Special

MmuINT0104399 @ mm9

Intron Retention

Gene
ENSMUSG00000034593 | Myo5a
Description
myosin VA [Source:MGI Symbol;Acc:MGI:105976]
Coordinates
chr9:75012103-75015037:+
Coord C1 exon
chr9:75012103-75012211
Coord A exon
chr9:75012212-75014825
Coord C2 exon
chr9:75014826-75015037
Length
2614 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
ATGTTTTTCCTCTAAAATAGGAC
3' ss Score
9.39
Exon sequences
Seq C1 exon
GTGGACTTACCAAGAGTTTTTCAGCCGGTACCGGGTCCTAATGAAGCAAAAAGATGTGCTGGGAGATAGAAAGCAAACGTGCAAGAATGTATTAGAGAAACTAATATTG
Seq A exon
GTGAGAATGGTTTTCACTTAACTGTTTCTGGAAAGGTCTTGTCATTCTGAGCAGAAAGGCCCTGCAAACTTCTGTGTTAAACAGCATAACCTGGATTATTTGACAGATAGTTAAGTAGGGAAACATAAGTAGACAGATAGTTAAGTAGGAATGACATAAGGTCATTCTCCGTGTTTAGTGTGATAGAAGGAATTGGATGCTGATAGCCAACACCGGACAGTTATTATAAAGGCTAGACTTGAACTTGAGGTACAGTCCTTCAGATAGTTTGATCATTATCAACAAAAATGTTTTTAGTACTTAGTTATGGAAAACAACAGATATAATTAAGGAGGAAAGTCTATTTTTATTTTTAAAGACAATGCATTTTGAAGATGAGCCTTTAGATTATGTCTACATCGCATGTTGGGTAAGGACTGGAGAAATGGCTCAGTAGAAGAGCATCTACTTGACTCAAGAGGACTTGAGTTCACTTTCCAGGACCCATGTATGGTGACCCACAACCACTTGTAACTCTGGCTCCCAAGGGAGCCAACACATCTGGCCTTCTCTGCCACTTATACTTTCACATCAATATCCTTGCAGAGACACACACATGCATACATATAGCTGAACATCTTAAAATAATAAGCATGCCCAAATACAATGCAGAGGAAGTAGAACCATTATGAGAAGGAAGAATAATTTTATGAGGTGTGAGATTTGAATCAGGCACTAAAGAATGGGTAAGTCTGAATAAAAGTGGACCTAAGCTATAAAGAAGTAGAAAATACAGAATTTGCTTATGTGGCTGGAGAAATGTTTTAGAGTTCTTGCTTGCAGAGGACTTGAGTTCGATTCCCAGCATCCACACTGGATGGCTTGCAATTGCAATTCCAGCTCCAGGAGATCCAATGCCTTCTTCTGATTTATGTGGGCACTACATATACTCATATACTCATATACTCATGTAGACCATACACATAATGAAATAAATCTTTAGAGCTAGATGACCTAGGTTTGATTCCCAGCACCCACATGGCATATCATAACCACCTTTCAAGTTCCAAGAGATCCAGCATCTTCTTTTGGATTCCACAGATACTTATCACAACAAAGTAAATTTTGTTGGCCTGGGATGGGCCCAATAATTTAACAACCTTCTTCCCTATACTTTTTTTTATTATTATTCTGTAGATAGGACCCAGGGTTTTGCATATGCTAGGCAAATATTGTACCACTGAGCTAAATCCCATTATCATTTGCATTTCTAACAGTTCCCTGGGTCTACACAGTACATATAGAAAAATCTCTAATCTAGTCTTGATGAATTTGAGATTCATGAAATGGTTGATTAAAAACTATTTTTCTTGTATCTCACTATGAAGTACTTATAATTACTAGCTATTAATTAAATGTAATTCTTCTATGATAATGTTTTTCTCCTTTGAGAGAAATAAGGATTCCTTTTTAGTAATGATTTTTAAGATTTAATGTGGTTTTTGTTTTAGTTTTATGTTTGTTTTTTCAGTTTAGCCCCACTCCTTTCTAACTTGGTGTAGATGGGAATATGAAGCAGATGCTAAGACAACCATGCAGCTGCCTCCTCACCCAGACCACTCCAGGCCTGGGCCCAGTGGAGGCAGAGGCAGTAGCTGAGAGCCGCAGTGGAAAAGGAATAGCTAGGCTTCCTATGTAAATGTTATTAAGTTATTTTAGATTTTTCAAATATATGTTATAGTTTCTAATTTTTAGCTTCATGTTTAAAGGGATGCGTACTTACTGCAAAGACTGAGTTTCTCTATTTTTTGCTTAGAATTTCAGACACAGTAGTGATTAATATATGTAAATTCCACTCTTCTTTTGATTAGAATACAGGCGATGATTTGCATTCCTGCACCTGAGGTAAATCACCTCAGTCACATGCCTGTCTCCACTTACCCTACAGCTCCGCTACAAACATCAGTGCAGTATGCAGAACTGTGTTTTAGGAAAGAAATCTGATGCAATCTTCTAATATCTTGTAAGTCTTCTACAAGTTTTAGAAGGTTTGAAAGACATTTATGAGGTTGTATCTATTTTTAGATCCTGTTAAGGTAAACTGATAACTACGTAGAAGCATCGCCTTCATCTGAACACAGGGGTTTGGAAGGATTGGTTATTGGTTTGTTTTTGTTTGTTTTTAACTTTTTATTTTGTGTGGTTTTCTTCCTGCCTTATTCTTCATCCTGGTGTTTTTGTTTCTTCAGCTGCTCATGGAGTGTACAGCCTGATGTAATCTAACAGCGGGTCAGTCAGAGGGAGTGTCAGCATCTCCATTTCCTTGAGGTGTTTAAAATCCAAACAAGCAAATAGTAGCTGCGTAGAATCCACAACCAGTTTTGGGCCTCAGATAATAATTCCAGGTAGAATAATTCTGGAAAATAACTCTTAGGCTACCATTTTCTCTACAATCCTTTCTATTTAAACAACTTATAAAGGATCAACAATCTGGCTCCATTAGTTCGTTGAAATGTATGTAGCTCAGGTTTTAGATGATAGATTCATCTTTTTACTGATTCTACTTCTATATTTTTCCATCTTTAATTTCTTTTATACAGTCATTATTTCTCCTTATGTTTTTCCTCTAAAATAG
Seq C2 exon
GACAAGGATAAATACCAGTTTGGTAAGACAAAGATCTTTTTCCGTGCTGGTCAAGTGGCCTATCTTGAAAAATTGAGGGCTGACAAACTTCGGGCTGCCTGCATCCGGATCCAGAAGACCATTCGTGGGTGGCTTCTAAGGAAGAGATACCTGTGTATGCAGAGGGCAGCCATCACAGTGCAGCGATACGTGCGGGGCTATCAGGCTCGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034593-Myo5a:NM_010864:18
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:
PF0006316=Myosin_head=FE(5.3=100)

							
A:
NA

							
C2:
PF0006316=Myosin_head=PD(2.1=19.7),PF0061222=IQ=WD(100=29.6),PF0061222=IQ=PU(81.0=23.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000117493





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000116028, ENSMUSP00000120444
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:52376559-52379624 
LOW PSI
HsaINT0108761
(MYO5A)
Human
(hg19)
chr15:52668756-52671821 
LOW PSI
HsaINT0108761
(MYO5A)
Rat
(rn6)
chr8:82086912-82091849 
LOW PSI
RnoINT0097224
(Myo5a)
Cow
(bosTau6)
chr10:58086726-58088926 
LOW PSI
BtaINT0098156
(MYO5A)
Chicken
(galGal4)
chr10:8300367-8301489 
ALTERNATIVE
GgaINT1018701
(MYO5A)
Chicken
(galGal3)
chr10:10046508-10047624 
GgaINT0029956
(MYO5A_CHICK)
Zebrafish
(danRer10)
chr18:39010772-39010915 
LOW PSI
DreINT0100827
(myo5aa)
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"