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LOC130005957 ATAC-STARR-seq lymphoblastoid silent region 3490 [ Homo sapiens (human) ]

Gene ID: 130005957, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005957
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3490
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 LOC130005957 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 (64802844..64803023)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64796154..64796333)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64570316..64570495)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64520964-64521574 Neighboring gene glycogen phosphorylase, muscle associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64525447-64526151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526152-64526855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526856-64527560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64527561-64528263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64530587-64531460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64532334-64533208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64533209-64534081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64534082-64534955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4914 Neighboring gene splicing factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3488 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:64545791-64546392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64557481-64557982 Neighboring gene mitogen-activated protein kinase kinase kinase kinase 2 Neighboring gene Sharpr-MPRA regulatory region 11124 Neighboring gene MPRA-validated peak1298 silencer Neighboring gene Sharpr-MPRA regulatory region 2965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3491 Neighboring gene menin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64594480-64594980 Neighboring gene CDC42 binding protein kinase gamma Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64609163-64609975 Neighboring gene Sharpr-MPRA regulatory region 8286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64610788-64611600 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3494

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 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_185402.1 

    Range
    101..280
    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
    64802844..64803023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64796154..64796333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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