Special

MmuINT0045449 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:32807950-32810942:+
Coord C1 exon
chr17:32807950-32808220
Coord A exon
chr17:32808221-32810875
Coord C2 exon
chr17:32810876-32810942
Length
2655 bp
Sequences
Splice sites
5' ss Seq
AAGGTCGGC
5' ss Score
6.12
3' ss Seq
GAACCTTGTCTCGTGTCCAGGAT
3' ss Score
7.7
Exon sequences
Seq C1 exon
GAAGCCTAGCCAGTATATTGCTGCCATCTTGGAGCTCAGTACCCTGGCTGTGAAGAGAAACGAGCAACTGCTTATGCATGTGGACCTGCTCTACCGCCTCACGCCCGATGGAATGCGCTTCTATAAGGCCTGCCGTCTGGTACACGACTTCACCGATGCCGTCATCCAGGAGCGACGTCGCACTCTGCTGAAGCATGGTGGTGATGATATCATCAAGGCCAAAGCCAAGTCCAAGACTTTGGACTTCATTGATGTACTGCTGCTAACCAAG
Seq A exon
GTCGGCTTCTTAAGAGGTGCAATGGAGCTTTTTAAAATGAATTAGATGAAGTTTTTGTTTTGTTTCCTTCTTTTAGACAGAGTCTCACTGTAGACCAGGCTGGCCTCAACCTCATGATCCTCCTACCTCAGCTTCCTCAGTGCTAGGATTACATATCCATGTCAACCCTTTGGGTTTTGGTAGCTTTCTTGTGATGTGTCTTACTATGTTGCCAGGCTCATCTTCAGGGCTGGGTACATATCTCACTGCCCCACTGGCACTACATGTTTATACCACTCCTCATGACTTTAAAAGCTAATTCATTTATTTTTGTTTTGTGTGTATGAGTGTTTGCATGCATGTTTGTATGTGCATCACACGCATGCTTGGTGACTGCAGAGGCCAAAAGAAAGAACTGAATTTCCTAGAACTAAAGTTATAGGTGAGGCACCATATGATTATTGAGCCATCTCTCCAGCTCCAACCCTTTATGATTTTATAAAAAATAGAGTGAATGCTTGTACTGAATGTGAGATGATATGACTTTTTTATATTTCAGTAATGACTTGGGCTTGATGTAGAGAACACCTAGAATCCATAGAATGCATTTGAGGTAAAGAGAGACGAGTCAGAGAAAAACACATTGTAGAGAGCAGACTGGGGCCAATACAGTCTTTCTAGGTGGACCTGAAGGGCCTTACTTGGTAAGTTAGTAGATCATAGTATCCGTATTTGGGAGACGCTGCACATAACTTCATAATCAGTGTGGATCACACATTATAGCAGTCATGCTATGAAGGTAGCAGTCACTCCCTATTACTAGATCTTTCCTTCCCAGGTGATTTGACTATTTTACCTGACAAATATGTGTACAAAAATGTCACCGTGAAATGCATTATTTTATAGTTAAAAACCAATCTTAGACTTGATGTGCCAGGGTTGGGAGATACTCAAGGGGACTCCCACTTGCTCAGAGGAGAAAGGGAAGGAGATGGGGGAAGGATTGTTGGAGAAGGTGACTGATGACAGCTGTCTTAGTTACTGTTCTACTGCTCTGAAGAGACAAATGACTAAAGCAACTCTTATAAAAGAAAGCATTTAACTGGGGGCTTGTTTACAGTTTCAGAGGATTAATCCATGATCATCATAGTGGGAAGCAGACAGGCTGGAGCTGGAGCGATAGCTGAGAACTTTACATCCTGATTCATAGGCAGCAAGCAGAGAAGGAGAGAGAAGGAGAGAGAGAGAGGGAGAGGGAGAGGGAGAGAGGGGGAGAGGGGGAGGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACCTGGCCTGGAATGGGCTTTTGAAACTTCAAAGCCCAATGGTGGTACACTTCCTCCAACAAGGTCACACCTCCTAACCCAAGCAGTTCATCAACTGAGGACTAAGCATGCAAATGTGTGGGTCCAGGGGACAATTCTCATTCAAACAGGATTCACACAACAGGAGAAAGACCTATATATTAGGAGTCGTGGAGGCTTATAGGACAGCACATCTATGTCTTCTTGGTTTCAGAGAAAGCAATGGGATAAACAGAGGAAGAGGGAAGAGAACAGGAGAGGTAACATAGATGAAGGGTAAACAGATAATAGAGGAGACAGGAGAAGAGGCAAGGGATAGAAGATCATTTTTAACTATAAAATAATGCATCTCACAGTGACATTTTCGTGCACATAAATCACCCTGCATTTCTCTCAAATTTTCTCAAGTAAAGAGAAGACTTTATTGTTGAATATAAACAACTTTAACCAAGTGCCAAGGTAAGTTTTATAGGTTTGTAAACCTGATAGCTTCTAAAGGAAATAAGATAAATTCCTAATATTTAGACCCAGTAGTGGGACAGAAGAGCAGGGAAGGAATTAGAGAGTAAGATGAGAGAAGCCAGAGAGGGGACACGTTTGAAAACTAGCAAGTGAGAAAGAGAGGAGAAGGGGAAGCCAGCCCACTTACCAACCACACACACTATGACATCATCTGAACTCACAAAGTTACATACTGCTCCTATTTCTCCCATCAGTCTAAATCTTCCCACCCTGCAGACACAACCTTTGTGACAAATCAAGTAGCAAAAAGGGAAGAATGGTACAAAGGAAACCCACTCTTCCCACCCAGTGAGCAAAGTTAAAGATTTAGGGCAGTGGTTCCCAACCTTCCTAATGCTGTGAGCCTGTAATACAGTTCCCTATGTTGTGCTGACCCTGAACTATAAAATGATTTTTGTTGCTGCTTCATACCTATAATTTTGCTACTGGTATGAATTGTAATGTAAATATTTTTTGGACATAGTGGCTTGCTATGTGTTGAGGAACACTGACTTAGAGCAATGTTTAGTCTCTAACTTTCAAGACAAGTTGTCCTACAATGATTCTACTTGAAGGTGGCTAGTCACTCATCACACAGGAGTAGAAAATATCCACGAGTCTTTGATTCCCTCAACTAGGAAAACACAGGAAGCCAAGAAAATGCCTGTGTGTTGGTGACCAAGAGAAATGCAGGAATATGAAGGTCTTGTGTGCATAGTCAGAAAAGGATCTCTAGATGTTATTTTATGTTAGACATGGGAGCCATCAGAAGTTGTGCAATATAAGAACCTTGTCTCGTGTCCAG
Seq C2 exon
GATGAAGATGGAAAGGAGCTGTCAGATGAGGACATCCGAGCTGAAGCTGACACCTTCATGTTTAGGG
VastDB Features
Vast-tools module Information
Secondary ID
-Cyp4f40:NM_001101588:6
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)
chr19:15683764-15684815 
ALTERNATIVE
HsaINT0044473
(CYP4F12)
Human
(hg19)
chr19:15760994-15763378 
HsaINT0044519
(CYP4F3)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:8516861-8528393 
LOW PSI
BtaINT0007900
([1])
Chicken
(galGal4)
chrUn_AADN03027099:3346-4444 
Chicken
(galGal3)
chr8:22596979-22597378 
GgaINT0039280
(E1C120_CHICK)
Zebrafish
(danRer10)
chr12:48574122-48575310 
DreINT0054414
(cyp4f3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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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