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LOC129993608 ATAC-STARR-seq lymphoblastoid silent region 15896 [ Homo sapiens (human) ]

Gene ID: 129993608, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993608
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15896
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 LOC129993608 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 (6448822..6448891)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (6379188..6379257)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (6448935..6449004)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22330 Neighboring gene mediator complex subunit 10 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:6408294-6409493 Neighboring gene uncharacterized LOC124900933 Neighboring gene uncharacterized LOC105374639 Neighboring gene ubiquitin conjugating enzyme E2 QL1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15898 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:6583428-6583589 Neighboring gene long intergenic non-protein coding RNA 1018

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_173054.1 

    Range
    101..170
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    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
    6448822..6448891
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791776.1 Reference GRCh38.p14 PATCHES

    Range
    152632..152701
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    6379188..6379257
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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