Special

MmuINT0033355 @ mm9

Intron Retention

Gene
ENSMUSG00000061048 | Cdh3
Description
cadherin 3 [Source:MGI Symbol;Acc:MGI:88356]
Coordinates
chr8:109068903-109071731:+
Coord C1 exon
chr8:109068903-109069127
Coord A exon
chr8:109069128-109071521
Coord C2 exon
chr8:109071522-109071731
Length
2394 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
AAATGTGTGTGTCTCTCCAGGAG
3' ss Score
9.86
Exon sequences
Seq C1 exon
GAAACCCTCCCACCACCGGCACTGGGACCCTCCTGCTTACACTTACTGACATCAACGACCATGGCCCGATCCCTGAACCCAGGCAGATCATCATCTGTAACCAAAGCCCTGTGCCTCAAGTGCTGAACATCACTGACAAGGACCTGTCCCCCAACTCCTCCCCTTTCCAGGCCCAGCTAACACATGACTCAGATATCTACTGGATGGCAGAAGTCAGCGAGAAAG
Seq A exon
GTAACTCTGGTGGTGACAGGGGGCTGTCGTTCAGCTGGGTGGGTGTCATTCCCCCACAGTAGGACCCACACACATCCCTGTCCTAGCATCTGTGGGTCACAGAATTGTGGTCTCAAAAATGGCCACCAGGGGTCCTTCCTTAGCATTATATGTCTTTGAAATCTCTCAGGAGCCCTAAACAAATTAACAGGGCTAGGCATGATTGCACTTAATCCCAGCACTCAAGAAACAAACAAACAAAAGAAGCAGATTTCTATGGGTTCAAAGCCAACCTGATATAGAGCTATATAATGAGACCCTGTCTCAAAAGAACAAGCAAATAGCAACATCCACAGTAAAAACACAAATAAAACAGAGAGAGCCAGGACTGGAGAGATTTCTCAGTGGTTAGGAGCACTGGCTGGCCTTCCAGAGGACCTCGGTTCAATTCTCAGCACCCACATGGTGGCCACAACTACCTGTAACTCCAGTTCCAGGGGATCAGATGTTCTCCTCTGGTCTCCACAGCACTGGGTACACACGTGGTGCACAGATGTATGTGCAAGTAAAACACCTGTACACATTAAATAAAATGTAAAAATTTAAAAAACAAAACCAAAAAGCACATGTTGCAGCCGGGCGTGGTGACGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTTTACGAAGTGAGCTCCAGAACAGCCAGGTCTACACAGAGAAACCCTGTCTCGAAAAAAATAAATAAATAAATAAATTTTTAAAAACACATGTTGCTCTTGCAGAGGAGCCAGGTTTGATTCCTGGCACCCACATGGTAGCTCACAACCATCTGTAACTCAGGTGCCAAGGGTCTGACATCTTTTTTGACATCCATGGGGCACCAGGCACACCCATTGTGCACATACAACATGCAAGCAACACACACATACCATAAAATAAATATCTGTTTAAAGATAAGCAATGAAGTTAAAGAATAATGTACTTTTCTTTTTCGTCTTTTTTTGGTTTTTCAAGACAGGGTTTCCCTGTGTAGCCTTGGCTGTCCTGAAACTCACTCTGGAGATCAGGCTGGCCTCGAACTCAGAGATCCATGTGCCTCTGCCTTCTAAGTACTAGGAGTAAAGGTGTGCGCCACCACTGCCACGCTTATAATGTATTCTTTTGAGGCAAAGAGTAGTCTAGCAGCTGATGATCCCAAGAATATTGGTCCAACATTTCACGACTTCCAGAGCCTCACAGTTTACTATCATCAATTTCTTGTTTGTTTGTTTGTTTGTTTGTTTTAAATAACACCCAAGCTCGGAAGCTCAAACCTGTGATCCTGGCACTCAGAAGACAGAGGGAAGTGAATTGCCATGAGTTTGAAACCAACCCAGACTACAGAGTAGAACTCTATCTTGTAAAAGATGAATTAATTAATTTAAAAATAATGAACTGGGAGCCGGGCAATAGTGGCGCACGCCTTTAATCTCAGCACTTGGGAGGGAGGCAGGGCAGGTGGATTTCTGAGTTCCAGGCCAGCCTAGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACCAAGAGAAACCCTATCTCGAAAAAAAACAAAAAAGCAAAAACAAAAAAAGAACTGGGGCTGGAGAGAGAACGCAGTGGTTAAGAGCACTGGGTTCAGTTTCCAGCAGTCACGTGGCGTCTCACAACCGTCCGTAACCACAGCTCCAGGTGATCTTACACCACAGTCTTCTGGAGTCCAAGAACACCAGCCACACACATGGTGCACAGACATGCAAACGTACATGTAGGCAAAATACCCATACATGTAGGGAAAAATAACCATACACATTTTGGGGGGATGAAATAATTTTTGTGAGCTAGCAAGATTTCTCTGTAGATGTAAGTGCAGCCCAGCTTAATGGGACGTTAAGTTCGACTCCCAGAACCCAGAGGTGGAGGAGAAAACTGATTCCCAAAAGACTTGTCTCCTGCTCCTCACATGTGCATCATAGCACACACGTGCCCACATTCATGCATACACACACGCATACACACATACACACTCACCAGCAACAAAAACAATAGGTGACATTTTTGGGGGGAAAAAAGATACTGAAAAATGAATTAATTTTGGTAACCGAATAATCCTCACAGCAGCAAAGTTTTGCTGTGCCAGGGTTCTAGAGATCCTCTATTTGTTTTGCTTGTCTGTTGTGGGGCTTGAACCCAGGGCCTCATGGATGCTGAGCAGGTACTCTGTCACAATGCTACACTTAGACTAAACCTGCCTTTTGTTCCTTGGGTGCTGAGGCTGTGTTGGCTCAACGTTTTGCAGTCTTGTATTTGGTGTTCAACCCGAATGACACCCCTAAGCTAATAAATGTGTGTGTCTCTCCAG
Seq C2 exon
GAGACACCGTGGCCTTGTCCCTGAAGAAGTTCCTGAAACAAGACACGTATGACTTGCATCTTTCTTTGTCTGACCATGGCAACAGGGAACAGCTAACCATGATCAGGGCCACTGTGTGTGACTGCCATGGCCAAGTGTTCAATGACTGCCCCAGACCCTGGAAGGGTGGTTTCATCCTCCCCATCCTGGGTGCTGTCCTGGCACTGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061048-Cdh3:NM_007665:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.329 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0002812=Cadherin=PD(15.8=19.7),PF0002812=Cadherin=PU(54.5=63.2)

							
A:
NA

							
C2:
PF0002812=Cadherin=PD(44.3=54.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000079613





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000126504
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr16:68687737-68691719 
LOW PSI
HsaINT0032171
(CDH3)
Human
(hg19)
chr16:68721640-68725622 
LOW PSI
HsaINT0032171
(CDH3)
Rat
(rn6)
chr19:38707096-38709625 
LOW PSI
RnoINT0033106
(Cdh3)
Cow
(bosTau6)
chr18:36130617-36133795 
ALTERNATIVE
BtaINT0035457
(CDH3)
Chicken
(galGal4)
chr11:18315624-18315708 
LOW PSI
GgaINT1008872
(CDH3)
Chicken
(galGal3)
chr11:20833300-20833501 
LOW PSI
GgaINT0026004
(F1NUS5_CHICK)
Zebrafish
(danRer10)
chr7:52830355-52830445 
LOW PSI
DreINT0043962
(cdh1)
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"