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LOC130005133 ATAC-STARR-seq lymphoblastoid silent region 3066 [ Homo sapiens (human) ]

Gene ID: 130005133, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130005133
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3066
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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Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (2377842..2378041)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (2467210..2467409)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene CD81 antisense RNA 1 Neighboring gene uncharacterized LOC124902611 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2359685-2360602 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2360603-2361518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2381313-2382101 Neighboring gene uncharacterized LOC105376520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2396527-2397285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2400391-2401372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2401373-2402355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4297 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4298 Neighboring gene nonconserved acetylation island sequence 93 enhancer Neighboring gene CD81 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4301 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2421638-2422140 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2422141-2422641 Neighboring gene tumor suppressing subtransferable candidate 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2435338-2435838 Neighboring gene transient receptor potential cation channel subfamily M member 5 Neighboring gene Sharpr-MPRA regulatory region 9407

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

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_184578.1 

    Range
    101..300
    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
    2377842..2378041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    2467210..2467409
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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