Special

MmuINT0045430 @ mm9

Intron Retention

Gene
ENSMUSG00000061126 | Cyp4f39
Description
cytochrome P450, family 4, subfamily f, polypeptide 39 [Source:MGI Symbol;Acc:MGI:2445210]
Coordinates
chr17:32623891-32626698:+
Coord C1 exon
chr17:32623891-32624020
Coord A exon
chr17:32624021-32626564
Coord C2 exon
chr17:32626565-32626698
Length
2544 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CACAGTTCCTTTCTCTTCAGGGA
3' ss Score
8.91
Exon sequences
Seq C1 exon
GTCATGACACAACATCTAGTGGGCTGTCCTGGGCACTGTTCAACCTGGCAAAGTATCCAGAGTACCAGGAGAAGTGCCGGGAGGAGATCCAAGAAGTCATGAAAGGCAGAGAGCTGGAAGAGCTGGACTG
Seq A exon
GTAAGTTTGGAGGGTCAGGAGGATGGAAGGGAGGAAAATGAGTCTTGGGTGTGAATCTCTGAGCTGCCACTTTCTGATTGTGTGGTCTTAGACAAGTCCCTGCAGCTTTCTGAGTTCCAACTCATATTGGGATGATTGCGATGCCTGACCCTGGTTCAGCAGTTTCCAGGACAACTTCAGCAGCAGCTGTTGCTGCCCCACCACAGAACATATAGCCCTCAAATTCAGTGGCTTGGGGCAAGCATTTAGTTGCAGCTTTGACCTACACAAGATTTCCATGGCTACTGGGCTTCGTTGAATGGAGTGAGGCTGCTTCCAAATTGTTGGCTGGGTTCAGGTCTTCTCCAAGTGCCTCCTAACTCTCCTAGGATCTGGGGCTACTCTGGGGCGTGTTCTTGTCAATGCAGATTCCAGAAGTGTCAAAAAAGTTCTATGTGCACTGAAACATTGTGGAGGAGGCAAGTCACATGATGAAGCTCAGTATGCGTGGGGCAGCGAAGGCCTGTAAATAGTGCCTTTGGACACATCACCCTTTGGGATGGAATGGCATGCCATGTGATTGTGATGCAGAGAGGAAGTGCAGAATAGAGAGCAGGAAGATAGTCTTAAGATGTAAGTTGACTCTGAGTGGTACAGAGAGCCCAGCACTGAAGCCAGGCATGGTGGCACACCTGACATTCCAGCTTTTAAAAGGATGAAGCAGGAGGATCAGGAGTTCAAGGCCAGCCTAGTCTACATATTAAAACTGAGGCAAGCCTTGGCTAATTGAATCACTTTCAAAAAAAAAAAAAAAAGAGTTTGGGAGATGTCCCATTGGTAAAATGCTTGTCTTGCAAACGTGAACGAAAATCCATGCTAAAAGAAAAGCTGGTGTCTTAGTCAGTGTTCTGTTGCTGTAAAGAGACACCATAACCATGGCAGCTCTTATAAAATTTAATTGGGGCTGGCTTACAGTTTCAGAGGTTTAGTTCATTTCCATCACGATGGGAAGCATGGCAGTGTGCAGGCCGACGTGGTGCTGGAGAAGGAGTTTAAGAGTTGTGCACTTAGATCTATAGGCAGCAGGAAGAGAGAGACATTGCCCTGCTTTGGGCCCTTGAAATCTCAAAGCCCATCCTCAGTGACACACTTCCTGTGATAAGGTCACACATCCTAATTATTTCAAATATATGAGCTGATAGCGCCTATTATTCAAAACACCACAGCTGGATATGGTGTCAAACTCTTGTCGTCCCAATTCTGGGGAGGTAGAGACAGGTGGACCCCTGGGCTCCCTAGAAGTCTAGGGGCTTCTTGGCCAACGAGAGACCTTGTCCAAATATAAACAAATAAAGTAGATGGTGCATGGTGCCTGAGAAATGACATTGGAAGTCCTCTGGCTTCCAAGGTATTCACACATGACATGTGGATAAATACCTAAGTGTATACATGAACCCACACATTCTGTGTACACCTTCAGGAAGACTGTCAGTTGGGTACCACAGTACCCTAAACATCCTGTCACTTTTGCCTTTATAACAAAGGGAGACAGCAGAGGGTCTGACTAGGAAGTCCAGCAGCAGATGATGCCTGCCAGGATCTAAGTGCTCTTTTGTTTTCTTGGTCGTGTTTATTTATATCTATTGGTATCTGTATGACAAGGGTTTCTTTGGCTCTTTATAACAGGAACACAAAGCTTCTGTCAGGGCTGGAGAGGGGCATAGTGGTTAAAGATGCCTGCTACTCTTCCAGGGCTCCCAAAGTCCAACCCTAGCACCCACACTGGGCAGCCAGATCACCATTGCTTGTAACTCCAGCTCCAGGGATCTGATGCCCTTTTCTGGCATCTACAGGCACCTGCATATGTGTGAGAAGCCCCAAACCAACCTGCTAGAGCTAGGTGCGGTGATGCACAACTGTAATACCAGTATCCTGGAGGTTGAGGCAGGAGGGGTGCTACAAGATAGAGACTAGCTTGGTCTACATAGTGAAAACTTGACTCAAAACAACACACACACACACACACACACACACACACACACACACACAGTGTCTTGATCTTAAAAAAATGAACTAGACCATAAACTAATAGTTATAATTAGTTTAATCTGAGCTCCCAAGTATAATAAACTATTCTGAAATCTGCAATAAAGCATTTTAAAATAAATACAACAAATGAAATCTGGAAAGAATGCATACAAACTAGTAACTTGCTGTGACTTTGAGGTTCCCAGCTGCCCTCACATCTCCCATGATTATACAACAATTCATCAATGGTAGGTTAGTCTGGGGCCCAGTGGCAGCCCCAGCAACCAGGACCATTGCTTTCTGTTTTCATTTGTCATTATTGTGATTGGTGGATGGACAGATAGTTTTTTCTGAACCTAGGACCTCATGAATATCAACCAATTGGACTGTCACTGAGCTATATTCCCAGTCACCTCTTCCTTTTTTTGTTTCAATTGATTGATTGATTGATTGTGTGTGTGTGAGCATGTGAGTGTGCGTATGTGGGTACCTGCATATGTGCATGTGTTCAGGGAGTCACAGTTCCTTTCTCTTCAG
Seq C2 exon
GGATGACCTCACTCAGTTGCCCTTCACCACCATGTGTATCAAGGAGAGCCTTCGCCAGTTCCCACCTGTGACCCTCATCTCTCGTCGCTGCACAGAGGACATCAAGCTGCCAGATGGACGTGTCATCCCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061126-Cyp4f39:NM_177307:10
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(9.2=100)

							
A:
NA

							
C2:
PF0006717=p450=FE(9.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000003413





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:15544280-15548107 
ALTERNATIVE
HsaINT0044489
(CYP4F22)
Human
(hg19)
chr19:15655091-15658918 
ALTERNATIVE
HsaINT0044489
(CYP4F22)
Rat
(rn6)
chr7:14505743-14510611 
LOW PSI
RnoINT0044588
(Cyp4f39)
Cow
(bosTau6)
chr7:8632425-8633959 
LOW PSI
BtaINT0046306
(CYP4F22)
Chicken
(galGal4)
chr8:20777885-20778166 
ALTERNATIVE
GgaINT0039282
([1])
Chicken
(galGal3)
chr8:22599896-22600177 
ALTERNATIVE
GgaINT0039282
(E1C120_CHICK)
Zebrafish
(danRer10)
chr12:48572202-48572371 
ALTERNATIVE
DreINT0054404
(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
  • 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"