Special

MmuINT0028736 @ mm9

Intron Retention

Gene
ENSMUSG00000026509 | Capn2
Description
calpain 2 [Source:MGI Symbol;Acc:MGI:88264]
Coordinates
chr1:184404013-184407439:-
Coord C1 exon
chr1:184407382-184407439
Coord A exon
chr1:184404078-184407381
Coord C2 exon
chr1:184404013-184404077
Length
3304 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGT
5' ss Score
10.74
3' ss Seq
ACATCCATTTTATCTTTTAGGCC
3' ss Score
10.69
Exon sequences
Seq C1 exon
GATGCAGAGATCTCTGCCTTTGAGCTGCAGACCATCTTAAGAAGAGTTCTAGCCAAAC
Seq A exon
GTAAGTGTCCCCTTTGCAAATCCATCATCACACTCTTCCCGCTTTGGACATGAGGGGACATGGGATCCCCCCTTCAGGCACAAGTCAGCAGCTACTCTCTGCTTCTACACCAGTGACCTTTGCAGTGTCAGTACTGGGGAGATATAGGACGGAGCAGACTCTGGGTGAGGTAGTGCCCTAGAGCAGAGGTTCCTGGGTCTAGAGATCACAGATCAAATCCAGGTTCTCCCATGTCTGAGCTCTGTGATGTAAACCAGGTTTGACCATCTGTTGGACTCCCCCGACCCCCATCTGAAAAATAGACATACTATGACTTTCTCTTCCCAGTGGTTGAATATCACTTCGTGAGATAACATATAAAATCTGCCTGCACGCTGTAAATGGAAGCTCTTATAATGACTGGCTGGTAAGAAAAGGCTAAGTCGGCCCAGACGATGGACACCACAGTCCTGAGTTTCTAAGTTCTCTGCCTACCTAGGGGAGAGGTCGCCTGTCACTGATTGGCCAGAATGGTGGACAATATGTCATCTTACCCTCGGGCTAGGAGAGATCGATTGCAAAGTCTCAACTCCTCACGTTGAATTAAATGAGCTTCAACTCACTTGAGCCAATGGGACAAATAAATAGCGTCTAGATTCTGGAATTACATGCTCAAACCCAAGCCGGAGGCGTCCATAGAGCAGGGAACAAGACTAGGTGGAGGCCGGAGAAAGAGGCAGAGCCAAGGATATCGCAGCTTTTTTTTTCTTTTTTTTTTTTCCTTTTTAACCTTATGGTTATTACTTTAAATTTTTTCTTTTGCTTTTAAAAAGTATGGCTATTATTTTTCACATGTATATATGTGTGCACATGTACATATGTGTGTGTGCACTTGAATTCCACAGTACACACGTAGAGGACAATATTCAGGAGCCGTTCTTTAAATTTCTACTGCATGGGTTCTAAGCATTGAACTTCAGTCATCAGACTTGCTGACAAGCACCTTTACCTGGTGACCCACCTTGATGGCCTTTTTGGCTTCTATAGCCTAGAATGACCTCCTTGAACTTGGTGTGTAGCCCAGACTGGTCTTGATCTCACAGCAATCCTCCTGCCTTGGGCTCATAAGTATTGAGATTATAGGTGTGATCAGCCATGACAGCTTCTCTAGCTGTTTCTTAAATAAGAAGTTAGCCAAAGGCCTGGAGAGATGACTCAGCAGTTAAGGGAACTAACTGCTCTTCCGAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATTCATAATGAGACCTGACGTCCTCTGGTGCGTCTGATGACAGCTACAGTGTACTTAGATATAATAATAATTAAATCTTTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTGATTGAGAGAGATTTAAAGAAAGAATTTATCCAAAGACTACTGCTCACCTCCCCTGCTGTTGCTCATCCCTAGAGAAGAGGGGAAATATATTTCTCCCCTCCAACCCTTACAAATCATGATGCCCCGACATGATAGTGGATAGTTAGCATGCCATGCCTGAAGTCATGCAGATTAGAAACAGGCACACATCCCAAGCATCAGTTCTACCTGTCATCATGGATGCCCCATGGACTCCAGGGACTGCCGTTCTATCTGACACCACCAGATGGCCTCCTACTTGACCCCTCCGAACAAAAGCAAATCCTTGTTTTAAAGCCAAAGAGTAGCCCAAGGTCTGTAGGGTCTTCCATACTTGGTGTGTGTCCCTCACATGGGAGACAGTGGGTTGCAGCATGCGGTTCGTGCTGTAGGATAGCATCTATTCTTCACAGAACACTCAGCAGTCAGAGTGAGGGTGGCTGGAGCCAGCATCCAGGCAGGCCAATGCAGGGCTTCCCCAGGGCTGGGCTTAGCTGCACTCTCCCTCTTCCAGGACAAGAGAATAATAGTCTTTACCCTTGTGGCTGCCTGGCACAAGGATGGTGAGAGGACTCCTTGAATGTTGGCTGTAGTGCATGCAGAAGACAGAGTCTCTTTGTCTCTCACAGCTGAAATGCAGGAAGAGCCAGGCCATGCTTGGTCCAGGCTGCTTCTAGTTGAGGAAAAGCATGTGTTGTTGAGCTCAGGCCCCTCCTCTGCCTGCCTGGTGACTCTGGCCTTCTGCCTAAGTGTCCCCACACAGCCTCATGACCATACTGGACAATGGGTTGCTGTCTAGTGGAACAAGTTTAGTGTTGAGATGTAAGCCCAAATAGTCTACAAAAACATCACCAAAAGGGTTATTCCGTGTGGCCTGGAGAGATGGTATGGGGGTAATGTGCTTGCCGTGCTGGCACGAGGGCCTGAGTTTGAATCCCTAGAACCCAAGTAAAGCCAGGCACAGTAGCATGCACCTGTAACACAGTGTTCCTATGGTGAGATGGGAGATGGAGACAAGAGTCCCCAGAATCTTATGGGCATCCCAGTCTAGCATCCACAAGGGCTAACAACAAAGAGACTCTGTCTCAACCAAAGTGAAAAGTTACTACTGACACCCAAGGCTGTCCTGACTTGTATGTACCATGAGCCAAGGTACATACCCATCCATACTCACACACATGCAGACACATCCATCATACACACACATTACTGTCATCCTCGTTACACACATATACGCTTGCACACACACATGCACACGCACACAGTTGCTCCTCATGAAGCCCACGGAGAGTGTGACAAGAGTCTCATGCCACCTGCCACCACCAATGGACTCACCTACAAAAGTGCAGTAGGTTCTGGGTCCTCAGCCCTCTCTGTCATCTCAGACAGAGATACAACTGTCTGCAGATAGACCAGTGGAACTGCTGCCTTCCTCTCTCTGCTCGGAACCTACAATGAACACACGTGCTCTCTGGCTGTGTGTGACCACCAGCAGTTTTCTACCCTGTCAGCATTTAAAGGCCCAGCTATAATCAGGTGTGATAGCACATGTCCATGATCCTAGCCCTTGGGAGTCAGAAGAAGTGTTGAGTTTGAAGCCTGCCTGAGCTCAATCACAAAACTCAAAAAGTCCAGTCATATTTTTTATTCCTTTATTGCTTATTTTGATATTAAACCCTGTTTAATATATCCATGGCAGTCATACAAAGAAATCAAACACGCCTAAGACTTTCTGTACCGTCCCCATTTGACAGCCAGTCAAACATGGCTAAACTAATCCGATTGGCTGTTGTAGTGGTCAGCACAGAGGAAGAACATGTTTATCTTTGTAGAAAGTTCTGGGAGACAGTGCTGGTCTGGAAGGCTCTCCTCATACATCCATTTTATCTTTTAG
Seq C2 exon
GCCAAGACATCAAGTCAGACGGCTTCAGCATCGAGACCTGTAAGATCATGGTGGACATGCTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026509-Capn2:NM_009794:15
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:
PF138331=EF-hand_8=FE(31.1=100)

							
A:
NA

							
C2:
PF138331=EF-hand_8=FE(34.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000068895





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000106631
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:223764208-223766366 
LOW PSI
HsaINT0027441
(CAPN2)
Human
(hg19)
chr1:223951910-223954068 
LOW PSI
HsaINT0027441
(CAPN2)
Rat
(rn6)
chr13:100885721-100888837 
LOW PSI
RnoINT0029042
(Capn2)
Cow
(bosTau6)
chr16:27830142-27833083 
LOW PSI
BtaINT0031357
(CAPN2)
Chicken
(galGal4)
chr3:17024717-17025835 
ALTERNATIVE
GgaINT0078834
(CAPN2)
Chicken
(galGal3)
chr3:18802157-18803275 
LOW PSI
GgaINT0078834
(CAPN2)
Zebrafish
(danRer10)
chr22:26313034-26313114 
LOW PSI
DreINT0041151
(capn2b)
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"