Special

MmuINT0045442 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:32796428-32799207:+
Coord C1 exon
chr17:32796428-32796628
Coord A exon
chr17:32796629-32799062
Coord C2 exon
chr17:32799063-32799207
Length
2434 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CTTATCTTTTTTTTCCCCAGTCC
3' ss Score
10.57
Exon sequences
Seq C1 exon
AGGATGCGATATCTGGACTTATCCTGGCTAGGACTGGGGCCCATGTCAGCCTCACCGTGGCTACTCTTTTTCTTGGTTGGGATTTCCTGGTTCTTGGCCCGGTTCCTCACGCAGCTATACACTTTGTATGCAAAGTGTCAACGTCTCTGTGGTTTCCCTCAGCCACCCAAGAAGAATTGGTTTTGGGGTCACCTGGGCATG
Seq A exon
GTGAGTATGTTAACAGGATGAGTCTGGATTATGAGGGTGCAGGGACCTCCCAGTGGTCAAGGAGTTTGTTAGAAGGATGTCCCGGGATGTGGGTATGAGGTATATGGACAGAAAGTCGGGGATTAGGTGGGCTAGGGGCTGGGGTGCGAGGGTGCAGAGATCCTCATGGATATGGGAATTGAGGATAGAATGGGTTAGGGTCTTTGGGTGCTACATTTCAAACTCTTTTCAGATTTCTGTTTTTCTATTCCCAGTCTACTCTGGGTTGATTTCTAGCCTCTTTTGCTGTTTCTGGTACACACTGAAGGGCTCCCAGAATGGGCTTCATAGATCCAAGACCCCTCACATTCATTCTGCTGCTTAGGCCTCCTGAAGGGTTCTGGTTTAGAGTCAGCTTCCTGTCTGGTCCATTTCTTTCTGCTAGTCTATCTTTGGGTTTCTGCTTTATTCCAGAAGGGATTTTTATGCCCTTCTCATACACCTCCAGCACACCTGTGCCCCTGGCGAGTTCTTTTCTGACTCCTTGCTTCACTTTCCTGAATCATATCTTGCTTAGACTGCTCTTTTCTACTAAGATTAATCACTGAGGTCTGCTGCACAACCTGGATTAGACTAGAAGCCTCATCTTTTGGTGATCTTCCTTGATCCTAACAATTACACAGCATTTGGACTGTAACATAGGACCGTTCTCTCCTTTGGTTAACTTGGTCTTGATTGCTTCATTCACAGTTCTCAGATCTCACAGCATGCATGCAAGTCCTTGTGGGTGGTGGTTGCTTGTTGGGGAGCTGTCACTTTTATGGAGTCTTAGGGGTCCTCTTTGCTATCTTGGCATCTGCTGAGCATCCAGTGTTTGAACCCTTCTGCCTAGTTGGAACTGGAGACTTTTGGTGTATGCAGTCAGAAGAGCATGTGCGAGAAATCTTAGGGACAAACCTTGAGCCTGCAGTGCAGTCCACACATTTCCCTGTCAGGACCTTGCCTTGAGGCTTTTTCTGGGGCTGAAATTGAGTCCACCTGAGAAATTAATTTTCTTAAGACAAAGGAGTCTTCTCTGAGGTGGACAGTGTGACAATATAGCTTGTCTATTGACCATGAGTTACAGGCTTGATACCAGGACATGACTGATAAAGACAAAGCAAGAAGAAGCAGGGATTTACTCCTATGTCTTGCAACATCCAGACACATGTTCACTACAAAGGCTTCAGGAGAAACATATTACAGGTGCTGAGGAAGTATATTAGTGATCTCCGGAGCTCCAGAACCAAAGCATGAACACACATGTGCACACAAACAGTAAAATAAACATACCCCAACACAACTGCACACACTCACACACACACACACACACACACACACACACACATGCATATACACACTTACATATGCACACAGATACATCATTTTGCATTAGTTAGTGATAGGGACAAATTTTAAAAATTCATCGCTGGATGATTTCATCATTTGGCTATCGCTATAGAGTACACTGAATCAAACCATCTTGGCAGAGCCTACTGCATATCTAGGTTATGAGAGACCACTTATTGGTCCCAGCATACAAACCTGTACCTCACGGTACTATTGAGAAGATTGCAGAGAGTTTTTTGATAAAGGTATTTATTTAGCCAAATGTACACTAAACATAACAATAATAGTAAAAATTGAAAGACACAGATAATCTTCAGGTGTGTTATAGTTTTGTGTGACCAAGGTTGTACATGCAGACTATCAAAGAAGGGGATGGAAGATAAGGAAAGAATTGTGGGAGAGGGTTACCAGGAAGGGGGCAGTGAGCAGATTGTAAAATGAATAAGTAGAAAAATTAAATTAAATTTAAAAATCATTATGCATCACAATTCTATACATAGTTATACAGATATGCGAATGAACACAATATACATATAACATATACAGGTATGCAAATGAGAAAGAGAAGAAGGTAGGGATCGATAGATAGGTAGATAGATATGTAGATAAAGTTTGGACTTAAGTAATAAAGGAGGTTGAGAAATCTCACAATACCACACACAAATTTGGAGGACCAGGAAGCTGGTGGTGTAGCAAGTTAGTGTTAGAACAAAGGCCCAGTGTAAAGTGGAGTGTCAAACATGAATGCTGGAGTCCAAAAGTCAAGTACCAGAAGTTTGCTATTTGAGAGCATGAGAAGCTGAGTGTCCCAGCTTGGGCAGGAAGAGTGAATTTCCCCTTCCTCTGTCTCTTGTTTCATTTGGATCCTCACTGGGTTGGATGGTACCACCCATGCTGTGAAGGGAGGGACATCCTGACTCAGTCTACTGCTGTGAATACTGTGTTCTGAGAATATTGCGGATGCAACAAGAAGTCATGTTGCATCAGCTTATGTGGGCATCCAGCCGATTTGATCCCTGAAAAGAGCCATGTCAAGAGGGATTGCACTTATCTTTTTTTTCCCCAG
Seq C2 exon
TCCCCTCCTACAGAAGAAGGCATGAAGCAGGTGACTGAGCTGGTGACCACCTATCCCCAGGGCTTCATGACCTGGTTAGGCCCTATAGTTCCTCTCATCACTCTGTGCCACCCTGATATCATCCGATCTGTCCTCAGCGCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
-Cyp4f40:NM_001101588:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





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)
chr19:15641614-15645718 
ALTERNATIVE
HsaINT0044514
(CYP4F3)
Human
(hg19)
chr19:15752424-15756528 
ALTERNATIVE
HsaINT0044514
(CYP4F3)
Rat
(rn6)
chr7:14866905-14869138 
Cow
(bosTau6)
chr7:8508671-8510493 
ALTERNATIVE
BtaINT0007895
([1])
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr12:48581766-48588585 
LOW PSI
DreINT0054403
(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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