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LOC130008752 ATAC-STARR-seq lymphoblastoid silent region 4858 [ Homo sapiens (human) ]

Gene ID: 130008752, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008752
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4858
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 LOC130008752 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110583141..110583470)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110560833..110561162)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (111020946..111021275)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903015 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene Sharpr-MPRA regulatory region 4252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7006 Neighboring gene VPS29 retromer complex component Neighboring gene ReSE screen-validated silencer GRCh37_chr12:110953094-110953337 Neighboring gene RAD9 checkpoint clamp component B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978258-110978758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978759-110979259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7008 Neighboring gene protein phosphatase targeting COQ7 Neighboring gene HNF4 motif-containing MPRA enhancer 250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7013 Neighboring gene RNA, 7SL, cytoplasmic 387, pseudogene Neighboring gene tectonic family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111099215-111099717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7016 Neighboring gene uncharacterized LOC124903017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7017 Neighboring gene hydrogen voltage gated channel 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7019

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_187321.1 

    Range
    101..430
    Download
    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
    110583141..110583470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110560833..110561162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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