| Accession | HsInv0055 | Region of the inversion | chr5:63797584-63813599 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 11,135 bp | Supporting predictions | 2 |
| Inverted allele frequency | 0.7887 | Mechanism of origin | NAHR |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr5:63797584-63802465 |
| Ancestral orientation | NA | Breakpoint 2 | chr5:63808718-63813599 |
|
|
 |
|
|
Human Polymorphic Inversion DataBase
|
General information
- Region map
+ Predictions
| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr5:63800180-63800180 | Breakpoint 2 | chr5:63811001-63811001 | ||||
| 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 | chr5:63773587-63802965 | Breakpoint 2 | chr5:63808317-63841542 | ||||||||||||||||||||
| D/C Score | 0.38 | Disc. Support Prob. | 0.99739 | ||||||||||||||||||||
| Support | 18 probes  | ||||||||||||||||||||||
| Individuals |
| ||||||||||||||||||||||
+ Validation and genotyping
| Description | Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes | ||||
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | Validated |
| Genotyping | 98 individuals: 96 HapMap/1000GP, 2 Other 5 STD/STD - 31 STD/INV - 60 INV/INV - 2 ND |
- Frequency
|
|
+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
Yoruba in Ibadan, Nigeria (YRI) (Vicente-Salvador et al. 2017) | 4 | 5 | 0.3750 | 0.6250 | > 0.3 |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 5 | 0.3750 | 0.6250 | > 0.3 |
|---|
+ 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) (Vicente-Salvador et al. 2017) | 63 | 101 | 0.1984 | 0.8016 | > 0.5 |
| Europe (EUR)
|
Europe (EUR) summary | 63 | 101 | 0.1984 | 0.8016 | > 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) (Vicente-Salvador et al. 2017) | 1 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
|
Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| 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 (Vicente-Salvador et al. 2017) | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Unknown
|
Unknown summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr5:63797584-63802465 | Breakpoint 2 | chr5:63808718-63813599 | |||||||||||||||
| Study | Vicente-Salvador et al. 2017 | |||||||||||||||||
| Description | Breakpoints defined by comparison with the HuRef Human Genome assembly and two sequenced fosmids | |||||||||||||||||
| Definition method | Manual curation | |||||||||||||||||
| Mechanism of origin |
NAHR
|
|||||||||||||||||
| Flexibility | 11.12 | GC content | 0.47 | Stability | 1.88 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between inverted L1PA7 and L1PA3 elements with 96.6% 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
- 2018-10-26 16:37:48
| Breakpoint 1 | chr5:63797584-63802465 | Breakpoint 2 | chr5:63808718-63813599 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with the HuRef Human Genome assembly and two sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr5:63797584-63802403 | Breakpoint 2 | chr5:63808780-63813599 |
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr5:63799180-63801180 | Breakpoint 2 | chr5:63810001-63812001 |
| 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.