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LOC116158492 CRISPRi-validated cis-regulatory element chr4.1627 [ Homo sapiens (human) ]

Gene ID: 116158492, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158492
Gene description
CRISPRi-validated cis-regulatory element chr4.1627
Gene type
biological region
Feature type(s)
regulatory: 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 both the NMU (neuromedin U) and SRD5A3 (steroid 5 alpha-reductase 3) genes on chromosome 4, and also at lower confidence for the PDCL2 (phosducin like 2) gene, based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (55730465..55730928)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (59218642..59219105)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (56596632..56597095)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15443 Neighboring gene neuromedin U Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:56501035-56501786 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:56501787-56502538 Neighboring gene uncharacterized LOC105377660 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:56573715-56574216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:56574217-56574716 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1625 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1626 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1628 Neighboring gene Sharpr-MPRA regulatory region 7030 Neighboring gene RNA, U6 small nuclear 276, pseudogene Neighboring gene uncharacterized LOC105377661 Neighboring gene exocyst complex component 1 like

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

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_066634.1 

    Range
    101..564
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    55730465..55730928
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187541.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    52399..52862
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    59218642..59219105
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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