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LOC130009601 ATAC-STARR-seq lymphoblastoid silent region 5279 [ Homo sapiens (human) ]

Gene ID: 130009601, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009601
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5279
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 LOC130009601 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (40517576..40517775)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (39736583..39736782)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (41091713..41091912)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene RNY3 pseudogene 9 Neighboring gene Sharpr-MPRA regulatory region 8959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40926515-40927014 Neighboring gene long intergenic non-protein coding RNA 598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40956871-40957426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7604 Neighboring gene LINC00598 intron ENCODE-defined enhancer Neighboring gene RN7SK pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41019797-41020402 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:41092118-41093317 Neighboring gene Sharpr-MPRA regulatory region 6999 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:41114319-41114868 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:41114869-41115418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:41115419-41115966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:41119870-41120370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:41120371-41120871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41137465-41138218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7610 Neighboring gene forkhead box O1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7612 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41225852-41226373 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41226374-41226894 Neighboring gene ring finger protein, LIM domain interacting pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7613 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:41254046-41254810 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41254811-41255575 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41255576-41256340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5285 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:41286412-41286912 Neighboring gene microRNA 320d-1

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_189174.1 

    Range
    101..300
    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    40517576..40517775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    39736583..39736782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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