Special

MmuINT0140907 @ mm9

Intron Retention

Gene
ENSMUSG00000029189 | Sel1l3
Description
sel-1 suppressor of lin-12-like 3 (C. elegans) [Source:MGI Symbol;Acc:MGI:1916941]
Coordinates
chr5:53572961-53576118:-
Coord C1 exon
chr5:53576003-53576118
Coord A exon
chr5:53573020-53576002
Coord C2 exon
chr5:53572961-53573019
Length
2983 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
TATATTTCTCTCCGATGTAGATA
3' ss Score
8.58
Exon sequences
Seq C1 exon
GCAGTTTGCACATTCAAATGCATCTCGTCAAAGGAGAAGACCTGGCTGTAAAAACCAAGTTCACCATCCCATTGAAGGAGTGGTGCCGACTGGATATCTCGTTCAATGGAGGCCAG
Seq A exon
GTATCTGCTTCTACTCTGCCTGGAGTCCTGGGGACATCTCTTTTGAGCTACAAAAAAACATTGTTGCAAAGGCAAAGAGCCACAAAACCTGGGAGGGGATTTGGCGAAGGATGCACCCTTTACAATTACACACTTGCTAAATCGAACTTTATAGATGGAAGTTTAAATCATAAGACTCTCATCCCATTTAATTAACTTTTAAAGTGCTTCTTTCCGCTCTGCGGTGAATGAGTAAATAATATAGCCAGCTCTGTAGCCACAATTATCTGAGTTATTCAGTCCTTCTCCCCTAAGGACATAGGCTTCTTACACTTAAGTGTCAAAATCACATCGGCCATGTTTACATGGCCTTATTAGATCTACAACTTTTTTTTTAAGGGAATTTATTGGCTAGTTCCGCTTAGAAATGATTTGACTGCTTTTGGCAGTTGAAACAATTGCTTACGCTTGGCACTAAACACACTCGTAATAACCAACGCGTATAAGTGATGATTGTGTGGGGAGGGAGGGTCTTTATCTATTCTGTACATAAAACATTGCTCATAACTCTCTCAAACCCCACTAACAGAGGTTTTTATGGATTGTGGGAAATCTGTTGTTGTAACTGAAGACGATTCCATTTCTCCATTGATGCGATGCCTGCATGCTAGCTTTTTCTGGTTACTTTATTTTCTCATCAGCTTTTCTTATTGATTTGTGATTTTCCTGGAACAAAACTGGAGGCGGCGTTTTGTTTGTCTCGTGCATTAGATAACGCGTGGTCCTCCCTTGTGCTTGATGTCCCCATGTTCTGAAGCAAGGGAAAAAAAAATTAATCAGGTCAGCTCTTGCCACCTCCCTGAGAGGACTGTGTGAGATGCTAGCTGGGGATTTTTGTATGTTACTTTTTCCTTAGAAAATCTTCAGTAACATAGCTGAGGTCCATGTTACCCATGCCCGTGGTATGTGAGGCACATGCTGCGCCACCAAGACAGGCATCAAATCATCAGAGCAGCTACACAGATCTGACGCTGCACCTGCTGTATGGAAGGCACAGGCTCCAGTTACTTATAGACTATTTATGGAAGTCACATTAAGCACGTGAAGAGAAGTCATAAGGCAAGCTTAATTGCCAAATGATTCATATTGATTTCTAGAAGGAAGACAGCGTTCCATGCTGGGATGCTCAGGGAAGCGGTGTTGTACAAGGCTTTTATGTTTGGGCAGAATTTAAATGGAGAAGAAAGGAACAGGGATTTCTGCTATGATTGGGAAGTTCACAGATGAGCCAAGTTGACTGGGTCTGTTGCTAGAGACTATCCAGAGACAAAAAGTTAGTTCCTCACAGTTTTGAAAGCTCTTACTGGCATCTTGTGGGAGCCCTCTTGCTGTATTACAGCATATATGGTAGCCGGAGAGAATATTCTGGCTGAGGTCACTCTCTTTCTTTTTTTCTTAATTTTTATTATATCTATACACATATACTTAGTTTAGTGTGTATATGTGATATATATATATATATATATATATATATATATATATATGTAAGTGCAGGAATTTTCATGCCACAGTAATGATATGGAGGTCAGAAGACAACCTATGGGAGTCAAGTCTCTCCTTCCACCGTGTGGAATGCAACTCAGGTCTTCAGTCTTGGTCCATCTCCCTTTACCCATTAGGCCATCTTTTGGGTCTTTTCTTCTTAGGTAGCTGTTAACCCCATCAAAGAGACTCATCCTCATGGCTTCATATAATATGAATCCTAGAGTTTTCACCTCCACATACCATAAGCATACATGTTTAGGAATTAAATTTCCAATGTATGAACTTGAGGAGCATAGAAAACTAAAAGAAAAAAAAGTTATGACTTTGGAGCTAGAATGTGCAGAAACGTCAATTTGGATTTTAGCTTGCAAGGCAGTAGAGAATCATAGTGTTGAACAACCAAAGGATACAGTTCCTTAGGTAGAGAGAAGAGCTGCATGGTGCAATGTGTGATGTGATGAAGCCACAGAAAGGCAACACAGAAGGGCAACAAGGTGGGGAAAAGCAGGGTTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCTCTTTTGCCAGTGGGTTTCAGATACTTCTAGACTCGTCTTTCTCGCTGCCTCCTCTGGTCTCCTTTGTAGATTTAAACCTCTGGTGGGATTGCCACACTCCCTGATCTGATCAAGCAGTCACTTAGAGTGATTGCCAAGAGAGACAACTGGTTGGGTTCTTTTCTTTCCTCACATGCCCTGTGACTGGTTGGGTTGGTTTCTAGTGGTTTTGTTTGTCTTCCTTAAGCATAGGGTGATCTCTAAGTCTTTGAGACTCTAGAAAGGTCAGGACACCTTTGCTAAACACTTCCCATGGAAGTGTCTGAAAAAAGTGTCTCCATTAGTCCCAAGGACTCACACAGTAGTCTTAGCTCTAAGAGGAACCTACTTGAGACAACACAGAACATCATGAGCAAGACATTGTCCTCACAGAAATGAGGGGGAGGACTCTTGCTGCTTATGGGAAGGGCGGCGGCAGGATCAACGGGCAGTGAAGACCATAGAGCATCAGGCTTCTCTCCCCTACCATGGCTCTGGTAAAATCAATAAAACTTCTAAGCCTGCTTGTCCTGTCAGGTGTACTTCCTTGTCTTCTTCACAAGAAGTTTGGAAGCACAGACAGACCCATCCAGTCAACCTCTGGCTTAAAGTCTGGAAGCATAAAAAACCCACTGGCAGAAATTGCATTGTAGATATTTTTAGACACAGCATCCAGTCATTTGGGGAGAGCTAAATTTATTAAGTCTTAAAATATACACAGGGCTAGTAAACTGTTAATTTTATTTTTGTAGAAATTAATCAGGAGAAGGACAAGCACATTTCACGAGTAATTTATACCAAGGATCATATATATTTATAGCGTGGGGTGTGCGGCCTTATCTGACCTGTATATTTCTCTCCGATGTAG
Seq C2 exon
ATAGTGGTCACTGCCAGCATTGGATGGGACTTGAAAAGCTACCATAATCAGACCATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029189-Sel1l3:NM_172710:5
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:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031090





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:25830157-25832994 
ALTERNATIVE
HsaINT0147116
(SEL1L3)
Human
(hg19)
chr4:25831779-25834616 
LOW PSI
HsaINT0147116
(SEL1L3)
Rat
(rn6)
chr14:60151252-60154308 
LOW PSI
RnoINT0132693
(Sel1l3)
Cow
(bosTau6)
chr6:46863526-46865818 
LOW PSI
BtaINT0130604
(SEL1L3)
Chicken
(galGal4)
chr4:73003104-73004033 
LOW PSI
GgaINT0072900
(SEL1L3)
Chicken
(galGal3)
chr4:75837787-75838716 
LOW PSI
GgaINT0072900
(SEL1L3)
Zebrafish
(danRer10)
No conservation detected
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"