Special

MmuINT0139164 @ mm9

Intron Retention

Gene
ENSMUSG00000035236 | Scai
Description
suppressor of cancer cell invasion [Source:MGI Symbol;Acc:MGI:2443716]
Coordinates
chr2:38954896-38957919:-
Coord C1 exon
chr2:38957841-38957919
Coord A exon
chr2:38954996-38957840
Coord C2 exon
chr2:38954896-38954995
Length
2845 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAA
5' ss Score
6.82
3' ss Seq
TCTTCCCTCTGTTCTTTTAGGTC
3' ss Score
13.12
Exon sequences
Seq C1 exon
GAGCTGCCTGCCAATAGTGTGCTTCTGATTTACCTGTCAGCCACTGGCGTTTTCCCCACAGGTCGTTCTGATGGTGAAG
Seq A exon
GTACAATAAAGGAATGCTCCCACTGTGAGCAGGGCTTGAATTATCTGTTTTCTACAAGACAATGGCCCACAGCCCAGAGACCGCCTCAAGCTTTCTAAAAAAGCTTTTAAATTTAAAGCCTGGTCTGTTTGTTTAGTGACATTGTTGGAAAGAATCTGGTTAATTCTCTCTACTCATTTATTATTCCTTGAAGCCCAAAAATCTTGACACAATATTTATGTCTAATGCACATTTCCCTATCATATTTGTCAAATGTGTCGTATGTAGATTTATACATTATGGCTGAAAGTCTTTGTAGAAATCAGTGTACTTTTGTAACTATGAAAGTTCAAGTCCTTGTTATAATTTTATTTTCAGGCCTTTTTATGTTGTTACTACAGGTTCAGTCCATGCAGTATTGGGATGCTGCTTCAGAATAAAACCCTAAACTATCAGAATATACAAGCCCAGAACTTGTTCAGACTATGAACAACTCAGATGCAAATGAAGGACTTAAGTCTTTGGAGAAAAATAGTTTAACATTTTCACCATTTTCCTCCTCATTTGTCTGTGGCAATTGGCATTCCTTTATAAAATGCATGACCTACCATCTTCCTTGCATGACCTACAAAGTAGTAAAATGTTACAGTTAAAACAAAACAAAGTGGGTGGAACAACATTATGAACTAACCAGTACCCCGGAGCTCGTGTCTCTAGCTGCATATGTATCAAAAGATGACCTAATCGGCCATCACTGGAAAGAGAGGCCCATTGGACACGCAAACTTTATATGCCCCAGTACAGGGGAACGCCAGGGCCAAAAAGTGGGAGTGGTGGGTAGGGGAGTGTAGGGGGAGTATATTGGGGACTTTTTGGATAGCATTGGAAATGTAAATGAGGAAAATACCTAATAAAAAAAATAATTCTAAAACAAAACAAAGCAAATCGCTATAGTCTTTACGTTGCAGTGATTTTTTTAAAGGTCTGTAATCCAGCTGTGACCCGAGGGGTTGGGGTATAGTGGAGCACTTACAGGATGTGTAAGGGAGGGAGAAGACAACTGCATGAGTAACTGCCTTACTTCTTATTTAATGTTAGTGACTTTACTTATATTTAAGTATTTCTTGTCTGAAAACATGTTATTAAGACAACTATTCTGGGTCTTCACATTAGACTTTTGGCTTCTTCCTTTTTGTAATTAGTATAGGTAATAAACTAAATTTCTCTCAGAACTTATCTGAACATCTCACAATCACTGTTCGACTTAGACAAGAGTTACAGAACACTTATGATCAATTGGGAAAGACTAACATGTAAATCAACAGTTTAAAAGTTTACATGATAGTAGAATAATGAATTTTTTATATACTGAAATTTGACAGAATATTTCATAAAAATGAAGTTTTGTTAATCAGAATTTTCAAGTTAATTCTAATTTTTCTTCAAATTTTTCACTTAACAGTTAATTTAAAATTATCTTTACTGGATCAGGTGTTATAGTGCATCCCTATAGTGCCCGCTACTCAGAATGCTAAAGCAGGAGGGTCACTTAAACCTAGAGCTCAAAACCAGCCTAAGCAACATGATAGACCTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAGAATGAATATATATCATATACTAAACATGCATGTTTAAATAGAAAGAAAGAGGGAGATTTCAGTTTGCAGTTAATCAGCTTTCTTTATAACCAGAGATTGAGATTTTATTTGCAATTTAAACTTTAGTTTAGTTTAACTTTTTATTGATTCTTTGTGAATTTCACATGATGTACCCCAGTCCCACTCATTTTCCCGTCCTCTGTATCTGCCCTCTACCCTTGCAACCTCTCCCCCAAAACAAAACAAAACTCTTTCCCTGGAAGCTGTGATGTGTCACAGTCTGTCACACAGCATGCCCCTGGAAGCTCTAGTGTGTCACAGTGTGTCACACAGTATGCCCCTGGAAGCTGTGGTGTGTCACAGTCTGTCACACAGTATGCCCCTGGAAGCTGTGGTGTGTCACAGTCTGTCACACAGTATGCCCCCAGAAGCTGTGGTGTGTCACAGTCTGTCACACAGTATGCCCCTGGAAGCTGTGGTGTGTCACACAGTATGCACCTGGAAACTGTGGTGTGTCAGTCTGTCACACAGTGTGCCCCTTTGCCCATGCAGCTTTACTTGTAAGTATTTGTCACAAGGAGTCATTGGTCTGGTTTGAGGCCTCTGGCTTCTGGCTACACCACCAATACTGTGTCCGCACCATGACTCCTCTCAAATGTCCTATAAATGTTATTTTAAACATCCAGGTCTCCATCCCTTTTTTACCACCCAAATTAATGGGATGCTATAGATTATTGTTTTTGTTGTTGTTGCTGGAGGTTTTGTCTGTTTATTTGTTTCGTGTTTTTTGTTTAGTGGAATTTTTTGAGACAGAGTCTTTCCGTGTAACCCTGGCTATTCTGGAGTTCACGGTGTAGACCAGGCTGGCCTCTAACTCAGAGATCTACCTGCCTCTGCCTCCTGAGTGCTGGAATTAAAGGCATGTGCCTCCATGCCTGGCTATAGATTCTTATTTTGTTTCTCAATATATTATATTTGAAAAGCTAGTAAACAATTTAGTGTTTTTTTAAACGTTGAAGGCAATGTGCTGAGATCATCTAATATTTCATTATAGTATAATGTTAAATTTAAAGAGAATACTCTGTGATTCTGTCAAAGGGAGATTCACTGATGCTCTTGAACCTGGGCATCAGATCACTTGGTGTTACCCTCCAATTGAATTCTAGGTTTCTTCCCTCTGTTCTTTTAG
Seq C2 exon
GTCCTTATGACTTTGGAGGTGTACTTACTAATAGTAACCGGGACATTATCAATGGAGATGCTATCCACAAGCGAAATCAGTCTCACAAGGAAATGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035236-Scai:NM_178778:12
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=0.304
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF120703=DUF3550=FE(5.2=100)

							
A:
NA

							
C2:
PF120703=DUF3550=FE(6.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037194





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037194f3378A, ENSMUSP00000037194f3379A
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:124999991-125001964 
ALTERNATIVE
HsaINT0145300
(SCAI)
Human
(hg19)
chr9:127762270-127764243 
ALTERNATIVE
HsaINT0145300
Rat
(rn6)
chr3:23384485-23387048 
ALTERNATIVE
RnoINT0131098
(Scai)
Cow
(bosTau6)
chr11:95954430-95956265 
LOW PSI
BtaINT0128946
(SCAI)
Chicken
(galGal4)
chr17:9548320-9550443 
HIGH PSI
GgaINT0125709
(SCAI)
Chicken
(galGal3)
chr17:10269312-10271435 
HIGH PSI
GgaINT0125709
(SCAI)
Zebrafish
(danRer10)
chr5:31436347-31439087 
LOW PSI
DreINT0131103
(scai)
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"