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LOC130010079 ATAC-STARR-seq lymphoblastoid silent region 5487 [ Homo sapiens (human) ]

Gene ID: 130010079, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130010079
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5487
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 LOC130010079 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (102846771..102846820)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (102064967..102065016)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (103499121..103499170)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5486 Neighboring gene protein O-glucosyltransferase 2 Neighboring gene BIVM-ERCC5 readthrough Neighboring gene NANOG hESC enhancer GRCh37_chr13:103478160-103478661 Neighboring gene basic, immunoglobulin-like variable motif containing Neighboring gene ReSE screen-validated silencer GRCh37_chr13:103485696-103485895 Neighboring gene RNY5 pseudogene 8 Neighboring gene H3K27ac hESC enhancers GRCh37_chr13:103497312-103498136 and GRCh37_chr13:103498137-103498959 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:103518038-103519237 Neighboring gene ERCC excision repair 5, endonuclease Neighboring gene methyltransferase like 21E, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7975 Neighboring gene solute carrier family 10 member 2

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_189559.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    102846771..102846820
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    102064967..102065016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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