Special

MmuINT0033358 @ mm9

Intron Retention

Gene
ENSMUSG00000061048 | Cdh3
Description
cadherin 3 [Source:MGI Symbol;Acc:MGI:88356]
Coordinates
chr8:109076766-109080047:+
Coord C1 exon
chr8:109076766-109076912
Coord A exon
chr8:109076913-109079140
Coord C2 exon
chr8:109079141-109080047
Length
2228 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GCTGCTCTCTGCTTCCCTAGAAC
3' ss Score
9.02
Exon sequences
Seq C1 exon
GACTATGACATCACCCAACTCCACCGGGGACTGGAGGCCAGGCCTGAGGTGGTTCTCCGAAACGATGTAGTGCCAACCTTCATCCCCACCCCCATGTACCGACCCCGGCCCGCCAACCCAGATGAAATCGGGAACTTCATCATCGAG
Seq A exon
GTAAGGCATGGCAGGTTTACCAAACACAAGCATGGGTCAGGCACAACCATAGGAGAACAAACATGGGCTTTCTGCATAGACTGAGTTCTAGTCCCGGCTCTGCCCTCCAACTACTTGATCTCTGCATACTTGAGTATCTGTGGGTTTCTCTTTCCTCCTCCATAAACTCCAGGTTTAAACACTGAGTTACTAGCAAAATACTCTGGAGTCAGTCAGGCAACTTAGGTTTTATTTGGGGTTTTTGGTGTTTAAGATTCTCTCTCTCTCTCTCTCTCTCACTCACTCACTTACTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTGCCTACATTCATGTTTGTAAACAACATGTGTACAGTGCCCTCAGAGTCCCTGGGACTGGAGTTGGAGACAGTCATGAGATCCCAAGTGGGTGCTGGTGCCTGAAACCCTGTCCTGTGGAAGAGCAGCCAGTGCTCTTAGCTGCTGAGCCATTGCTCCAGCCTCGGCTTGCTTGGTTGGTTGGTTGGTTGGTTGATTGGTTGGTTGATTTGAAACAGGGTTTTTCTCTGTGTAGCCTTGGATGTTCTGGACCAGGGCTCTCTGTGTAGGTCAGGCTGACCTCAAACTCACAGAGACTCTCCTGCCTCTGCCTTCCGAGTAGTGCAGTTAAAGCCTTATGATACCATTCCTGGCCTCTTGGCTTTTTACTTTGTTTTTGTTTTATGTTTTGTTTTGTTTTTTTTTAAAGATTTATTTATTATATGTAAGTACACTCTAGCTGTCCTCAGATACTCCAGAAAAGGGCGTCAGATCTCGTTATGAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATGTGAACTCCGGACCTTTTTGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCTGTTTTTATGTTTTATTTATGTATTTAGTGTCTATCCCCCATATCTGCCATGGTACACATGCATTAAGAGTATTCGCTGCTCTTCTAGAGGACTGGGACAAAGATTTGAAACCTTCTAGAGGACAGGATTTGAAACCCTGTCTCAAATCAACCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCCCAGTCTGAAAACCCATACGGAGACCCACAGCTCTCTGTAATCCAGTTCGGTTCTAGGGGTGTCCAGTGCCCTCTTCTGGCCTCCACCGGCACTGCATACACATGGTGCATAGACATACGTGCAGACAAAACACCAGTGCACATAAAATAAATAAAGCTTTTAAAAATAAAAGTAACAAAAAAATTGAAATTAAAATAAAAATAATTTTTAGGCCTGGCTTGGTGGTATACACCTTTAATTCCAGAACTCAGAAGGCAGATGGATCCCTCTGTGTTGGCCTGGTCTACAGAGTGAATTCCAGGACAGCCAAGGCTATGTAGAGAAACCCTGTCTCAAGCCCCTCCACATAATAATAATAATAGTGATTTTATTTATTTATTTATTTATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCGTCAGATCTCGTTACGGATGGTTGTGAACCACCATGTGGTTGCTGGGATTTGAACTCCGGACCTTTGGAAGAGCAGTAGGGTGGTCTTACCCACTGAGCCATCTCACCAGCCCTATTTTTTTTCTTTAAGTTCAGTGTAGTAGTACATGTCTTTAGTCCCAGAATTTAGTAGGCAGAAGCAGGCAGATCTCTGTGAGTTCAACACCGGCCTGGCCCACAGAGCTCAGAACAGCGAGGACTACATAAGGAGACCCTGTCTCAAAAACAAACAAACAAAAAACCCACAAAGGTCTGGAGAGGTGGCTCAGCAGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGTTCATAACCATCTGTAATTGGATCCAATGCCCTCTTCTGGTGTGTCAGAAACAGTGACAATATACTCATTATACAATAAATAAATCTTTAAAAAACAAAAACAAAAGAATTTTAAAAATAATTACGTTTATGTGTCTAGGAAGAAAAATGTCGATGTGGAGATGTGGAGATGTGGAGGTGGGGGTGGGTATAGAGGCTCGGCAGGTGTACTGATTTGTCAAAACCCAGGTCGCTGGCAAGGGTCTCCATCCAATCAATGCTGACCGCTGCTCTCTGCTTCCCTAG
Seq C2 exon
AACCTGAAGGCTGCCAACACTGACCCTACTGCCCCGCCCTACGACTCCCTGCTGGTTTTTGACTACGAGGGCAGCGGCTCTGATGCCGCCTCCCTGAGCTCCCTCACCACCTCCGCCTCCGACCAGGATCAGGACTACAACTACCTTAACGAGTGGGGAAGTCGATTCAAGAAACTGGCGGACATGTATGGTGGCGGTGAGGATGACTAGGCTGTCCCTGCCAAGCTGTCCAGGCAAGAACTACAGACGGGTCACAGCAGCATCTCAAGGGAGCCTGGCTCCCGCTCCAGCCAGGACTCTGAAGTTTGCCCAGAAGTGGCCTGCGTGGCACGCTGCATCTGACCAGAAGGCTGGACTGTGAGCCTTTCCGATGGAAGGATGTGACTCTGACGACAACACTGATCCCCACCTCAGCCATGGCTGAGCCCCTCTCAGAGCGGGAATGTCTAAAGGTCTCCCGCCTGCCACACAGCACTCAGCTCTGCCCTCTCAGGGCTTGAACTTGCTCCGATGCCCTCGGTGACTTTCCCCACTTGGAATGGCTCCCTCTCTTTAGAAAGAGGCCCCTAACTAAGGCCCTGTTTTTCTTTAATGCAGTTTTCAAAAAGAGGCTGGGGTGGGTGGGGCAGGGTGCGGACATCAGTGTCCCCTCAGGCCCTCCAGAAGAGAAGCCTACAGGGCACTGGCCCTGGTACATTTCTCTGACATTTCTTGAGGCCTCACATTGGGGAGGGGTCACTGCCTTTTTTTTTTTTTTAATACTGAGTATATCTAAGTTGTCTCGTATTTTTTTATTTTCCCTGTTATGTGCTGTAGATGGAGAGTGATGACAATCGTGTAAATGTACTAGAATTTTTTTATTAAAATGAACTTTTTTTTTTCCCAGAGGTGCTAGGGGAGTGGATTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061048-Cdh3:NM_007665:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.245 A=NA C2=0.333
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0104912=Cadherin_C=FE(32.0=100)

							
A:
NA

							
C2:
PF0104912=Cadherin_C=PD(43.3=92.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000079613





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000126504
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr16:68695924-68698190 
ALTERNATIVE
HsaINT0032174
(CDH3)
Human
(hg19)
chr16:68729827-68732093 
ALTERNATIVE
HsaINT0032174
(CDH3)
Rat
(rn6)
chr19:38716800-38718947 
LOW PSI
RnoINT0033109
(Cdh3)
Cow
(bosTau6)
chr18:36137476-36140085 
ALTERNATIVE
BtaINT0035460
(CDH3)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr11:20834923-20835035 
LOW PSI
GgaINT0026007
(F1NUS5_CHICK)
Zebrafish
(danRer10)
chr18:7443237-7443600 
DreINT0145636
(si:dkey-30c15.12)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"