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LOC129994633 ATAC-STARR-seq lymphoblastoid silent region 16351 [ Homo sapiens (human) ]

Gene ID: 129994633, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994633
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16351
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 LOC129994633 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 (134005239..134005288)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (134528874..134528923)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (133340930..133340979)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23112 Neighboring gene chromosome 5 open reading frame 15 Neighboring gene uncharacterized LOC105379183 Neighboring gene MPRA-validated peak5471 silencer Neighboring gene voltage dependent anion channel 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23120 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133382518-133383158 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133383159-133383798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133385203-133385778 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:133387505-133388080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133394172-133394770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133394771-133395367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23121 Neighboring gene short transmembrane mitochondrial protein 1-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133422388-133422888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133422889-133423389 Neighboring gene Sharpr-MPRA regulatory region 10905 Neighboring gene Sharpr-MPRA regulatory region 12956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133437181-133438148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133438510-133439380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133441120-133441988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133442973-133443520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23127 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133457701-133458202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133464814-133465636 Neighboring gene transcription factor 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133465637-133466458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133475053-133476030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23134

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_174079.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    134005239..134005288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    134528874..134528923
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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