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LOC129993061 ATAC-STARR-seq lymphoblastoid silent region 15682 [ Homo sapiens (human) ]

Gene ID: 129993061, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993061
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15682
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 LOC129993061 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (128287693..128287742)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (131591792..131591841)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (129208848..129208897)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5106 silencer Neighboring gene La ribonucleoprotein 1B Neighboring gene ribosomal protein L15 pseudogene 8 Neighboring gene FOSL1 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr4:129186588-129187089 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:129197563-129197760 Neighboring gene Sharpr-MPRA regulatory region 13521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15684 Neighboring gene Sharpr-MPRA regulatory region 12082 Neighboring gene progesterone receptor membrane component 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129242766-129243328 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129271007-129271585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129271620-129272158 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129283869-129284407 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:129308825-129310024 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73985 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73994 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129337187-129337688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129337689-129338188 Neighboring gene long intergenic non-protein coding RNA 2615 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:129390695-129391894 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15685 Neighboring gene NFE2L2 motif-containing MPRA enhancer 199 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129456135-129456788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129456789-129457442 Neighboring gene uncharacterized LOC101927259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21891

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 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_172507.1 

    Range
    101..150
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    128287693..128287742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    131591792..131591841
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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