcin like 1) gene on chromosome 2 based on multiplex CRISPR/Cas9-mediated perturbation in K562 erythroleukemia cells. A subregion was also 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC115804260 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10297812..10298424)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10326390..10327002)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10437938..10438550)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:10422935-10424134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10424193-10424793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10425933-10426432 Neighboring gene uncharacterized LOC101929691 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10429268-10430467 Neighboring gene RNA, 7SL, cytoplasmic 66, pseudogene Neighboring gene small nucleolar RNA SNORA51 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10443229-10443426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11161 Neighboring gene hippocalcin like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10459734-10460234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10460235-10460735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10471739-10472326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10484271-10484771 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr2:10508004-10508811 Neighboring gene Sharpr-MPRA regulatory region 2000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10513139-10513866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10513867-10514592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10522419-10523074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10523075-10523728 Neighboring gene uncharacterized LOC124905972 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10547784-10548983 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10559385-10559972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10559973-10560560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10564889-10565701 Neighboring gene uncharacterized LOC124907732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10572745-10573710

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. 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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 12273

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_066143.1 

    Range
    101..713
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    10297812..10298424
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    10326390..10327002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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