| Accession | HsInv0266 | Region of the inversion | chr4:189106589-189114664 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 6,580 bp | Supporting predictions | 2 |
| Inverted allele frequency | 0.3889 | Mechanism of origin | NAHR |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr4:189106589-189108085 |
| Ancestral orientation | NA | Breakpoint 2 | chr4:189113168-189114664 |
|
|
 |
|
|
Human Polymorphic Inversion DataBase
|
General information
- Region map
+ Predictions
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||||||||||||
| Method | Long-read sequencing | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr4:189106420-189106420 | Breakpoint 2 | chr4:189114832-189114832 | ||||
| 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 | chr4:189077854-189108977 | Breakpoint 2 | chr4:189113000-189144348 | ||||||||||||||||||||
| D/C Score | 0 | Disc. Support Prob. | 0.99797 | ||||||||||||||||||||
| Support | 8 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 2 STD/STD - 7 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 | 1 | 0.7500 | 0.2500 | > 0.5 |
| Europe (EUR)
|
Europe (EUR) summary | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
|---|
+ 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)) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| Unknown
|
Unknown summary | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
|---|
+ Breakpoints
| Breakpoint 1 | chr4:189106589-189108085 | Breakpoint 2 | chr4:189113168-189114664 | |||||||||||||||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | |||||||||||||||||
| Description | Breakpoints defined by comparison with one sequenced fosmid | |||||||||||||||||
| Definition method | Manual curation | |||||||||||||||||
| Mechanism of origin |
NAHR
|
|||||||||||||||||
| Flexibility | 10.58 | GC content | 0.41 | Stability | 1.85 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 1.9 kb inverted L1PA5 elements with 98.5% identity |
|||||||||||||||||
|
Sequence features |
||||||||||||||||||
Transposable elements:
| ||||||||||||||||||
+ 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
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2018-11-07 18:29:18
| Breakpoint 1 | chr4:189106589-189108085 | Breakpoint 2 | chr4:189113168-189114664 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with one sequenced fosmid | ||
| Definition method | Manual curation | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr4:189101420-189108977 | Breakpoint 2 | chr4:189113000-189119832 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr4:189077854-189108977 | Breakpoint 2 | chr4:189113000-189144348 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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.