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LOC129992365 ATAC-STARR-seq lymphoblastoid silent region 15335 [ Homo sapiens (human) ]

Gene ID: 129992365, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992365
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15335
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 LOC129992365 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (26319318..26319587)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (26304309..26304578)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (26320940..26321209)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene recombination signal binding protein for immunoglobulin kappa J region Neighboring gene uncharacterized LOC124900690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26206221-26206722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21392 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26239970-26240520 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26240521-26241069 Neighboring gene uncharacterized LOC105374542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15334 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26301633-26302396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21396 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:26323092-26324013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15336 Neighboring gene Sharpr-MPRA regulatory region 12863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26353747-26354248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26354249-26354748 Neighboring gene Sharpr-MPRA regulatory region 2944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21397 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:26407341-26408540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26454493-26455031 Neighboring gene cholecystokinin A receptor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:26569763-26570962 Neighboring gene Sharpr-MPRA regulatory region 5841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21398 Neighboring gene TBC1 domain family member 19 Neighboring gene Sharpr-MPRA regulatory region 1278 Neighboring gene small nucleolar RNA SNORD74

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_171811.1 

    Range
    101..370
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    26319318..26319587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    26304309..26304578
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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