| Accession | HsInv0095 | Region of the inversion | chr4:89066188-89077724 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 11,537 bp | Supporting predictions | 5 |
| Inverted allele frequency | 0.8000 | Mechanism of origin | NHEJ |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr4:89066188-89066188 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr4:89077723-89077724 |
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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 | chr4:89066187-89066187 | Breakpoint 2 | chr4:89077723-89077723 | ||||
| Individuals |
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| Description | Paired-end mapping analysis of the J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr4:89064966-89066187 | Breakpoint 2 | chr4:89077010-89077766 | ||||
| Individuals |
| ||||||
| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr4:89066185-89066405 | Breakpoint 2 | chr4:89077736-89077963 | ||||
| Individuals |
| ||||||
| 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 | chr4:89069504-89069504 | Breakpoint 2 | chr4:89078070-89078070 | ||||||
| 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 | chr4:89039691-89066885 | Breakpoint 2 | chr4:89075737-89102298 | ||||||||||||||||||||
| D/C Score | 0 | Disc. Support Prob. | 1 | ||||||||||||||||||||
| Support | 37 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| 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 CH17-144M16 BAC sequence (AC255484) obtained with PacBio long reads |
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||||||||
| Method | Genotype predicted by tag-SNPs |
| Status | Genotyping |
| Genotyping | 207 individuals (No genotypes available) |
| Comment | Inversion genotypes estimated from association with tag SNP rs1477602 (r2 > 0.8) |
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Comment | Inversion genotyped in 42 individuals of diverse origin (19 STD alleles/65 INV alleles) |
-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 | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals: 8 HapMap/1000GP, 2 Other 1 STD/STD - 2 STD/INV - 7 INV/INV |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
All samples and studies | 4 | 8 | 0.0000 | 1.0000 | NA |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 8 | 0.0000 | 1.0000 | NA |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
All samples and studies | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
|
All samples and studies | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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All samples and studies | 1 | 2 | 0.0000 | 1.0000 | NA |
| 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)) | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Unknown
|
Unknown summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr4:89066188-89066188 | Breakpoint 2 | chr4:89077723-89077724 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and three sequenced fosmids | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ
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| Flexibility | 10.71 | GC content | 0.35 | Stability | 1.84 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) with a 1 bp deletion in each breakpoint |
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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) | Pang et al. 2013 |
| Orangutan | Inverted | Polymerase chain reaction (PCR) | Pang et al. 2013 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-29 00:00:00
| Breakpoint 1 | chr4:89065805-89066785 | Breakpoint 2 | chr4:89077363-89078336 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-03-11 17:00:34
| Breakpoint 1 | chr4:89066188-89066188 | Breakpoint 2 | chr4:89077723-89077724 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and three sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr4:89065805-89066785 | Breakpoint 2 | chr4:89077363-89078336 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr4:89065805-89066785 | Breakpoint 2 | chr4:89077363-89078336 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr4:89065805-89066785 | Breakpoint 2 | chr4:89077363-89078336 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr4:89066188-89066189 | Breakpoint 2 | chr4:89077723-89077724 |
| Study | Pang et al. 2013 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by sequencing | ||
| Definition method | Manual curation | ||
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Contact us at invfestdb@uab.cat
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.