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LOC129994671 ATAC-STARR-seq lymphoblastoid silent region 16362 [ Homo sapiens (human) ]

Gene ID: 129994671, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994671
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16362
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 LOC129994671 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (134525870..134526129)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (135051490..135051749)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (133861560..133861819)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901070 Neighboring gene RNA, 7SL, cytoplasmic 541, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:133868144-133868644 Neighboring gene jade family PHD finger 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133873253-133873806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133874500-133875431 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133875432-133876362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133876363-133877294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133884143-133885142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16365 Neighboring gene U7 small nuclear RNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133916765-133917297 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133917298-133917829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23156 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133928109-133928702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23158 Neighboring gene secretion associated Ras related GTPase 1B Neighboring gene HNF4 motif-containing MPRA enhancer 267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133968413-133968969

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_174117.1 

    Range
    101..360
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    134525870..134526129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    135051490..135051749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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