Special

MmuINT0045448 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:32806719-32808220:+
Coord C1 exon
chr17:32806719-32806840
Coord A exon
chr17:32806841-32807949
Coord C2 exon
chr17:32807950-32808220
Length
1109 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
TTCGTGTTCTCATTGTGCAGGAA
3' ss Score
9.2
Exon sequences
Seq C1 exon
GCCAAGTGGCTGCGCCTGGCCTCAGGGGGTAGCACCCGTCTGAACATGTTTGAGAACATCAGCCTCATGACCTTGGACACTTTGCAGAAATGCGTCTTCAGCTTCAACAGCAACTGTCAGGA
Seq A exon
GTAAGTTTCACCTTCAGGTCTTGGATGAGTTTTGGTCCACAGACTTAAGGCAAGAGGTAGAAGAGGGAAGGCTGGCCAGAGCAAGCAGAAGAGACTCATGGAAGAAGTGGGTCAGAACTGACACTGAATCAACCCCACGGGGGACAGAGTAGCCTCTTCTATAAGGTGGAATTATTCAGAAGAAGGCACAGAGATTCAGGTAGTCATGAGCACCTGGCAGGAAGCGTTTGGAAAGAGGTTGGGAGAACAGACAGTAACTAAAGCATGGAGACATTAAAGTCAAGAAAAGTGTGGAACTTCGTTCTGTGAATTAAGGTCATAGTTTCTAGGAAACTATGAGAGATCTTCATTATCTATCACTATAATAAAATATCTAAGATTATAAAATAGAGGAAATATTTATTTCAGCTTATGGTTTCAGTGTAATTTGGGTCTGTGCCCAAATTTGTATTATGGTGGGGACCATGTATTTGAGGAAACACAGGCAGCCAAGAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGTCAAGGTTTTAACAACCCTTTAAAGGCACACCCATAATACAAAAGAGCTCTATAGACAGTAACTGTCTTTTAAAAGAAAATAGGATTGATGTTGTAAAAGGGGGTAGGTGAGACTGGCCATAGCATATTGCAAGAATTGATGAGTTCTAATCTGGGTGGACAATATTGGGAGCAGGAGAAGCAGAACTGGACCCTGTGTCAGAAAGGAAAGAGAGGAGTCTGGTGTCTACACTATGTGGCAGATGCTTAGGGAAATGCCTAGGCTCATGTGATTGGAATGAAGGGAGAGAGGAAACTGAGTATACAGTGCTAGGATTACATATATAATAAAATTACATATGATAAGCCTTTTGGCTTGAGATAGCTTTTTTGAGACGTGTCTTACCATGTCACCATCAAGGCCCATGTCTATCACATGTGACCATTGTTTCTAGATGAGTTAGGCTACTTGGTATCCTGTTAGAAAATAGTTCCCTCCTTCTGCTGAGAGATGCCCCTCAGGTTTTAGGTCTGCAGCATTCCTGCTTCTCTTCGTGTTCTCATTGTGCAG
Seq C2 exon
GAAGCCTAGCCAGTATATTGCTGCCATCTTGGAGCTCAGTACCCTGGCTGTGAAGAGAAACGAGCAACTGCTTATGCATGTGGACCTGCTCTACCGCCTCACGCCCGATGGAATGCGCTTCTATAAGGCCTGCCGTCTGGTACACGACTTCACCGATGCCGTCATCCAGGAGCGACGTCGCACTCTGCTGAAGCATGGTGGTGATGATATCATCAAGGCCAAAGCCAAGTCCAAGACTTTGGACTTCATTGATGTACTGCTGCTAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
-Cyp4f40:NM_001101588:5
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:
ENSMUSP00000129536





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:15682511-15683492 
ALTERNATIVE
HsaINT1010523
(CYP4F12)
Human
(hg19)
chr19:15733271-15733567 
HsaINT0044518
(CYP4F3)
Rat
(rn6)
chr7:14899050-14901580 
ALTERNATIVE
RnoINT0044598
(Cyp4f4)
Cow
(bosTau6)
chr7:8516180-8516589 
LOW PSI
BtaINT0007899
([1])
Chicken
(galGal4)
chr8:20787396-20787489 
ALTERNATIVE
GgaINT0035773
([2])
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr12:48575594-48575722 
DreINT0054413
(cyp4f3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGTAGCACCCGTCTGAACATG

				
R: 
GCAGCAGTACATCAATGAAGTCC

				
Band lengths: 
358-1467

			

		

	





	
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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