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LOC130005123 ATAC-STARR-seq lymphoblastoid silent region 3062 [ Homo sapiens (human) ]

Gene ID: 130005123, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005123
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3062
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 LOC130005123 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 (1840137..1840256)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (1925936..1926055)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (1861367..1861486)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902610 Neighboring gene actin beta pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1844971-1845472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1854181-1854796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1854797-1855410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3063 Neighboring gene uncharacterized LOC107984299 Neighboring gene synaptotagmin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1870712-1871698 Neighboring gene troponin I2, fast skeletal type Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4293 Neighboring gene lymphocyte specific protein 1 Neighboring gene microRNA 4298

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_184568.1 

    Range
    101..220
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    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
    1840137..1840256
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160004.1 Reference GRCh38.p14 PATCHES

    Range
    30640..30759
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    1925936..1926055
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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