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LOC110121284 VISTA enhancer hs2229 [ Homo sapiens (human) ]

Gene ID: 110121284, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121284
Gene description
VISTA enhancer hs2229
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. A subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic trigeminal nerve of transgenic mice. An overlapping subregion was also validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. This locus also includes three 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177389135..177392188)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177932353..177935406)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176816376..176819189)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene lectin, mannose binding 2 Neighboring gene ribosomal protein S20 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23706 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:176778754-176778968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176784977-176785477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23712 Neighboring gene regulator of G protein signaling 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176793955-176794594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176794595-176795233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176796333-176797184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176800703-176801203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176814616-176815116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176815117-176815617 Neighboring gene solute carrier family 34 member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176823005-176823660 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:176824881-176825056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176828971-176829828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176830685-176831542 Neighboring gene profilin 3 Neighboring gene coagulation factor XII

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  3. 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 23714
  • ATAC-STARR-seq lymphoblastoid active region 23715
  • ATAC-STARR-seq lymphoblastoid active region 23716
  • P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:176816136-176817335

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_053899.2 

    Range
    101..3154
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    177389135..177392188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177932353..177935406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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