Special

MmuINT0140034 @ mm9

Intron Retention

Gene
ENSMUSG00000007279 | Scube2
Description
signal peptide, CUB domain, EGF-like 2 [Source:MGI Symbol;Acc:MGI:1928765]
Coordinates
chr7:116987391-116990562:-
Coord C1 exon
chr7:116990437-116990562
Coord A exon
chr7:116987508-116990436
Coord C2 exon
chr7:116987391-116987507
Length
2929 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TTGATTCGTTTTGACCTTAGTGA
3' ss Score
5.67
Exon sequences
Seq C1 exon
AAGGCCTGAGCTGTATGAACAAGGATCATGGCTGTGGTCACATCTGCAAGGAGGCCCCAAGAGGCAGCGTTGCCTGTGAATGCAGGCCTGGTTTTGAACTGGCCAAAAACCAGAAAGACTGCATCT
Seq A exon
GTAAGTATGAACTGTCAATAAGTGAGGTGGGTACAGCCTACACAGAGGTCAGAAAAACAACCACGGGGACAGCCACAGGTATAGCCACAGGTACATGCACAGGCACAGGCAGAGTCAAAGCCACAGGCAGAGGCACAGGAACAGACACAGACACAGGCACAGTCACAGCCAGAGCCACGGTCACAGCCAGAGTGACAGGCACAGGAACAGGAACAGCCACAGTCACAGAGACAGGCACAGCCAAAGTCACAGACACAGGCACAGGCACAGGCACAGCCAAAGTCACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGTACAGGCACAGGCACAGGCACAGGTACAGGCACAGGCACAGGCACAGGCACAGCCAAAGTCACAGGCACAGGCACAGACAGAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGCCAAAGTCACAGGCACAGCCAAAGTCACAGGCACAGGGACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGACACAGGCACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGTACAGGCACAGGCACAGGCACAGGTACAGGCACAGGCACAGGCACAGGCACAGCCAAAGTCACAGGCACAGGCACAGACAGAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCACAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCACAGCCAAAGTCACAGGCACAGCCACAGGCACAGGCACAGGCACAGACACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCACAGCCAAAGTCACAGGCACAGCCACAGCCACAGCCACAGTCACAGAGACAGGCACAGCCAAAGTCACAGGCACAGACACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCACAGCCAAAGTCACAGGCACAGACACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCACAGGCACAGGCACAGGCCTAGGCTCAGGCTCAGGCTCAGGCACAGCCAAAGTCACAGGCACAGGCACAGCCAAAGTCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCACAGGCACAGGCACAGGCCTAGGCTCAGGCTCAGGCTCAGGCTCAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAGGCACAAGCACAGTCACAGTCAGAGGCACAGGTACAGGCACAGCCACAGCCACAGGCACAGGTACAGGCACAGGCACAGGTACAGGTACAGGTACAGGCACAGGCACAGGCACAGACACAAGCACAGGCACAGACAGAGGCACAGGCACAGGCACAGGCACAGCTTAGGAACAAAAGAGCAGCTTGTGGGAATCATTCTTTCCTTCTATTCTATGTGTCCCGGGGATTTAACTCAGTTATAGATGTCTTTACCCTGTTCTATCTTACCCGACCAACCAATAAACCTTTTTTCTTTTTCTTTTCACTAAATGTTTTTTATTGTCACTGCTTAAATGCTTTTGTTAGAACATTTGCATTCCTGTGATCTCAGCACTTAGGAGGTAAAGGGAGGAGCATTGGGAATTCAAGGTCATCTTTGGATACTTATCTGTAGAGTCAGTTGGAGGCCAACCTGGGCTACATGAGACCTTATCTCCAAAGACACCCCCGCAATCAAACCAACCAACCAACCAAACCCTCAAATACCTAAAAAGGAGGATGGGGAACATATCCCAGAATCACACGATCTAGCCAGTTCACCTTTTCCATATTCCTATTTTGTCATCTTACACATTAAATAATGTCAGTTTGTTCCAAACATGAAGTGCTAGAGAACTTCTAGAGGCCCTGTGTACAGCTGGGCTAAGAGGCAGACTTCACCAGAGAGAGGGAAGGTACAGTCAAGAATCACTTGGCATAGTCTCCCTACATAGTGGGATGCTACTCTACCCCAGGCTTCGGAGCTCCATCTTTCTGTATCACTCCATTCAAGTCGGGCTATGGTTCTATGTGGTTTATACTGTGACACACGATACACTGTATACACTGCATACACAAAGAACATTCTAGAGGGAAGTCTTTTATCTCAAGAGTCAGGCACGCACTGGATACTCAGATACCTGCAGAGAAGAAGAATCAGCACTCGGGGGGCTGGGGGGGGGGAAGTGTGGTGATGGACACCTTTAGTCTCAGCAGAGTAGAAGCAGGCAGATCCTCGTGAGTTCAAGGTCAGCTAGGGCTACATAGTGAGTTACACAGGCCAGTTACATAGTGAGACCTTGTCTTTAAAAATACAAAAATTCTTGGGAAACAAACCCAACCCTGGTTGTGGAAACCTCAGCGCTTTAAGTATTGATTCGTTTTGACCTTAG
Seq C2 exon
TGACTTGTAACCATGGAAATGGTGGGTGTCAGCACTCCTGTGAAGATACAGCAGAAGGCCCTGAGTGTAGTTGCCATCCACGGTATAGGTTGCATGCTGATGGGAGAAGCTGCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000007279-Scube2:NM_020052:5
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:
PF146701=FXa_inhibition=WD(100=86.0)

							
A:
NA

							
C2:
PF146701=FXa_inhibition=WD(100=90.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000007423





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000102339, ENSMUSP00000102340
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:9066814-9069369 
ALTERNATIVE
HsaINT0146211
(SCUBE2)
Human
(hg19)
chr11:9088361-9090916 
ALTERNATIVE
HsaINT0146211
(SCUBE2)
Rat
(rn6)
chr1:174474964-174476073 
ALTERNATIVE
RnoINT0131927
(Scube2)
Cow
(bosTau6)
chr15:44110190-44113389 
LOW PSI
BtaINT0129761
(SCUBE2)
Chicken
(galGal4)
chr5:8937311-8937690 
ALTERNATIVE
GgaINT0057955
(SCUBE2)
Chicken
(galGal3)
chr5:10462642-10463021 
LOW PSI
GgaINT0057955
(SCUBE2)
Zebrafish
(danRer10)
chr7:28333704-28333791 
ALTERNATIVE
DreINT0131772
(scube2)
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"