| Accession | HsInv0374 | Region of the inversion | chr17:25967879-25981879 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 8,864 bp | Supporting predictions | 2 |
| Inverted allele frequency | 0.4444 | Mechanism of origin | NAHR |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr17:25967879-25973016 |
| Ancestral orientation | NA | Breakpoint 2 | chr17:25976743-25981879 |
|
|
 |
|
|
Human Polymorphic Inversion DataBase
|
General information
- Region map
+ Predictions
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||||||||
| Method | Paired-end mapping (PEM), Long-read sequencing | ||||||||||
| Name | |||
| Breakpoint 1 | chr17:25973712-25973712 | Breakpoint 2 | chr17:25975967-25975967 |
| Individuals | 2 out of 2504 individuals
 | ||
- Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr17:25938379-25973376 | Breakpoint 2 | chr17:25976637-26010875 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.98946 | ||||||||||||||||||||
| Support | 12 probes | ||||||||||||||||||||||
| Individuals |
| ||||||||||||||||||||||
+ Validation and genotyping
-Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | Validated |
| Genotyping | 9 individuals: 8 HapMap/1000GP, 1 Other 3 STD/STD - 4 STD/INV - 2 INV/INV |
- Frequency
|
|
+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
Yoruba in Ibadan, Nigeria (YRI) (Martinez-Fundichely et al. 2014 (in preparation)) | 4 | 4 | 0.5000 | 0.5000 | > 0.5 |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 4 | 0.5000 | 0.5000 | > 0.5 |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
Utah residents with Northern and Western European ancestry (CEU) (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 0 | 1.0000 | 0.0000 | NA |
| Europe (EUR)
|
Europe (EUR) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
|
Han Chinese in Beijing, China (CHB) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| Japanese
|
Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
|
Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| Unknown
|
Unknown summary | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
|---|
+ Breakpoints
| Breakpoint 1 | chr17:25967879-25973016 | Breakpoint 2 | chr17:25976743-25981879 | |||||||||||||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | |||||||||||||||
| Description | Breakpoints defined by comparison with a sequenced fosmid | |||||||||||||||
| Definition method | Manual curation | |||||||||||||||
| Mechanism of origin |
NAHR
|
|||||||||||||||
| Flexibility | 10.87 | GC content | 0.49 | Stability | 1.96 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 5.8 kb inverted SDs with 99.5% identity |
|||||||||||||||
|
Sequence features |
||||||||||||||||
Segmental duplications:
| ||||||||||||||||
+ Evolutionary history
| Ancestral allele | NA | Age | ND |
| Derived allele | NA | Origin | ND |
+ Orientation in other species
Not defined
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
| Gene position | chr17:25927608-25988610 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-18 00:00:00
| Breakpoint 1 | chr17:25968712-25973376 | Breakpoint 2 | chr17:25976637-25980967 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:29
| Breakpoint 1 | chr17:25967879-25973016 | Breakpoint 2 | chr17:25976743-25981879 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with a sequenced fosmid | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:29
| Breakpoint 1 | chr17:25938379-25973376 | Breakpoint 2 | chr17:25976637-26010875 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:29
| Breakpoint 1 | chr17:25967879-25973016 | Breakpoint 2 | chr17:25976743-25981879 |
| Assembly | hg18 | ||
| Description | Complete sequenced Fosmid analisis | ||
| Definition method | Manual curation | ||
Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona
Contact us at invfestdb@uab.cat
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.