Special

MmuINT0140052 @ mm9

Intron Retention

Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28305327-28308290:+
Coord C1 exon
chr17:28305327-28305406
Coord A exon
chr17:28305407-28308140
Coord C2 exon
chr17:28308141-28308290
Length
2734 bp
Sequences
Splice sites
5' ss Seq
AAGGCAAGT
5' ss Score
3.24
3' ss Seq
CCACCTGCCATCTCCTGCAGGAC
3' ss Score
11.13
Exon sequences
Seq C1 exon
AGGACTATGAGCAGCTGGTGGAAGACATAGTGCGTGATGGCCGGCTGTATGCCTCAGAAAACCACCAGGAGATCCTAAAG
Seq A exon
GCAAGTGAGCGTTCGCTGTGGTGCGGATGGAAATGGGTATGCACCGATGTGCAAGCAAACTGCTAAGTACAGCCTGCCTTTCTACTCCTGGCTCTGTGGGGCATGCGCTTTCTTCACTGCCGCTTTCCAGATGAGAGAGGTAAAGGGCTTTCCCATGATAGGCCTGGGCTCTGGACCCAGCTCACAAAACCAGTGTCAGCATACTGCGTCACCCCTGGGAGGACAGGAGACATCCTCTGCCTTGTCCATCACAGAGGCAGAGAGGGTAAACTGCACAACGATATACGTTGTTTACTTTTTTGAGACAGAGTCTTAAGAGTCTAGGTTGGCTTTGAACTCCGGGTTCCCCTGCTTCCCGCTCCTAAGTGTTTGGTGGGATCACAGGCCCAGAGGAACGAACACCACCCTGGGTCTGTGGATCCCGATTTGAGTCCCGCCTGGCGTAGTGCTGCTCCCCTTTGATCCCAGCACTCAGGAGGCATAGGCGGGTGGATCTCCGAGTTTAAGGCCAGTCTGGTCTATATGTGCAGTGCTAGGGTAGCCAAGGAGACATACTGAGACCCTTCCAAATATTTTTTTTTTAACTTCACTCTTTTAGTTATGGCTATTTGTGTGGATATGTGCATGGGATTGCAAGGCGGCCAGAGGTGTCAGATCCTCCTGGGGATGGGGTAGCAGGCAGTTGTGAGCCATCTAATATGGGTGCTGGAACCTAAACGCACATCCTTTGCAAGAACTATGTGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCCACGCCACTGTTTGAAATCAAATGTAACTGGGTGTGCTGGTGCACATATGGCCCGGCTATTCAGGAGCTGAAGTGGAAAGATCATTCAAGCCCAAGAGTTAAGAAAACAGCCTGGGTGACATGCTGGACTCCATCAGACAGCGAATCAAATGCACCGTGCAACTGTATGCACAAAGTAGTGCAGCCATGCTGGAGCTGGGGTGGCGCACCTTTGACTGCAGTACGTGGGAGGCAGAGGCAGAGGCAGGAGGATCTCTGGGAGTTCTAGGTCAGCTTCAGGCCAGCCCTAGCCACACAGTGAGACTCTGTCCTAAAGGAAGGACTGTATAGAACAATCGTCTTGGTTAGAGTGGAGTTACGAGGCTGAAAGCCCCAACTATCTTAGAACTCTGTGTGCAACCTAGAAGCCAGGAGATTCATTGGTAGTTGGGTTGGGTCTCTGTGGGCACGGGGCTTGTGCATGTGTGTGGGTCTTGGGAATTAAACTGAGGTTGTTAGGCTTGGTGGTAGGGGCCTTTCCTCATGAATCACCTCAGTAGCCCCTAGAGAGGAGTTTTAAGGAGGCGGTGGAGAGGTGAGCTGGAGAGACCTACGAGGAAAGGTTTGAAAGGAGCTGTGGGATGACCAAGGAACAGTGCAGACCAGTGAGTGCAGCACTAGTGTGTTGTATTGAAGGACGCCAAGACTACTGTCATTCCACAGGGGAGGAAGAGGAGAGGGAAGCAGGACACAAGTGACGTACAGCTAGCATGTCACACAAGGGACCTGACTCTTCCTGTGAGTGAGGACAGAAACGGGCTGATATGTAATCAGTGGCAGAGAAAGGTTTGTCAGGCACACAGCCGTGGTGTGGCTCCTGGAGCTAATCACTGTCATCATTATAAAAGAATAAACTTTCATCAGACATTATAGCACCTGCCTGTGGTCCCAGCTACTGGGGCAGCTCAAATGCAAGGATCACCCAAGATAACAGGAAATGAAAACCAGAGAGCAGAAAATGGGTTCCAAACATGAAGCAGACTAACTGAGCGCCCCACTGTGGCTGCCGTGAGGAGGGAACGCTATGGTGGGCCAAGGATAGAAACACAGAGATCAATCCCAGGCCCAGTGGCTCACACCTCTCGGACTAGTTATTCAAAAGGCTGAGGCAGGAGGATGGTGTGTTGTGGGTCAGTTGGAGCTACAAAGCAAGTCCAAAGCCAGTTTGAGCAACTTAGAGAGACTCTATCTCAAGTAACAAGAGTGCTCAATAATAGAATTGCTATTGCAGAGTAATAGGGTATAATAGAATTCGATTATAGCAATAATAAAATTGCTGACACTGGAGTGGCCTAGGTGCTGGAGAGTTGGCTCAGTAGTTAAGAACATCTGTTACTTCTTGCAGAGGAACTGGGCTCAGTTCCCAGTGCCCACACAGTGACTCATAACCATCCATAACTCCAGTTCCAGGGAATCTAACACAATTCTGACCTCCTCAAGCACCAGGCATGCATGTGGTGCACACACATACACACAGGTGAAATTCACATAAAATAAGTAAATCTAGGAGGAAAACAAAAGAAGAATACTAGGCTATTGTGTCTGAGGGCCTAGTATCACAAAGGAAAGGAATAGACCAGCCATTGGAATAGCCCAGGTGAGAGTTTATGGTGGTGTCACTCCGCGTGGCAGCTGTGGGCTGGCAAGCTGCTCAGACAGATGCTGGGCATACGCTGAAGGCAGAGTCAACAGCTGGCTGTAGCTGAGACACTACGGAGTCAAGGATGCCCCACAGGCCCAGCCTGAGCAGCGGAGGCCTAGACCTGTGGCTAACTGAGCTTTGGGGTTCCAAAGGAGCAGGGGGAGGCCCTCTGAGCATGCTCAGTGTGAGCTGCTGTTAGACAGGAAGAGGGGCTGCTGAGTATTCCTCTCCCCCACATGCCACTGAAGCTGACAACTGCCACCTGCCATCTCCTGCAG
Seq C2 exon
GACAAGAAGCTTATCAAGGCCTTCTTTGAGGTCCTGGCCCACCCTCAAAACTACTTCAAGTACACAGAGAAACACAAGGAGATGCTGCCAAAATCCTTCATCAAGCTACTGCGCTCCAAAGTCTCCAGCTTCCTGAGGCCTTACAAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677-Scube3:NM_001004366:21
Average complexity
IR-C
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:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000073961





     
                   









    
Main Skipping Isoform:
ENSMUSP00000038366f3866A





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000117490
          









    
Other Skipping Isoforms:
ENSMUSP00000038366
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:35246286-35248555 
ALTERNATIVE
HsaINT0146229
(SCUBE3)
Human
(hg19)
chr6:35214063-35216332 
ALTERNATIVE
HsaINT0146229
(SCUBE3)
Rat
(rn6)
chr20:7743190-7746181 
ALTERNATIVE
RnoINT0131945
(Scube3)
Cow
(bosTau6)
chr23:9164397-9166078 
ALTERNATIVE
BtaINT0129779
(SCUBE3)
Chicken
(galGal4)
chr26:4079335-4079490 
LOW PSI
GgaINT0141281
(SCUBE3)
Chicken
(galGal3)
chr26:3969019-3969174 
LOW PSI
GgaINT0141281
(SCUBE3)
Zebrafish
(danRer10)
chr4:8906966-8907053 
LOW PSI
DreINT0131747
(scube1)
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"