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LOC117038779 CRISPRi-FlowFISH-validated COPZ1 and HNRNPA1 regulatory element [ Homo sapiens (human) ]

Gene ID: 117038779, updated on 12-Sep-2024

Summary

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Gene symbol
LOC117038779
Gene description
CRISPRi-FlowFISH-validated COPZ1 and HNRNPA1 regulatory element
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 was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. A subregion was validated as a negatively-acting cis-regulatory element for both the COPZ1 (COPI coat complex subunit zeta 1) and HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1) genes based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC117038779 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 (54300787..54301902)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (54267363..54268478)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54694571..54695686)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene chromobox 5 Neighboring gene S-phase cancer associated transcript 2 Neighboring gene CRISPRi-FlowFISH-validated NFE2 regulatory element 2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 regulatory element Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 and NFE2 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated COPZ1, HNRNPA1 and NFE2 regulatory element Neighboring gene nuclear factor, erythroid 2 Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 and NFE2 regulatory element 2 Neighboring gene RNA, U6 small nuclear 950, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54722975-54723665 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:54723666-54724355 Neighboring gene COPI coat complex subunit zeta 1 Neighboring gene microRNA 148b

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. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, Free PMC Article
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54694946-54695686

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_068105.2 

    Range
    101..1216
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    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
    54300787..54301902
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    54267363..54268478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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