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LOC129993456 ATAC-STARR-seq lymphoblastoid silent region 15834 [ Homo sapiens (human) ]

Gene ID: 129993456, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129993456
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15834
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 LOC129993456 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (184307195..184307244)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (187651000..187651049)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22202 Neighboring gene RNA, 7SL, cytoplasmic 28, pseudogene Neighboring gene uncharacterized LOC124900825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22204 Neighboring gene MYL12B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185234973-185235474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185238635-185239134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15835 Neighboring gene long intergenic non-protein coding RNA 2363 Neighboring gene Sharpr-MPRA regulatory region 724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22213 Neighboring gene long intergenic non-protein coding RNA 2362

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

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_172902.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    184307195..184307244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    187651000..187651049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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