Special

MmuINT0045470 @ mm9

Intron Retention

Gene
ENSMUSG00000047155 | Cyp4x1
Description
cytochrome P450, family 4, subfamily x, polypeptide 1 [Source:MGI Symbol;Acc:MGI:1932403]
Coordinates
chr4:114794462-114797073:-
Coord C1 exon
chr4:114796946-114797073
Coord A exon
chr4:114794590-114796945
Coord C2 exon
chr4:114794462-114794589
Length
2356 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
ATCTTGGCCTCCTCTGGCAGGAT
3' ss Score
7.76
Exon sequences
Seq C1 exon
GACGAGGACTCCTGAATTTAGATGGGCCCAGGTGGTTCCAACACCGCTGCCTCCTAACTCCTGCATTCCATCAGGACATCCTAAAACCATGTGTGGACACGATGGCCCACTCTGTGAAAGTGATGCTG
Seq A exon
GTAAGTGAAACACTATATTAGTTTATATAGTGGATTGGGAAAAATCAAAGCTGATTTCTAGAAACTAATCAGAATGCAAGTACCCAGTGAGTAAGGATGTCTAGGTAAACCTTTCCTGAATTCTTCAGGTGATTAAAACACAAGAGCTGGTCCTCTGACTTAGAGTCTAACACTCTGTGGTGGTAAGACTTACATATTAGGCACTGTGGGAGACAGGTAAGGAAGCCACGTGCAGCTAACTGGTTTCAAATTTCAGATTTACCACAAATAAATGCTGGTTGCAGAACAAGAAAACCATAGGCAGAGTGATGTGAGAAAAGGTTTGAGGCTGAAATGGACTTGGCTGATGGGTATGAAGGACTGGGCAAGGAGTGAGTGCCTCTCACAAGTGGTGGAAGATCTTTAAGGGAGTAGCACCTTCCAAAGGGGCAGGGCATTGCCCTGAGGGGCACCCCTATTACATGGCTTTCTGGTTTAGAGATGAGTTTTACCAAAAGCTCTATTGACATAGAGGTTTCACTTTTTTAATGTTAAAAGTAGACAACCAATTAATACAGTTTCTTCATAAACTTCAAATACCACAAAGCCAAATTTCCCTCCTTATCTGCAAGCCCATACTCTGTTCCCAGGAAACAGCTGTTACAGGCTTGTGGCTGGGCCAAACTTCTGCAGGAATGGAGCAGGACATCAATGGGAAGGAGTTCTCAAGGCAGAGACTGGGAGAGCACCAGGATCAAGAAAGCAGGCCGGGTTACTGGGAGCAGGGGGAGGATAGCATCTTCCTTAGCGCTGCTCAGTGTTTGGAACAATTCAGTTACACCAGTGACCATTTCATCCCCTTGTTTCTGCCCTCTGCACTTGTCAGGCCCTTGTTTCCCTGCTCACATCCTTCCTCCTTCTGCTGAATGCTTCCAGGGCACCACAAGCTCATTTCTTCCAAACCTAGCACATGGGCTCATCAGCTCTTCTCAAATGCCTGAATTCTATTAATAGGTAAAACGAATATATATTCATAAAAAAGCTTGATCCTTTACAAAGGTTAACCCCTCTAGCTATCGGCCTTCTGGCCAAATAATAGACACTTCAGTGAAAGGCTTTCAAATTCTACTTTGCAATCAGTCTCCAAGCTTTCAGTACATAATTTGTCACCTGTCGGTACTCGACATTCAGCACCTAGGCTGACACCTATAGTTGCTCCACAAACATAGATTGAACTAAATTTAAACATTTCCATTCATTCACATTTTTATACAAAAAGTGTTTGTTGTGACAAATACATTTATAACTGGAGGATGGGCACTTTGGGCAGTTTAGCAGTTAGACCACACACTTCAGGCTGTGTGAATAGGCCTCTTTCTGTGGGAAAGTAAGAGCTAGCTCCCTGTAGCAACTCCTTTTCCAGGTCTTTTTCTGTTCCCAATGATTGACTCAGAATTATTTTTATTGTTTTTATTTGCAATTTTTAAGTGAAATATAATTATAGCATCCCCTCTTCCTTCTTCTCCCATCAACTCCTTTTGTGTTATCATCCCCTGTTTCCTCTCAAGTCTGTTATCTTTTTCTTTAATAATTATTGTTCCATGTATATATAAATATACAAATATGAATACAACCATTTAGTGTTGCTTGTATGTATGTATTTTCAGAGCTGATCATTTGGTATTGAATGACCATTTAGGGGGCTCATTCCTGGGGGAGACTTATTGGCCCTGTCACATGTTATATGAAATTACTACTTGTATATATATACTAATATATATATGTATGTATGTATGTGTGTGTATATATATATATATATATATATATATATATATATATCAAGGGGCATTTAAGATTGCAAAATATACATTGCATGTAGCTTTCTTGTGCAGTAATTTCAGTCATTACTTGCCTGTAGCTCCTCATCTAAAATTGGGGCCTCAGACATCTCCTTCCACGTTAGCATGTCTATTGGTGTTGTCCATAGCTGAATGTAAGATGATCTGAGATGTGGTGTGATGGTTGAGAGGTGTGATGGGGTACCTAGCAGGTTGGAGGTTGAAGGTAGAGGAAGCCCTGGGGTTTCCACGTTGCAGTCTCACTTAGATGGTGTGTGGAACTCTGTACCATTTGTTGCAGAGCTGAGACAGTTGTTGAAAGACCATTTGCCAGACGTGAAGTGCGAGTCATGCTCCTTCTCACTGGCCTAGCGTGTGCTTCCTTTCCTTGTGCCCAGAATAAACACATGGGTGATTTACTCCTGGCCTTCAGTTCCTGTCAGGTTGGGGGTTTTGTCCCTGAGACAATAAGGGAAAAAGCAGTCAAGTTAAGGCCATTTGATGATGGTGATGATATTGATCTTGGCCTCCTCTGGCAG
Seq C2 exon
GATAAATGGGAGAAGATGTGGACCACTCAGGAAACAACCATCGAGGTTTTTGAACACATCAACTTGATGACCCTGGACATAATAATGAAATGTGCTTTTGGCCAGGAGACCAACTGCCAGATAAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047155-Cyp4x1:NM_001003947:4
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(13.5=100)

							
A:
NA

							
C2:
PF0006717=p450=FE(13.5=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000059545





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000059545f4610A, ENSMUSP00000102155
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:47033369-47035805 
ALTERNATIVE
HsaINT0044549
(CYP4X1)
Human
(hg19)
chr1:47499041-47501477 
ALTERNATIVE
HsaINT0044549
(CYP4X1)
Rat
(rn6)
chr5:133942447-133944001 
ALTERNATIVE
RnoINT0044641
(Cyp4x1)
Cow
(bosTau6)
chr3:99687619-99690534 
BtaINT0046333
(CYP4X1)
Chicken
(galGal4)
chr8:20775435-20776142 
ALTERNATIVE
GgaINT1002648
([1])
Chicken
(galGal3)
chr8:22596335-22596339 
GgaINT0039931
([2])
Zebrafish
(danRer10)
chr16:4805256-4807143 
LOW PSI
DreINT0054420
(cyp4t8)
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"