Special

MmuINT0045406 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:32664786-32665056:+
Coord C1 exon
chr17:32664786-32664919
Coord A exon
chr17:32664920-32664991
Coord C2 exon
chr17:32664992-32665056
Length
72 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGG
5' ss Score
5.28
3' ss Seq
GACTTTTTTCTTGTCCAAAGGAA
3' ss Score
9.03
Exon sequences
Seq C1 exon
GGACGACCTGGCCCAGCTGCCCTTCCTGACCATGTGCATCAAGGAGAGTCTGCGGCTGCACCCCCCAGTTACGGTCATTTCCCGTTGCTGCACCCAAGACGTTGTGCTTCCAGATGGCCGGGTCATCCCTAAAG
Seq A exon
GTGTGGACTGTATGGGGAGGTGGCTCCTGATGGTCCCCAAGGGGGCAGCACTGACTTTTTTCTTGTCCAAAG
Seq C2 exon
GAACCGACTGTGTCATCAGCATCTTCGGGGTTCATCACAACCCTGAAGTCTGGCCAGACCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
-Cyp4f17:NM_001101445:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000129514





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr19:15694295-15694390 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:8585846-8585927 
LOW PSI
BtaINT0046309
(CYP4F3)
Chicken
(galGal4)
chr8:20789347-20789749 
ALTERNATIVE
GgaINT0035777
([1])
Chicken
(galGal3)
chr8:22611358-22611760 
LOW PSI
GgaINT0035777
(F1NNP0_CHICK)
Zebrafish
(danRer10)
chr12:48570962-48572067 
LOW PSI
DreINT0054405
(cyp4f3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCCTTCCTGACCATGTGCATC

				
R: 
GCCAGACTTCAGGGTTGTGAT

				
Band lengths: 
169-241

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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