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LOC130009101 ATAC-STARR-seq lymphoblastoid silent region 5043 [ Homo sapiens (human) ]

Gene ID: 130009101, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009101
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5043
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 LOC130009101 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 (123389554..123389663)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123386125..123386234)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123874101..123874210)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene strawberry notch homolog 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7260 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123855180-123855353 Neighboring gene SBNO1 antisense RNA 1 Neighboring gene microRNA 8072 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123867650-123867872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123867837-123868567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5042 Neighboring gene lysine methyltransferase 5A Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123886419-123887182 Neighboring gene Rab interacting lysosomal protein like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123920207-123921136 Neighboring gene uncharacterized LOC124903041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7269 Neighboring gene COP9 signalosome subunit 5 pseudogene 2

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_188768.1 

    Range
    101..210
    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
    123389554..123389663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    123386125..123386234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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