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LOC129994806 ATAC-STARR-seq lymphoblastoid silent region 16429 [ Homo sapiens (human) ]

Gene ID: 129994806, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129994806
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16429
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 LOC129994806 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (139748239..139748288)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140273313..140273362)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901085 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139104350-139104850 Neighboring gene RNA, U6 small nuclear 236, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139117735-139118662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139121544-139122093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139122094-139122642 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139123561-139124154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139125678-139126325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139128271-139128918 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139131846-139131997 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139137793-139138691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139138692-139139589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139141892-139142555 Neighboring gene PSD2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139143219-139143882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139142556-139143218 Neighboring gene pleckstrin and Sec7 domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139169627-139170127 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139174912-139175111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139194145-139194646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139259501-139260264 Neighboring gene neuregulin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23255 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:139364881-139366080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139422349-139423018 Neighboring gene uncharacterized LOC124900193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16442 Neighboring gene mitosis associated long intergenic non-coding 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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_174252.1 

    Range
    101..150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    139748239..139748288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    140273313..140273362
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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