| Accession | HsInv1065 | Region of the inversion | chr11:55121099-55214331 |
| Status | Validated | Prediction type | Complex |
| Estimated Inversion Size | 53,776 bp | Supporting predictions | 3 |
| Inverted allele frequency | 0.3478 | Mechanism of origin | FoSTeS |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr11:55121099-55188126 |
| Ancestral orientation | Standard | Breakpoint 2 | chr11:55202445-55214331 |
| Comments | Complex rearrangement including two inversions of 2.9 kb and 1.8 kb, four deletions of 66 kb, 12 kb, 9.5 kb, and 0.4 kb, and a small duplication, which delete RefSeq genes OR4C11, OR4P4 and OR4S2 and invert OR4C6
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| 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 | chr11:55120813-55120813 | Breakpoint 2 | chr11:55188486-55188486 | ||||||
| Individuals |
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| Comments | prediction outside of the current location of the inversion breakpoints | ||||||||
- 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 | chr11:55084529-55133686 | Breakpoint 2 | chr11:55201499-55237487 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0 | ||||||||||||||||||||
| Individuals |
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| Comments | Below the threshold of the Discordant Support (DS) probability | ||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr11:55143598-55190359 | Breakpoint 2 | chr11:55202675-55249446 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.0089 | ||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | High-resolution copy-number variation analysis of human olfactory receptor diversity using oligonucleotide tiling microarrays and validation by quantitative and regular PCR | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Comment | Quantitative and regular PCR confrmed the presence of homozygous ORC4C11 deletions in NA12003 and NA12246 |
| Description | Analysis of copy-number variation of the human olfactory receptor gene family and validation by MLPA and PCR | ||||||
| Method | Multiplex ligation-dependent probe amplification (MLPA) |
| Status | Validated |
| Genotyping | 46 individuals: 44 Other, 2 unknown 21 STD/STD - 18 STD/INV - 7 INV/INV  |
| Comment | Genotypes were inferred from results of MLPA for OR4C11 and PCRs for OR4P4, OR4S2, OR4P1P and OR4C6, which support the predicted structure of the inverted allele |
-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 | Fosmid sequence analysis |
| Status | Breakpoint refinement |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
African American
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African American in North America (Young et al. 2008) | 9 | 3 | 0.8333 | 0.1667 | > 0.5 |
| Biaka
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All samples and studies | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
| Mbuti
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Mbuti Pygmies in Ituri Forest in northeast Zaire (Young et al. 2008) | 3 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
|
Africa (AFR) summary | 16 | 4 | 0.8750 | 0.1250 | > 0.5 |
|---|
+ Middle East/North Africa (MENA)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Druze
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Druze from Galilee, Israel (Young et al. 2008) | 5 | 3 | 0.7000 | 0.3000 | > 0.3 |
| Middle East/North Africa (MENA)
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Middle East/North Africa (MENA) summary | 5 | 3 | 0.7000 | 0.3000 | > 0.3 |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Caucasian
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Caucasians (Young et al. 2008) | 8 | 6 | 0.6250 | 0.3750 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 8 | 6 | 0.6250 | 0.3750 | > 0.5 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Cambodian
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All samples and studies | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
| East Asia (EAS)
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East Asia (EAS) summary | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
|---|
+ Oceania (OCE)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Melanesian
|
Melanesian from Bougainville in the Solomon Islands (Young et al. 2008) | 5 | 8 | 0.2000 | 0.8000 | > 0.5 |
| Oceania (OCE)
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Oceania (OCE) summary | 5 | 8 | 0.2000 | 0.8000 | > 0.5 |
|---|
+ America - Natives (AMN)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Karitiana
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Karitiana (Young et al. 2008) | 4 | 4 | 0.5000 | 0.5000 | > 0.5 |
| Maya
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Mayan from Campeche State in Yucatan (Young et al. 2008) | 4 | 6 | 0.2500 | 0.7500 | > 0.5 |
| America - Natives (AMN)
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America - Natives (AMN) summary | 8 | 10 | 0.3750 | 0.6250 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr11:55121099-55188126 | Breakpoint 2 | chr11:55202445-55214331 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with three sequenced fosmids | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS
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| Flexibility | 11.96 | GC content | 0.33 | Stability | 1.78 |
+ Evolutionary history
| Ancestral allele | Standard | Age | ND |
| Derived allele | Inverted | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Genome sequence comparison | Hasin et al. 2008 |
| Chimpanzee | Standard | Genome sequence comparison | Young et al. 2008 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
HsInv0522 and HsInv0136 merge into HsInv1065
- 2015-02-23 10:15:27
| Breakpoint 1 | chr11:55084529-55190359 | Breakpoint 2 | chr11:55201499-55249446 |
| Assembly | hg18 | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:15:27
| Breakpoint 1 | chr11:55121093-55121094 | Breakpoint 2 | chr11:55214331-55214332 |
| Study | Young et al. 2008 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with two sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:15:27
| Breakpoint 1 | chr11:55121099-55188126 | Breakpoint 2 | chr11:55202445-55214331 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with three sequenced fosmids | ||
| 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.