Special

MmuINT0028754 @ mm9

Intron Retention

Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120317530-120320677:+
Coord C1 exon
chr2:120317530-120317690
Coord A exon
chr2:120317691-120320507
Coord C2 exon
chr2:120320508-120320677
Length
2817 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TTTCCTTTCTTGGGTCACAGACA
3' ss Score
8.91
Exon sequences
Seq C1 exon
GATGTCATATGATGACTTCGTCTACCATTTCACGAAGCTGGAGATCTGCAACCTCACAGCTGACGCCCTGGAGTCCGATAAGCTTCAGACCTGGACGGTGTCTGTAAACGAGGGCCGCTGGGTGAGGGGCTGTTCTGCTGGAGGCTGCCGAAACTTCCCAG
Seq A exon
GTGGGAGAGCCTCTGGATGGGGGAAGGTCTAGGCAGAACTCATTCCAGGCAGAATAATATTAGCTATCACTTATGGAGCCTGTCCTAAATTCAGGATGCACTGTCTTATTAAAGCCTCCTCAGTTAAGGAAGGAAACATGCCAAGGGACCTCCGACAGGGAGCTTGTAGCAACTTGAGCTTGAAGCAGGAAACTGTCAGAGCGCCACGCCAATCCTGCTGGAGGTGCATTTGAGGACCTGGTGGCCATGGCACTTGCCCATAGCAGAGATGCTGAATGCATGGCCAAGGCAGTGGCCTCAGAGATGGGGCAGCAGAGAGAATGCAGATTTAGGGAAGGAATAATGAACGATACCAAGGGTCCTGCTGTTTTTATGTGGCTGGTTGTGGAGTTACAGTAAGAGGAGTTTAGTTTGTGACATGAAAAGTTTGAGGTACATATTGACTACCATGGTAAAGATTTGTAGTAGAGAACTGAAGTCATCTACATTTTAGAGTAGACTTGGTTATATGATAAAAATTCAATGAAGATGACAGAAAGATGGTTCGGCCTATAAAGAATTTTCCGGGTAAACTGAGTCTGGATCCTCAAACCCCCACAAAAGTCAGGTGCACTAAGTTGTGTGTCCAAGACCCCAGGGATGGGAAATGGAGACAGGAGAATCCCAGAAGCTCAGGGGCCAGTTAGCCCAGCATACACATCAGCAGACAACAGAGGCTCCCAAGAAGGTGGAAGGAGGAGGACTGATGGTCAACATTGCCCTTTGACCTCCATGCACATGCCATGCCATGCCGTGCATACATCTGCTTTCGCAAACACACACACACACACACACACACACACACACACACACACCATATACACACAAAACTCAGTATTTTATGATGAAAAAAAAAAAAACCAAACGAGTAAATAGATGAGAAGAAAAGGGTGGTAGAGAGTGGGAAGCCAGATAGGAAACTGAGCCTAGACATGTACCTCAGGTGTCATTGGAATGTAGGGCTCAGTTAGAAAGTAGAGGTCACACAAAGCTATGGTGGTGCACTCCTTTAATCCCAGCACATGGAAGGCAGAGACAGGCAGATCTCTGTTTGAAGCCAGCCTGATCTTCAGAGAGAGTTTAGGACAGCCAGGGCTACACAGAGAAACTCTGTCTCTGGAAAAAAGAAAAGAGACACTAACACCACACATACACACACACACACACACACACACACACACACACACACACACCACCACCACCACCACCACACCACATACACCACATACACCACACCACACACACACACACACACACACACACACACACACACACACACACACACACATCACATCACAGTGGAGAGGGTCAGATGCCTAGGGAAACAGCATAGGTGAAATCAGAGGAGAAACAAAGCCTCATTCACTTGAGACCAGTGACACTTGAGGAGTAGGCTAAAAAGTTAAACAGCTGTCATGTGTCAAAGACAATGAACGTTCAGAAAGGACATGACAGCATTGCACATCCAGACCGTGCAATGCCAGAAGCGCTGGTTTAGCTTTCTACAGCTGTGGTGAAATACCAAGACCAAAACAACTTGGGGAGAAAAGGGTTTATTTGGCATCACTGTTCATCAGAGGAGGAATTCAGGAACTCAAACAGGCAGGAACCTGGAAGCAGACGCTGATGCAGAGACCATGGAGGGGTGCTGTTTACCAGCTTGCTTGATTTTTTTATAGAACACAGGACCACAGGTTGTCTGCTTACAGCCCAATCTTAGGGAGACATTTTATCAGTGGCTGAGAGGAGGAGATTCCCTCTTTTCTGATGACTCTAACTTGTATCAAGTTGATATAAAATTAGCCATCATAAGGGTAGGGGGTCTCACTCACCAATAATTACACAAACGCTTGGATCATGCTTTCCATAAATAACTGTGCATCTTACAGTTGTCCGGAATGGGAAGCAGGCCTCTTAAACTTTTTTTACATATATCTTCTTTTCAATGAGGAATTTTTACACAACCCCGTGTATAGGTGTATAAAATAGGTATGCAAATCAGACACTTACTGATAAATCATTAAGACATTTACTTGGGAGTCTGGGAGTGTAACACAGTTGATAGTTTGCTTGTCTAGCATGCATGAAGTCACACCCTCACACACATACACACAGAGAATAAAGCATGTATGGTGGCACATGCTTCTAATCCCAGCACGAAGGAGTCAGGAGAATTGTCACAAAAAATGAAAAGAAAATAAATTTATTTTATTTTAAAACAGTTCATGGTGCACATGTAAGTTTGCCATTTATTTTATGTTAATGAGATAGGTGCACTTGTTCGCTTTTGCTCAAAAAAATTAAATCTTGTGGAATATTAGATACCGTAGGACACAGAGCATCTTCTTTTTGGAATTGATGGATATTTTGATGTCATAATTGTCAATCTTGAGAATCCCATTTATATAAATAAGTAGTACGAATCGGCAGCAGTTCTTAGGGCCATTTCAGAAATTTCTGGGAATTCTGTCCTAATTCTAAGTCAAAATCCATTTAATGGGAACTGGCGAGATGACTCAATGGTAAAGAGCTCTTACTGCTCTTGCAGAAGACCTCGGTTCGGTTCCCAGCAATCACATGGTGGCCCTCTTCTGATCTCCATGGGCACCAGACATGCATGCGGTACACAGACATAGGCAAACCATCCATACACATAATTCAAAACCTTAACGTTACCCATCATAGGGAACAAAGGAGACCGGATCTCTGTCCTACTTTCCTTCCTGCCCTTTCTCATAGAGGCGTATCTGAACACGCATTTCCTTTCTTGGGTCACAG
Seq C2 exon
ACACTTTCTGGACCAACCCGCAGTACCGTCTCAAGCTTCTGGAGGAAGACGATGACCCTGAGGACTCTGAGGTAATCTGCAGCTTCCTCGTGGCTCTGATGCAGAAGAACCGGCGCAAGGACCGGAAGCTGGGGGCCAACCTCTTCACTATTGGCTTCGCCATCTACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110-Capn3:NM_007601:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0064816=Peptidase_C2=PD(12.8=34.5),PF0106717=Calpain_III=PU(15.5=43.6)

							
A:
NA

							
C2:
PF0106717=Calpain_III=FE(36.1=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028749





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028748, ENSMUSP00000028749f6296A, ENSMUSP00000087482, ENSMUSP00000106344, ENSMUSP00000106347, ENSMUSP00000106349
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:42399653-42401640 
ALTERNATIVE
HsaINT0027459
(CAPN3)
Human
(hg19)
chr15:42691851-42693838 
ALTERNATIVE
HsaINT0027459
(CAPN3)
Rat
(rn6)
chr3:112264868-112267534 
ALTERNATIVE
RnoINT0029057
(Capn3)
Cow
(bosTau6)
chr10:37872922-37874290 
LOW PSI
BtaINT0031372
(CAPN3)
Chicken
(galGal4)
chr5:24950369-24950929 
LOW PSI
GgaINT0054921
(CAPN3)
Chicken
(galGal3)
chr5:27831687-27832247 
LOW PSI
GgaINT0054921
(CAPN3)
Zebrafish
(danRer10)
chr17:45339810-45342193 
DreINT0041196
(capn3a)
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"