| Accession | HsInv0040 | Region of the inversion | chr2:138720715-138725814 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 4,346 bp | Supporting predictions | 6 |
| Inverted allele frequency | 0.7986 | Mechanism of origin | NAHR |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr2:138720715-138721469 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr2:138725059-138725814 |
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Human Polymorphic Inversion DataBase
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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 | chr2:138720714-138720714 | Breakpoint 2 | chr2:138725814-138725814 | ||||
| Individuals |
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| 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 | chr2:138720840-138721430 | Breakpoint 2 | chr2:138725150-138725793 | ||||
| Individuals |
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| 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 | chr2:138719674-138719674 | Breakpoint 2 | chr2:138723811-138723811 | ||||||
| Individuals |
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| Name | |||||||||
| Breakpoint 1 | chr2:138720361-138720361 | Breakpoint 2 | chr2:138722119-138722119 | ||||||
| Individuals |
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| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr2:138721419-138721419 | Breakpoint 2 | chr2:138725673-138725673 | ||||
| Individuals |
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- 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 | chr2:138689837-138721370 | Breakpoint 2 | chr2:138725284-138761059 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99999 | ||||||||||||||||||||
| Support | 22 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes | ||||||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals: 8 HapMap/1000GP, 2 Other 1 STD/STD - 1 STD/INV - 8 INV/INV |
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | Validated |
| Genotyping | 98 individuals: 96 HapMap/1000GP, 2 Other 6 STD/STD - 26 STD/INV - 64 INV/INV - 2 ND |
| 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 | Sequence analysis |
| Status | Validated |
| Comment | Inversion validated by analysis of CH17-215F16 BAC sequence (AC255436) obtained with PacBio long reads |
| 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 | Genome sequence comparison |
| Status | Validated |
| Comment | Inversion confirmed by comparison with the Celera Human Genome assembly |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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Yoruba in Ibadan, Nigeria (YRI) (Vicente-Salvador et al. 2017) | 4 | 5 | 0.3750 | 0.6250 | > 0.3 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 5 | 0.3750 | 0.6250 | > 0.3 |
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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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Utah residents with Northern and Western European ancestry (CEU) (Vicente-Salvador et al. 2017) | 64 | 102 | 0.2031 | 0.7969 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 64 | 102 | 0.2031 | 0.7969 | > 0.5 |
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+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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Han Chinese in Beijing, China (CHB) (Vicente-Salvador et al. 2017) | 1 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017) | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
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East Asia (EAS) summary | 2 | 4 | 0.0000 | 1.0000 | NA |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Vicente-Salvador et al. 2017) | 2 | 4 | 0.0000 | 1.0000 | NA |
| Unknown
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Unknown summary | 2 | 4 | 0.0000 | 1.0000 | NA |
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+ Breakpoints
| Breakpoint 1 | chr2:138720715-138721469 | Breakpoint 2 | chr2:138725059-138725814 | |||||||||||||
| 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
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| Flexibility | 12.11 | GC content | 0.25 | Stability | 1.66 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 0.8 kb inverted repeats formed by unique and different types of repetitive sequences with 99.9% identity |
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Sequence features |
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Inverted repeats:
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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 | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Gorilla | Inverted | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Rhesus macaque | Inverted | Genome sequence comparison | Vicente-Salvador et al. 2017 |
+ 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 12:47:04
| Breakpoint 1 | chr2:138720715-138721469 | Breakpoint 2 | chr2:138725059-138725814 |
| 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 | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr2:138720419-138721370 | Breakpoint 2 | chr2:138725284-138726673 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:31
| Breakpoint 1 | chr2:138720715-138721469 | Breakpoint 2 | chr2:138725059-138725814 |
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:31
| Breakpoint 1 | chr2:138720419-138721370 | Breakpoint 2 | chr2:138725284-138726673 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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