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LOC130005100 ATAC-STARR-seq lymphoblastoid silent region 3039 [ Homo sapiens (human) ]

Gene ID: 130005100, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005100
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3039
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 LOC130005100 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 (830166..830775)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (881601..882210)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (830166..830775)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:811306-812046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:812047-812787 Neighboring gene ribosomal protein lateral stalk subunit P2 Neighboring gene small nucleolar RNA, H/ACA box 52 Neighboring gene Sharpr-MPRA regulatory region 11801 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4287 Neighboring gene patatin like domain 2, triacylglycerol lipase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:827342-827880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:828421-828958 Neighboring gene calcium release activated channel regulator 2B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:828959-829498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:829499-830036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:831115-831654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:831655-832192 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 CD151 molecule (Raph blood group) 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 RNA polymerase II, I and III subunit L

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_184545.1 

    Range
    101..710
    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
    830166..830775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    881601..882210
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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