Special

MmuINT0104402 @ mm9

Intron Retention

Gene
ENSMUSG00000034593 | Myo5a
Description
myosin VA [Source:MGI Symbol;Acc:MGI:105976]
Coordinates
chr9:75016732-75019585:+
Coord C1 exon
chr9:75016732-75016888
Coord A exon
chr9:75016889-75019345
Coord C2 exon
chr9:75019346-75019585
Length
2457 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTATCTTCCTTTTTCTGCAGATA
3' ss Score
12.31
Exon sequences
Seq C1 exon
CTATGCTAAGTTTCTGCGCAGAACCAAGGCAGCAACCACCATTCAAAAGTACTGGCGCATGTATGTGGTCCGCAGGAGGTACAAGATTAGACGAGCTGCCACGATTGTTATTCAGTCTTACTTGAGAGGCTACTTGACAAGAAATAGGTATCGCAAG
Seq A exon
GTAAGACACTATTTTCATAGTCTCCATCTGTACAAAGTACCATCCAGACTGCAGTGGGCAAAGAAGCCATGAAGAAACAGCCAACAATTAAATTGTATGCTAGTATTAAGTAATTAGATATACTTGTTAAGACAACACAAAAGAAAATGTACATCCCATTTCCATTTGTCTGTACAACTTGTAAAGCTGAATAAGTGAATGTAAAATGAAAATCACAATTGCTAAAAACAACAGTACTTATTTTCTCAGCCTTCAGCAGTACCACATTCACCAAAAGCCCAAGATAGAATGCATTCGTCATTCCTCCCAGGGGTGGCCTACAATCCTATACCTGTGCTCACATTGCTCCTATCTCTGCTCTATTTTACATCATCTGTCTCTTACAAAAATAATCATGGGGCTGGTTAGACCCCTAAGACCCTCATCATGGAAGGAGACAATCAGCTCACACATATGTTCCCCCACAAAATAATTATTTTTTTAAAGATATTTTTTAAAAATTATGATGGTATTTAGATCCCACCTTCATAGTTCAGGATAATATCCCTGTCTCAAGATCTTTAACCTAGTTATGAAGTCCCTTTTTCCAAATAAAATAACAACTACAGGTTCTAGGGATTAGTACATTATGCCATTGGGCCTATTATTCAGACAGATACAGAGAGGTAAGCTATACAGATCGGCTAAGTCTATGACAGAAGATCAACCTAAGGAGAAGAGCTTAGAAGAATTTATCATGAGGAAATAAAGAGGAAATAACTATAATGTTTGTATAGTTAAAATTATATTGACTAGAATGTGGTGTGTCTTTGATTCAGTGTGTGTGCACGCGTGTGTGTATGCAAGTTGTGCATACATATGTAGACACCGGAGCAGGACTCCAGTTGTCTTCCTTATTACCTTGAGACAGACTCTCACTGAACCTGAGGCTCATTGTCTTGGCCAGGCTGGTCAGCCAGCAAACTCCCAAGATCAACTTGTCACCACCGCTCAGTTCTGGGGTTGGGTTATGGAGATAAGAGTCTATGCTCAGGTTTTTATGTGGGTTCTGGGGATTCACACCAAGGTCCTCCTGTTTGTATAGCAAGCAGTTCTTGTCCACTGAGCCATCTTCCAAGCCCAATAAATCTTTTTTGCATGTGGCACTGGGATTGAATTCAAGACTGCATGTATAATAACCATGCAGTTGTCTACTAAGTTGTCTGTATTAAAAGTGTCCTTTGTATCTTAGAATAATTAATATTACTCTATAGATCATAGATCACCAATGAATCTTTTTAAAAGCGTGTGTGTGTGTAGAAGGGGCAGATACATATATGCCATTGTATAAGTGTGGATGTCAGAAGACAACTTTCAGGACTTAATTCTTTCCATTATGTGGGCCCCAGGGAACAAACTTTCAAACTCTTCCTTAAAAATTGTTCACATTGTCTCTGCTTAATGGTTTTTAGTGACAATAAATTTATTTCATGAGGCAATCATTTCATCATTTCATATATATATATGTACATGTGTGTGTGAATATATATACATATACACATATATATATACATATATGTATATATAAAAAATTGAAGAGACTATCATGACTTTATTTTATATTTTCATGCTTTTAGCTTTTACTTTTAAGCTCTCTATTCTTCTACCTTAGCATTCATAACAGACTCCTGCTGCATTAGAAACAACAGCAATAGGAAATCCTACTAGAATGGTATACCTCAAATGTGGCAGACAAGTACATCAGCTTTAGGCTGAGGAGGTGGCACTCACCTTTAATCCCAACACTTAGTAGACAGAGGCAGTTGGACCTCTGTGGGTTTGAGCCCAACCCGGTCTACTTAGTGAGTTCCAGGCCAACCAGGGCTACCTAAAAAGACCCTATCTCAAACAAACAAACAAACAAAGTCACCTTCTGTGTACAAGATGGGGGTCAAAAAGTCATTAATAACCTTTCACTATATCAGGGGTCAGCCTCTCAGCCAGTTTACTGGCTGTCCCCATGAACTCAGCAACTCAGTGTAATGGGACAATCTCTGATTTTAATAATACATAGTTCATAAAGTACCTGGTTCTTAGTTTTATAAGGCCTCCTATCAGCAGAAATCATATACCAAGAAGAATACTGATGGACTTTGTGTGTGTGTTCCTCATAGAACTTTTTCCTTTTTGCAATCTGGTGATTTTTATTTAGACTGCTTTCAATTTTGTTTTGTTTGTACACACGCACACAATAAAATGTAATTAGAAAAGTGGATATTGAAAGTTTATTTGGAAAGGAATATATTGATACACACACACACACACGTGTGCCTTTATATTTCTGTGATGTATAATCCATGTAAGAACACTGTTGATTTAATTTTTCTTCCTCTCTAAGTATGGATTCTCAGTTTGACACACATAGACTTGAACTTTGAGTCTAGTGTAGAGTCTCAGGTTATCTTCCTTTTTCTGCAG
Seq C2 exon
ATACTCCGTGAATACAAAGCAGTCATCATTCAGAAACGTGTCCGTGGCTGGCTGGCCCGTACACATTATAAGAGGACCATGAAAGCCATCGTCTACCTTCAGTGCTGCTTCCGGCGGATGATGGCCAAGCGTGAGCTGAAGAAACTCAAAATTGAGGCTCGCTCTGTGGAACGCTACAAGAAGCTCCATATTGGCATGGAGAACAAGATTATGCAGCTGCAGCGCAAAGTGGATGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034593-Myo5a:NM_010864:20
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:
PF0061222=IQ=PD(14.3=5.7),PF0061222=IQ=WD(100=39.6),PF0061222=IQ=WD(100=39.6)

							
A:
NA

							
C2:
PF0061222=IQ=WD(100=26.2),PF0061222=IQ=WD(100=26.2)

						

					

				








    
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)
chr15:52372364-52375303 
LOW PSI
HsaINT0108764
(MYO5A)
Human
(hg19)
chr15:52664561-52667500 
LOW PSI
HsaINT0108764
(MYO5A)
Rat
(rn6)
chr8:82092986-82095252 
LOW PSI
RnoINT0097227
(Myo5a)
Cow
(bosTau6)
chr10:58090834-58096580 
LOW PSI
BtaINT0098159
(MYO5A)
Chicken
(galGal4)
chr10:8302793-8305616 
ALTERNATIVE
GgaINT1018704
(MYO5A)
Chicken
(galGal3)
chr10:10048928-10051751 
GgaINT0029958
(MYO5A_CHICK)
Zebrafish
(danRer10)
chr18:39013799-39017074 
LOW PSI
DreINT0100830
(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"