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LOC130001325 ATAC-STARR-seq lymphoblastoid silent region 19618 [ Homo sapiens (human) ]

Gene ID: 130001325, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001325
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19618
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 LOC130001325 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143368633..143369092)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144516267..144516726)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144450803..144451262)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902037 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144389476-144389976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144389977-144390477 Neighboring gene DNA topoisomerase I mitochondrial Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144403237-144403900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144403901-144404564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144404565-144405228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144405229-144405890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144414065-144414598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144416274-144416958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144421307-144422044 Neighboring gene RNA, U6 small nuclear 220, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144450004-144450559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144451300-144452207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144452208-144453114 Neighboring gene RHPN1 antisense RNA 1 (head to head) Neighboring gene rhophilin Rho GTPase binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144482673-144483320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144483321-144483968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144483969-144484616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144484617-144485263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144487803-144488782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19621 Neighboring gene MAFA antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144504663-144505250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19622 Neighboring gene MAF bZIP transcription factor A

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_180771.1 

    Range
    101..560
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    143368633..143369092
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    144516267..144516726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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