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LOC130005152 ATAC-STARR-seq lymphoblastoid silent region 3079 [ Homo sapiens (human) ]

Gene ID: 130005152, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005152
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3079
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 LOC130005152 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 (3423079..3423288)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (3468488..3468697)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (3444309..3444518)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene tumor suppressing subtransferable candidate 2 (pseudogene) Neighboring gene Sharpr-MPRA regulatory region 4578 Neighboring gene olfactory receptor family 7 subfamily E member 12 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3425235-3426069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3426070-3426903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3427261-3427774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3427775-3428286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3430516-3431016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3431017-3431517 Neighboring gene family with sequence similarity 86, member A pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3078 Neighboring gene MPRA-validated peak1172 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3456375-3456993 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:3458797-3458965 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 15 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:3480157-3480658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:3480659-3481158 Neighboring gene uncharacterized LOC105376526 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:3510409-3510910 Neighboring gene uncharacterized LOC101927708 Neighboring gene uncharacterized LOC107984301 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:3533122-3533622 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:3533623-3534123

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_184597.1 

    Range
    101..310
    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
    3423079..3423288
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    3468488..3468697
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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