| Accession | HsInv1000 | Region of the inversion | chr3:164008436-164030338 |
| Status | Obsolete | Prediction type | Simple |
| Estimated Inversion Size | 21,902 bp | Supporting predictions | 2 |
| Inverted allele frequency | 0.3333 | Mechanism of origin | NHEJ or FoSTeS |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr3:164008436-164008437 |
| Ancestral orientation | Standard | Breakpoint 2 | chr3:164030337-164030338 |
| Comments | Inverted allele includes two deletions of 19.6 kb and 16 bp flanking the inverted region
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Paired-end mapping analysis of the J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr3:164007964-164009561 | Breakpoint 2 | chr3:164030337-164031814 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr3:164008271-164008434 | Breakpoint 2 | chr3:164030071-164030328 | ||||
| Individuals |
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+ Validation and genotyping
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 6 individuals: 4 HapMap/1000GP, 2 Other 1 DEL/DEL - 1 INV/DEL - 1 STD/DEL - 1 STD/STD - 1 STD/INV - 1 INV/INV  |
| Comment | Quantitative and regular PCR confirmed the presence of a 19.6 kb deletion associated to the inverted allele and the existence of an additional 114.2 kb deletion including the entire inversion region |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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Yoruba in Ibadan, Nigeria (YRI) (Pang et al. 2013) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
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Africa (AFR) summary | 1 | 0 | 1.0000 | 0.0000 | NA |
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+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
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Utah residents with Northern and Western European ancestry (CEU) (Pang et al. 2013) | 3 | 2 | 0.6667 | 0.3333 | > 0.1 |
| Europe (EUR)
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Europe (EUR) summary | 3 | 2 | 0.6667 | 0.3333 | > 0.1 |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Pang et al. 2013) | 2 | 2 | 0.5000 | 0.5000 | 0 |
| Unknown
|
Unknown summary | 2 | 2 | 0.5000 | 0.5000 | 0 |
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+ Breakpoints
| Breakpoint 1 | chr3:164008436-164008437 | Breakpoint 2 | chr3:164030337-164030338 | ||
| Study | Pang et al. 2013 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ or FoSTeS
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| Flexibility | 11.55 | GC content | 0.22 | Stability | 1.69 |
| Comments |
Inverted region is flanked by two deletions of 19.6 kb and 16 bp and was probably generated by NHEJ or FoSTeS mediated by microhomology. Current inverted region include the deletion in BP1. |
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+ Evolutionary history
| Ancestral allele | Standard | Age | ND |
| Derived allele | Inverted | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Polymerase chain reaction (PCR) | Pang et al. 2013 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
HsInv1000 and HsInv0052 merge into HsInv1122
- 2015-02-23 10:15:07
| Breakpoint 1 | chr3:164008436-164008437 | Breakpoint 2 | chr3:164030337-164030338 |
| Study | Pang et al. 2013 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:15:07
| Breakpoint 1 | chr3:164007834-164008871 | Breakpoint 2 | chr3:164029728-164030671 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:07
| Breakpoint 1 | chr3:164007834-164008871 | Breakpoint 2 | chr3:164029728-164030671 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:07
| Breakpoint 1 | chr3:164007834-164008871 | Breakpoint 2 | chr3:164029728-164030671 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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