Special

MmuINT0045083 @ mm9

Intron Retention

Gene
ENSMUSG00000081362 | Cyp2j7-ps
Description
cytochrome P450, family 2, subfamily j, polypeptide 7, pseudogene [Source:MGI Symbol;Acc:MGI:2449816]
Coordinates
chr4:95866027-95868867:-
Coord C1 exon
chr4:95868680-95868867
Coord A exon
chr4:95866166-95868679
Coord C2 exon
chr4:95866027-95866165
Length
2514 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACA
5' ss Score
5.19
3' ss Seq
ATCTTGGCTTTCTCCTTTAGGGC
3' ss Score
11.12
Exon sequences
Seq C1 exon
AAAGAGTACACTCTGAGATTGATGGAGTGATTGGACAATGGAGGCAGCCAAGCACTGGTGACCGAGACTCCATGCCCTACACCAATGCTGTCATCCATGAGGTGCTGAGGATGGGCAACATCGTCCCCTTGAATGTTCCCAGGGAGGTAACAGCAGATAGCACGTTGGCTGGATTCCACCTGCCTAAG
Seq A exon
GTGACATTACACTTGCAGCTTCCCATCTTCAGTCTATTGTCATTATTTGAGTAACCTAGTCACAAAAGTAAAATTTACTTCTGCCCCAAGAAATCATTTAAAACTGAAGAGAGATTTTATTCATAGCAGAACATGAGCATTCCTCCTATGTGTGTCAGTGATGTTTATGTGTATCATGGGGAATACAGAAAAGGCAATTTCTTTTTGGAATTTGCTTAGTAAAAGACAGCTTTGTTTGCTAAAGAACATCCTCTTGTACTCCTGTGCTAATGTTCACTCATAAGAGTCAATATTTTTGCCATATCTGAAGTCACAGGTGGTTTTCCAGAGTTTTCTTAACATTCCACAGTTGAGAACATTCTATCACATAAAGAAATCTAGTCCAAAGTGAATCAGTAATTCTAAGAAAGGGACAGAAAAACACAGATAGTTGCCTAGAAAACATATATTGAGAATTCTCTTTATATCAAAATTTCATAATCCCCTTTTCATGAGTATTGATCACCTCTTTATTCAGTAAAAATTGTGATTAGGTGAAATAAGTTTGCATAATGTCTCTCTGCTACATTATACAATGTCCTAACCTTGGGATTTGGGAAGAAACTTGTTCAGATTATTTGTCCTGCCCAGGATTTATTATATTCATCATTAAAAGAGCTCCCTTATACTTTTATGCATGGGTCTTTCTTGCAATCCCACTGTTCCCAGACCCTAGCTTATAATCTACTCAGGATTTCTGCAGAGAGCTTTCCGGAGTACATTATACTCATTCTGCTTAAGGCACAATTATTATCCTTTCCATTCTTTCTCTATACTGTGTGCCAAACAAAATCAGACAGTTCTCTGCAGTAGCAAAATAAAATGTCTGGGGTTTTAGTTCAGCATGGTAGAAAAGGGGGAGCACAGCTGATCATTCTCATTCTGCCAGGAAGCAGAAAGAAAATCTTCAGGAAGTTTCCATCTCACTCCATTTATTCTACCCAGTTCTTCAGCATTGGAGAAGGTGCCACATATCAGGAAAGTCTACTGTCATTGTATAATGAGCTTTGCAGATGGTCTCACTGCTACTCTTACTGGTGTTCTATTATAATTTCCTGGACAATTCTAAATTACTCAGAATGTGTTGTTCTTAGGAAAGTTTTCAGAGTTCAGAGCAGAAGAGTCCATTCTGGAAACACAGATACAACCACTATAACACTTAGAAATAGAAAGCCTTAAATATACTATCAGCTCTAGACATTGACCGTCTAACTAGATACTATGCAAGTGAGTCAAAGAGCCATGGCTTTGATTTTACATGGACCTAGTTTCAGAAATGGCTGCATCTCTGCCTAGTATATGGCTGTAAGAAAACTGTTAATTTCTCATAGCATTGATCCCTGTATCACTATCATGACATAGAATAATGTACAGTCCTCACAAGAAGAGGTCATTCATGCAAAGCTTCCCACGCCATATAAGAGTTATAATTTTTATTTTTTACACATCTAAGATTTTCTGTCTGTAAAACATCCTAAAAAGGTGACCATGTAAGTGGAAGATTATAAATCATGAGAATGGCCAGAGGAAAGCACTCTGGCACTATCTAGAACTAGGTGCTCTGGGATGAAGCCCAGAGCCTGGGAGAGAACAAGAAAGGTTCTAAAGAAAACGATACAGGTTCTGACAACATGCAAGAGGATTAGTTTTATATCAGAGAGAAAATCTTTAAAGGGGATTGGTATGATTACCAATCTAAGAAAATAAATGCCAGCATATGATGTCTTAAGCAGTAGGGAAAACTGGCTTTGGGGAATCAAAGAATACCTCTTTATATTAGTACTGATGTAATTATACTACAGAATGGTTCATTAAAATAATGGAAGATGTGCATTTATAGTTATTAATGTGTATTTATGGCATAAGCATTGTCAGGTGTGAGCTAGATGAGGGTCTAAGTTATCAAGGAGGCAGGGGGATATTAGTACTGACATGACTCAATCAAGAGAGATTGAAAGAATGGTTTGGGACTTGGATGGAGTGAATGAGACAGTATGAGGTAAAGGCACACTCTAGGGAATCCAGGCATCATGCCAGGGAGGCTGGTGGACTGAGCTTGCTTACTCTACATGTTTGATGTGTTCCTACCCCTGCTGAGAGATTGAGTACAGCTACATACTGAAGGCTATGATGAGAGAGAGAAAGAGATGGTAGACACACGATCTTCTTTTGCAGACCTTCCATAGTCCTCACTATAGGAAGTAGCTATTTTGAAGGTTATCACCTCCAGTCAAATTATATTCCCATTGATGGTCACATGTCTTCTCCCTACCATATCCTGACCTATTCCCACAGACCAGCATTTTGTAATAAAACAAAGCCTAATGTCCCTGAAATGCGCTAAGCAAACACTGTCCATCAATGATCTGAACAAGGACAGGTTTTTGTGGGAGCTTAGGGTGTGAACAGGAATGGGATATTGGCAAGCCTCATCCATTGTGTTTATATCTCTTAGATCTTGGCTTTCTCCTTTAG
Seq C2 exon
GGCAAAATGATCCTCACCAATTTGACTGCTCTGCACAGGGACCCCAAAGAATGGGCCACTCCAGATATATTCAATCCAGAGCACTTTTTGGAGAATGGACAGTTTAAGAAGAGAGAATCCTTTCTGCCTTTCTCAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000081362-Cyp2j7-ps:NM_001104926:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
NonCoding





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0006717=p450=FE(13.6=100)

							
A:
NA

							
C2:
PF0006717=p450=FE(10.1=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000134331





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:59901104-59904870 
LOW PSI
HsaINT0044317
(CYP2J2)
Human
(hg19)
chr1:60366776-60370542 
LOW PSI
HsaINT0044317
(CYP2J2)
Rat
(rn6)
chr5:119550225-119552253 
LOW PSI
RnoINT0044407
(Cyp2j4)
Cow
(bosTau6)
chr3:86538695-86542216 
LOW PSI
BtaINT0002936
([1])
Chicken
(galGal4)
chr8:25601313-25601784 
ALTERNATIVE
GgaINT1001531
([2])
Chicken
(galGal3)
chr8:27487072-27487998 
GgaINT0039183
(E1BVV4_CHICK)
Zebrafish
(danRer10)
chr20:25617175-25617896 
LOW PSI
DreINT0054259
(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"