Special

MmuINT0028854 @ mm9

Intron Retention

Gene
ENSMUSG00000031981 | Capn9
Description
calpain 9 [Source:MGI Symbol;Acc:MGI:1920897]
Coordinates
chr8:127118529-127121567:+
Coord C1 exon
chr8:127118529-127118662
Coord A exon
chr8:127118663-127121398
Coord C2 exon
chr8:127121399-127121567
Length
2736 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
CTGCTCTTGCATCTTTGTAGGCT
3' ss Score
8.65
Exon sequences
Seq C1 exon
TTCTGGCAGCACAGTGAGTGGCTGGACGTAGTGATTGATGACCGCCTGCCCACCTTCAAGGACCGCCTGGTCTTCCTCCACTCTGCTGATCACAATGAGTTCTGGAGCGCACTGCTGGAGAAAGCCTATGCCAA
Seq A exon
GTGAGTGGGGCTGGGGTGGGTGGGGTCCCTCCTCCTGCTCCTAGAAGCCTGGACTCATCCCCTCATGGGGATGTTTGGTGGAGAGACTGGGATGCAATCAGTAGGGAAGAATGGTTGCTACCTGTCGGGGACTTGGACCACTAGGACATTCTCATGAGATGACCTAGACATTTCCAGCTTCAAACATGGTGGCCATGTTTCCTGTCTCCCCAAGAAACTGATCGGACCTTCACAATGCTGGCAGGAAAGATGTTAGGAGGAAGGTAGGCCCTTGGCTATGCCCACATGGCACAAGGGTCCTTCAGGTCTCATACCAGGATTTGCCACAGCTTAGGTGCGTGGCTTTAAGCCACATGAATAGAAAGACATCAGCTGGCCCCAAGGGCTCATTTCCTTCCTTTTAAAAATGTTATGAGCTGGGCGTGGTGGTGCATGCCTTTAATCCCAGCACTCGAGAGGCAGAGGCAGGAGGATTTCTGAGTTCGAGGCCAGTCTGGTCTACAAAGTGAGTTCCAGGATAGCCAGGACTATACAGAGAAACCCTGTCTCAAAAACAACAACAACAACAAAAATGTTATGAAACACTCATGCCATAAAATTTACCACTGTAACATTTTGAGGGCATAGTTTAATGGTATTAACACACTTATCTGGCATGTGACCAACTACAGCATCCACCCTCAGAAGTGGCTGCCTTGCAAAACTAAAACCTAGTCCCTGATAGACACTGGTGTCCCATCCCTCTCTTTCCAGCTCCCTCTTGGCACCATCCACTTCCTGTCTCTGTGGTTAAACCAGTCCAGGAGCTTCACATAAGAAGAGTTAGCATGGACTGGAGAGATGGCTCAGTGGGTAAGAGCACCCAACTGCTCTTCTAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAAGAAGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTAAAAAAAAAAAGAAAAAGAAGAGTTAGCACAGTTGTTTCTTTTTTTAAAAAAAGTTATTTATTTATTTCATGTATGTGAGTGCACTGTTGCTGTCACTGTCTTCAGACACACCAGAGGAGGGCATCTGATCCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCGGGACCTTTGGAAGAGTAGTCTGTGTTCTTAACCACTGAGCCATCTCTCCAGCCCCAGTGCATTCATTTCTAATCCCTAGTCAAATGGCCCCAACTCCCCCCAGTCCTCCAGTTCCAGCCTGCTAGTAAAATTCAGGTCCAATCACCTCACAAATGTATAAGATGAAACTTGATTGAGTTGGGAAGACAGTGGGTGTCTTGGTCACCCTAGAAACACATGTACTCTGGTAGATAGGGCACATCCTATAGGATTCAGGCAGGGTATTCTGATGCAGTGGTCCACACAGTGACTGAGCAGTTGGTAAGATGGAAGGCAGGAAGGGAAGCCAGCTGCTAGCGGTTGGAGGGTAATGTTTCCCACCCGGATAGAAGGGCCTCTACATATGCTAATGGATGGTGCTGGAGTTCAGGGTGGGCTTATGATGATCCCACCAGAGCAGTAACGGATGTGCGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTGTGTGTGCGCGCGTGCGCATAGGTTATGCACACAAATGCAAAGGGCTAGACTTGGTCATGAATGCCTATAACCCCAGTGCAGTGGGGAGTCGAGACAGGGGAATCTCTGGGGTTTTCTAACTTCCAGCCTTGCTCCAGGTTCAGTGAAAGACTGTCTCAGAATAAGGAAGAGTGTCATAGACCAGGACACTCAGTGTCCTCCTCTGGCTTCTGTGTGTGCACATAGACACATGCATCCATACACAAATGTGAAAATACACTACACCTATCACATAAATTCACACACACATATGCACCACACACACACACACACACACACACACACACACACCAAGAGGAAGCTGGGCATGTTGATGAATATCTATAACTGCAGCCCTGGTGAAGCTGAGGCAGGAGGATCACCACAAGTTTGAGCTCAGCCTGGTCTGCATATAGAGTTTCAGGCTAGCCTGGGCTATATAGCAATATTGTGTCTTGATTTCCCCCCCCCCTTTGGGCTTGATAACTTACTCCCACAATCCTAGAACTGGAGATTCTGAGACAGAAGGATTGCTATGAGTTTGAGGCCATCCTGGTCTGTGGAGTGAGAGTCTGGCTCACACCCAAGCATATACATTCACACACACACACACACACACACACATACACACACACACACACACACACACAGACCACAAATCAAGGTAAAGCTGGGTGTTGTGATCAATGCCTGTAACCCCAGCTCTGAGTCAGAAAGATCACCATAACAACAATAAAAAAGCAATCTCAGTACTTCAGAGACTGAATCAGGAGAACGAATAAACAACTGAGCATTCAAACATTAAAAAACAAACAAACAAGCAAAAACCATGTTTGTGAGGAAGATGGCAGGACTGGCTCAGACTACGATCCCCTCAAGGTGTCAGCCTCAGTCACTATCTTGCCAGTACCAGGGCTTGCCCCACTGCCTCTCCTCCCTGAGTCTGAGCTCCTCTGTGAGCTGAGCATACCTTCCACCTCATCCTGTCCCTCCACTCCCTCAGCCAATCTGCTCTTGCATCTTTGTAG
Seq C2 exon
GCTTAACGGGAGTTATGAGGCACTGAAGGGAGGCAGTGCCATTGAAGCCATGGAAGACTTCACTGGGGGTGTGGCTGAGAACTTCCAAATCCGAGAGGCACCAGAGGATTTCTTTGAGATTCTGGAGAAGGCTTTGAAGCGTGGTTCCTTGCTGGGATGCTCCATAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031981-Capn9:NM_023709:4
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=FE(14.9=100)

							
A:
NA

							
C2:
PF0064816=Peptidase_C2=FE(18.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000090717





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:230762787-230767540 
LOW PSI
HsaINT0027562
(CAPN9)
Human
(hg19)
chr1:230898533-230903286 
LOW PSI
HsaINT0027562
(CAPN9)
Rat
(rn6)
chr19:57354015-57356016 
LOW PSI
RnoINT0029145
(Capn9)
Cow
(bosTau6)
chr29:44067082-44067167 
LOW PSI
BtaINT0031246
(CAPN1)
Chicken
(galGal4)
chr3:39822142-39822723 
ALTERNATIVE
GgaINT0087005
(CAPN9)
Chicken
(galGal3)
chr3:42369556-42370137 
LOW PSI
GgaINT0087005
(CAPN9)
Zebrafish
(danRer10)
chr1:53238441-53238517 
LOW PSI
DreINT0041267
(capn9)
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"