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LOC130005593 ATAC-STARR-seq lymphoblastoid silent region 3270 [ Homo sapiens (human) ]

Gene ID: 130005593, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005593
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3270
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 LOC130005593 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 (43942225..43942354)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (44097575..44097704)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (43963775..43963904)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene alkB homolog 3, alpha-ketoglutarate dependent dioxygenase Neighboring gene ALKBH3 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:43941776-43942975 Neighboring gene uncharacterized LOC124902663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:43949635-43950136 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:43955407-43955585 Neighboring gene 1-aminocyclopropane-1-carboxylate synthase homolog (inactive) like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:43964814-43965643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:43965644-43966472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:43968482-43968982 Neighboring gene chromosome 11 open reading frame 96 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:43977126-43977352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44003904-44004404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44004405-44004905 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44026425-44027286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:44028815-44029314 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:44035825-44036324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4649 Neighboring gene 1-aminocyclopropane-1-carboxylate synthase homolog (inactive)

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_185038.1 

    Range
    101..230
    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
    43942225..43942354
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    44097575..44097704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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