Special

MmuINT0140892 @ mm9

Intron Retention

Gene
ENSMUSG00000029189 | Sel1l3
Description
sel-1 suppressor of lin-12-like 3 (C. elegans) [Source:MGI Symbol;Acc:MGI:1916941]
Coordinates
chr5:53535281-53536793:-
Coord C1 exon
chr5:53536674-53536793
Coord A exon
chr5:53535422-53536673
Coord C2 exon
chr5:53535281-53535421
Length
1252 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGG
5' ss Score
9.13
3' ss Seq
GAGTTGCTATTGTCTTTAAGCAA
3' ss Score
4.13
Exon sequences
Seq C1 exon
GCATATGTTGAAACTATTAGGCTCAAAGATGATGAAATACTCAAAGTCCAAACCAAAGAAGATGGCGATGTCTTTATGTGGCTGAAGCACGAAGCCACCCGTGGCAACGCAGCAGCACAG
Seq A exon
GTGCGGGCAAGCCCGTCTTGGAGCATTTGTCAGTCATTTCAGATGAGGTTACAAAGTAACAAAGCCTCCCCATCCTCTGCGGCTTAAAGCGATGCTGCTGTATCTTCTGCTTGCGCTCACGTCTCCTGGAGTCCTTGCCTCTTTAGAGCCAGGTGGCTGGGGCTTCTGCATGTACTTTAATTCTTTATTCTCAACCTAAGCCGTGTTATATGCGATAACTAGCATATATTAATTGTTATGTGATATGGGTTTCATTATGATATTTTCATACACATGCATAATGTATTCCAATTTCAGTTACTCCTCCCACTATTCCCTCTTCTCTTCCCAGCAAGTTCCCTTCTACTTCCCTGAGAGAAGAAAGGAGAGGGAGAGAGAAAGGGAGGGGAGGAGGGAGAAGGAGAAAACCCAGCAAGTTCTGCTAGGGTTGTTTACAGGAGCAAGCTCACCGCTGGAGACAGCATCTTCCTAACCCTCATTGGCTCTTAACCTCTCCCCCTTCCATGGCAGATCTCTTAATAGATGTCGCATGCAGGTAATCACACCTGCTGTGGATTCCAGAGTGGCAGGTGTAGTGAGAGGACTGGAGCAACAGCTCAGCCCTTCAGAGCATTTCCTGCTCTCGTAGAGAACCCAGGCTCAGTTCCTAGCACCCACACGGGAGGCTCACAACTGCCTGTAACTCCAACTCCAGAGGACCTGGTGCCCTCTTCTGGTCACCAGGGGCTCCTGCATGTATGTGGTGCACCCCAAACTTTCTTGGGTATACACATATACCCATAAAATGGTAAATAACCCCTTTTTAAAAGCAGACAGGGGTCTGGTGATATGGCTCAGTTGGATAAGGTTACTTGCCACCAAGCTTGATGGCCAGCTTATCTGAACTTGATCTCTGGGACCCACTGGTAGAAGAGAGAACTAACTCCCAGAAGTTGTTTCAGATCTATGTTAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCACACTCCCCCTCCCGCCCCCTGGCCCCCATACACACATAGGAGTGTAACAGTCATGCTATGCCTGGAAGGCAGCATCCTACACCTCTCCCCACTGCATCCTCTGGCCCTGGTGTTCTTTCTGCCCCCACTTCTAAGACATTCCCTGAGCCTGTGCAGGGTTGATACAGATATCCCATTTGTGGCTGGTCACTCAGCCCCTTCTCCCATTCCCTCAAGTGCAAAACATTACCCAGGAAACTCACTGTTCTGAGTTGCTATTGTCTTTAAG
Seq C2 exon
CAACGATTGGCTCAGATGCTCTTCTGGGGACAGCAAGGGGTGGCCAAGAACCCTGAGGCCGCTATCGAGTGGTACGCGAAGGGGGCCCTGGAGACGGAGGATCCGGCGCTGATATATGACTACGCCATTGTGCTATTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029189-Sel1l3:NM_172710:12
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF082387=Sel1=PU(8.6=7.5)

							
A:
NA

							
C2:
PF082387=Sel1=PD(85.7=63.8),PF082387=Sel1=PU(27.3=19.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031090





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:25788365-25790454 
ALTERNATIVE
HsaINT0147101
(SEL1L3)
Human
(hg19)
chr4:25789987-25792076 
LOW PSI
HsaINT0147101
(SEL1L3)
Rat
(rn6)
chr14:60190048-60191244 
LOW PSI
RnoINT0132678
(Sel1l3)
Cow
(bosTau6)
chr6:46826737-46828603 
LOW PSI
BtaINT0130590
(SEL1L3)
Chicken
(galGal4)
chr4:73010298-73010859 
LOW PSI
GgaINT1024689
(SEL1L3)
Chicken
(galGal3)
chr4:75846509-75847070 
LOW PSI
GgaINT0072907
(SEL1L3)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCATATGTTGAAACTATTAGGCTCA

				
R: 
TGAATAGCACAATGGCGTAGTC

				
Band lengths: 
259-1511

			

		

	





	
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






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