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LOC115995531 CRISPRi-validated cis-regulatory element chr3.4789 [ Homo sapiens (human) ]

Gene ID: 115995531, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995531
Gene description
CRISPRi-validated cis-regulatory element chr3.4789
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 the GOLIM4 (golgi integral membrane protein 4) gene on chromosome 3 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:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (168116229..168116729)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (170900113..170900613)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (167834017..167834517)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 26 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:167729036-167729547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20773 Neighboring gene golgi integral membrane protein 4 Neighboring gene NANOG hESC enhancer GRCh37_chr3:167799674-167800287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14868 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:167813739-167814240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20774 Neighboring gene Sharpr-MPRA regulatory region 6960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20777 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:167990063-167990598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20779 Neighboring gene NANOG hESC enhancer GRCh37_chr3:167993395-167993896 Neighboring gene EGF like and EMI domain containing 1, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:168102881-168103380 Neighboring gene MPRA-validated peak4911 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:168231986-168232502 Neighboring gene RNA, U2 small nuclear 20, pseudogene Neighboring gene microRNA 551b

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

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_066612.1 

    Range
    101..601
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    168116229..168116729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    170900113..170900613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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