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LOC106992256 t(11;20)(p15;q11) topoisomerase (DNA) I recombination region [ Homo sapiens (human) ]

Gene ID: 106992256, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106992256
Gene description
t(11;20)(p15;q11) topoisomerase (DNA) I recombination region
Gene type
biological region
Feature type(s)
misc_recomb: mitotic
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region is known to undergo somatic cell DNA recombination with another region, the nucleoporin 98kDa (NUP98) recombination region, located on the p arm of chromosome 11. Recombination between these two regions results in a translocation known as the t(11;20)(p15;q11) rearrangement, and produces an in-frame gene fusion involving the nucleoporin 98kDa (NUP98) gene and the topoisomerase (DNA) I (TOP1) gene. The NUP98-TOP1 chimera, but not its reciprocal TOP1-NUP98 chimera, has been implicated in tumorigenesis. This chromosomal rearrangement has been observed in multiple tumors including acute monocytic leukemia (AMoL), therapy-related myelodysplastic syndrome (t-MDS), and de novo acute myeloid leukemia (AML). This recombination region is located within an intron of TOP1, while its recombination partner is located within an intron of NUP98. Both of these intronic regions are rich in repetitive elements. [provided by RefSeq, Dec 2015]
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Genomic context

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Location:
20q12-q13.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (41082685..41084304)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (42814362..42815982)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (39711325..39712944)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100128988 Neighboring gene uncharacterized LOC105372621 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:39625651-39626225 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:39631901-39633100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17885 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:39657161-39657512 Neighboring gene origin of replication in promoter of TOP1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12912 Neighboring gene RNA, U2 small nuclear 52, pseudogene Neighboring gene DNA topoisomerase I Neighboring gene Sharpr-MPRA regulatory region 14849 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:39686360-39687559 Neighboring gene PLCG1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12914 Neighboring gene translation initiation factor IF-2-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39764698-39765482 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:39766267-39767051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17889 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39774494-39774994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39774995-39775495 Neighboring gene phospholipase C gamma 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39786713-39787233 Neighboring gene microRNA 6871

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. Treatment-related acute myeloid leukemia characterized by t(11;20)(p15;q11) and del(9)(q22). Haimi M, et al. Cancer Genet Cytogenet, 2006 Jun. PMID 16737924
  2. A t(11;20)(p15;q11) may identify a subset of nontherapy-related acute myelocytic leukemia. Potenza L, et al. Cancer Genet Cytogenet, 2004 Mar. PMID 15036893
  3. Generation of the NUP98-TOP1 fusion transcript by the t(11;20) (p15;q11) in a case of acute monocytic leukemia. Chen S, et al. Cancer Genet Cytogenet, 2003 Jan 15. PMID 12645654
  4. Potential role for DNA topoisomerase II poisons in the generation of t(11;20)(p15;q11) translocations. Ahuja HG, et al. Genes Chromosomes Cancer, 2000 Oct. PMID 10959088
  5. Retroviral integration site analysis identifies ICSBP as a collaborating tumor suppressor gene in NUP98-TOP1-induced leukemia. Gurevich RM, et al. Exp Hematol, 2006 Sep. PMID 16939812

See all (11) citations in PubMed

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)

General gene information

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Other Names

  • NUP98-TOP1 recombination region
  • t(11;20)(p15;q11) TOP1 recombination region

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_046336.1 

    Range
    101..1720
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    41082685..41084304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    42814362..42815982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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