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LOC129930317 ATAC-STARR-seq lymphoblastoid silent region 752 [ Homo sapiens (human) ]

Gene ID: 129930317, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930317
Gene description
ATAC-STARR-seq lymphoblastoid silent region 752
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 LOC129930317 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 (41699675..41699734)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (41570216..41570275)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (42165346..42165405)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene vir like m6A methyltransferase associated pseudogene Neighboring gene HIVEP zinc finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 868 Neighboring gene uncharacterized LOC128125817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:42136496-42137086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:42138269-42138858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 871 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:42156217-42156717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:42198929-42199430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 888 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:42289027-42289544 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 754 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:42353785-42353994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 890 Neighboring gene Sharpr-MPRA regulatory region 8090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 755 Neighboring gene uncharacterized LOC124904160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 756 Neighboring gene heterogeneous nuclear ribonucleoprotein F pseudogene 1

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_163369.1 

    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
    41699675..41699734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    41570216..41570275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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