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LOC129993999 ATAC-STARR-seq lymphoblastoid active region 22624 [ Homo sapiens (human) ]

Gene ID: 129993999, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993999
Gene description
ATAC-STARR-seq lymphoblastoid active region 22624
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 LOC129993999 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 (67195623..67195772)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (68017775..68017924)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (66491451..66491600)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22621 Neighboring gene peptidylprolyl isomerase A pseudogene 78 Neighboring gene microtubule associated serine/threonine kinase family member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22622 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:66075742-66076941 Neighboring gene NANOG hESC enhancer GRCh37_chr5:66125559-66126060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16068 Neighboring gene NANOG hESC enhancer GRCh37_chr5:66137580-66138081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:66145039-66146238 Neighboring gene Sharpr-MPRA regulatory region 1390 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:66199778-66200630 Neighboring gene Sharpr-MPRA regulatory region 14441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16069 Neighboring gene Sharpr-MPRA regulatory region 14150 Neighboring gene MAST4 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:66354795-66355337 Neighboring gene Sharpr-MPRA regulatory region 2367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:66462629-66463134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22623 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:66501978-66503177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22625 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:66515108-66515295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22626 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:66528881-66529430 Neighboring gene CD180 molecule Neighboring gene TCL1A interacting lncRNA, retroperitoneal liposarcoma associated Neighboring gene uncharacterized LOC124900989

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_173445.1 

    Range
    101..250
    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
    67195623..67195772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    68017775..68017924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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