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LOC120285839 VISTA enhancer hs2613 [ Homo sapiens (human) ]

Gene ID: 120285839, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120285839
Gene description
VISTA enhancer hs2613
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 includes a conserved genomic element that can function as an enhancer. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic hindbrain and midbrain of transgenic mice. An overlapping subregion marked by the H3K4me1 histone modification was also shown to be an active enhancer by ChIP-STARR-seq in naive human embryonic stem cells. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (66828982..66830794)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (67704809..67706621)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (64825100..64826553)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene protein kinase C alpha Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:64640965-64642164 Neighboring gene Sharpr-MPRA regulatory region 6976 Neighboring gene RNA, 5S ribosomal pseudogene 445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64672313-64673082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64710611-64711307 Neighboring gene NANOG hESC enhancer GRCh37_chr17:64718354-64718855 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64726459-64727144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64743608-64744108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64778583-64779084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64803038-64803887 Neighboring gene microRNA 634 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:64874747-64874957 Neighboring gene calcium voltage-gated channel auxiliary subunit gamma 5 Neighboring gene RNA, 5S ribosomal pseudogene 446

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. 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

  • H3K4me1 hESC enhancer GRCh37_chr17:64825981-64826912

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_074540.2 

    Range
    101..1913
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    66828982..66830794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    67704809..67706621
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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