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LOC130006770 ATAC-STARR-seq lymphoblastoid silent region 3908 [ Homo sapiens (human) ]

Gene ID: 130006770, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006770
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3908
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 LOC130006770 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 (113314394..113314643)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (113324834..113325083)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (113185116..113185365)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RNA, U7 small nuclear 187 pseudogene Neighboring gene neural cell adhesion molecule 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:113017979-113018497 Neighboring gene NCAM1 antisense RNA1 Neighboring gene TTC12 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 9915 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:113202304-113203503 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:113214693-113215892 Neighboring gene tetratricopeptide repeat domain 12 Neighboring gene Sharpr-MPRA regulatory region 12815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5539 Neighboring gene ankyrin repeat and kinase domain containing 1 Neighboring gene dopamine receptor D2 Neighboring gene microRNA 4301

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_186215.1 

    Range
    101..350
    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
    113314394..113314643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    113324834..113325083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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