Special

MmuINT0005188 @ mm9

Intron Retention

Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108283894-108284287:-
Coord C1 exon
chr3:108284182-108284287
Coord A exon
chr3:108284044-108284181
Coord C2 exon
chr3:108283894-108284043
Length
138 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
ATACCATTCTTTCTTCCTAGGGG
3' ss Score
10.37
Exon sequences
Seq C1 exon
GTTGAGCTAAATAGAGGCAATAACGTCCTCTATTGGAGAACCACAGCTTTCTCGGTGTGGTCCAAAGTGTCCAAGCCCGTGCTTGTTAGAAACATCGCCATAACAG
Seq A exon
GTACAGAAAACAGCTTGGATCTGGGTCTGCTGCTGGCTTCCTGGACTCCTGGCTTCTAGGGAGGGATGGGCATTTGGTCCCCAGGGCCTTGGTGTCTGGGCTCAAGCTTTGATCGTCTATACCATTCTTTCTTCCTAG
Seq C2 exon
GGGTGGCTTACACCTCCGAGTGTTTCCCCTGCAAGCCTGGCACATACGCTGCCAAGCAGGGCTCCCCTTTCTGCAAGCTTTGTCCAGCCAACTACTACTCAAACAAAGGAGAAACGTCCTGCCATCCGTGTGATGCTGACAAATACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412-5330417C22Rik:NM_001033304:5
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:
PF076998=GCC2_GCC3=PU(0.1=0.0)

							
A:
NA

							
C2:
PF076998=GCC2_GCC3=WD(100=64.7),PF075629=NCD3G=WD(100=56.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000102236





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000040128
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr1:109716202-109716309 
LOW PSI
HsaINT0086695
(KIAA1324)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr3:34343800-34343930 
LOW PSI
BtaINT0081102
(KIAA1324)
Chicken
(galGal4)
chr26:1131305-1131371 
ALTERNATIVE
GgaINT1016114
(KIAA1324)
Chicken
(galGal3)
chr1:8090988-8091644 
LOW PSI
GgaINT0113139
(KIAA1324L)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGAGGCAATAACGTCCTCTATTGG

				
R: 
GAGTATTTGTCAGCATCACACGG

				
Band lengths: 
242-380

			

		

	





	
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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