| Accession | HsInv0098 | Region of the inversion | chr3:41337147-41338809 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 1,308 bp | Supporting predictions | 4 |
| Inverted allele frequency | 0.3000 | Mechanism of origin | FoSTeS or NAHR |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr3:41337147-41337165 |
| Ancestral orientation | NA | Breakpoint 2 | chr3:41338116-41338809 |
| Comments | Inverted allele includes a small duplication and a 0.7 kb deletion flanking the inverted region
|
||
|
|
 |
|
|
Human Polymorphic Inversion DataBase
|
General information
- Region map
+ Predictions
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||
| Name | |||
| Breakpoint 1 | chr3:41337149-41337149 | Breakpoint 2 | chr3:41338118-41338118 |
| Individuals | |||
| Description | Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr3:41337147-41337417 | Breakpoint 2 | chr3:41338113-41338404 | ||||
| Individuals |
| ||||||
| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||
| Name | |||||||||
| Breakpoint 1 | chr3:41337863-41337863 | Breakpoint 2 | chr3:41342037-41342037 | ||||||
| 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 | chr3:41296664-41337147 | Breakpoint 2 | chr3:41337482-41374815 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99923 | ||||||||||||||||||||
| Support | 3 probes  | ||||||||||||||||||||||
| Individuals |
| ||||||||||||||||||||||
+ Validation and genotyping
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Comment | Tested in sample A105c |
| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
-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 | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals: 8 HapMap/1000GP, 2 Other 4 STD/STD - 6 STD/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 | 3 | 0.6250 | 0.3750 | > 0.2 |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 3 | 0.6250 | 0.3750 | > 0.2 |
|---|
+ 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 | 1 | 0.5000 | 0.5000 | > 0.3 |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
|---|
+ 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)) | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
| Unknown
|
Unknown summary | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr3:41337147-41337165 | Breakpoint 2 | chr3:41338116-41338809 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with split reads of two fosmids and sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS or NAHR
|
||||
| Flexibility | 11.09 | GC content | 0.27 | Stability | 1.74 |
| Comments |
Inverted region is flanked by a small duplication and a 0.7 kb deletion and was probably generated by several FoSTeS events mediated by microhomology or NAHR between inverted AluSz and AluSz6 elements with ~86% identity followed by a deletion and a duplication. Breakpoint 2 position comprises the deleted sequence. |
||
+ 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
- ULK4
| Gene position | chr3:41263093-41978664 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-29 00:00:00
| Breakpoint 1 | chr3:41332149-41337147 | Breakpoint 2 | chr3:41337482-41343118 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:32
| Breakpoint 1 | chr3:41331856-41337147 | Breakpoint 2 | chr3:41337482-41343674 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:32
| Breakpoint 1 | chr3:41337147-41337165 | Breakpoint 2 | chr3:41338116-41338809 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with split reads of two fosmids and sequencing of inverted PCR fragments | ||
| 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.