Special

MmuINT0045407 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:32664992-32665303:+
Coord C1 exon
chr17:32664992-32665056
Coord A exon
chr17:32665057-32665220
Coord C2 exon
chr17:32665221-32665303
Length
164 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGA
5' ss Score
5.51
3' ss Seq
TAGTCTTGGTTGACCTGCAGGTC
3' ss Score
5.95
Exon sequences
Seq C1 exon
GAACCGACTGTGTCATCAGCATCTTCGGGGTTCATCACAACCCTGAAGTCTGGCCAGACCCTGAG
Seq A exon
GTGCGACACCTCCCACTCTCTAATTCTGGGACCCGGGGAAGAGGTGTGGCCCTTACCTGGAAAACCAGATCTGTCACTCTTCTGTTTCCATGTCCATCTTTTCTGGGACTGTCTCCATGTGAATAGAGACGCGACCCATAAGCCTAGTCTTGGTTGACCTGCAG
Seq C2 exon
GTCTATGACCCCTTCCGCTTCGACCCAGAAAACCCACAGAAGAGGTCTCCTCTGGCTTTTATTCCCTTTTCTGCTGGGCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
-Cyp4f17:NM_001101445:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





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)
chr19:15694456-15694934 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:8585669-8585780 
ALTERNATIVE
BtaINT0046310
(CYP4F3)
Chicken
(galGal4)
chr8:20789815-20790269 
ALTERNATIVE
GgaINT0035778
([1])
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr12:48570787-48570896 
ALTERNATIVE
DreINT0054406
(cyp4f3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAACCGACTGTGTCATCAGCA

				
R: 
TAGGCCCAGCAGAAAAGGGAA

				
Band lengths: 
147-311

			

		

	





	
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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