Inversion Report: HsInv0472

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0472

General information

Accession	HsInv0472	Region of the inversion	chr4:3866029-9373835
Status	Validated	Prediction type	Simple
Estimated Inversion Size	5,028,236 bp	Supporting predictions	2
Inverted allele frequency	0.0625	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chr4:3866029-4235076
Ancestral orientation	NA	Breakpoint 2	chr4:8783740-9373835

- Region map

+ Predictions

+ Validation and genotyping

-Giglio et al. 2002

Description

Analysis of two inversions involving olfactory receptor-gene clusters that mediate a recurrent translocation

Method	Fluorescence in situ hybridization (FISH)
Status	Validated
Genotyping	40 individuals: 40 unknown 35 STD/STD - 5 STD/INV
Comment	Inversion genotyped in 40 control individuals

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

Please be aware that this information will be displayed in the Frequency section of the Inversion report, but the following will not be available: Hardy-Weinberg test and genotype file for download. Also, data will not be averaged with other studies of the same population.

Population
Analyzed individuals
Inverted alleles
Standard frequency
Inverted frequency

+ Manually curated breakpoints:

Only modified sections are submitted. All the corresponding fields must be complete because they will be overwritten. In the Frequency without genotypes section multiple populations can be added if the editing process is repeated for each one of them.

-INVFEST curation

Description

Information update by manual analysis of InvFEST curators

Method	Sequence analysis
Status	Breakpoint refinement

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

- Frequency

+ Unknown

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Unknown	Unknown (Giglio et al. 2002)	40	5	0.9375	0.0625	> 0.5

Unknown	Unknown summary	40	5	0.9375	0.0625	> 0.5

+ Breakpoints

Breakpoint 1	chr4:3866029-4235076	Breakpoint 2	chr4:8783740-9373835
Study	INVFEST curation
Description	Breakpoints defined by InvFEST curators as the largest blocks of inverted segmental duplications
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

10.92

GC content

0.27

Stability

1.79

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between large blocks of inverted SDs with high identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr4:3852863-3869313	16,451	chr4:9117207-9132641	15,435	0.941	Inverted
chr4:3853832-3869797	15,966	chr4:9061630-9078084	16,455	0.937	Inverted
chr4:3854619-3869758	15,140	chr4:9085996-9101693	15,698	0.937	Inverted
chr4:3869911-3879166	9,256	chr4:9074731-9083982	9,252	0.940	Inverted
chr4:3872142-3883456	11,315	chr4:9356347-9367485	11,139	0.927	Inverted
chr4:3875779-3879166	3,388	chr4:9128287-9131695	3,409	0.924	Inverted
chr4:3876591-3879166	2,576	chr4:9099126-9101693	2,568	0.922	Inverted
chr4:3963457-3980496	17,040	chr4:9341265-9357304	16,040	0.952	Inverted
chr4:3986695-4068416	81,722	chr4:9239625-9322946	83,322	0.957	Inverted
chr4:4066147-4108559	42,413	chr4:9198179-9234791	36,613	0.947	Inverted
chr4:4108349-4218498	110,150	chr4:9085997-9197018	111,022	0.950	Inverted
chr4:4171888-4175283	3,396	chr4:9360464-9363837	3,374	0.924	Inverted
chr4:4171895-4187667	15,773	chr4:9062112-9078084	15,973	0.929	Inverted
chr4:4202883-4205458	2,576	chr4:9360466-9363045	2,580	0.931	Inverted
chr4:4202886-4218509	15,624	chr4:9061659-9077297	15,639	0.939	Inverted
chr4:4220723-4231786	11,064	chr4:9360463-9373834	13,372	0.917	Inverted
chr4:4225987-4235075	9,089	chr4:9071467-9081758	10,292	0.909	Inverted
chr4:4229435-4235075	5,641	chr4:9125039-9131685	6,647	0.911	Inverted
chr4:4230458-4235075	4,618	chr4:9095872-9100431	4,560	0.908	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Ancestral allele	NA	Age	ND
Derived allele	NA	Origin	ND

Breakpoint 1	chr4:4070653-4118519	Breakpoint 2	chr4:9193969-9238919
Assembly	hg18
Definition method	Default informatic definition

Name
Breakpoint 1	chr4:3866029-4235076	Breakpoint 2	chr4:8783740-9373835
Individuals
Comments	Breakpoints defined by INVFEST to include all pairs of inverted segmental duplications located at both predicted breakpoint regions

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)