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LOC130002643 ATAC-STARR-seq lymphoblastoid active region 29037 [ Homo sapiens (human) ]

Gene ID: 130002643, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130002643
Gene description
ATAC-STARR-seq lymphoblastoid active region 29037
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 LOC130002643 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127268294..127268413)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139474772..139474891)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Ral GEF with PH domain and SH3 binding motif 1 Neighboring gene uncharacterized LOC124902273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129985710-129986210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129986211-129986711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20300 Neighboring gene uncharacterized LOC124902274 Neighboring gene GTPase activating Rap/RanGAP domain like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130047596-130047803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20301 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:130094714-130095913 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:130098321-130099520 Neighboring gene DENR pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 1510 Neighboring gene uncharacterized LOC124902275

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_182089.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    127268294..127268413
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139474772..139474891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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