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LOC129929116 ATAC-STARR-seq lymphoblastoid silent region 63 [ Homo sapiens (human) ]

Gene ID: 129929116, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929116
Gene description
ATAC-STARR-seq lymphoblastoid silent region 63
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 LOC129929116 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1349550..1349869)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (781176..781495)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1284930..1285249)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene taste 1 receptor member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 61 Neighboring gene dishevelled segment polarity protein 1 Neighboring gene microRNA 6808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1281421-1282299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1282501-1283130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1283131-1283760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 62 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 64 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1288877-1289508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1289509-1290140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1290141-1290771 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1291896-1292448 Neighboring gene matrix remodeling associated 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1293036-1293618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 65 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 66 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1307318-1308085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 67 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1310373-1311278 Neighboring gene aurora kinase A interacting protein 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_162173.1 

    Range
    101..420
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1349550..1349869
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    781176..781495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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