Evolutionary novelties in genomes have recently attracted increasing attention. Studies on young genes have afforded great insight into the mechanism of origin of new genes and their subsequent evolution. Rapid evolution is a common phenomenon in newly evolved genes, often driven by positive Darwinian selection. Since exon shuffling is widely recognized as important in the generation of new genes, how new exons, the basic units of gene and exon shuffling, originate and evolve becomes an important question at the genome level.

In this study, we foucsd on the rodent lineage, and use human and pig as outgroups to detect newly evolved exons in mouse, and use rat to calculate the evolutionary speed in rodent. All results of this project list as following, if you want do some further analysis, you can just download these data freely.
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1. Mouse and Human transcript unit position on chromosomes (genomic TU):
    
Mouse:

Mouse.RefSeq.GC2.tab (0.6 M)  Display Download
Mouse transcript unit on every chromosome. In this file, you can find which ESTs or
mRNAs are clustered into one group.Readme

Mouse.GC2.tab (26.6 M)  Display Download
Mouse transcript unit position on every chromosome. Readme

Human:
Human.RefSeq.GC2.tab(0.61 M)  Display Download
Human transcript unit on every chromosome. In this file, you can find which ESTs or
mRNAs are clustered into one group.Readme

Human.GC2.tab (25.5 M)  Display Download
Human transcript unit position on every chromosome.Readme
2. Mouse and Human exons' position, splicing type and phase information:
    
Mouse.splitExon.orf.revise(7 M)   Display Download
Mouse exon basic information. In this file, you can find all the usefull inforation of
mouse exons in this project, which include the exon position on mouse genomic TU, the
include-level, and the exon phase et al.Readme

Human.splitExon.orf (8.9 M)  Display Download
Human exon basic information. In this file, you can find all the usefull inforation of
human exons in this project, which include the exon position on human genomic TU, the
include-level, and the exon phase et al. Readme

3. Mouse exons to human genomic TU align info:
    
Mouse_exon_evolution_type.Fasta.MajorMinor.tab4(11.2 M)   Display Download
Mouse exons to human genomic TU align info. In this file, you can find the mouse exon to
bhuman alignment result. This can show you which exon aligned to human exonic regions,
which to intronic regions and which without obvious homologous.Readme

4. Mouse exon to rat SNP, InDel and ka/ks info:
    
71039.kaks.tab (18.1 M)  Display Download
Mouse exon to rat SNP, InDel and ka/ks info. This file can show you the exon evolution
info in the rodent lineage. The Ka/Ks ratio is based on the Li93 method. The mouse to rat
alignment is based on the UCSC genome align info.Readme

5. Big table include all useful info:
    
71039_Mouse_splice_evolution_type_KaKs_Li93.Fasta.2004-06-04.tab( 10 M)   Display Download
summary of all usefull info in this project, which include the splice include-level,
evolution type, and the evolution speed info et al.

6. The alignment of mouse exons and pig ESTs:
    
Mouse_splitExon_cut.pig_unigene.blastn (300 M)  Display Download
Mouse exons to Pig EST alignment. This file show all mouse exons align info to all pig ESTs.
File is in blast m8 format.Readme

7. Mouse new exon fasta sequences:
    
true.intron.list.fa (0.65 M)  Display Download
Welll defined newly evolved exons in intron-category. These mouse exons are which aligned
into intronic regions of the human orthologous. This file includes all these intron-category
exons, and is in fasta format.

true.none.list.fa (0.18 M)  Display Download
Well defined newly evolved exons in none-category. These mouse exons are which can not
find obvioushomologous in human orthologous genomic regions. This file includes all these
none-category exons, and is in fasta format.

8. The exons whose evidence is based on a single EST are labeled as 'singletons' :
    
singleton.list (13 K)  Display Download
 


      the methods and glossaris are described in the paper, you can see more details in it. PDF

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