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LOC116268448 CRISPRi-validated cis-regulatory element chr12.3588 [ Homo sapiens (human) ]

Gene ID: 116268448, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116268448
Gene description
CRISPRi-validated cis-regulatory element chr12.3588
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 cis-regulatory element for the C12orf76 (chromosome 12 open reading frame 76) gene on chromosome 12 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC116268448 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110079425..110080255)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110055125..110055955)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110517230..110518060)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene GIT ArfGAP 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6990 Neighboring gene Sharpr-MPRA regulatory region 2512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6991 Neighboring gene ankyrin repeat domain 13A Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110460576-110461076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6992 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:110465819-110467018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110480304-110480817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6993 Neighboring gene chromosome 12 open reading frame 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6995 Neighboring gene uncharacterized LOC105369976 Neighboring gene Sharpr-MPRA regulatory region 13461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110546777-110547368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110547369-110547960 Neighboring gene CRISPRi-validated cis-regulatory element chr12.3595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4853 Neighboring gene intraflagellar transport 81 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110610112-110610892 Neighboring gene MPRA-validated peak1945 silencer

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 6996
  • ATAC-STARR-seq lymphoblastoid active region 6997

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_066963.1 

    Range
    101..931
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    110079425..110080255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110055125..110055955
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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