Special

MmuINT0139975 @ mm9

Intron Retention

Gene
ENSMUSG00000008226 | Scrn3
Description
secernin 3 [Source:MGI Symbol;Acc:MGI:1921866]
Coordinates
chr2:73157360-73160251:+
Coord C1 exon
chr2:73157360-73157556
Coord A exon
chr2:73157557-73160041
Coord C2 exon
chr2:73160042-73160251
Length
2485 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGA
5' ss Score
4.59
3' ss Seq
TTTCTGCCCTTTACCAATAGGCG
3' ss Score
9.9
Exon sequences
Seq C1 exon
GCTGGGCCTTGAGAGAGCTGACACGGCTGAGAAAGCTCTGGATGTCATTGTTGACTTACTAGAAAAGTATGGCCAAGGTGGAAACTGCGCAGAGGGCAAAGAGTTCAGCTATTACAACAGTTTCCTGATAGCTGACAGGAATGAAGCCTGGATCCTGGAGACGTCGGGGAAGTACTGGGCAGCAGAGAGAGTCCAAG
Seq A exon
GTGTGAACAGCTACCTGCAGTTTGGTTCATAATTATGTAATTGATAAAACCGACTGTAACTTTGGGTGATACATTGGCTTGCCTTTAGAGATTTATAATCCATTGCAGAGCAAGGCTTAAATTGGAAAGAACAGAAGGGAACGAGAACTGTGATGAGCTTTCGTACAAAAATACCAGGAGCATTATCTCCAGTGGCCTGTGGCTGCTGATAGTGTGGTGGTGGTGGTGGTCGTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTGATTGCAGTTTGATTGCTTTGGAATTGATTTCTCCAGGTGATTTGTTTGTGGCCATACATTCCTCTAATTTCTTCTTGTGTGTGTTTCTTTGTGACACGTATGCATGTATATATGTGGAGGGAGGCATATTAGACCGCTGTGTTCAAGTGAAGGTCAGAGGACAACCCACGGTGACTCGTGGTCCCTGTGGTTTACTGCTCCTGTGTGAACTTGACTGTGACCCCCACACTTCTGGGGATTTTCTCCCATCGCCTTCCGTCTCACCACAGAAGTCCAGGGACTGTAGACACCACCGTCATCCCTGACCTTATCTACGTCCTGGGGGTTCGAATTCGCATCATCCATTAAGCTTTCTCCAAAGCCAGTCCTCTTAATTTCAGGTGAAGAAATCCAGAGATAGAAAGTAACTTAGTGTGCTGAGTGCAAGTCTTCATCCCCTTTCCTTACTCTGGAGAGCACAGCCTGGTGTGGAAACATAATCTCACGCTTCTTGTGAACCGACATCTTGAATCTCCTAGTTTTACAAAGGAGATAAGGGATGTCTGTAAACATCCTAGCGGAGGTTAGCCCAGTTGCTGTTGCTTATCTGGCACACACAAGTCCTGGTTGAATCCCCAGCAGTGTGTAAAATGGAGACGGGTGGGACACAGCTGTAATCCCGCCATCTGGGAGGGAGAGAGGTAGGGAGAGCGGAAGTTGGAGATCAGTGTCGACTGCACAGAGTCTGAGTCTAGCCTTGGACTCAGGAGAACCTGCCTCGACTAAGTAGTTAATGAACTGGGTGAACGATGAATGATGTGGACCCAGGGGCACTGTGAACATCAGAGGAAGGAAAACCATTGTGAGCTTCTGGGGGCAAAAGGACGTCACGGGAGCCTGTGCTGGAAGATTTCACCGTTACCTTTCAAAATAGGGCACTGCCAGTTATTTCCATCGGCTTTAGAAATGCTGTTGTTATATTCTAAGTTTGACACTTTCTATGTATTAATAAAATATATAAAATTAAATTTAATCCATTTTATTATTACACTGATTACTTTGGTTGTATCAATGACCACTTTTTCTTTTATTAAACATGCTACCCGAAAGGCAAAGGCATACAAATATCATTGAAAAACATCTTACCTGATCATGCAAAACAAATGCCTTTCTGGGTGTGATCATCCTGTTGAAATAACCTTGCTAGTGCTTCCTTGTTCCATAAAGAACTAGATTGTTGCTTTGAGTATCTCCAACACAGAAATCATACATCTATGATAGATTGCTAATCACCTGCATCTGGCCATTGAGTATTATATACATGTACTGAAATGCTAAACAAAGTGGCATGCATCATACAAGATACAAATGAACTGTTGATAATACAATGGGTCTTCCTAGAATTGGCTGACTTAGAAAGGCCAGAAGGCAGGACAGCAAGATAGCTCAGCAGGTAAGGGTGCTTGCTGTCAGTCCCAACAACCCGAGTGATTCCCAGAACACAGTGGTGAAATGTGACCTCAGCACATGTACACACAAGAAAACAAATGTACATTTAAACATTTTAAAATAATTTTTTAAAAGACAGAAGGCTATTTACTATATAATTCTACACATATAACATTCTTTTAAAAAATGCATATGTAGGCATATGTGCTATGGCATGTGTGTGAAGGTCAGAGGGCAACGTGGAGAATCAGCTTTCTTTTTCTATCGTGTGAGCTCTGGGGATTAAACTCAGATGGGTCAGCTTGTGGCATGTACCTTTACCCAATATATATAAATTCACACACACATGCTGTGTGTGAGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTATGCATGCTCATGCAAGCATGGTTTTAGATACCAAATATACCTAGAGCTAATGAGTCATTAGGATTGGGAGATGCACTGCTCTGGTATGAAAGGGAAAGATGATGGATGGTCCAAGTATTCTTTTCCTTGACACTCTCACTACCAATGTTCTTGATGTGATAATATTCTATATTTTTAAAAATGTGATGGGTAGAAACAGTGAAGTATAATTTCATATTACTGCATCTGAGTGTACAGTTACCTCAAAGTTTAATTTTAAATTTTATTAATTGTTTAGGACATGCAGTAGATGTCCATGGCCAGTCTTATGTTGAAGTATGATTGAGAATCATAATGTAGAGATAGATACTTTATGTTAAAGGTAGTTTTTCTTCGCCTTTCTGCCCTTTACCAATAG
Seq C2 exon
GCGTTCGTAATATTTCCAATCAGCTTTCCATAACAACCAAGATTGACCGGGAACATCCAGACATGAGGAACTACGCTAAGCAGAGGGGCTGGTGGGATGGCAAAGAAGAATTTGATTTTACTGCGGCCTATTCTTACATTGACACGGCTGCTATGATGACTTCACCAAGCAGGTACTGCCAGGGCTACAAGCTTCTGGATAAACACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000008226-Scrn3:NM_029022:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.007
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0357710=Peptidase_C69=PD(41.3=92.2)

							
A:
NA

							
C2:
PF0357710=Peptidase_C69=PD(29.1=95.8)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000107681





     
                   









    
Main Skipping Isoform:
ENSMUSP00000088320





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000088320f304A
  



Associated events






Conservation


Human
(hg38)
chr2:174401190-174404102 
LOW PSI
HsaINT0146148
(SCRN3)
Human
(hg19)
chr2:175265918-175268830 
LOW PSI
HsaINT0146148
(SCRN3)
Rat
(rn6)
chr3:60029843-60032561 
ALTERNATIVE
RnoINT0131869
(Scrn3)
Cow
(bosTau6)
chr2:22422818-22425766 
LOW PSI
BtaINT0129704
(SCRN3)
Chicken
(galGal4)
chr7:16410640-16411077 
ALTERNATIVE
GgaINT1024593
(SCRN3)
Chicken
(galGal3)
chr2:33827977-33831497 
GgaINT0049538
([1])
Zebrafish
(danRer10)
chr9:2517228-2518462 
LOW PSI
DreINT0131726
(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"