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LOC130006599 ATAC-STARR-seq lymphoblastoid active region 5402 [ Homo sapiens (human) ]

Gene ID: 130006599, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130006599
Gene description
ATAC-STARR-seq lymphoblastoid active region 5402
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: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (94129154..94129413)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (94045925..94046184)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene hephaestin like 1 Neighboring gene uncharacterized LOC124902735 Neighboring gene PHB1 pseudogene 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:93821850-93822408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:93822409-93822965 Neighboring gene NANOG hESC enhancer GRCh37_chr11:93838940-93839521 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:93852752-93853716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5401 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:93866399-93866898 Neighboring gene Sharpr-MPRA regulatory region 4215 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:93885086-93886285 Neighboring gene pannexin 1 Neighboring gene uncharacterized LOC105369435 Neighboring gene actin related protein 2/3 complex subunit 3 pseudogene 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:93970861-93972060 Neighboring gene NANOG hESC enhancer GRCh37_chr11:93995336-93995837 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:94011033-94012232

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_186044.1 

    Range
    101..360
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    94129154..94129413
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    94045925..94046184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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