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LOC129993887 ATAC-STARR-seq lymphoblastoid active region 22548 [ Homo sapiens (human) ]

Gene ID: 129993887, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129993887
Gene description
ATAC-STARR-seq lymphoblastoid active region 22548
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: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (54390529..54390658)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (55218115..55218244)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ADP ribosylation factor like GTPase 15 Neighboring gene microRNA 581 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:53313399-53314173 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:53314174-53314947 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:53315686-53316592 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 ribosomal protein L37 pseudogene 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:53735813-53736314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22550 Neighboring gene heat shock protein family B (small) member 3

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_173333.1 

    Range
    101..230
    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
    54390529..54390658
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    55218115..55218244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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