Special

MmuINT0139973 @ mm9

Intron Retention

Gene
ENSMUSG00000008226 | Scrn3
Description
secernin 3 [Source:MGI Symbol;Acc:MGI:1921866]
Coordinates
chr2:73153489-73156484:+
Coord C1 exon
chr2:73153489-73153649
Coord A exon
chr2:73153650-73156302
Coord C2 exon
chr2:73156303-73156484
Length
2653 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
ATGACTTTTTCTTTTTACAGTGT
3' ss Score
9.46
Exon sequences
Seq C1 exon
AAATGGAACCCTATTCCTGTGACACTTTTGTGGCATTACCTCCAGCAACAGTAGGAAATAGGGTTATTTTTGGAAAAAATTCAGACAGACTCTTTGATGAAGTACAAGAAGTAATTTACTGTCCAGCTGCAGTTCATAATGATTTGGAAAAACGTCTCAAG
Seq A exon
GTAGGTGAAGTATATGTTGTAGTAGAAATATCTGTTGTTTAAGATATTCATGGATAGTTTTATTTTATATGCATGACTGTTTTAACTATATGTATGCTTGCATATCACATGTGTATGCCTGGTGCCCAAGGAGGCCGGGAGGGGGTGATGGATCTCTTGAGACTACAGTTCCAGACAGTTGTGAGCTGTCATGTGGATGTCATGGATTGAGCCCTGGTCCTCTATAAGAGCAGCAAGTGCTCTTAGCCACTGAGAAATTTCTCCAGCCCCATAAATGGTTTTTTCTTTCATTAGCTACCAATTGACAGAAGACCATTGAAATTAAAATTCAAGAATTTAAAGTTGAAAATAGTTTGAATAAAAAATAGACTTCTGATCTTTTATTTAGATAATTTAGAGGAAACTGTTAAAAATAGTAAAACTTGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTTTTCCGAAGGTCCGAAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCACCCGTAATGAGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATAAATCTTTTAAAAAAAATAGTAAAACTTATCTCTTTGATCAAATATTTGAATACTTTCTATATATTATGTATGTTGGATATGATAAGGGTTTTCTTAAGTCAGTTTATTAAAACCTGGGCAACATCTTACAGAAATTAAGAATGTACAAATGGACTATGGATGCAACCAACTTCATAATAGTGTAGGATGGTTTAAATGTGGGACTTAGGTAGGAGTAGTGGTTGGGGCAGCAGAGAAGGAACATCTAGGTTAGATTAAAGAATGGGGATGGAGCATTGGCTCATTGGTTGAGAGCACTTGTAGCTCTTGCAGAGGACCCTGGTTTGATTCCCAGCACCTAAGTGGTGGTTCACAACCATCTATAACTCCAGTTGCATGAGATCCAGTGCTGTCTTCTGTCTTCTGTGGTCTCCAGGCACATATGTGCACAGAAACACATGCAAGCAAACTACTCATAAAATAAAATAAATCGGGGCTGGAGAGATGGCTCAGCAATTAAGAGCATTGACTGTTCTTCCAGAGGTCCTGAGTTCAATTCCCACCAACCACATAGTGGCTCACAACCATCTATAATGGGATCTGACGCTCTCTTCTGGTGTGTCTGAAGACAGCTACAGTATACTCATATAAGTAAAATAAATAAGTAAAATCTTTTACAAAAATGTTTAAAAAATAAAATAGGTCTTTCAAAAAATTATTTAGTTAGAGCTGGAGTTTTAATTGACAGATCAAAAGGATTCTGCTTGAAATAGATGAGAAAAATTATTCCAGGTTTTATAAATAACAGGTTTTGTTTCTTTTCCTATAGTGCTGGGGACCAAACCTATGGTCTCTTGTATGGTAGGCACATATTCTAGCAATTGAGCCACATTTTCAGCCCCATAAATAAGTTGTTTTGTTTTGTTTTGGTTTTTCAAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGGGCTGGGATTAAAATAAGTTTTGCAGTTTATCAAAAAGGTTTATTAGACATCTGATACATACATTTTATATATTTCTCTTCACCCCTTATATACACATTAAATAAAATGTCCTTTAAAATTTTTATTTAAAGAGTATATTTACATGGAACTTAACGGTTATATTATCTTCTATTGTTATGAACTTTTTGGATTCTTGATGTTCTCACATTACAGACATTAAGCATAAGACTTTTTGTATTCTATATCTGTGTTTAAATGTGACCCGTCCTGTACGTCAGGTTCTCACTCTTCCCACTGCAGTGGAGATGCCTCAGAGGTCACAGACACGGAACTGTGGGCCCCTGGCCATTCTCACCTGACTGAGGGTCTCACGTACCTATGATACGTGTCACTAGTCAGGACAGGCTAAACATTGAACTCAAGGACTGCTTCATGCTCTTCAACTCATATTAATCATTCTCCATGAAACAGTTTGAAGATCCGTAACCATCACCCCGAAGCTCCGAGAGCAGCTCTGTTCACCTTCCTCCTGGCCTTCATACTTAATGTTTGTTGTATCCTCGTTAATGGGGAAGCCTTTGTTTTTTGAATGAAGCTCTGTTTTGAATTCTCTTTGTAACTGACCTGTCTTAGCAGGGTATATTATGATAGGACACACTCAGGAAGTCCTTAAATGGTAAATGCTTTAGAGTCAATTCTGCATGAGGTTTTTTTTTAAAGACCATCTTTTTTTTTTTTTTTGATTTATTATATATATTTAGACACACCAGAAGAGGGCATCAGATCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTAGAACTCAGTACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACTGAACCATCTCTCCAGCCCCTGCATGAGTTTTATTATTGAAAATTTAATGTAGCCCCATTTCTCCTACCTTCATAGTGATCGCCTCTTCCCAACGGTGTTTTAAATTCTGGGATTTGGTAACTTTTCATTTTTGGTTGTGTAGTTGTATGACTTTTTCTTTTTACAG
Seq C2 exon
TGTACTTATATAGAAGTTGATCAAGTTCCTGAAACATATGCTGTTGTCCTTAGTCGCCCAGCTTGGCTGTGGGGGGCAGAAATGGGTGCCAATGAGCATGGAGTCTGCATTGGGAATGAGGCTGTATGGGGAAGAGAAGACATTTCTAAGGAGGAAGCACTTTTGGGCATGGACCTTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000008226-Scrn3:NM_029022:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0357710=Peptidase_C69=PU(12.8=60.4)

							
A:
NA

							
C2:
PF0357710=Peptidase_C69=FE(24.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000088320





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000088320f304A, ENSMUSP00000107681
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:174398443-174399921 
LOW PSI
HsaINT0146146
(SCRN3)
Human
(hg19)
chr2:175263171-175264649 
LOW PSI
HsaINT0146146
(SCRN3)
Rat
(rn6)
chr3:60026907-60028716 
LOW PSI
RnoINT0131867
(Scrn3)
Cow
(bosTau6)
chr2:22426901-22429501 
LOW PSI
BtaINT0129702
(SCRN3)
Chicken
(galGal4)
chr2:34395851-34405770 
ALTERNATIVE
GgaINT0096077
(SCRN1)
Chicken
(galGal3)
chr2:33835853-33845772 
LOW PSI
GgaINT0096077
(SCRN1)
Zebrafish
(danRer10)
chr9:2519248-2522077 
LOW PSI
DreINT0131724
(scrn3)
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"