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LOC129992787 ATAC-STARR-seq lymphoblastoid silent region 15544 [ Homo sapiens (human) ]

Gene ID: 129992787, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992787
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15544
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 LOC129992787 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 (84503950..84503999)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (87833946..87833995)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (85425103..85425152)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:85165003-85165976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:85165977-85166950 Neighboring gene heart enhancer 9 Neighboring gene PLAG1 like zinc finger 2 pseudogene Neighboring gene VISTA enhancer hs680 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:85257789-85258318 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:85258319-85258846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:85263663-85264162 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:85283860-85284085 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:85299952-85300636 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:85306108-85306821 Neighboring gene NANOG hESC enhancer GRCh37_chr4:85334758-85335365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:85402785-85403285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:85404850-85405688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:85413525-85414416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:85416773-85417273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15545 Neighboring gene uncharacterized LOC102723338 Neighboring gene NK6 homeobox 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:85486943-85487584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:85504073-85505026 Neighboring gene ribosomal protein L3 pseudogene 13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:85517394-85518371 Neighboring gene Sharpr-MPRA regulatory region 8979 Neighboring gene CDP-diacylglycerol synthase 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 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 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_172233.1 

    Range
    101..150
    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
    84503950..84503999
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    87833946..87833995
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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