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LOC129931725 ATAC-STARR-seq lymphoblastoid silent region 1463 [ Homo sapiens (human) ]

Gene ID: 129931725, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129931725
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1463
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 LOC129931725 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160751763..160751822)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159888850..159888909)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160721553..160721612)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene endogenous retrovirus group K member 18 Env polyprotein Neighboring gene CD48 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1947 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160695816-160696558 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160696559-160697302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1951 Neighboring gene uncharacterized LOC124904440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1952 Neighboring gene SLAM family member 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1955 Neighboring gene uncharacterized LOC105371470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:160751105-160751606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1958 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:160759219-160759411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1961 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:160771561-160771810 Neighboring gene lymphocyte antigen 9

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_164768.1 

    Range
    101..160
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    160751763..160751822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    159888850..159888909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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