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LOC129937454 ATAC-STARR-seq lymphoblastoid silent region 14669 [ Homo sapiens (human) ]

Gene ID: 129937454, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129937454
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14669
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 LOC129937454 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (125915795..125915844)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (128648214..128648263)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (125634638..125634687)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene translation initiation factor IF-2-like Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 11 Neighboring gene long intergenic non-protein coding RNA 2614 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 4 Neighboring gene NANOG hESC enhancer GRCh37_chr3:125609269-125610164 Neighboring gene uncharacterized LOC102723696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:125635188-125635778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125650034-125650534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125650535-125651035 Neighboring gene family with sequence similarity 86, member A pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125655344-125655844 Neighboring gene ALG1 like 1, pseudogene Neighboring gene FBRSL1 pseudogene 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_170464.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    125915795..125915844
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    128648214..128648263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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