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LOC130061175 ATAC-STARR-seq lymphoblastoid silent region 8705 [ Homo sapiens (human) ]

Gene ID: 130061175, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061175
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8705
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 LOC130061175 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (50560535..50560914)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51427671..51428050)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48637896..48638275)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48620417-48620917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8704 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:48626222-48626443 Neighboring gene epsin 3 Neighboring gene spermatogenesis associated 20 Neighboring gene CACNA1G antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48639035-48639624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48646614-48647600 Neighboring gene calcium voltage-gated channel subunit alpha1 G Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48670255-48671063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48673674-48674174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48686338-48686945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48702910-48703682 Neighboring gene uncharacterized LOC101927253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8706 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:48715992-48717191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48717641-48718411 Neighboring gene ATP binding cassette subfamily C member 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:48738547-48739746 Neighboring gene Sharpr-MPRA regulatory region 5804 Neighboring gene ABCC3 (B) eExon liver enhancer Neighboring gene Sharpr-MPRA regulatory region 2031

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_194915.1 

    Range
    101..480
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    50560535..50560914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    51427671..51428050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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