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LOC114827862 VISTA enhancer hs2547 [ Homo sapiens (human) ]

Gene ID: 114827862, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114827862
Gene description
VISTA enhancer hs2547
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This locus represents a conserved genomic element that can function as an enhancer. It can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic hindbrain and midbrain of transgenic mice. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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 LOC114827862 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (22401875..22405162)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (22459424..22462711)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (22382513..22385800)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372561 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:22245080-22246279 Neighboring gene long intergenic non-protein coding RNA 1427 Neighboring gene Sharpr-MPRA regulatory region 5495 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:22370619-22371818 Neighboring gene Sharpr-MPRA regulatory region 10803 Neighboring gene uncharacterized LOC284788 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:22392180-22393379 Neighboring gene FOXA motif-containing MPRA enhancer 246 Neighboring gene uncharacterized LOC105372562 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:22436641-22437455 Neighboring gene uncharacterized LOC105372563

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. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 17626

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_065218.1 

    Range
    101..3388
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    22401875..22405162
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    22459424..22462711
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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