Special

MmuINT0173992 @ mm9

Intron Retention

Gene
ENSMUSG00000031600 | Vps37a
Description
vacuolar protein sorting 37A (yeast) [Source:MGI Symbol;Acc:MGI:1261835]
Coordinates
chr8:41626379-41629307:+
Coord C1 exon
chr8:41626379-41626447
Coord A exon
chr8:41626448-41629163
Coord C2 exon
chr8:41629164-41629307
Length
2716 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
3' ss Seq
ATTTTTTTGTTTGTTCACAGAGT
3' ss Score
10
Exon sequences
Seq C1 exon
TATGAATTACTTCTACAAATGAAATCTACCTTTGAAAAGAAGATGCAAAGGCAACATGAACTCAGTGAG
Seq A exon
GTAGGGCTGATGAGTTCTTTCTGTCCCTCAGGAGCTGCTCAGCCACAGGAGCTGGCCCCGCCCTGTGCATCTGACTTTATAAAGCTGACTGACAGCTGGAAACAGAGTTCTTGTTCTTTCAGGGTTTGTCTATTTCCAAATCCTATAAGGAATGAAACCCCAGCAAAGCAGGAAAGTAGTGTAACTGCTATAATAAAACCTAGTAACAAAAAGATACTTTACATTAAGTATAATTTAAAAGATTAGACTGCTACTTAGGAAAAATAATCTTTAAAAATAAAATAGAAGATGTAATCTTTATAGCTTATTGCAGCAAGAAACATTGTAGTTAATAATTTGTTTCCCTTAAGAGATGCTTATATTCTCTAGTTAGAATAGCATAGAATATTAAGTAGAATGAAAGAGTATTAATAAGACTTGATTCTTTAGCATATGACTTAAAAGTTTAATATTTCCAGTAATCTCCCAAATATGGTTTTAAAAATCTGAGTGGATTAAAGTAGTTAGGAAGGAGTTGAATATAAAAGGGTTGGGAAAAACATGCTTCATCAACATCAAAATATTGTGTAAATGTCATTTAAAATGATGCAGTAGTTTTGTAGGAAGATGGAAAATAGTTGTATGGAGCAGGCTGCAGTTCTAAAATAGATTCGTGTATGTGACTAATAACTAGAAAAACTTCAGGAGTCAACAAATTGTGTAATTGCTTATTGGTTTAGGATCTGATGAAAAATTGCCTTCATCTTTTATATCAAACTTCATAAAGGTCATATTCTACAGAATATAGAAAAGTACAATACATATAGTATCAGAACAAAGTATAAAAATCAGTTAATTCCTAGGAATATTTTTAAATGGTTTTTTAATGTGAAAAAATTAAAAAGTCCTGTTTTCTAATTGTAATAGAAGGCAAAAGCATAGAGGAAAATGTTCACATTTGAATATATAAATTTAAAATTGAGAAGTACTAAAAATAAAAGTGAATGCTTTTGTTAAGAACACATGTATAATATAGACAACACAAAAGTTGCTAGTGGATTATAAAGAGCAAATAAGAAAGTAGGAAACTCCCCTAAGAGAAAATGTCTCGTAAAGAATTCTGTGTAGGGGCTGAGCGGTAGAGCATGTGCCAAACATTTGTAAGGCCTCAGCTGCACCTGACACAACACAGGTCAGCTTTACCACTTTTTCTCACCCCTGGACATGTATGTAAGAATTACTTGAGGTGATTCTAGAAATACTTAAAAATTGTCCTGAGGTAGTGGCGCACACCTTCACCCACATACTTGGAAGGCAGAGGTAGGCTGATCTCCGTGAATTTGAGGCTAGCCTTGTCTACAGAGTGAGTTCCAGGATGGCCAGAGCTACAGAGGGAAACCTGTCTCAAAACAAAAACAAAAAACAGAAAACCCATAGATATGTTTGTGGATTAACTTCTGACATTACTAGGAGACGGAAGTCTCACAGGAAATTCCCTGATCCTTTGCTTCTTATAATCTTTCTAAATTTCCTTGAATCTTAGCTACAGGAGTTGTTTTGTATCTGTTTGGACTGGGTTCTACAACTCTGTACTTGATTAGTTGTGGTCTTCTATAATGGTCTTTCTGGTATATTGCAAAGAGACGTGTTCCTTATGGAGGCGAGGACTGCACTTACCTGTGGATTAAGGGTTATGCTGGATTGGTAATGTGGTGGTTGTAGGTTCTTTAAGATCCACAACTTCACTAGTCCCGGCTAGTTAGTTGGCTAGGTTCCCAGTTACAGGCATGAATTCCCCCTTTGTTGAACAGGTCCTAGTCTTATTAGAAGGCTGAGCAACAAATCAAAAGAGGATTTCTCATGCCTAATGTTTGATTTTTTTTTTTTTTTTTTTTTGGTTAGGTGGTCTTTGGTTCTTGGAGGGAGCATTGTCAACCCAGAAGGGATGTCATTTGAATATTAATATTCTTTTTTATACTCTTGGAATGTATTAGAGTGCATTGATTTTGTAGATCTTTTGCGTTATCATTGTCATCGTAACCTAACAAAGACAGACAAGAACAGGAATACAAGGAGATGCAGGTCATTGGGTCATTTGAGTAGGTATTCTCACAATGATTTAATTCCAAAATATCTAGGATATAACAGTGGATTTTCAGTTTCTCATTTAACAGTTTTACAGTTTGTGATTTGGTTTCTTTTGTGCTTGCTATCTGTATTTGCTAATTGTAGGTCAAATTGACACAAGCTATAGTTATCAGAAAGGAAGGAGCTCCAATTGAGAAAATACCTTCATAAGATTGGGCTGTACAAGAATTTATAGTACATTTTCTTAATTATTCATTGATAGGGGGAGGACCTAGCCCATTGTGAGTGGTACAATCCCTGGGCTCTATAAGAAAACTAAGTAAACCATGAGGAACAGATACAATAGCAGCATTCCTCCATGGCCTCTGCATCAGCTCTTGCCTCCAGGTTCCCACCTAGCTTGAGTTCCTGTCCTAACTTTCTTCAATGATGAATGGTGATGTGGAACAGTAAGCCAAACAAACCCTTTCATCTCCAGTTTGCTTTTAGAAGAAACCCTAACTAATGACTAAGGCAGGATCCATCCAAGTAGCCAATGCTGAAGACCCCCGTGGATCTTGCTTCTCATATCTCTGCCTCATTTCCCCGTCTGTAGTTTATCTGAGAATTATAGACTAATGCATTGCCTGATTTTTTTGTTTGTTCACAG
Seq C2 exon
AGTTGTAGTGCAAGTGCTCTACAGGCAAGATTGAAAGTAGCTGCACACGAAGCTGAGGAAGAATCGGATAATATTGCTGAAGACTTCTTGGAGGGAAAAACTGAAATAGATGATTTTCTCAATAGCTTCAAGGAAAAGAGAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031600-Vps37a:NM_033560:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.083 A=NA C2=0.115
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF072008=Mod_r=FE(14.7=100)

							
A:
NA

							
C2:
PF072008=Mod_r=FE(31.3=100)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000127557





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096415





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr8:17280444-17284472 
LOW PSI
HsaINT0180814
(VPS37A)
Human
(hg19)
chr8:17137953-17141981 
LOW PSI
HsaINT0180814
(VPS37A)
Rat
(rn6)
chr16:54863741-54867980 
ALTERNATIVE
RnoINT0163613
(Vps37a)
Cow
(bosTau6)
chr27:19023513-19025888 
LOW PSI
BtaINT0160231
(VPS37A)
Chicken
(galGal4)
chr4:62746558-62747636 
ALTERNATIVE
GgaINT0069620
(VPS37A)
Chicken
(galGal3)
chr4:64983698-64984776 
LOW PSI
GgaINT0069620
(VPS37A)
Zebrafish
(danRer10)
chr1:15783874-15784656 
LOW PSI
DreINT0174214
(vps37a)
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"