Special

MmuINT0172733 @ mm9

Intron Retention

Gene
ENSMUSG00000033721 | Vav3
Description
vav 3 oncogene [Source:MGI Symbol;Acc:MGI:1888518]
Coordinates
chr3:109485724-109488612:+
Coord C1 exon
chr3:109485724-109485875
Coord A exon
chr3:109485876-109486485
Coord C2 exon
chr3:109486486-109488612
Length
610 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CCATTCCTTATCTTCCATAGGTG
3' ss Score
10.24
Exon sequences
Seq C1 exon
TGTTGAGTCCCAAAGTACTGGGTATTGCCATCGCTCGGTACGACTTCTGTGCAAGAGATATGCGGGAGCTCTCCCTATTGAAAGGAGACATGGTGAAGATTTACACGAAGATGAGTGCAAATGGCTGGTGGAGAGGTGAAGTAAATGGCAGG
Seq A exon
GTGAGTCGTCCCTTTGATTGTCCCAGTTCTTTGTGAATGAGAGAGCTGGACAGTCACTGGCAGCTGTCACGTTGTAGACTTGTCCTTTCAGCGGTATGGCTTCAAGGGGCTGGAGGCATGCATTACTATTCAAAATGGATTGAGTCAATACAATGGGGGCCAAGAGTTAACTAGCACATCAGAAGAGTTGAGGAGCATTTCAGATTTTTTTCCCAGGAGCTAAGTACTGGGGCATGCAGTTTATATAAGCGCCAAGCATTTCCAAAAGCTCCCAATCCCACTTAGAAAGACTGGGATAGAGTACCTCTGCTTTTCATCTACATCCTGTGCTACAAAAGAGATGAGAATCATAATGGTGAGCCCCATATTGCCCCTATGTATATATTCATTTGTGAGCTAGTGGATGGATTTGAGCCTGGCTTAAGCTCCTTTTACTACTTAGTTGCTATCACTATCTCTATGAGGCCTATCCTAGCTGTTAAGGCAGTCTTCTTACAGTGGGCATAAAACCCCAGCATAATTAGAGTATTAGGAAAAAGAGGAATTCTCTGTCTATAGAATCCTTTGAAGCAGTAGAGGTGTTAATATGTCCATTCCTTATCTTCCATAG
Seq C2 exon
GTGGGCTGGTTTCCATCCACATATGTGGAAGAAGATGAATAAAGTCCTATCCAGTGTTGACCCTGCACTAAAATCTCAAAGACAACATAAGCAGAAGCCTGCACGGCATTGAGTTAACTGAAGTGTTTAAAAAGCAGCGTTCTTGGCTGTTCAACACCCTCTTTTTTTCTCTTCCTAAGTCTTAATGCTGGGATTTCTAAAGATGCTGGTACTGACAGATTAATGGCTCGCCTAGAGCAGTGCAAGAAACAGCCTGCCAGTCTGTCATTGTCAGGAACCAGGGCAAAACCAATGGCTTTTCTACCCCCAAAGAGTCCAGCAAACCCATCAGTTTAGCTTTCTCTTACTTCATTGGGCCAGACACCATGGATCCAGCCATTAGGAAACGCTTTTTGCATATTTACTTTGTTCTCACAGTTTTTGATGATACAAAGAAACAGAAGTTTAATTTTGCTTTTCCCCAGCATGAAGAGAAAGTAGAGCCTGCCATCTGGGAAAGATCCAGCTTGCTGGAAAGATCCAGCATTTCTCGTCTTAAATTGTTCAACAGGTGACTCACTGCCTGGCAAACCCTTTTATCCCCAGATGTTACTCATGATAACAAAAAAGAGGCTCATGCTCAGGTTTGCATCATAAGTGATAAATTACAGAGAGGGTTTTAATTATTCATTTGATGTCCTGATTATATTTCCACACTTCTTTATGAAGAAGAAAAAGAGAAGCACATGAAAGGAGGTGTCTTTGTGTTAAAGCTTCACAGCTTTCGTGATTTCGTGGAGTGTTTTGGAAATGTCGTGCTTGACAAAGGGAATCATGGCCGGCCAGATCATGCTTAGTTGCCAGGAATCCCAGAAAGGTAGAGGTGTTTACAGAGACAGATCAAGCACTGTAATCAATCCACAGGACATCACTGTATAGCTGCAATAGCTATTAACACAAGCCTTTTCCTTCTCTCTAGAAGGACCCAGGGCAGATTTGCTGATTTACAATCTTTTTTTTTTTTTAATAGTAGCACAAAAGAGCTTTATTGAGGATTTGGGAAGAAAGGCAGCCCGAGTCCTTCATTTCTTTCTGAGACGGATGGAAGGGCACCTGATGTCCGTGTCCTCCTGCCTGCTCTGTTGGTCCTTCTGATGCCTTTCTAGCTATGTCTTAATCAGTAGGAAGATCCACCTTGCAGCATGTTTCTTTCTCTAAGCTTTCACTGTGTTCCATGAGGAGTCTTCAGTATCTTCCTCCTGAGATGCATGGGGTCCCTAGCCCAGGCTGACAACTCGGCTCTTCCATGGTGGAGTGTTTCTTTGGTAGCAGTAGCTGTGTTCTGACAAGCTTCTGAAAATGTTTCTTCTTGGGGAAAAAAAAGATGTATTTTTATCTTACAAGTGATCTAGAAGCTTCTCTTGTACCAGACTTTCTTGGTCACCTCTTACATGTAAGGGCTGAGACAACCTGTTCTCTCCCATCTCACAGGAGTGCCAGAACCTGGAAGAGACCCCATGGGGGCTAGGACTTCTCATTTAAATAGACTCAAGACCTTTACCTCAGAATTATGTAAACTGTGATTGTGTTTTAGAACAATTGAGCTTTTGTATGTGTGTAAATGGTCAGGAAAATGTATTTTATAAAATGTCTATAGAGTCAACTTGTGCTGGCAAGGTCTACTCTTGGAATGGATTCCTACCTATAAGGTCTTACTTGTGTCTTGGGGATGTTTTGTCTGTTCATGCCAGCAAGTGTTGCTATGGAGAGTACAGCTTCCCACAGATTGTAACACTCCTGTGTACAGTATTGTAGCATGTATTGTTTATTTCAGTCAATAGACTCCCTGCCTCACAAATGGTATGTGGTCTTCCTGTTGCATTTCATTGGCCTCAGAGTTTCATAGCAGAGGATACAGAGCCTCTTTTCATGACATTACCAATGACAACTTTGTCTACATTTAATACTTTATATTGGAGGTTTTAAATGCCACGATCTGTGTAGATTTCTAATACCAAAGACAGACATAAATGTTTTCCATAGACTTTGTCTTGCCTGTCTGTAGCCCTTGTGTCATATGGTGAGTTAGAATGACATTTTACTTTGTAATATTTTGTAAATATGTCAATAAAATAGTTACTACTTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033721-Vav3:NM_020505:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0765312=SH3_2=PU(75.9=80.4)

							
A:
NA

							
C2:
PF0765312=SH3_2=PD(20.4=78.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000036270





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000102186, ENSMUSP00000121660
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:107573373-107574046 
ALTERNATIVE
HsaINT0179972
(VAV3)
Human
(hg19)
chr1:108115995-108116668 
ALTERNATIVE
HsaINT0179972
(VAV3)
Rat
(rn6)
chr2:212583078-212583678 
LOW PSI
RnoINT0162683
(Vav3)
Cow
(bosTau6)
chr3:35860045-35860712 
LOW PSI
BtaINT0159575
(VAV3)
Chicken
(galGal4)
chr8:989394-991004 
ALTERNATIVE
GgaINT1029629
(VAV3)
Chicken
(galGal3)
chr8:994116-995726 
LOW PSI
GgaINT0039993
(Q8UUX6_CHICK)
Zebrafish
(danRer10)
chr2:16325460-16332061 
LOW PSI
DreINT0173576
(vav3b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGCTGGTGGAGAGGTGAAGTA

				
R: 
TTGCTGGACTCTTTGGGGGTA

				
Band lengths: 
352-962

			

		

	





	
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"