Special

MmuINT0028714 @ mm9

Intron Retention

Gene
ENSMUSG00000043705 | Capn13
Description
calpain 13 [Source:MGI Symbol;Acc:MGI:2685789]
Coordinates
chr17:73675815-73679018:-
Coord C1 exon
chr17:73678962-73679018
Coord A exon
chr17:73675873-73678961
Coord C2 exon
chr17:73675815-73675872
Length
3089 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
TCTCCTGCGTTTTGAACCAGGGG
3' ss Score
7.65
Exon sequences
Seq C1 exon
GAAAGTCTTCCAGAAAATGGATCCCGAAATAGCATTTCCTACACATACATGGATCAG
Seq A exon
GTATGCTATCTTGCAACCATGAACCTCACCGTGGTGAATGGGGAAAAGTCTAGGGACTGAAACATCTCCAGTTGCTTATTGGAAATGCACAAAGGCAAAGGACTTGATCATATTAGCCCCTTCCTATCCCTGGACCATCCCCAGATACTCTGGTTGCCAAGCTCTGGAGACAAGTGATGTCCCAATGTGGGTGGAATCCCATTGGAACATAAAGCTTAGGCAAGGAGAAGATAATTATGAGCTGTGTGTAAAGGATATATTGTGGCTTAAGCCTTTAGACAAGCAGTTGGCAGAAATCTTTCTTTCTGGGGCTCGGCCATTCCCCCCACCCCAAACCTGGCACTGTTCCTCCCTGGAGCTGGCCAGCTTCAGAAAGCCCCAACAGCTCTCTTCCTGCCAAGCCACCTATGTGCACACGGGGCTTTCCTAATGGTTTAATAAACTGTAATAAAGAACTCCTTGACTCCTCGGGATAAAAGAGCTGCCAATGGTTTCGTGGGATGGGCCTTTTTACCATTAATAACAGTGTCGGTGTGGGAAGCAGAAAATGATATAGATGCTTTTGTGTACCATGGGCCAAGCAGAAGCTGAAGGAAGGAAGGATGCCTGCCCCCTGCCTCTGTACTCAGAGGGCTAATAGCATGGTGGTATCTCAGATGTAGATTGGACCCACACACCAGAAGGAGAGGGGGATGGATGGATAGTGTGGCTAGAATGAGGGGTGACTGTTGGCAAGAGCAGCCCTTCCACACTTGTCCAGGATTCAGGACAGTTCTCACTGAAACAAGGCTGACCCAGAAGACCACTGTCCCTGTCTGTGAGTTCCTGAAGGCAGAGACAACTTCATATGCATTTCTTGTCCCCAGCCACTGATCACTGTCCTTGGCCCAGAGGAGGTGCTCAATCATTTCTGTCAGATTGAATTAAGACAGATTAGCTCCCCTGGAGCAGATGCCTGAGCCTGGGTTAGCTTCTCTGAGGTGGTCAGCAGGACCTGATTAGGATGCCTAAGACCAGGCTTCTTCAGGGCAGGTGGTACATTTTCAGACAGGGTCACACACCTTGTACTTCTAAAATAAAAATATAATCTGCCGTATGATAGGATGGTCCAGACTCCCTAATCAGGACTTTTCCAAGCACCAGCGAAACGTTTGGCACCCTCTAGAGTGATTGTTAGCTGGTATTGGACATTGGTCAGAATTAGAATAAGGCAGACGGGGCATTGTGCCTAGGTCACCTCTTAGGCAGGTATCCTTGACCAAAGCACCCCTGGCACCATCCTGTGCAACCTGCAAACCATGCTCAGAGGTTGTGGCTCCCAAGACATTTTAAAGCAAAGCATTTCTCATGCATTCGCTATAACCTCTCTCCTGGTCCCTCACATTGGCTTTAACTAGACATATTCATACAGTACTTACCAACACCCATTGATGCTAGTCACTTTTATTAGCCACTGCAGTTGTGATAGCATAAACAGACGTGCCTGTCAGAAAGGACTCATGTTGGGACTGGAGAGATGGCTCAGCAGTTAAGAGCACTGACTGCTTTTCTGAAGATCCCGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAATGAGATCTGATGCCCTCTTCTGGTGCGTCTGAAGACAGCTACAGGGTACTTAGACATAATAATAAATAAATCTTTAAATCTAATCTCCAGGATTAGACAGAGCAGATCTAACCACCATCCTTTATGAGTGCAATTGGCACACAGTTTCCAAACTCCTAGGACATTTCCTGCAAATACCTCTACCTCTCAAAGCTTTGATGCTCCACAGTCCCTACATGCAATCCTTGGGGAACTTGTCTGAACAGTCATCATTGTTATGCCTGCTATGAGTCTGTGAATGCTTCTAACAGGTGATAGAGTTACATCCCAGGACCACGTGTGCCCTAGGTGTAATATGGAGAAGGAAGTAGATGTGGTCCACACTCAGTTCAGTTGGCTAGTGGATAATCCTGTGAAAGTGAGTCCTTCCTTACCGTATCAACTTCTGTAAGGGGTCCAGAATCTTTGGAAGAAAAACTCAGTTAATGATAGGCACATAAAGACAACTTCTCTGATATCCCCCAAACTATAAGGTTAGAAAAATGGCCAGAGGACCAGCATCAGACACAAACAGCTTAGAGTTTATGCTTCTCTCTGTGGGGCTTTGCAAAGACAGGATATGAGGCTGCTCTCTTGCTTTTGGAGCAAGGTGGTGCTGTCAATGTTAGGAGGAGAAGGGACAGTGTGTGGAGGCTGTGAAGGCTGTCTTCTGTGAGGAGCAGCTCTCAGAAGGCCGCTAGGAAGCACTTTCTGAGACATGGACTGCCGCTCTACAACTCCACCACTGAGAGACCTAACTCCAGCACCAGCTCCCTGAAGCACAACAGCCATACTTCTCTATAAAGCTGTCATCAAAGGCACTACCCACCAGGCTGCCCAGTGCCTGTCTGCTGGAAAGGGTTAAGAGCATGACCCCACCCCAAGAGCAGACCTAGAAAATGTCCTCTTTATCCATAACTGTAGTTCTGTTTTTAATCTAAGGGAAGTTATGACACCCTCCTTTTTCCCTCAGTACCTGAAAGACTAAGTATTATCTTCCCCGACAGCAGCTTCTAGTAGCCTAGATTTTGAGTACGGTTAGCTCCAGTTGTCACACACATACGTATACAAAGTCATCACACATCTCATGGTCTTTCTGAAAGTGGAGAATACACCTAAAGGGCTGCACTGGTCATCCTGCTATGGTCCTCCTGATGGGGACCCTCAGTGTCAGCCATAAAGATAAAGGGAACAAGAAACACTTGTCCCATAATAAATGGAGGGAGACAGTATGAGGAGCTCACGCCAGCATCCCAGTGTCAGGATCAACCATTATGATGGATATTCAAGGAGGGAGTTATCAACATAGCCAGAACCCAGGGCAGGCCCAGGACAAAGAACAGGTAGACGTGCTATGGAAAGGAAGGGCTCAGAAGTCAGAGAGCTGTTACAGACTTTTGGAGATGTGTTCCTTGGTTACTGACTCCCATCTCACAACCCATTTTTCTCCTGCGTTTTGAACCAG
Seq C2 exon
GGGCTGGACATTGATGCCACCCAACTTCAGAGCCTTCTCAATCAGGAGTTCCTAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043705-Capn13:NM_001033444:15
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:
NO

							
A:
NA

							
C2:
PF138331=EF-hand_8=PU(30.4=85.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000092832





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:30738458-30741907 
ALTERNATIVE
HsaINT0027398
(CAPN13)
Human
(hg19)
chr2:30961324-30964773 
ALTERNATIVE
HsaINT0027398
(CAPN13)
Rat
(rn6)
chr6:24597413-24600220 
ALTERNATIVE
RnoINT0029009
(Capn13)
Cow
(bosTau6)
chr11:69118842-69120461 
ALTERNATIVE
BtaINT0031305
(CAPN13)
Chicken
(galGal4)
chr3:7773851-7774864 
ALTERNATIVE
GgaINT0079544
(CAPN13)
Chicken
(galGal3)
chr3:7792079-7793092 
ALTERNATIVE
GgaINT0079544
(CAPN13)
Zebrafish
(danRer10)
No conservation detected
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"