Special

MmuINT0028822 @ mm9

Intron Retention

Gene
ENSMUSG00000038599 | Capn8
Description
calpain 8 [Source:MGI Symbol;Acc:MGI:2181366]
Coordinates
chr1:184527078-184527839:+
Coord C1 exon
chr1:184527078-184527196
Coord A exon
chr1:184527197-184527705
Coord C2 exon
chr1:184527706-184527839
Length
509 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGA
5' ss Score
5.29
3' ss Seq
GTTCTGTTTCCCACCCCTAGTTC
3' ss Score
8.89
Exon sequences
Seq C1 exon
GAGACTGTTGGCTTCTGGCAGCCATTGCCTCCCTCACCTTGAATGAAAAGCTGCTTTATCGAGTGGTTCCTAGAGACCAGAGCTTCCAGAAGAACTATGCTGGCATTTTTCATTTCCAG
Seq A exon
GTGTGAGTCCTTGCTTGTGACCTTTGTCACTACTTTTGTATCATAGATATTACTCCAGATCTGTGGCATCAGAAACTCTGGAAGCGCAGCCAAGTTACTACGTGAGATTATCCCTCTGGGTGATTTGGATACACACTCCAGTTTGAGAACCATTCCTTTATACATCTATCCAATCATCTTCATTCTGTCTCCTTTTCCCTCCAGGCCATGGGCCAAGAGAATCACTGTGGACTAAGGACCAGGAGATGGGTGTCTGAGTTACCCACTCTGGCTCCCTGGGTGATGTTTGAGCAAGCTCTCTTCTCCACAGACTCCAAGAAAGGCTAAGTGCTTCTTGGTGTCTGTGGTATATCCTGTGTGCAGATGGGGCATAAAGCCTTCTCTCGGGGCATTTAAGGCTCATGAAGGTTGGAGTCTTGCTCACTGACTGCAGAAACCGCATCCAAGGATGCCACTGAAGGACCGGCTCTGCTTCTACATGTGATCCGTGTTCTGTTTCCCACCCCTAG
Seq C2 exon
TTCTGGCAGTATGGAGAGTGGGTGGAGGTGGTCATTGATGACCGGCTCCCCACCAAGAATGGACAGCTGCTCTTCCTACACTCCGAAGAAGGCAATGAGTTCTGGAGTGCTCTGCTGGAGAAAGCCTATGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038599-Capn8:NM_001145806:3
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(13.0=100)

							
A:
NA

							
C2:
PF0064816=Peptidase_C2=FE(14.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047164





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000129549
  



Associated events






Conservation


Human
(hg38)
chr1:223628143-223628661 
ALTERNATIVE
HsaINT0027542
(CAPN8)
Human
(hg19)
chr1:223815845-223816363 
ALTERNATIVE
HsaINT0027542
(CAPN8)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr16:27711719-27712232 
LOW PSI
BtaINT0092732
(MGC151839)
Chicken
(galGal4)
chr3:17055619-17056431 
LOW PSI
GgaINT0081349
(CAPN8)
Chicken
(galGal3)
chr3:18833059-18833871 
LOW PSI
GgaINT0081349
(CAPN8)
Zebrafish
(danRer10)
chr18:36691620-36701984 
LOW PSI
DreINT0041081
(capn12)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAGACTGTTGGCTTCTGGC

				
R: 
GGCATAGGCTTTCTCCAGCAG

				
Band lengths: 
251-760

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"