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LOC130004262 ATAC-STARR-seq lymphoblastoid silent region 2582 [ Homo sapiens (human) ]

Gene ID: 130004262, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004262
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2582
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress 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 LOC130004262 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (87537240..87537289)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (88420835..88420884)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (89296997..89297046)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268063 Neighboring gene Sharpr-MPRA regulatory region 7232 Neighboring gene uncharacterized LOC112268064 Neighboring gene CRISPRi-validated cis-regulatory element chr10.3228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3708 Neighboring gene microRNA 4678 Neighboring gene multiple inositol-polyphosphate phosphatase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:89311461-89312660 Neighboring gene uncharacterized LOC105378412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3710 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:89386301-89387109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3711 Neighboring gene NANOG hESC enhancer GRCh37_chr10:89398621-89399136 Neighboring gene NANOG hESC enhancer GRCh37_chr10:89399137-89399651 Neighboring gene ribosomal protein S26 pseudogene 38

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. 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)

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_183707.1 

    Range
    101..150
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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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    87537240..87537289
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    88420835..88420884
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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