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LOC129994334 ATAC-STARR-seq lymphoblastoid active region 22880 [ Homo sapiens (human) ]

Gene ID: 129994334, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994334
Gene description
ATAC-STARR-seq lymphoblastoid active region 22880
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 LOC129994334 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 (109409199..109409318)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (109913814..109913933)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (108744900..108745019)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene FER tyrosine kinase Neighboring gene uncharacterized LOC124901040 Neighboring gene NANOG hESC enhancer GRCh37_chr5:108506215-108506770 Neighboring gene MPRA-validated peak5411 silencer Neighboring gene MPRA-validated peak5412 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr5:108533816-108534023 Neighboring gene uncharacterized LOC285638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:108626441-108626942 Neighboring gene Sharpr-MPRA regulatory region 6746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22879 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22881 Neighboring gene praja ring finger ubiquitin ligase 2 Neighboring gene uncharacterized LOC105379117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22882 Neighboring gene Sharpr-MPRA regulatory region 13215 Neighboring gene keratin 18 pseudogene 42

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_173780.1 

    Range
    101..220
    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
    109409199..109409318
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    109913814..109913933
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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