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LOC129936977 ATAC-STARR-seq lymphoblastoid silent region 14500 [ Homo sapiens (human) ]

Gene ID: 129936977, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936977
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14500
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 LOC129936977 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (63864324..63864543)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (63907932..63908151)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (63850000..63850219)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene cadherin related family member 18, pseudogene Neighboring gene chromosome 3 open reading frame 49 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14497 Neighboring gene THO complex subunit 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14499 Neighboring gene THOC7 antisense RNA 1 Neighboring gene ataxin 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20031 Neighboring gene ataxin 7 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20032 Neighboring gene SCA7/ATXN7 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:63946089-63946588 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63950216-63950720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20035 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:63956153-63956804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:63958786-63959286 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63986120-63986621 Neighboring gene PSMD6 antisense RNA 2 Neighboring gene PSMD6 antisense RNA 1 Neighboring gene proteasome 26S subunit, non-ATPase 6

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_169988.1 

    Range
    101..320
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    63864324..63864543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    63907932..63908151
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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