Special

MmuINT0028691 @ mm9

Intron Retention

Gene
ENSMUSG00000054083 | Capn12
Description
calpain 12 [Source:MGI Symbol;Acc:MGI:1891369]
Coordinates
chr7:29673631-29674134:+
Coord C1 exon
chr7:29673631-29673839
Coord A exon
chr7:29673840-29674091
Coord C2 exon
chr7:29674092-29674134
Length
252 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGC
5' ss Score
3.73
3' ss Seq
CCTTTTTCTGTAACTTGCAGGGA
3' ss Score
10.61
Exon sequences
Seq C1 exon
CTGCTGGACCTCTGGGACTCCCCGCGCAGCCGCGCGCTCTTGCCGGGACTGCTGCGCGCCGACCGCTCGGTTTTCTGCGCCCGCCGCGACGTGAGCCGTCGCTGTCGCCTGCCGCCTGGCCACTACCTGGTGGTACCCAGCGCCTCGCGCGTAGGCGATGAAGCCGACTTCACTCTGCGCATCTTCTCGGAGCGCAGCCACACCGCAGT
Seq A exon
GTGAGCCAGTGTACCCTCCATAAGCCTTACCAGGGGCATCCCGACCCCGGCCCAGGAACCTCAATCTAGAATCATAGGCCCCGCCCCTGGCACCAAGCCCCGCCCAGGAATCACAAATCCCTGTCCCTGCATCTTCAGCCCTGCCCTACCCAGGGATTCCCTTCTCCCCAAAACCCACACTGCCTTTGACTATATCCACTTCCTCTGCTGAGACCTCCGCCCGAACGCCTCCCCTTTTTCTGTAACTTGCAG
Seq C2 exon
GGAGATCGATGACGTGATCAGCGCAGACCTGGACGCCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054083-Capn12:NM_001110807:12
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=0.056
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0106717=Calpain_III=FE(39.0=100)

							
A:
NA

							
C2:
PF0106717=Calpain_III=PD(1.8=50.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000069055





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:38735545-38736109 
HsaINT0027375
(CAPN12)
Human
(hg19)
chr19:39226185-39226749 
HsaINT0027375
(CAPN12)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr18:48749141-48749376 
LOW PSI
BtaINT0031282
(CAPN12)
Chicken
(galGal4)
chr3:29684411-29684572 
LOW PSI
GgaINT0088805
(CAPN1)
Chicken
(galGal3)
chr3:31554218-31554379 
LOW PSI
GgaINT0088805
(CANX_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTGCTGGACCTCTGGGACTC

				
R: 
CGTCCAGGTCTGCGCTGAT

				
Band lengths: 
244-496

			

		

	





	
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






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