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LOC129993537 ATAC-STARR-seq lymphoblastoid silent region 15866 [ Homo sapiens (human) ]

Gene ID: 129993537, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993537
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15866
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 LOC129993537 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 (343767..343866)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (334732..334831)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (343882..343981)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:270110-270802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15861 Neighboring gene PDCD6-AHRR readthrough (NMD candidate) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:278988-279488 Neighboring gene PDCD6 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:279489-279989 Neighboring gene programmed cell death 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:295122-295292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:296594-297122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:297123-297651 Neighboring gene PPP4R2 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:301361-301866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:301867-302372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:306908-307792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:322065-322632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22273 Neighboring gene aryl hydrocarbon receptor repressor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:372826-373456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22281 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:399561-400760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15871 Neighboring gene mitochondrial translational initiation factor 3 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85003 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85008 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85009 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85011 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85012 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85017 Neighboring gene AHRR intron CAGE-defined high expression enhancer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:415251-415804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15872 Neighboring gene EXOC3 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_172983.1 

    Range
    101..200
    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
    343767..343866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    334732..334831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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