Special

MmuINT0021505 @ mm9

Intron Retention

Gene
ENSMUSG00000038023 | Atp6v0a2
Description
ATPase, H+ transporting, lysosomal V0 subunit A2 [Source:MGI Symbol;Acc:MGI:104855]
Coordinates
chr5:125083460-125086693:+
Coord C1 exon
chr5:125083460-125083538
Coord A exon
chr5:125083539-125086595
Coord C2 exon
chr5:125086596-125086693
Length
3057 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCTGCATCTTATTTTCACAGTGT
3' ss Score
7.47
Exon sequences
Seq C1 exon
CTCAATCAAAATGTAAGTTCTTTTCAAAGAAAATTCGTCGGTGAGGTAAAGAGGTGTGAAGAGCTCGAACGAATACTGG
Seq A exon
GTGAGTTTGTCTTCCACTTTAATCTAAATGCCTTTTATCTTAATACAAGCATAGCTGTTTCTTTCAGAAAATACAGATGAAGAGAAGAGAGGGAAGAAGCCAGGCGGTGGTGGTGCACGCCTTTAATCTCAGCACTTGGGGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGTCAGCCTGGTCTACAGCCTAAGTTTTAGGACAACCAGGGCTGCAGAGAGAAACTCTGTCTGGGGTGAGGAGAAGAAAGAAAGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGAGATGCTGTGTGGGGGTAGGGAGTTGATCCCTGTTCTGTCCAATTGTAGGCTCATTGTTTTTGATGGCAGCTGAGTAGGATTTCATGGTATCGACGTGTCATGGCTTATTCAGGCCATATTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAGCCTGTCTTAAAAAAAAAAAAAAAAAAGAACCCTGTACCTTGTATACATGCTGATACTCGCCACTCAACCCAAGCTGTTACTTAGGGATAGGACAGGCAGGAAATGGCTGACAGCTGGCTTGATAACACTTGGTGTGTTTGCAGGGCTTCCTTTGTGAATGGGGTAGTTTGGTGCTTCCTGCTTGACTCTTACAACCCAGGAGCCCATGCGTGGGGCTTCCCTCATCTCTAAAATCTAAGATGCACTGCAGAGTAGTTGGGGTGTAAGAGAGTCTTGGCTTTTTCAATGATTTTTCTTTTAAAGATTTATTTATTTATTTATTTTATGTATATGAGTGCTCCAACTACATGTACACCTGTGTGCCAGAAGAGGTTGTGACTCACTATGTGGTTGCTGGGAATTTGAACTCAGGACCTCTGGAAGAGCAGCCAGTGCTCTTAACCGAGGAGCCATCTCTCCAGCATCTTAGAATGATATCTGACTGTTAATCATTACTTAGGTTTTTTTTGTTTTTTGTAAATTTAAAATTTTTTTTATTTATTTACTATATGTAAATGCACTGTAGCTCTCTTCTGACACACCAGAAGAGGGCGTCAGATCTGAAAACAGATGGTTGTGAGCTACCATGTGGTTGCTAGGATTTGAACTCGGGACTTCTGGAAAAGCAGTCAGCGCTCTTAACTGCTGAGCCATCTCTCCAGCCCCCAAGTTGTTTTGTTTTTTCAAACTACGGATTTTTTTTTAATTCTTTGAAATTTTGTACACATATACAGGGCATCTGGATCATATTTATTCCCACCACCACCACTGTCTTCCTGCAGCTGCACACCCCCCCTCCCCTCCAAACACTTCCCTCTCCCACCTTCCTGCCCTGTTTTCCTTTAGTGACCTACCTAGTCCACCTAGTGATGTGTTTGTGGCTGCGGGACACCCACTAGTACACGGCTAGGTGACAGGTGGCCAGAGCCCCCAAGAGGACAGACTGCCAGTGCCAGTTGTCCTCAGTGAGGCGTCCCCTTCATCTAGAGATTTTTCTTCTCCTTCTCGTCTGGAGGGGGGACCTGGTGTGGGGCGGTCAGGGTCTCATGAAGCCCAGACTGGATTCAGGCACAGTGTGTGGCTGAGGCAGACCTTAGACTGCTGATCCTCTTGCCCTCTCTCCCATGTGGTAGGACGACAAGCCTTTTTTTTTTTTTTTTAGAGATTTATTTTTATTGCTTTTAATTATGTGTGTGTGTATGTTTGTCTGTCTGTGTGTGTGCATGAGTGCAGATAAACCCGTGGAGAACAGAGGTGTGTGGTGTCTCCTAGAGCAGGAGTTACAGGTGGTTGTGAGCTGCCCAGTGTGGGGGCTGGGGGATTGGACGTAGGCCTTCTGGAAGAGCACTCATGGCTCACTCCGTGCAGTTAAGTGCTGAGCCATTTCTCTGAACACCACCTGAACTTTTAGTTCAGGATTTTAAATTAACAATAATATTTTTAAAAGATTTAGTATTATTATTATTATTTTTTTTAAAGATTTATTTATTTATTATATGTAAGTATACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGATCTTTTTACGGATGGTTGTGAGCCACCATGTGGTTCCTGGGATTTGAACTCTGAACCTTTGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCAAGATTTATTATTTTTAACTGTGTGTCAGCGTGTAGCTATGTACATATAAGTGCAGTGCCCAACAACGCCAGAAGAGGGCATCAGATCTTCTGGAACTGTTGTCCACTTGAGGTCCAGTTGTGAGCTGCCTTACAATGCTGAGAACTGGGTCCTCTGCAGGAGCAGTGCTCTGAACCACCTCTCCAGCCCTAGTATTTATTTATCAGATTTTTGTTTGTTTTTCAAGAGTATTTCTCTGTGTAACCCTGGCTGGCCTGGAACTATTTCTGTAGACCAGGCCGGCCTTGAACTACGAGATCCACTTGTCTCTGCCGCCCAAGTGTTGGGTTTGAAGGCATGTACCACTTCCCGTGGCTTCCAGCCCTAATGTTAACAATACCATTTAGTCATGTGGAATCTCTAGATATTTGCATATTAATAGTTCATGTGTCTGAGTGACATCACTTGTGGACAGGTCAGTTGTGTAGAATGAGGCTCCTAAAAGCAGAGCAAAGCACAGCCTGGTGCCTCGCTGGGAGCCTGGCTCTGCTGTGACTCTGACCTCTGTGGGGAGCGCCAGTTCACTGCATCTGGTGCGGTACAGGTCTACACCGTCAGTACATCTTTGGCTACCTTCCATGGGAGGAGGTACCCAAACCTGTTTTAGCCTGGGTTTTAGTTATGAAAGAACCTGAGTAGCTCTAGCCAGTGAATGCAGGCGGTGACAGGGACAGGCGGAATCTGTGCACACAGTAGGTTGGGGCTGCCAGGATTCAGATTGCAAAGGGTCACAGTGAGACTCTCTGACTCTGCATCTTATTTTCACAG
Seq C2 exon
TGTACCTGGTGCAGGAAATCACCAGAGCTGATATTCCCCTGCCTGAAGGAGAGGCCAGTCCTCCCGCACCACCTCTTAAACATGTCCTAGAAATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038023-Atp6v0a2:NM_011596:2
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=0.394
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0149614=V_ATPase_I=FE(3.2=100)

							
A:
NA

							
C2:
PF0149614=V_ATPase_I=FE(3.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000039737





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:123718702-123722350 
LOW PSI
HsaINT0015086
(ATP6V0A2)
Human
(hg19)
chr12:124203249-124206897 
ALTERNATIVE
HsaINT0015086
(ATP6V0A2)
Rat
(rn6)
chr12:37391669-37394273 
LOW PSI
RnoINT0023474
(Atp6v0a2)
Cow
(bosTau6)
chr17:54232772-54235882 
LOW PSI
BtaINT0023665
(ATP6V0A2)
Chicken
(galGal4)
chr15:4921161-4922453 
ALTERNATIVE
GgaINT0007378
(ATP6V0A2)
Chicken
(galGal3)
chr15:4968545-4969837 
LOW PSI
GgaINT0007378
(ATP6V0A2)
Zebrafish
(danRer10)
chr5:24041264-24041588 
LOW PSI
DreINT0035510
(atp6v0a2b)
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"