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LOC129993889 ATAC-STARR-seq lymphoblastoid active region 22550 [ Homo sapiens (human) ]

Gene ID: 129993889, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993889
Gene description
ATAC-STARR-seq lymphoblastoid active region 22550
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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See LOC129993889 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (54440761..54440820)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (55268320..55268379)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (53736591..53736650)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ARF like GTPase 15 Neighboring gene RNA, 7SL, cytoplasmic 801, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr5:53476360-53476866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:53592529-53593029 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:53600502-53601165 Neighboring gene CRISPRi-validated cis-regulatory element chr5.1314 Neighboring gene GATA motif-containing MPRA enhancer 36 Neighboring gene long intergenic non-protein coding RNA 1033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:53735813-53736314 Neighboring gene ribosomal protein L37 pseudogene 25 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:53813343-53813584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:53814497-53815441 Neighboring gene heat shock protein family B (small) member 3 Neighboring gene sorting nexin 18 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:53935341-53935915

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_173335.1 

    Range
    101..160
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    54440761..54440820
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    55268320..55268379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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