| Accession | HsInv0290 | Region of the inversion | chr7:5899796-6839043 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 842,925 bp | Supporting predictions | 3 |
| Inverted allele frequency | 0.0800 | Mechanism of origin | NAHR |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr7:5899796-5995202 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr7:6741802-6839043 |
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Identification of human inversion polymorphisms by comparative analysis of human and chimpanzee genome sequence assemblies | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||
| Breakpoint 1 | chr7:5899796-5995202 | Breakpoint 2 | chr7:6741802-6839043 |
| Individuals | |||
| Comments | Breakpoints defined by InvFEST curators as the most identical inverted segmental duplications | ||
- 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 | chr7:5985750-6013078 | Breakpoint 2 | chr7:6716051-6751483 | ||||||||||||||||||||
| D/C Score | -1.96 | Disc. Support Prob. | 0 | ||||||||||||||||||||
| Support | 5 probes  | ||||||||||||||||||||||
| Individuals |
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| Comments | Below the threshold of the Discordant/Concordant (D/C) ratio score. Below the threshold of the Discordant Support (DS) probability | ||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr7:5904402-5911101 | Breakpoint 2 | chr7:6824446-6826687 | ||||||||||||||||||||
| D/C Score | -6.8 | Disc. Support Prob. | 0 | ||||||||||||||||||||
| Support | 11 probes | ||||||||||||||||||||||
| Individuals |
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| Comments | Below the threshold of the Discordant/Concordant (D/C) ratio score. Below the threshold of the Discordant Support (DS) probability | ||||||||||||||||||||||
+ Validation and genotyping
| Description | Identification and validation of polymorphic micro-inversions in humans and chimpanzees | ||||||
| Method | Fluorescence in situ hybridization (FISH) |
| Status | Validated |
| Genotyping | 5 individuals: 5 unknown 3 STD/STD - 2 STD/INV |
| Comment | FISH was done with BACs RP11-1275H24 (AC0921714), RP4-810E6 (AC004895) and RP11-425P5 (AC009412) |
| Description | Identification of human inversion polymorphisms by comparative analysis of human and chimpanzee genome sequence assemblies | ||||||
| Method | Fluorescence in situ hybridization (FISH) |
| Status | Validated |
| Genotyping | 20 individuals: 20 unknown 18 STD/STD - 2 STD/INV |
| Comment | FISH was done with BACs RP11-237F7, RP11-119N18, RP11-164P11, RP11-188M14, and RP11-419C12 |
-INVFEST curation
| Description | Information update by manual analysis of InvFEST curators | ||
| Method | Sequence analysis |
| Status | Breakpoint refinement |
- Frequency
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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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Caucasian individuals with European Ancestry (CEPH) (Feuk et al. 2005) | 20 | 2 | 0.9500 | 0.0500 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 20 | 2 | 0.9500 | 0.0500 | > 0.5 |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Szamalek et al. 2006) | 5 | 2 | 0.8000 | 0.2000 | > 0.5 |
| Unknown
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Unknown summary | 5 | 2 | 0.8000 | 0.2000 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr7:5899796-5995202 | Breakpoint 2 | chr7:6741802-6839043 | |||||||||||||
| Study | INVFEST curation | |||||||||||||||
| Description | Breakpoints defined by InvFEST curators as the most identical inverted segmental duplications | |||||||||||||||
| Definition method | Manual curation | |||||||||||||||
| Mechanism of origin |
NAHR
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| Flexibility | 11.26 | GC content | 0.29 | Stability | 1.68 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 95-97 kb inverted SDs with 99% identity |
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Sequence features |
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Segmental duplications:
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+ Evolutionary history
| Ancestral allele | Inverted | Age | ND |
| Derived allele | Standard | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Inverted | Fluorescence in situ hybridization (FISH) | Feuk et al. 2005 |
| Gorilla | Inverted | Fluorescence in situ hybridization (FISH) | Feuk et al. 2005 |
| Chimpanzee | Inverted | Fluorescence in situ hybridization (FISH) | Szamalek et al. 2006 |
| Bonobo | Inverted | Fluorescence in situ hybridization (FISH) | Szamalek et al. 2006 |
| Gorilla | Inverted | Fluorescence in situ hybridization (FISH) | Szamalek et al. 2006 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2015-02-23 10:14:40
| Breakpoint 1 | chr7:5904402-6013078 | Breakpoint 2 | chr7:6716051-6826687 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:40
| Breakpoint 1 | chr7:5899796-5995202 | Breakpoint 2 | chr7:6741802-6839043 |
| Study | INVFEST curation | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by InvFEST curators as the most identical inverted segmental duplications | ||
| Definition method | Manual curation | ||
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Contact us at invfestdb@uab.cat
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