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LOC107980440 ABL breakpoint recombination region [ Homo sapiens (human) ]

Gene ID: 107980440, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107980440
Gene description
ABL breakpoint recombination region
Gene type
biological region
Feature type(s)
misc_recomb: meiotic, mitotic
misc_structure
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 mitotic DNA recombination with other recombination regions found within the BCR, RhoGEF and GTPase activating protein (BCR) gene, including the major-, minor-, micro-, p195, p225, and p230 breakpoint cluster regions, located on the q arm of chromosome 22. Recombination between these regions results in t(9;22)(q34;q11) translocations, and can produce different gene fusions involving the BCR, RhoGEF and GTPase activating protein (BCR) gene and the ABL proto-oncogene 1, non-receptor tyrosine kinase (ABL1) gene, depending on the location of the recombination region within BCR. The smaller derivative chromosome resulting from this translocation is commonly known as the Philadelphia (Ph) chromosome. Translocations resulting from recombination events produce different chimeric transcripts. Recombination with the major-breakpoint cluster region produces e13a2 and e14a2 transcripts, recombination with the minor-breakpoint cluster region produces the e1a2 transcript, and recombination with the micro-breakpoint cluster region produces the e19a2 transcript, the e6a2, e8a2, e15a2, and e18a2 are produced as a result of recombination with the p195, p200, e15a2 and e18a2 breakpoint recombination regions, respectively. The abnormal tyrosine kinase activity of the chimeric proteins can result in leukemias such as chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL), and acute myelogenous leukemia (AML). It has been noted that this region contains a palindromic sequence with 243 nucleotides of perfect reverse complementarity, separated by about 2 kb. Analysis of recombination breakpoints is consistent with recombination occurring through a non-homologous end joining (NHEJ) pathway. A mechanism to explain this recombination event has yet to be determined, but it has been noted that BCR and ABL tend to be in close physical proximity during cell division in hematopoietic stem cells. This close proximity could provide opportunities for aberrant recombination in the event of double strand break formation. [provided by RefSeq, May 2016]
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Genomic context

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Location:
9q34.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130710129..130854140)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142915086..143059013)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133585516..133729527)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:133541982-133543181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133556829-133557504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29155 Neighboring gene PR/SET domain 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29157 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133587784-133588460 Neighboring gene umcharacterized LOC128092248 Neighboring gene exosome component 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133604882-133605718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133605719-133606555 Neighboring gene ribosomal protein L37 pseudogene 17 Neighboring gene ABL proto-oncogene 1, non-receptor tyrosine kinase Neighboring gene ReSE screen-validated silencer GRCh37_chr9:133635228-133635409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29161 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133642635-133643440 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133643441-133644245 Neighboring gene uncharacterized LOC124902288 Neighboring gene uncharacterized LOC124902287 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133709696-133710222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133710223-133710748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20408 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:133722835-133723457 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133735115-133735964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133735965-133736812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133737874-133738374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133738375-133738875 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:133741863-133742364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29164 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:133756258-133757457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133759146-133759916 Neighboring gene Sharpr-MPRA regulatory region 3771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133769017-133769531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133770320-133771007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133771008-133771694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133789692-133790384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133794286-133794826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133796861-133797810 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:133798030-133798213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133798761-133799708 Neighboring gene pyroglutamylated RFamide peptide Neighboring gene fibrinogen C domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133805119-133805663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133814336-133815266 Neighboring gene FIBCD1 antisense RNA 1

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. A novel BCR-ABL fusion gene (e6a2) in a patient with Philadelphia chromosome-negative chronic myelogenous leukemia. Hochhaus A, et al. Blood, 1996 Sep 15. PMID 8822944
  2. A novel e8a2 BCR-ABL1 intronic fusion through insertion of a chromosome 22 BCR gene fragment into chromosome 9 in an atypical Philadelphia (Ph) chromosome chronic myeloid leukemia patient. Chen L, et al. Leuk Lymphoma, 2016 Dec. PMID 27118564
  3. Multiplex RT-PCR Assay for Detection of Common Fusion Transcripts in Acute Lymphoblastic Leukemia and Chronic Myeloid Leukemia Cases. Limsuwanachot N, et al. Asian Pac J Cancer Prev, 2016. PMID 26925663
  4. Simple multiplex RT-PCR for identifying common fusion BCR-ABL transcript types and evaluation of molecular response of the a2b2 and a2b3 transcripts to Imatinib resistance in north Indian chronic myeloid leukemia patients. Mir R, et al. Indian J Cancer, 2015 Jul-Sep. PMID 26905124
  5. Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients. Alikian M, et al. J Mol Diagn, 2016 Mar. PMID 26857065

See all (310) 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

  • ABL proto-oncogene 1, non-receptor tyrosine kinase recombination region
  • Philadelphia Chromosome ABL 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_050744.1 

    Range
    101..144112
    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
    130710129..130854140
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    142915086..143059013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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