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LOC130008879 ATAC-STARR-seq lymphoblastoid silent region 4911 [ Homo sapiens (human) ]

Gene ID: 130008879, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008879
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4911
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 LOC130008879 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (117098982..117099091)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (117080030..117080139)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (117536787..117536896)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4909 Neighboring gene ribosomal protein L36 pseudogene 15 Neighboring gene F-box and WD repeat domain containing 8 Neighboring gene uncharacterized LOC100506551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117443824-117444346 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117447522-117448273 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:117461930-117463129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117473629-117474381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117474382-117475133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117477181-117478126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117478127-117479070 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:117479989-117480493 Neighboring gene Sharpr-MPRA regulatory region 12461 Neighboring gene Sharpr-MPRA regulatory region 12935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117490883-117491488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117492095-117492700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117500218-117500994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117500995-117501771 Neighboring gene tescalcin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4910 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:117537215-117537353 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:117538220-117538437 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117540353-117540852 Neighboring gene uncharacterized LOC105370010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7102 Neighboring gene TESC antisense RNA 1 (head to head) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117556298-117556892 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:117580597-117581796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4913 Neighboring gene F-box protein 21 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4915

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_187448.1 

    Range
    101..210
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    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    117098982..117099091
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    117080030..117080139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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