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LOC130065833 ATAC-STARR-seq lymphoblastoid silent region 12894 [ Homo sapiens (human) ]

Gene ID: 130065833, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065833
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12894
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 LOC130065833 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (37750264..37750313)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (39474338..39474387)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (36378666..36378715)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100287792 Neighboring gene uncharacterized LOC105372609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12893 Neighboring gene catenin beta like 1 Neighboring gene uncharacterized LOC124904895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36414145-36414646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36414647-36415146 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:36416862-36418061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36504902-36505402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36505403-36505903 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12895 Neighboring gene uncharacterized LOC124904896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36530829-36531792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36537707-36538207 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36542615-36543462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36543463-36544310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36545629-36546130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17852 Neighboring gene V-set and transmembrane domain containing 2 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36568310-36568810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36568811-36569311 Neighboring gene MPRA-validated peak4207 silencer Neighboring gene RN7SK pseudogene 185

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_200250.1 

    Range
    101..150
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    37750264..37750313
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    39474338..39474387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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