Special

MmuINT0045123 @ mm9

Intron Retention

Gene
ENSMUSG00000027983 | Cyp2u1
Description
cytochrome P450, family 2, subfamily u, polypeptide 1 [Source:MGI Symbol;Acc:MGI:1918769]
Coordinates
chr3:130998306-131001339:-
Coord C1 exon
chr3:131000704-131001339
Coord A exon
chr3:130998468-131000703
Coord C2 exon
chr3:130998306-130998467
Length
2236 bp
Sequences
Splice sites
5' ss Seq
AAAGTAATT
5' ss Score
3.64
3' ss Seq
ATTCTTCCCTTCCTGCACAGAAA
3' ss Score
8.84
Exon sequences
Seq C1 exon
GAATCGTGTTTGCACACTATGGTCCAATTTGGAAACAGCAGAGGAGATTCTCCCACTCGACGCTTCGTCATTTCGGTCTGGGCAAGCTCAGCCTGGAGCCCAGGATCATCGAGGAGTTTGCATACGTGAAAGAAGCCATGCAGAAGCACGGGGAGGCCCCCTTCAGCCCCTTCCCAATCATCAGCAATGCCGTCTCCAACATCATCTGCTCCCTGTGCTTCGGCCAGCGCTTCGATTACACCAACAAGGAGTTTAAAAAGGTGTTGGATTTCATGTCCCGGGGGTTGGAAATCTGCCTGCACAGCCAGCTCTTCCTGATCAACATATGCCCCTGGTTTTACTACCTCCCCTTTGGTCCATTTAAGGAGCTAAGGCAAATCGAAAGGGACATATCCTGCTTCCTGAAAAACATCATCCGAGAGCATCAAGAGTCTCTGGATGCCAGCAACCCTCAGGACTTCATAGACATGTACCTTCTGCACATGGAGGAAGAGCAGGGAGCCAGCAGGCGCAGCAGCTTCGACGAGGACTACCTGTTCTACATCATTGGGGACCTCTTCATCGCCGGCACTGACACCACGACCAACTCTCTGCTCTGGTGCCTGCTGTACATGTCACTGAACCCCGACGTGCAAA
Seq A exon
GTAATTGGTGCATTTGTTCTTAACTCAGGGTAAAGGCAGGTTCTTTGAACCCAGTCACGGACTCTGTGATCTGCTGGCCCCGGAGCACCCATGTGTCCAGGTTGGAAAAACGCAGTAAACACTTGTATTCTATAGGGAGTTCGAGAGGTGAACAGCGGCGAAGCCTCGGGTTTCTAGACAGACTAGCGTCATAGCTTGCCCACCCCTGTTTAATCTCCCTGTCCAGTTCCCTTTGAAACCTGTGAAAGTGAAGGCCGTTAGAGAAGTGGCGTGTAGAGAGGGCTAAGGGAGTCTATTGCTCATCCATACCTTCATCTCGTTTTGAACACAGAGAACGCAAGCCCAAGAGTCAGCAGAAGTCACAGCCAGTGCCACCACAGTGGACAGCCAGTGGCGGGGGCTGAGTAAGGGAACGTGGTATATTGCTTTCAGCAGCAGCTCTAGCTATTTATTCACTACAAACTTAGTCACTTAAGCAAACCCGAATTTATAACAAATCTATATTAGAAGTGTGACAAATGCTTCACTGAACTGAAGACTGGGGTGTGAGCCAGGCTTGCGTTGCCCGCTGGAGGCCCCAAAGGGGAATTCTCTCCTTGCTATTTTCAGCTTCTTTGACCTGGTGGTCCTCTCTCCATCTTCAGAGCCAGCAGAGCTGTAGCCCTCAGGCCATGCTTCCGTATTCACATCTTCTTCTGACTGAAGTCGGTTAGGCAAGGCCATCTGATTTTAAAGCCCATGCGGTTTGGTGATAGGCGCATGTCCTAAGAATATGTCACTAGATGGTTTCACTATGTGCAAGCATCACAGAGTACACTTAAACTGACATAACCGTAGTGTCACTAGGCAATATAACCTCACAGGGCCATCTTGTTGATGTGGTCAGTGGTTGACTAAAGTGTCACCATATAGCATATAACTGTGCTTGGATGGAGATGCACTCAATAGTCCAGGATATGTCCCCATGCTTAGTACAGTCCCTTCAGCTATGTGTGTCAGTTGGATATGATTTTCAAGTATCCCCCCAAAGGTTCATGTGCTACAAGTTTGTGCCTTTGAGGTACCCACAGCAAGATTGTTTGTCATAGGACTTTTTAGAGCTCACTCTCGAGACCAAGATTCTTGAGGAGTTTGAGTGTCCCTCGCATCCTCAATCAGGTTGATGTAGTGCTTCCAGGAACTGAGTTCATGCCCATAAGAGGGAGTTAGCAGAAAAGGGGCAGCCTGGGCCCCTGAGTGCCTCTGGATTCTTGTTTGCCATGTAACATCTCTCTCACACACATGGTGTCACCATGGTGTCTGCCACACTCTGATGTAACCCAAGAGGGGTTTCTGAAACAGTGAGTTAAGGTTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGCACCCAGCTTTGTTTTCAGTTGTAGAGATTGGAAACAAAGACACTTGAAGATATCTTATTTGCAAGGCGCCAGAGGATGGAGTTACGAACTTCTTGAAGCGTCCACTTTTCTTTTCTTACCACAGACCTCATTGTGGCCATCTGCTTTAAGTAGCTACTACTAAGCAACACATTATCCCCAAAAATTTGCTGCTTAATCACACCAGCTTTATGATTTTAGAAAGTCTTTGAGGGGTACATGTACATGAACCCAGTGTTAACCAGTTTTTCAATGCTGTAACAATGCGTGATTGATAATTAACTGACAAGAGAAGTATGTTGTCTGGTGGTTGCAGCTCATAGCCAGCTGTCTCGGTGACAGTGGGGCCTGTGGTAAGGCAGTGGATTGTGGTAGGGAATTTCCTCAGGGTGGATGCAAAAGAGAAGGAAGGGGGAAGTGCGCTTTCTCCTCGGTTCTCCCACAGGGTCCCCCCTCATAATGTCACCACTGTAGAGAACAGACCTGCAACCACAGGCTTTAGAGGGTCATGCTCAACTGCAGCAACCCCAAAGGTCTGGTTTGCTGGCTATGATTTTGGACTTTTGCAGGGTGTTACAGCGTAGAGAGTCACATGAGCACGGAACGCTGCGTGCCCTGGAATCCAGAGGGCTGTTTCTTTTGCACAATCTCTTCTGCTGTCCATCAAAGCTCCAGTGTGGCAGGGCCCCACCCCCAGTGGCTTGCTGTCTCTGCCAAGCCTGCATCCAGCCACCGCGCCAACGGATGCCTTGATGGGGAGAGTCTGTATAAACAGCGCTGGCTCAACTCTCCCAGCCTTATCTCTGGTTTATTCTTCCCTTCCTGCACAG
Seq C2 exon
AAAAGGTTCATGAAGAAATTGAAAGGGTCATTGGCTGTGACCGTGCACCTTCCCTCACGGACAAGGCCCAGATGCCATACACAGAGGCCACCATCATGGAGGTGCAGCGGCTGTCCATGGTGGTGCCGCTCGCCATTCCTCACATGACCTCGGAGAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027983-Cyp2u1:NM_027816:2
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=PD(5.1=9.9),PF0006717=p450=FE(58.4=100)

							
A:
NA

							
C2:
PF0006717=p450=FE(34.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101944





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000087717
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:107945606-107947375 
ALTERNATIVE
HsaINT0044332
(CYP2U1)
Human
(hg19)
chr4:108866762-108868531 
ALTERNATIVE
HsaINT0044332
(CYP2U1)
Rat
(rn6)
chr2:236420766-236425992 
ALTERNATIVE
RnoINT0044430
(Cyp2u1)
Cow
(bosTau6)
chr6:18517509-18519266 
ALTERNATIVE
BtaINT0046218
(CYP2U1)
Chicken
(galGal4)
chr4:37412405-37415201 
ALTERNATIVE
GgaINT1010916
(CYP2U1)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr1:49283194-49285724 
ALTERNATIVE
DreINT0054290
(cyp2u1)
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"