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LOC129993347 ATAC-STARR-seq lymphoblastoid active region 22125 [ Homo sapiens (human) ]

Gene ID: 129993347, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129993347
Gene description
ATAC-STARR-seq lymphoblastoid active region 22125
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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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Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (168480511..168480750)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (171839498..171839737)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene DExD/H-box helicase 60 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22124 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76106 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76110 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76113 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76114 Neighboring gene DExD/H-box 60 like Neighboring gene small nucleolar RNA SNORA51 Neighboring gene uncharacterized LOC107986198 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:169408038-169409237 Neighboring gene uncharacterized LOC124900807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76181 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76192 Neighboring gene palladin, cytoskeletal associated protein Neighboring gene basic transcription factor 3 like 4 pseudogene 4

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_172793.1 

    Range
    101..340
    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
    168480511..168480750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    171839498..171839737
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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