| Accession | HsInv0030 | Region of the inversion | chr16:73797041-73814718 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 17,120 bp | Supporting predictions | 6 |
| Inverted allele frequency | 0.8611 | Mechanism of origin | NAHR |
| Functional effect | Breaks two genes | Breakpoint 1 | chr16:73797041-73797599 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr16:73814160-73814718 |
| Comments | Approximately 6% of inverted alleles include a 585 bp deletion that eliminates exon 6 of the CTRB2 gene
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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 | chr16:73795553-73795553 | Breakpoint 2 | chr16:73815532-73815532 | ||||
| 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 | chr16:73795974-73797620 | Breakpoint 2 | chr16:73814102-73814712 | ||||
| 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 | chr16:73795432-73795432 | Breakpoint 2 | chr16:73812778-73812778 | ||||||
| Individuals |
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| Name | |||||||||
| Breakpoint 1 | chr16:73799357-73799357 | Breakpoint 2 | chr16:73815672-73815672 | ||||||
| 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 | chr16:73797599-73797599 | Breakpoint 2 | chr16:73814159-73814159 | ||||
| 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 | chr16:73779640-73797445 | Breakpoint 2 | chr16:73814869-73833564 | ||||||||||||||||||||
| D/C Score | 1.17 | Disc. Support Prob. | 1 | ||||||||||||||||||||
| Support | 87 probes  | ||||||||||||||||||||||
| Individuals |
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| Comments | prediction outside of the current location of the inversion breakpoints | ||||||||||||||||||||||
+ 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 | 98 individuals: 96 HapMap/1000GP, 2 Other 2 STD/STD - 26 STD/INV - 70 INV/INV |
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 42 individuals (No genotypes available) |
| Comment | Inversion genotyped in 42 individuals of diverse origin (5 STD alleles/74 INV alleles/5 INV+DEL alleles). Genotypes of additional 871 HGDP-CEPH samples from 57 diverse populations showed that INV was the major allele and INV+DEL allele was most prevalent in Surui (47.2%), French Basque (20.5%), North Italian (17.9%), and Druze (15.4%), whereas it was completely absent in Yoruba, Yakut, Sindhi, and Mbuti Pygmies |
| Description | Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin | ||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| 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 | Polymerase chain reaction (PCR) |
| Status | Validated |
- 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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All samples and studies | 4 | 8 | 0.0000 | 1.0000 | NA |
| Africa (AFR)
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Africa (AFR) summary | 4 | 8 | 0.0000 | 1.0000 | NA |
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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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All samples and studies | 64 | 108 | 0.1562 | 0.8438 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 64 | 108 | 0.1562 | 0.8438 | > 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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All samples and studies | 1 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
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All samples and studies | 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 | chr16:73797041-73797599 | Breakpoint 2 | chr16:73814160-73814718 | |||||||||||||
| Study | Vicente-Salvador et al. 2017 | |||||||||||||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and several sequenced fosmids | |||||||||||||||
| Definition method | Manual curation | |||||||||||||||
| Mechanism of origin |
NAHR
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| Flexibility | 9.64 | GC content | 0.72 | Stability | 2.37 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 1.5 kb inverted SDs with 99.6% 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 | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Orangutan | Inverted | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Chimpanzee | Inverted | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Gorilla | Inverted | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
- CTRB1
| Gene position | chr16:73810384-73816323 |
| Mechanism | Breaks one gene |
| Study | INVFEST curation |
| Effect | The first exon and promoter are exchanged with CTRB2 gene. The first exon encodes a 18-amino acid signal peptide. 6 amino acids of this signal peptide are different between both gene copies but 3 are conservative substitutions. The rest of the protein shows a 98% identity between CTRB1 and CTRB2 with only 5 amino acid changes in positions with no apparent functional relevance. |
| Functional consequences | Unknown |
- CTRB2
| Gene position | chr16:73795494-73798573 |
| Mechanism | Breaks one gene |
| Study | INVFEST curation |
| Effect | The first exon and promoter are exchanged with CTRB1 gene. The first exon encodes a 18 amino acid signal peptide. 6 amino acids of this signal peptide are different between both gene copies but 3 are conservative substitutions. The rest of the protein shows a 98% identity between CTRB1 and CTRB2 with only 5 amino acid changes in positions with no apparent functional relevance. Approximately 7% of inverted alleles include a 585 bp deletion that eliminates exon 6. |
| Functional consequences | Unknown |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2018-10-10 16:27:35
| Breakpoint 1 | chr16:73797041-73797599 | Breakpoint 2 | chr16:73814160-73814718 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and several sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr16:73796599-73797445 | Breakpoint 2 | chr16:73814869-73815159 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:29
| Breakpoint 1 | chr16:73796599-73797445 | Breakpoint 2 | chr16:73814869-73815159 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:29
| Breakpoint 1 | chr16:73797041-73797599 | Breakpoint 2 | chr16:73814160-73814718 |
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly, two sequenced fosmids, and sequencing of inverted PCR fragments | ||
| 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.