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LOC130009117 ATAC-STARR-seq lymphoblastoid silent region 5049 [ Homo sapiens (human) ]

Gene ID: 130009117, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009117
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5049
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 LOC130009117 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 (123712178..123712727)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123711044..123711593)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (124196725..124197274)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7273 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124129599-124129794 Neighboring gene general transcription factor IIH subunit 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124143885-124145084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7274 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124184156-124184331 Neighboring gene tectonic family member 2 Neighboring gene uncharacterized LOC105370042 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124206184-124206364 Neighboring gene ATPase H+ transporting V0 subunit a2 Neighboring gene ribosomal protein L27 pseudogene 12 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124232793-124233992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5050 Neighboring gene uncharacterized LOC105370044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7275 Neighboring gene dynein axonemal heavy chain 10

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_187590.1 

    Range
    101..650
    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
    123712178..123712727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    123711044..123711593
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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