Special

MmuINT0005186 @ mm9

Intron Retention

Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108284700-108285396:-
Coord C1 exon
chr3:108285249-108285396
Coord A exon
chr3:108284781-108285248
Coord C2 exon
chr3:108284700-108284780
Length
468 bp
Sequences
Splice sites
5' ss Seq
TTTGTAAGC
5' ss Score
3.93
3' ss Seq
CCAACCCCCTTCTGCCTTAGGTC
3' ss Score
9.52
Exon sequences
Seq C1 exon
GTCCAAGTGGGTTCCCCGGGGAGACTACATCGCCTCCAACACAGATGAATGCACCGCCACACTGATGTATGCCGTCAACCTAAAGCAGTCTGGCACCGTTAACTTTGAGTACTACTACCCGGACTCCAGCATCATCTTTGAATTTTTT
Seq A exon
GTAAGCTCCCAGGCAGGAGGGAGGGAAGAGAGGGTTGGGGGAGGAGAGGTTGAGATTCCCCGAGGCTCAGATTCATTTTGTAGGGATCATTCACAAGTGTAGCCATGTCTGAGATTTTTTTTTTCCCTCTAGAGAAAACTGTGAGCAAAATGAGCTCAGGCCTGGGGGTCTGAGGAGAGAAGACCCCAGGCAAAGGACACTGATGGGGAGGACAGAGCCTGTGAAGTCCCTAGGTGTTTCATCCTGTTCAGACTTGTTATGACACGCAAGGGGCTAAGCTGCAAATTCTTTCTCTGAGGCCCATGCTCAGCCATGATTGTGTGCAGCTTCCTTGTTCTCAGTTTGGGCCTGGAGGGAATTGGCTGCTCCTCTGCTGTGAGAACAGTGTGAGAGCATCACACAGTATGACATAAGGCCCTCCTTTCCTCAGGAAACCGAACCTCTCCTCCCAACCCCCTTCTGCCTTAG
Seq C2 exon
GTCCAGAATGACCAGTGCCAGCCCAGTGCTGATGACTCCAGGTGGATGAAGACTACGGAGAAAGGATGGGAATTCCACAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412-5330417C22Rik:NM_001033304:3
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=0.047
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000102236





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000040128, ENSMUSP00000102237
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr1:109714636-109715109 
LOW PSI
HsaINT0086693
(KIAA1324)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr3:34344701-34345156 
LOW PSI
BtaINT0081100
(KIAA1324)
Chicken
(galGal4)
chr26:1130796-1130867 
ALTERNATIVE
GgaINT1016112
(KIAA1324)
Chicken
(galGal3)
chr1:8087319-8089037 
LOW PSI
GgaINT0113137
(KIAA1324L)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTTCCCCGGGGAGACTACATC

				
R: 
TGGAATTCCCATCCTTTCTCCG

				
Band lengths: 
215-683

			

		

	





	
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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