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LOC130068028 ATAC-STARR-seq lymphoblastoid active region 29478 [ Homo sapiens (human) ]

Gene ID: 130068028, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068028
Gene description
ATAC-STARR-seq lymphoblastoid active region 29478
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 LOC130068028 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (20141080..20141239)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (19723972..19724131)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (20159198..20159357)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29480 Neighboring gene EIF1AX antisense RNA 1 Neighboring gene eukaryotic translation initiation factor 1A X-linked Neighboring gene small Cajal body-specific RNA 9 like Neighboring gene ribosomal protein S6 kinase A3 Neighboring gene Sharpr-MPRA regulatory region 15471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20697 Neighboring gene Sharpr-MPRA regulatory region 100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29484 Neighboring gene RN7SK pseudogene 183

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_202443.1 

    Range
    101..260
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    20141080..20141239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    19723972..19724131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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