Special

MmuINT0021743 @ mm9

Intron Retention

Gene
ENSMUSG00000037685 | Atp8a1
Description
ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 [Source:MGI Symbol;Acc:MGI:1330848]
Coordinates
chr5:68167368-68172300:-
Coord C1 exon
chr5:68172227-68172300
Coord A exon
chr5:68167438-68172226
Coord C2 exon
chr5:68167368-68167437
Length
4789 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
TTTTCAATTATGAACAACAGTGA
3' ss Score
1.88
Exon sequences
Seq C1 exon
GTAAATGTTGGAGATATAGTTATAATAAAAGGCAAAGAGTATATACCTGCTGACACTGTCCTTCTCTCGTCAAG
Seq A exon
GTAGAGACACCTACTGATGCTCAAACAGTGTAGAGGATGGTTTCTCTACCCTGCATTGACCTTGTGATTTCTCCAAGGAAATAAAGAATAAACGAAGAATTTCAAAACCTCTCATGATTCTTAATTAAGCATTTACAAAACTGATTGGCCTCATGTGTGCCATATAGAATAAGTAACAGGTACTACATAACCCAGACTGAAAGTCGCCTCTTTCTCTGGCTCCAGCCAGATCCCTGTGGTGTGTGTGGACCACTCTGTTTATGAGTCCCTGTCATTTATATGATGCTGTCCATGGATTGGGCTCAGTTGCTTTTTTTTCTCTTTTCAGTCCTCACTTATAATAAATTCCTTTAATGTGCAGTCACCTCTCTCGCTAACTTTCCTATTCCTCGCAGTGAAATGATACAAGAGAATGGATGGGTGATTTCTTACTGTCATTGTGCCTTTCCGTATGACAGTTTTCCCACCAGACTGAGTACTTTATTCTTCCTTTCATGTCCTTTCTGTTACTGAATATAGATAATTTTTTTGTTGCATTCACATTTTAAGATAGTTGTGAATCAGTATTCAGAACATATGGCCTTAGGATTAAAAACTACCACACTAGTCCTTGTATAAATTTAGGATAATTTAAAACCTTACAATTTTAGTTCCGAAATAAACAAAGAAGAAATGTGTTTTAATGTACTTGAGGTTGTTTATCATCATTTCCTTGGACAGTTTGATTTGTAAAATCCACATAAAAATATGGACAGTGTCCTTTTTTCAAAATCTATTTAATCAGGTCATGATTTAAAATGATTGGATTATTTTTTACAAGCTAGTGATGCATAATCAGGGAGGCGGGTCATTCCTTGGCTATTTATAGAAACAGGTATTCCGGCGTTTGAAATAACTCAGGCTGTTTTGGTTTCCCTATGTGGCGTCTCTGTGTAGCACAAATGACTGTTTTCTTTAAGTCTGGCTTTCTGTCCTTAGTTACCTTTGTCGACAGCTTTGTCCGAGAGAGTTTCTAAGATGGCGTCATCAGCTTCCTGACTTTACTTGTCTACATGGGAGCGAGCTCGAAAGGAAGCTTCAGGTAGCTTCAAGTTCGAGGAGGAGTATCATGCCAGTTCTATTTTTTCATTAACTTTTAATCTGAAATGAGCAAACTGAAGTGTTAGCATGTAGCCATGAGTACATGTATGTAGCAGAAACATGGAAGAGAGCAACTATGGCTCTCATTCAAATCCAGGCAGATTCTTGGTATGACTTTCATATGTCTCTGGATACAAGGGCTTGCCCTCCTATACTCTCGGAACCACCACGTGTTACTTATACTTTATTAGTTATTAAATCACTTCAACTGGTGCAGTCATGGCCCCTCACAGCCTAAGACAGGAGTCTGTGCAGCCGTCCACTAAAGATAACACGATAGGGATGCAGTCAACTTTGAAAAACGTTTTGGAGCTGGAACAAAGTCACTTTTGTAGTGTATGAGAGAGGGGGCCGGACATACTTGTTTTTCAAATATCTCACAATTAGTTTTAAAATCATTTCTTTGCTGATTTGCGAGGAGTAAACAAAGTTCGCAGCAAATTGAGGAGTTTAAGGGAAGGAAATCTGTATGATAAAATAACTCTATAAAACGTTTTTATTTAATTTGATAAATGCTTATATGTAAACTTTAAAATGTTTTAAAGTTTCACTTTAGAAATTGAACATTGGACGGCTTAAAAAAAACCAAATGAGTTTATCTTTGAATGTTAAATATTTTCATTTCTCCCTTCAGGCCTGATCAAAATAAGTTTTGAAAAAAATCGGCATTAGACATTTTTATTAACATGAATCCTCTTCTATAATGATTTCAAACCTTCTGTCTCTTTTGTCCATTTGTTTGGTTTTTATTTTTTCTGTTATTCGTTTCTCCCCCCCCCCTCCCATTTTAATTCTTTTAAACTGGGACGTGTAGGTGGCAGTGGGGGAGATAGTGAAGGTGACCAATGGGGAACACCTCCCGGCAGATCTCCTCAGTCTGTCCTCAAGGTCAGAGCCTCAGAATGGGACAGGGTGTGTGTACGCGGGTCCTCGCCTTAAACCAAAGAACAACTGCACCCAAATGCAGTTGAGCTGGCTCTCCTTCTCTAACGCACAAATGCATATCCTTCTAGATGTGAATTGGAAATACTGTAAAGACGCTTTATGAGTATAGTTGCTGGATGTTCTTTGTCTCTCAGCCGGGCAGATTGAACTCCTATTACGCTCCATAGGAGTCCAAGAGATTTTAATCTCTCGTGCATTGAGTCACGTATGTTTTAACAACATGCCTTGCCTTTAAGGCTTTAGTTATTAATTCTCCAGGATACGGTATGTGAACAGTGTTAAGCTTTTCACGAGACAATCAATCGAAAACCGATTCCATTCTAAGGATGCTTTCTTATTCTATTTTAAATTATTTTACAAGTTCTGTGGAATTTCTGCAGTAACTGCGACTAAAATTTGGGCTTGTATAGGGTTTATAGAGGACCCCTGCACGAGGCTGGATGTCATATATTTTCATACTGCATGCTTTGGGCTCCGTCTTCATCCCAGCTGTAACTTGTGAACCAACGCACATTGCTGTGACCCGTGTCGGCCGTCTGCCGATGTCTGTCCTGTGGTGTGCATCTTGTTTCGTTTTTCCACTTACTAATCATAAAGCTTGCTTTGCCTCTGACCGTGGTTTGTGTCTTGGGTGTTACCATGACTTGCTGACGTCTTTATGAGCTAGCATGATTACTGACTCTGCTGCCTCTTCAGGGCCCTTAGAGCTACTGCAGTCACAGCTGTCTGAAGTCATTGTTAGGAATGTTCCAAATTGGGATGAATTTCATTGGCCTGGCATCAAGTGGAAGTCAGCCACTTAAACTTGCTAATTTCTTAATCCTTTCAAGCTCAATACAAATTGTTTTGTGTGGAGGGCAGTATTAGAAGGTTCTTTCTAGAAGTTTTACCCTAAGACTGGCTTTGGATAAGCATATTTATCAGTAACATTTTAATGAGTTTTACTGCCGAGATTAAAGACTTGGCAGTCTCAGTTGCTGTTCTATTTGTTGCCGTTTTTCTTTGTTAGCAGAGAAATGTGTTTTACAGCCTTTCCAATGACTATGTGGAAATTATAAAGTTGGGCAGCTGCCAGAGTGAGAATAACTATTGTGACCGTGAGTTGAAAATATTTTGGGGTGAATAGTTGAGACTGAAAATATTAATATGGAAAGATTTCTCTGATTGGGAAATAGCAGCCTAGGTGAAAGAAAGCTCGTAGGGAAACCTTGGAATGTGTGAGGTGACTTTAAAATTAATCTATAAAATTTGATTGATGTCTAAGTCTTTAAGTAAAGCTTTTGTTAATTTCAAGGGGACAAAATTAAGTTTATATGCTCATTTCTGGCACTTAGCGCAGTCTGGTTTGCACATGTACAAATTGGAGGTTGATTAAAAAAAATTCCAGTGTTTGCAACTTATAAATTTCTTTTCTATTTATAGTTATTTATCCGATAACAAACTAGGCTACATATTATGTAGCTAAGTGATAATGAGATTGGTTTAAGTTAAGAATACTTTTTGGGTTATCTTCAGAGTGCTTTTTTTTTTATAGATTTAAGGGTTAACTTTTTACAGTCAGGCCACACTCATACATCTGTAGCATCCAAGAAACAAAAAACAAACAAACAAAAACAGTGAGACGGCTATAATATAACTGGAGAACACAGGCCACAGGTCAACACATCTAGAGTTCACTTCAAACCTCAGATGCAGCTGCTTTAGGACAAGGAGCAATATGGCCAGGTGGACTGCTATTTGCTTCTCGGTCAGGCTGGGTTGATGGACCAGTTTGAATAGTGCTTGCTTATATACATGATGACCTGAGTCCAGTCCCTGAGACCCTGCATGAAAAAAAAAGCCCACTTGTGGTGTTGCACTTGTAAACCCACTGCTAAGGAGACAGACACCGGCAGACCCATTGAGCTCACTGACCAGTCAGCCCTGGTCTACTCTGCGAATTCAAGGCCAATGAGAAACCTTGCCTCAAAAATATATGGACAGCACCTGAGAAACCCACATCTCAGCTTATATTCTCACCTCCACACATCTGTATGTGTGCTACTCCACACACATGTACCAGGCCACAAATAACATGCATGAACACATACACACACACCTCTCAATCAAGTTTTTTTTTAATACTAAAAATATAAAGTGTAATGTCCACTTTCATTGTAAAATCCATCCTTTAAAAACAGCCTTGAGTTTTTACTATCACGTGGTCTATGCGATCTTGTGACCAAAGCTAAAAGGCTAAAATAATAAGTACAAGCTTGTAGATGGAGCAGTCTGGAAGTTTTTAATCAACCATTTTGCATAACCAATTTACATGTGGGCCATGAGCATGAAACAGGACATTTCTGAGCTGGAGATAAGTCTGGACGCAGACCTGCTTTACACTGGCAGAAACAGTCTGTGTTGTGCCTACATGGATAAGCGGTTTTAAAATAGGGTGGCTCTTTATGATGATATCTTGAAGACCATTACTGAGTGCTGTCAGGAAGTGGCTTTTGGGGGTCTTCTGGCTGGAAGGCTGATCCATGAGTGCCGTGCATGAGTTGTGCCTCACGCTGTCTTGCCATTAGAGTGAAACCCATCAAGAGGCTAGGTGGCTGTAGCTTTGTCTAGAATAAATGGCTTCGGTGAGTCTGAGCACTTAAGTAAGCTGGTCTCTTCCTTTCCTTTCCCAACTAAATCTTTGTTTTTCAATTATGAACAACAG
Seq C2 exon
TGAGCCCCAGGCCATGTGCTACATCGAGACATCCAACTTAGATGGTGAAACAAACTTGAAAATTAGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037685-Atp8a1:NM_009727:7
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.042
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0012215=E1-E2_ATPase=FE(8.8=100)

							
A:
NA

							
C2:
PF0012215=E1-E2_ATPase=FE(8.5=100)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000109282





     
                   









    
Main Skipping Isoform:
ENSMUSP00000118379





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000072738
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr4:42588330-42590810 
ALTERNATIVE
HsaINT0015330
(ATP8A1)
Human
(hg19)
chr4:42590347-42596305 
ALTERNATIVE
HsaINT0015330
(ATP8A1)
Rat
(rn6)
chr14:42035417-42045527 
ALTERNATIVE
RnoINT0023683
(Atp8a1)
Cow
(bosTau6)
chr6:63060263-63066621 
ALTERNATIVE
BtaINT0023896
(ATP8A1)
Chicken
(galGal4)
chr4:67777321-67781878 
ALTERNATIVE
GgaINT0067947
(ATP8A1)
Chicken
(galGal3)
chr4:70069399-70073958 
LOW PSI
GgaINT0067947
(ATP8A1)
Zebrafish
(danRer10)
chr14:46001530-46006658 
LOW PSI
DreINT0035666
(atp8a1)
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"