Special

MmuINT0045100 @ mm9

Intron Retention

Gene
ENSMUSG00000015224 | Cyp2j9
Description
cytochrome P450, family 2, subfamily j, polypeptide 9 [Source:MGI Symbol;Acc:MGI:1921769]
Coordinates
chr4:96235120-96238764:-
Coord C1 exon
chr4:96238626-96238764
Coord A exon
chr4:96235594-96238625
Coord C2 exon
chr4:96235120-96235593
Length
3032 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TGTTTTGTTTTGTCTTATAGGAA
3' ss Score
11.85
Exon sequences
Seq C1 exon
GGTATTATGGTTCTTTCCAACCTAACTGCACTGCACAGGGATCCTAGCGAGTGGACCACCCCAGATACATTCAATCCAGAGCACTTTCTGGAGAATGGACAATTTAAGAAGAGAGAATCCTTTCTGCCATTCTCAATGG
Seq A exon
GTGAGTTGTGATGTTTAGGAGAGAATTCAACCCCCTCCACATATTTTCCTTCCTTCTTCACTATAATTCTGTGCTGTAGTTGGGATGTTTCCAGATGAGCATGTCCATTGTGGATCTTTCCTTATCTAAAATAAAATTTTTATATAATATATTATGATAAGTGTCCTCTTTCCCAATTCCTCCATTGTCCATTGTCTTCCCTATCTTCTCACCTACTCTATGTTCTTTCACTTTCTTTAGAAAATAAGAAAAGATGGAGACATAGACACACACACACACACACACACAGACATACACAGAAATACAACAAAGAACTGAAAATTAACAAAAGAAACACCCACTCACATAGACACACACACACACACACACACACACACACACACACACACAAACTCCCCAAAATAGGAAACCATATTATACAAGCAAAATTATATTAGGCAAAGACCAATAAGGCATTGAAAAAATAAACCTAAACAAAGCAATATGAAACAAAATGTTTACAAAAATACCATTGAGCTCATTTTGCCTACTGTTGGTATGGAACCTAATGTCAAGTTTGATTAATACAGCCAATGAGACTTCACTGAAACAAACTAATGTGTTTTTTGCAAGAGGCTGCCAATTGTAGATAGCTTTTTATTTAAGGCTGAGAGACTATATACACTTCCTCCTCCAAGTGCTGGGACCCAGTCTGGCTTGAATCTGTGCAGGCCACAAGTGTGCTACCATAAACTCTATGCATTTATAAACATATCAGTCCTGTAATTTGGAAGGCACTGTTTCCTGGGATTCATTCATCCATTCTTCCCCCGGTAATCTTTCTGGCTCCACTTCCACATAGAGCCCTGAGCCCCGAGGGAAGGTATTTGAAGAAGATTTAGGACTGAGTGTTTCAAAATCTTTTAGTCTTTTCACTTGGTCCAGTTGTGAGTTTCTATGTTAGTTCCCACCTACAAGAGAATGTTTCCCTTATGCTGGCCAAGGAAGGCACTTACCAATAGGGATAGCAGAGTATCATAAGGAGCCATATTATTTCTATGTTCCTTTAACAGAACAGTAGTATTTACTTTTGTTTATAGATCTATGGCCTATGTAGTCTACTGTTCATGGCTACACAAGAAGTGTCAGGTATGGATTCCATATCATGGAGTGGGCCTCAAATCTAATCAGGTAGTGGTTGGTTACTTCTACAACATTGCAACAGTGTGTTTTCTAGACAGACCAGCATTATAGACTGCAGGATTTACATCTGGCTTGGTGATTACATTTCTACTCAGAGTATGTGGCCTAATATTGCAGTGTTTGAATGCCAGAATACTTTGTACATCACAGCTTCAGACAACTACTGCTTCAGCTTCCCTTGATATGTTTATCCCAACACCAAGCACAGAGACCCAGCCCCGTGACTCTTGTTAAAAACAAAGAAACTAGCTAAAAAACCAAAAACCAAGAAAAAAAAAAAACCAACAAAACAACAAATCCTGGATAGCTGTCATCTTTATTGACTTTTATTTTTTTTCCATGTTATTTCCATGTTCTCTCTCATTTAGAAATAAACTTGAACTTTAATAAAGATGTGGAAAGATGCCAAGCAGAAGGGTTCTCTATTTATCAAAATGGACACAGACAATAATTCTAAATGACATCGTCTTAACTAAGTGAGATTCTGCTCTAGTCGCAGTCTCTGGCAAGGTCTTATATTGTAATGTTAGGTTCTTATTTATAATCTAGGAGATGGGTTTATATGGTAAAAATATAAAATTTCTCTTTTAAGTTAAATAATTTTAACTTTTATGTCACAGCACTTAAATTGAGCAGAATGTAGAAACCTACATTCTGAATGTTTCTTGAATTAGCATTTTGCTACAAGGTGTCAGTATTTTCTGCCTCATCTTTGGTACAAGTCTACTTTTTCACCTACTTTCTCTTGACTTCCTATGTGCAGCATCCTTGTAGGAAGAAAATTCAGATATCAGCTATTTTTCTCTTGGCAACTATAAGAAGGCATTGGGTTATTACCTGTGCAGTATTAGAACAGATGGCACAATCCTTCTTGAAACTTCAAATCCTGCCTGTCTATAGACCAAAGCTCAGGCTGCTTTATGCTAACAAGAATCTTCTGCACCTTAATACATCAAAGTGCTTGGGAAGAACTTTGATAAAGGCCTGGGTCATTGCTTTCATTTTAGTACTGATGAAATTCAAGTGTGTTATGTGATGTGAAATGGCCCAACCACAGTTTTAACGAGGCAGTGGTGGTTAGCTGTCTGTCATTGTGGCAGGAAACAGACTGTTTGCATGTTTGTCAAGCAAGAAAGATTTAGCCCGTTGAAAATGGGTGAGTTAGTCAGAGTGACACAGTTGTGCCTGATGGAGCCTGCTGCTGAGCATGGGTTTCTGATTTTCCAGGTCATGTTTTGTCCTGACGGAGGAATTCTTCTAGAAGAATCTTGGGAATTTACAATGGAGTTGAGTTTTTTTTTTTTTTTCTCTTTGTAGCAAGTTACCAATCATATTCCTAGACATTCTTAATAAGATGAAGATGAAGAGAACAGACATGATTTAAATACATTGCTTGGACACACAGGCATAAACTATGATATCAGTCCTACTATAACACACAGTTACTAAATAGTTTTGCCTGTAGTATCTGCTTTTAAAGGTTAAAAACTTTCTTCTGGTTTTTGTTGCACCATTATCTGCCCTATTGCTTATGTTTGCTAAGTGAGTGTGAAAAGCACTTGAGTTATTCACACACTCCCAGTCAACACAGTTCCCTTCTCCTAGTCTCCTGTGTCATGCTCTCCCAGGATGGCCAGATCTGTGAGAGCATTCAATTTGTGATTCTGGATTTCACCTCCTGTGTTTGGAGGAGGCAAGACAGATGCTAGATCTAAGTAAGCAATTTATGGGGCTCAAATTCCAGCACCCACTGAAACTCTGAATGGTAGTTAGGGGCACCAGTCCCTGGACATACCAATGACAGCTGAATAAATTAACTTTTTGCTTGTTTGTTTTGTTTTGTCTTATAG
Seq C2 exon
GAAAACGTGCTTGTCTTGGAGAACAACTGGCCAGGTCTGAGCTGTTCATTTTTATCACTACTCTTTTCCAAAAATTTACCTTCAAGCCCCCAGTCAATGAGAAGCTAAGTCTGCAGTTCAGAATGGCTGCAACCGTTTCCCCAGTCAGTCACCGCCTTTGTGCAATTCCTAGGCTGTGATGTTGAAGGAGGAAAGTATGAAGAAATGGCATCTGCATGGGAGACACTGGTGTCTGCTCCCATTTGAGCCGGTAAAATTAAGGTGACAGAGAGTGCGTGCAATGAGACTAAGAAAACTGAATCAAGTTATGGGTTCAGTAAGTAGAAAGCCACTTGTGAGCTCAATAACACAGCTTCTCAACTGAAGACTTGCAGAGAAAAAATGATTCATCCAGAAATGAAAATGTTTGCAGAGATCATGAGGGAATGGATTAAGTAGATATGTAACTCATAAAAATTATTTAAAAAGTTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015224-Cyp2j9:NM_028979:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.191 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0006717=p450=FE(10.1=100)

							
A:
NA

							
C2:
PF0006717=p450=PD(11.9=90.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000126647





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000050464
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:59893830-59900964 
LOW PSI
HsaINT0044318
(CYP2J2)
Human
(hg19)
chr1:60359502-60366636 
LOW PSI
HsaINT0044318
(CYP2J2)
Rat
(rn6)
chr5:115022135-115076423 
LOW PSI
RnoINT0044387
(Cyp2j10)
Cow
(bosTau6)
chr3:86426940-86433195 
LOW PSI
BtaINT0007295
([1])
Chicken
(galGal4)
chr8:25611346-25611944 
LOW PSI
GgaINT0039184
(CYP2J2)
Chicken
(galGal3)
chr8:27486334-27486932 
LOW PSI
GgaINT0039184
(E1BVV4_CHICK)
Zebrafish
(danRer10)
chr20:25616530-25617032 
LOW PSI
DreINT0054260
(cyp2n13)
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
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"