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LOC129995352 ATAC-STARR-seq lymphoblastoid silent region 16662 [ Homo sapiens (human) ]

Gene ID: 129995352, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995352
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16662
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 LOC129995352 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176619192..176619461)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177165775..177166044)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176046193..176046462)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175976615-175977548 Neighboring gene RNA, 7SL, cytoplasmic 684, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175979197-175979830 Neighboring gene cadherin related family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175993117-175994082 Neighboring gene Sharpr-MPRA regulatory region 7457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16659 Neighboring gene G protein regulated inducer of neurite outgrowth 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16660 Neighboring gene Sharpr-MPRA regulatory region 11151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16663 Neighboring gene synuclein beta Neighboring gene microRNA 4281 Neighboring gene eukaryotic translation initiation factor 4E family member 1B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176070445-176071086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176071087-176071726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176072308-176072818 Neighboring gene Sharpr-MPRA regulatory region 4950

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_174798.1 

    Range
    101..370
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    176619192..176619461
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177165775..177166044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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