Special

MmuINT0173995 @ mm9

Intron Retention

Gene
ENSMUSG00000066278 | Vps37b
Description
vacuolar protein sorting 37B (yeast) [Source:MGI Symbol;Acc:MGI:1916724]
Coordinates
chr5:124454650-124457700:-
Coord C1 exon
chr5:124457618-124457700
Coord A exon
chr5:124456748-124457617
Coord C2 exon
chr5:124454650-124456747
Length
870 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
CTTTCTCCTGCCTCTTGTAGAAC
3' ss Score
10.93
Exon sequences
Seq C1 exon
ATAAACAGTCTAACAACGCTTCCTTGGAGACTCTGTTAGCGCTTCTTCAAGCGGAAGGGGCAAAGATTGAGGAGGACACTGAG
Seq A exon
GTAAGGCCTGACAGCCCTAGTGGCCGCCCTCCACATGGCTGGACTCTTAGGTCACCCTGTTCAGTCCCTGTCCTCCAGGACATGGGAGCCCCACAGCTCCACAGCCAGCCAGCGGCACTTCCAACACACAGAGGCCTGGATGCACGTGGCCATCTTGGCCTCTGGCTAGGGAACGTGCTAGGCCGGGATCAAGCGGTTCAGCTGGGGCCTGGGTGTGGATGCTCATGCTGCCCTGAACTAATGCCAGCCTCTTGGGTGCTAGTGTCTGCGGCGTCTGCTGTGGTCAACGAGGCAGCTAATCGCTGCTGCTACACGTGGCTGGCTGAATCCAGGGCTGGAGCCTTGTGAGGGGAGGAAATGAGTCAGGGTCACCTGTATGTATGCCTTAGCAAGTCAGGGCTGGCTACACATTGCCAGGTCAGGCTGGCTTTGTCTGACTAACCCATTAGGCCTCGGCAGGCCCCGATAGCCACAAGTAGGGTTCTTGCCTGCGAACTCTGTTCAGGGTGAGTCACTGGTCGGCTTGCAGCCAGGTGGAAACCAGAGGGCAGGGTCTGGGCCGTGGCAATCTCTCAAGAGTGAGAGAGCTGGGAAGCTCAGAACCATGTTGTCATAAGTAAGGCATGGCCTTGCCAGGCCTGCCATCTGTCTGTCGTGGCTCTGCGAGGTGACGGCTCCTGCCAGCATCACCCAGGCCCATAGGTCAGCAGCTCTGAGCATGTGGCAGAAGACAGGCACCCAGGAGTGCTCGCAGGAGAAAGGGGTACTACAGGGATCTGAGAGCCTCTTTCCCTTTGCCTGGGCTGTGAAGGGAGCCTTCTTCCTAACAGTTGGCCTATCTTATAACCTGCTTTCTCCTGCCTCTTGTAG
Seq C2 exon
AACATGGCAGAGAAGTTTCTGGATGGAGAGCTTCCTCTAGATTCCTTTATTGATGTCTACCAGAGCAAGCGGAAGCTGGCGCACATGCGCCGTGTGAAAGTGGAGAAGCTCCAGGAGCTGGTGCTGAAGGGACAGAGACACCCGCAGGCCGGGGCCCCGCCACCACCCAGGGTGCCTGAGCCCTCACCTGCCACCGCCCTTCCCTACCCCTCTCTGGAGGCCACTGGGCTCCCTTCTGTCGTGCCTCGGCGTATTCCCCCCCCTCCACCCCCGGTGCCTGCAGGACACGTAGCCACCCCTTTCGCTGCTGCCATGGGCTCGGGACAGGTTTCTGCATACCCGGGATTACAGTGCCCACCCCTGCCTCCCAGAGTGGGCCTCCCCTCTCAGCAAGGATTCTCCGCACAGTTGGTGTCACCGTACCCACCAGCCCTGCCCCAGAGACCCCCTCCACGGATGGCCCCACACCAGCCAGGCTTCATCCTGCAGTGAGCTCGGGTGCCTGCTCTTCCTGCAAGACATCCTCTGCCTGCCGTGCCGAGCTCTGCAAACAGAGGCTGTGCGGTTCAGCATCTGGGCCAAGGGCTTGGGTGCCCTGGGTCAGCGTGCCCACCTGATTTTAGAACTGTAGGTCCGTGGTAAGTAAGAGAGCAGGTTCTGTGCACCAAGGGAGCGCTGTTTGTGCCAGGCCAGTCTGCATCACCTCAATCTGTGTTGGGTGTGATTTCTGAGTGTCTCGGGCTGATGGACTTGTGCATTTGGAAAGATTACCCCCACCCCCAGGTTAGAATCCTGGCTCTCCTGTTGCAGCTTTATTTAATAAGCATGATTAATTATATGTTTTATTTTCGAGTCTTGGCCCACCAGCTGCCGTGGCGCTAGTAAAGACTGGTCTCAGCTGGCCAGCCTGGAATGTGTGCCCACGGCCAGGCCCTGCTGGGCAGCTGTGCTGTTCACCGAGTGTGCAGGGCAGGCCAGCCCAGTAACCTCCCACTCCTGCCATGCTGGGTGCTCTCATGGTTCAAAGCCACAGGCAGAGTTTGCACTTGGCTGCTGTGAGGTGTGCAGAGGCCAGGCGAACTGTGGCCCGGGGTGCGAGGCCAGTGTGAGCCCTCAGCCCTCCCCACACACCTCAAGCCGCGTCACGGTTTCTGTGAAGAAGAAAAAAAGATACTCAATGTTTTTACTACACTTGTAATTTTCCTGTTTTATATTTCAAAAGAAAACTTTTTTGACACTCTCAAGACCATTCAGGGAAACTTTTTTTAAAATGCAGATACTGTTTTGAGCTGGTTTAAAAAATGCAGATTTATTGAGTGCCGCTTCCTGTCGGGCAAGCAGTGCACGGTCACATCTGCCAGTGCCCGTGCTGTGCCTTAGCTTCACTGGTGCCAGGACTCGGAGCCCGCGGCGTGCCAGCCGCAGCTGCCCTATGGAGCCGAAGACCAGCTAGGTAGGGCCTGGCGGGCCTCGTCACTTTGTGATGGGTCAGGAGTGGTCCATCTTCCTCCACCCCGGATAATCTCAGGAGCAATGCTGCAGGTGCTGGCGTAGGCATGGGAGGGGTTTGGGGACAGCCCGCCCCACAGGGTTGGCAGTGGCCGCTCCCTCCTCTCTGGGATGTCATCTGCAGGTGCCACATGTGCAGAGTTCCCAGGGCCCGGCTGGGGAGGGGCAGCCCCACACCTGTTCCCAGAAGAGGGCTGCGAGCCTGTTGGTAGAACTTAGAACCCCACCTTCACCCTGCCAGCTGGCTACAGCCCAAGGTAACACAGTCAAGGCAGCGCTGATTAGTGAGCCTGCCCCAGCTGGGCCACCGGCAGGGCCATCAGCCTTTGTCCCCAAGTTGGACTGTTTTCCTCTCCATGGATTTGGACTCTGTACCCTACTGGAACCACTCTGTAAAGAGACAAAGCTGTATGTGCCACTTCAGTACCTCTGCCACCAGGAACGCCCACTGCCAGTCTCGGGCCGCAGCCACATGGGAGCTCCGGGTGGATGCAGTAAAGGGGCCGCCAGGCTGACCTTGCCAGGCCATAGCTGGCACTGGGGCTGTAAAGCTGTAGAACTCTTAATAAATTGAGAATTATTAATTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066278-Vps37b:NM_177876:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.179 A=NA C2=0.736
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF072008=Mod_r=FE(18.0=100),PF101464=zf-C4H2=FE(12.4=100)

							
A:
NA

							
C2:
PF072008=Mod_r=PD(24.0=22.0),PF101464=zf-C4H2=PD(71.9=95.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047980





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:122867608-122868479 
ALTERNATIVE
HsaINT0180817
(VPS37B)
Human
(hg19)
chr12:123352155-123353026 
ALTERNATIVE
HsaINT0180817
(VPS37B)
Rat
(rn6)
chr12:38020394-38021255 
LOW PSI
RnoINT0163616
(Vps37b)
Cow
(bosTau6)
chr17:54903683-54904381 
Chicken
(galGal4)
chr15:5234897-5236029 
ALTERNATIVE
GgaINT0008336
(VPS37B)
Chicken
(galGal3)
chr15:5290420-5291552 
LOW PSI
GgaINT0008336
(VPS37B)
Zebrafish
(danRer10)
chr5:27400581-27401507 
LOW PSI
DreINT0174217
(vps37b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCTTGGAGACTCTGTTAGCGC

				
R: 
CTACGTGTCCTGCAGGCAC

				
Band lengths: 
354-1224

			

		

	





	
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"