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LOC129995041 ATAC-STARR-seq lymphoblastoid silent region 16521 [ Homo sapiens (human) ]

Gene ID: 129995041, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129995041
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16521
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 LOC129995041 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 (151223965..151224044)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (151762913..151762992)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene annexin A6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150503406-150503906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23443 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:150537501-150538357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23444 Neighboring gene uncharacterized LOC107986463 Neighboring gene platelet derived growth factor receptor like 2, pseudogene Neighboring gene coiled-coil domain containing 69 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23446 Neighboring gene uncharacterized LOC105378230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23454 Neighboring gene Sharpr-MPRA regulatory region 974 Neighboring gene Sharpr-MPRA regulatory region 9347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16522 Neighboring gene uncharacterized LOC124901115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23455 Neighboring gene ganglioside GM2 activator

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_174487.1 

    Range
    101..180
    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
    151223965..151224044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    151762913..151762992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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