Special

MmuINT0045054 @ mm9

Intron Retention

Gene
ENSMUSG00000028571 | Cyp2j13
Description
cytochrome P450, family 2, subfamily j, polypeptide 13 [Source:MGI Symbol;Acc:MGI:2385197]
Coordinates
chr4:95735421-95738398:-
Coord C1 exon
chr4:95738236-95738398
Coord A exon
chr4:95735571-95738235
Coord C2 exon
chr4:95735421-95735570
Length
2665 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
GCTGAATCTCTTCTTTCCAGGAT
3' ss Score
7.32
Exon sequences
Seq C1 exon
TTTGTGAAGAAGTATGGGAATGTTATCAGTCTTGATTTCGGAATCAAGTCTGCAGTCATTATAAGCAGCCTGCCTTTAATCAAAGAAGCCTTTTCTCACCTGGATGAAAACTTTATAAATCGCCGTATATTTCCTCTACAAAGACAGATCTTTAATGGAAATG
Seq A exon
GTAAGTCTTTCATGTGTTGTAAGATATGTATTGTAATGTTTATGATACATAAAGGCACATATATGCCTTATTTATCCAACAGGCACATAAACCTTCATGAAAGGTTATCTTTAATGAGAGCTGGATGCCACCTTTCTTGAATGAAATCACCCAACAGATGACTTATACTAGGTCCTAGTAAAGACTGTGCACAACCACCTGTTTTGCAAAAGTACCTCTAGATGCTTTGGTAGGAAGTAACCATGCCACAATGGGTTCTCCTTTCCATTTCACCACTGCAGCCTTCTACCCAAGGAAAATGGAACCCCCTCTTCTACATCCTCTTTAGAGATGCTTATACTCTATGATTAAAATTATGGGGACTTCTAGGTTACTAGCCAATGTTATAACTTATTAGTGTAAATACTTCATATTAGCATCAATTAAGTCAAGTTGAAAACAAAATTTGAAATCTGTTAATCTAACAAACAGCAATTTAGATGCTAATTGCTCTTTGAAATAATCCATTAATTAATTCTACATCAATTCACTCTGTTGTCTGCTATGAGAAGCACAGTGCTAGACATATGTCTTCTTAAGGTTCTATTGCTAGGATGAAATACTGTGACCAAAAATCTTTGGAGGAAAGTGCTTATTTGGATTATGATTCTGTACCATTGTTCAACATCAATGGAAGTTAGGATGGGAACTCAAACAGGAGAAAAACTTGGAGGCAGAAGTTAAAACAGAGGCTATGGGGAAATACTGTTTACTGGCTTGCTCCTCGTGACTTGTTCAGCCTGATTTGTTATAGAACCCAAGACCACTACCCCAGGGTTGGCATTATCCACATTGCCTGGACCAAACACAAATTAAGACAATGCCCTACAGACTTACTTATAGCCCTATCTTATGAAGGCATTTTCTTAACTGTGGCTCCCTCCTCTCCAATGAATTTAGCTGTGTCAAGTTGACATAAAACCAGGAAGCATAGTATAAGTGACTAACAGGGAGCAAAATAGACTTTAAAATGTTCTTCTGTATTATCTTTATTGGATGAAAAAGAAAATCAAGTATGTACATTAATAAAATTGTGTAGTTTTATAAGTAAACCAATATTAAAGAAGAGGGCTTGTATTAGAAATGTCTATGTCTATAGATTCTTGAAAAACGGAGTAAATGATATTCATTTAATGACCTGAAGAGATAATTTGTCAAGGGGACATGATATCCTTAAAAAGGCCAGAAGGACAGAGGTATTGAAGAACTGAAATGCATCCAGTGTGACAAACATGGTATTTAAAGGACACAATTAAGTGTACATGACACTTCTGGGCCTGGTCAGAAAGAGCACAGTGTTCGCTAAAATACTGATTTTCATCCTAACAGCTGGGAAAGCTTCCAAATGGTTCTGAATAGAGGTGATCTTAGGATATTATGTCAAAATGGAGGGAAGATATTAGATATCATTATAAATATGAAAGGTCATTACATATTCCATATTCCAGTAGCAAAAATTACTGTGTATTAGACTAGAGTGATAGCATTGAATTCATATAGCCACAAGTCCATACATGCCTGATGAAAGCCAACATGATGTGTTCTACACCCCAAGAAAATAGGGTGCTGAGAATTCCACCATGAGTCTGGTGGCTAACCTTAACTTGTCAACTTAACTGCATTTGGAAGCAGCTACAGTCTAAGAATCTGAGCACAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAAAAGAGAGAAATTTTGCTTCATTGAATCATTTGAGGTGGGAAGATGCACCCTAAATCTGAATCATTTGAGATTTTGGAAACATTAAAGACTCAGCTTAAATCTGGGGCACACCTTCTGATTTCAGACCACATAAAAGAACATGAAAAAAAGGAAACTTTTGTCTTTTTCCTGCTTAGTCTCACTCTCACTGGCAAGTTCAACTGTCCTGCTGCTGAAGAACTCCTCCACCAGATTATTCAACTCTGGCATGTACTAGCCTGGCATTTACATCTCTACTTGCCAACCAGGAGGACAGTTATCCAGGGAGGACTTGGAAACTTACATTCATTTGATCAATATTCAAAATAGAAATTTTATTCAAAACAGCTTCAGTTTGGTTCCTTTCTACAACATATCTACCAAACAAAAATGTGGATACATTAAACACAACGTGTAGATGTGTTGGTTCTCTGGAGACTTAAAATTGATTACCTTGATAGCTAACTGTGTTCCCATGAAAATTTTACCTTGTCCTTGTATCTCATTTTTCCATCCATTGGAATGGGTCTAGTATGTTTTGGTAGTAAGCCTTTAAATTTTCTAAGAGTGCTAAATTAAAGAATATGTTAGAAATACTTACTAAACTGTGTGATGTTGCAAGCCACCAGGAGATGCTAACCATTATGTTCCTTGCTTGGTGATATTCTCTCTAGACAGCTATTAAGACCCTTATTGGCCCTTCTTCTTTACATTGCACACGTGTCCATAGAGCTCATGAGATAATTTTAGAACAGAATCACAATGCCGTGATGCTGAATCTCTTCTTTCCAG
Seq C2 exon
GATTGATCTTCTCCAGTGGCCAGACATGGAAGGAACAAAGGAGGTTTGCCCTGATGACACTGAGGAACTTTGGACTGGGAAAGAAGAGCTTAGAGCATCGAATTCAGGAGGAGGCCTCCCACCTGGTGGAGGCTATAGGGGAAGAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028571-Cyp2j13:NM_145548:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0006717=p450=FE(11.8=100)

							
A:
NA

							
C2:
PF0006717=p450=FE(11.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000030305





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000095587, ENSMUSP00000102693
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:59912312-59915937 
ALTERNATIVE
HsaINT0044312
(CYP2J2)
Human
(hg19)
chr1:60377984-60381609 
ALTERNATIVE
HsaINT0044312
(CYP2J2)
Rat
(rn6)
chr5:119562286-119564680 
LOW PSI
RnoINT0044402
(Cyp2j4)
Cow
(bosTau6)
chr3:86614496-86617000 
ALTERNATIVE
BtaINT0002104
([1])
Chicken
(galGal4)
chr8:25616923-25617545 
GgaINT1010913
(CYP2J2)
Chicken
(galGal3)
chr8:27492016-27492533 
GgaINT0039177
(E1BVV4_CHICK)
Zebrafish
(danRer10)
chr20:25620541-25623018 
LOW PSI
DreINT0054254
(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"