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LOC130010119 ATAC-STARR-seq lymphoblastoid silent region 5506 [ Homo sapiens (human) ]

Gene ID: 130010119, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130010119
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5506
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 LOC130010119 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 (110616015..110616174)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (109846640..109846799)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (111268362..111268521)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene collagen type IV alpha 2 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111155195-111156124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111159947-111160448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111160449-111160948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111164263-111164891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111166617-111167116 Neighboring gene COL4A2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111170170-111171006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8003 Neighboring gene Sharpr-MPRA regulatory region 8993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111183105-111183721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111186543-111187325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111209741-111210264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111210265-111210787 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:111213668-111213857 Neighboring gene RAB20, member RAS oncogene family Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:111253624-111254492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:111262660-111263160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:111263161-111263661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111266973-111267900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8005 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111284913-111285575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111286570-111287399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111287400-111288228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111289059-111289887 Neighboring gene NAXD antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111301435-111301934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8006 Neighboring gene NAD(P)HX dehydratase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8007 Neighboring gene cysteinyl-tRNA synthetase 2, mitochondrial Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8011 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:111364717-111364885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8013 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:111368201-111368894 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111371617-111372308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8015 Neighboring gene inhibitor of growth family member 1 Neighboring gene ribosomal protein L21 pseudogene 107

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_189592.1 

    Range
    101..260
    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
    110616015..110616174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    109846640..109846799
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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