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LOC129994383 ATAC-STARR-seq lymphoblastoid silent region 16244 [ Homo sapiens (human) ]

Gene ID: 129994383, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994383
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16244
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 LOC129994383 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 (114361138..114361347)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (114873954..114874163)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (113696835..113697044)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901047 Neighboring gene NANOG hESC enhancer GRCh37_chr5:113182507-113183008 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:113270609-113270841 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:113374279-113374780 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:113374781-113375280 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:113459198-113459408 Neighboring gene potassium calcium-activated channel subfamily N member 2 Neighboring gene NANOG hESC enhancer GRCh37_chr5:113590875-113591386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:113613789-113614290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:113614291-113614790 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:113643487-113644315 Neighboring gene RN7SK pseudogene 89 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:113695880-113696796 Neighboring gene NANOG hESC enhancer GRCh37_chr5:113724412-113724913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22922 Neighboring gene uncharacterized LOC101927078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:113880373-113880872 Neighboring gene long intergenic non-protein coding RNA 1957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:114117551-114118374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:114118375-114119196 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114364005-114364746 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114364747-114365486 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:114368052-114369251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22923 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:114404076-114405275 Neighboring gene Sharpr-MPRA regulatory region 9285 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114426221-114426720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114426721-114427222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22925 Neighboring gene tripartite motif containing 36

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_173829.1 

    Range
    101..310
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    114361138..114361347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    114873954..114874163
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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