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LOC130005107 ATAC-STARR-seq lymphoblastoid silent region 3047 [ Homo sapiens (human) ]

Gene ID: 130005107, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005107
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3047
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 LOC130005107 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 (849363..849422)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (900741..900800)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (849363..849422)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:834349-834888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:837986-838960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:840788-841532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:841533-842278 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:842279-843022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3044 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:843356-843524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3046 Neighboring gene CD151 molecule (Raph blood group) Neighboring gene RNA polymerase II, I and III subunit L Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:854507-855020 Neighboring gene tetraspanin 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:858925-859458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:859459-859992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:859993-860525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:860526-861060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:863729-864262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:865863-866396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:870607-871369 Neighboring gene extensin-like Neighboring gene chitinase domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:889730-890249 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:891289-891806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:891807-892326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:893960-894462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:897610-898120 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:903420-903590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3048 Neighboring gene Sharpr-MPRA regulatory region 4982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:920183-920682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:937789-938701 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:940609-941519 Neighboring gene adaptor related protein complex 2 subunit alpha 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:942997-943671 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:944346-945020 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:945021-945694 Neighboring gene Sharpr-MPRA regulatory region 620 Neighboring gene RNA, U6 small nuclear 1025, pseudogene

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_184552.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    849363..849422
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    900741..900800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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