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LOC130005697 ATAC-STARR-seq lymphoblastoid silent region 3342 [ Homo sapiens (human) ]

Gene ID: 130005697, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005697
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3342
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 LOC130005697 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (48031677..48031746)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (48201234..48201303)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (48053229..48053298)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902844 Neighboring gene SEC61 translocon subunit beta pseudogene Neighboring gene Sharpr-MPRA regulatory region 14057 Neighboring gene Sharpr-MPRA regulatory region 4641 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:47968069-47969268 Neighboring gene Sharpr-MPRA regulatory region 13015 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:47995557-47996216 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47996217-47996876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3340 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48015112-48015327 Neighboring gene GATA motif-containing MPRA enhancer 240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4711 Neighboring gene protein tyrosine phosphatase receptor type J Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48050132-48050706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48072419-48072920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48072921-48073420 Neighboring gene Sharpr-MPRA regulatory region 8111 Neighboring gene NANOG hESC enhancer GRCh37_chr11:48077877-48078378 Neighboring gene Sharpr-MPRA regulatory region 12058 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48092882-48093057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48112153-48112964 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:48119178-48119678 Neighboring gene microRNA 3161 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48149227-48149587 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48198445-48198617 Neighboring gene NANOG hESC enhancer GRCh37_chr11:48212556-48213092 Neighboring gene olfactory receptor family 4 subfamily B member 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_185142.1 

    Range
    101..170
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    48031677..48031746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    48201234..48201303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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