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LOC130067277 ATAC-STARR-seq lymphoblastoid silent region 13645 [ Homo sapiens (human) ]

Gene ID: 130067277, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067277
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13645
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 LOC130067277 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (33579662..33579731)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (34037195..34037264)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (33975648..33975717)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene LARGE xylosyl- and glucuronyltransferase 1 Neighboring gene uncharacterized LOC124905106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18881 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:33833834-33835033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18884 Neighboring gene microRNA 4764 Neighboring gene MPRA-validated peak4484 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18885 Neighboring gene Sharpr-MPRA regulatory region 960 Neighboring gene uncharacterized LOC105373007 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:34018247-34018422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34118270-34118798 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34134097-34134616 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34134617-34135136 Neighboring gene small nucleolar RNA, H/ACA box 50B Neighboring gene LARGE antisense RNA 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_201692.1 

    Range
    101..170
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    33579662..33579731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    34037195..34037264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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