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LOC129994757 ATAC-STARR-seq lymphoblastoid silent region 16408 [ Homo sapiens (human) ]

Gene ID: 129994757, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994757
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16408
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 LOC129994757 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 (139382598..139382657)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (139908691..139908750)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138718287..138718346)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 64 Neighboring gene poly(A) binding protein interacting protein 2 Neighboring gene solute carrier family 23 member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138716531-138717471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138723739-138724286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138724287-138724834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138724835-138725382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23225 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16409 Neighboring gene Sharpr-MPRA regulatory region 996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16411 Neighboring gene marginal zone B and B1 cell specific protein Neighboring gene spermatogenesis associated 24 Neighboring gene proline rich basic protein 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_174203.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    139382598..139382657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    139908691..139908750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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