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Relationship of Gene’s Type
and Introns
Chi K. To
Eukaryotes contain multiple introns per
gene.
Throughout eukaryotic evolution, the
length of introns had been changed by
either insertion, deletion or both.
How big of these lengths had been
change?
Do they just happen in specific type of
genes? What are those types?
Method:
Use the Browser to get introns in the
whole genome.
Do pairwise alignment between human
and dog genomic sequences with the
reconstructed sequences of their common
ancestor.
Only select introns have gaps that are
greater than 100bp.
Insertion (gaps on ancestral sequences) ,
deletion (gaps on human/dog sequences).
Get genes’ IDs
Upload data to the
http://gostat.wehi.edu.au/ - help to
calculate the Hypergeometric distribution
for the data
Gene ontology classification of introns.
Result:
GO ID
Description
p-val
GO:0030695
Mol. Function: GTPase regulator
activity [Modulates the rate of
GTP hydrolysis by a GTPase]
1.89E-05
GO:0005886
Location: plasma membrane
1.01E-04
GO: 0005887
Integral to plasma membrane
Biological process: NLS-bearing
substrate-nucleus
2.3E-04
GO: 0006607
Insertion in Human
5.42E-04
Go ID
Description
p-val
GO:0030695
Mol. Function: GTPase regulator
activity
Mol. Function: small GTPase
regulatory/interacting protein
activity
Mol. Function: guanyl-cucleotide
exchange factor activity
Mol. Function: cytoskeletal protein
binding
5.49E-06
GO: 0005083
GO: 0005085
GO: 0008092
Deletion in Human
3.65E-04
6.89E-04
1.96E-03
Go ID
Description
p-val
GO:0030695
Mol. Function: small GTPase
regulatory/interacting protein
activity
5.35E-04
GO:0006607
Biological process: NLS-bearing
substrate-nucleus
5.35E-04
GO:0030036
Bio. Process: Actin cytoskeleton
organization and biogenesis
2.67E-03
GO:0005587
Cellular component: collagen type
IV
2.67E-03
Insertion in Dog
Go ID
Description
p-val
GO:0030036
Actin cytoskeleton organization and
biogenesis
2.53E-04
GO:0030029
Bio. Process: Actin filament-based
process
2.75E-04
GO:0005083
Mol. Function: small GTPase
regulatory/interacting protein
activity
4.06E-04
GO:0005886
Location: plasma membrane
4.8E-04
Deletion in Dog
* In human: Genes have the molecular function
related to GTPase regulator activity or locate in
plasma membrane tend to change the lengths of
introns within the genes during the evolutionary
process.
* In Dog: Genes have the biological process
related to Actin cytoskeleton organization and
biogenesis and the mol. munction related to
small GTPase regulatory/interacting protein
activity tend to change the lengths of introns
within the genes during the evolution.
A big deletion of a intron in gene NM_018283 of Dog
Special thanks to:
1/ Baertsch, Robert – pairwise alignment
data
2/ http://gostat.wehi.edu.au/ - for the
G.O. statistics
3/ UCSC genome Browser