Special

MmuINT0130056 @ mm9

Intron Retention

Gene
ENSMUSG00000060224 | Pyroxd2
Description
pyridine nucleotide-disulphide oxidoreductase domain 2 [Source:MGI Symbol;Acc:MGI:1921830]
Coordinates
chr19:42823874-42827265:-
Coord C1 exon
chr19:42826827-42827265
Coord A exon
chr19:42823894-42826826
Coord C2 exon
chr19:42823874-42823893
Length
2933 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TCTTTCTTGTCTCGTTGCAGGAC
3' ss Score
12.05
Exon sequences
Seq C1 exon
TAGCCCACTACCGGGCCTGGGAGAACCTAGTTAAATTGTTCTCTCTTTGGTCCCTACTCGCTTGACTCCTGGAGGCTACTCAGACTCTGCCACCTACTCGCTTGACTCCTCGAAGCTACTCAGACTCTGCCAGTTCTTAGCCTACATGCCCCCTCCTCTAGGCTGGCTTGCGCAAACTCAGAGCCGCAGAAGCTCGGACCCTGGGAAACGGTGGCCCAAGGCCAAGGCTGACACTGAACTGTAACTCCCAGCCCCTCCCCTTGCCTGGGCCTCTGGAAAGCTGACTGTGCAAGCAAATTGCTGGGGGCAGAAATGGCTGCCGGCGGCCGAGGTCTCATCAGGGCCTTGCACTCCTCTCCCTGCCCTACTTGGAAACGAGCTCAGTCGGGAGCCAACGGGCGCCTGAAGCCCGAGTACGATGCCGTGGTGATAGGAGCAG
Seq A exon
GTAAAACCAAAGAGGGCAGAGCCAGAGCTCAGGGAAGGAAGGCAGCGTTCTGCCCACCGGCCTTGGAGGGGCCTCCAAGGAGCCTTGCTGCTGCCTCTCCTATGGGCACGACCTGGCCGGGAGTTCCAGTGAGCAGGACCTGGGATGGAAGTCCTCCCTGGCCTGGGAATCAGGATCCCTGGGTTCTAATTCCACCCTGGTGTGCTGTGTGGACTAGAACGGCTCTTGCCTTCTGGGTTTAAACCTTTCTCTCTAGAATGATAATGAGTGACTAAATAAACGCAGGAGTTTCCCTGTATCTCCCGCAAAATGAGTGAGTTCCTCCCGGGACCTTATGCAGGAAGCAAAGACCTCCGGACTGTAGACAAATGAGAGCCAATCTCACTTCTGCGATCATCCATTGGAAAAGGAAGCCAGAGTTGTTTCATAAAGAGAAAAGGTGGTTGAGGGGTTCCCAGACACCCTAATGCATCCACAAAGGGTGTCATCTCCCATGGCTTCCCTCAGACATAGATACCTGCTACAGTGGTGGTCCTGCAACATCTTGCTGACTCTCAGCCTCAAGTACTAGGTTAAGGCATAGCCTAGGGCCAGGCTGCACTCCACACCAGGGCCTTCCGGGTCACACTTTTGGGACCTGAAGGCTTTTATTCCCAGCTGGGCTTTTACATAGATGATAGCAGGTTCACATTTTTTTGTGAGACGCATCACACAGCTTTAAATAAATGCTGGCCTGGTTTGGCTTCTTCTTGTGTCTACTGAGAACCACCCTCTCCAATTTGTGCACGCATGAGTGAGTGTTTATTATACACAGACTTGGTTTTTTTTATTATCGATACTAAAATAAAGATATGTCTCACACAGTTTTTACAAATCAAATATATGCAACTCTTGATTTAAATACCAAGTTGGTTTTTTTTTTCTTTTCCCATTGAAAACATCCACTCAACACTCCACTGTGTGAAGACGATGGCAGAAGGGCCCAGGCTCAGTGGGCTCCTGCTGGGTGGGCATCCCCCTGAGGGCTGGGGATTAGCAGATCCTGCAGCAGAAAGGGACAGGTCACCTGAAGCCACAGGAGAGTCAGTCAGGACTTGGGGACTGGACTTTGGGGGTTTTGTTCTTTGTCACTTAAAATCTCCTTGTCATTCATTCATGGCTGAACTGAGACCAGTTGCCAAGGAAACTTGACAAGTTTTCCAAGACTGATGAGCCACCAATGAAAAGCCGATAGCCACCACGTTTGATGCAGCCTTGCAGCGGGCTGAGTGTTTCTTAGACACTGCTAAGTCTCCTCCCTCAGTACCACAAGGTTCCACATTATATATGAATATGTATGTATATTATATATATATTACATGCATATTACTCTCTGCCTTACAAATGGAGAACTTCAAAGCAGCCACTGGTTGTTAGATGCCTCTCTGGGGGTCAAGCCAGGTGAAGCCTGGGCTGCCTGCCTTGAGTTTATGTCTATATTCAGAGAATGGTTCCTCCAACTGCGGGTTCACACCAAGGACAGGCCCAACGGCATTTTTTTTAACTCTCATGAAATTTTTCTAACATTTTAAAAATAAAACCACATCGAGTCTCCCAACCTGTGGGTTGTGACTCCTTTGAGGGTCGAATGACCCTTTCACAGGGGTCAGATATCAGCTATCCTGCATATCAGATATTTACATTATGATTCATAACAGCAAAATTACAGTTATAAAGTAGCAACAAAAATAATTTTACGGTTGTTCACCACAACACGAGGAGCTGCATTAGAGCCACGGCATTAGAAAGCCTGAGAGGCACTGCATGGCATAGGTCATCGCATAAACTTACCACAGGATGGGTTACTGTGAGAGCATGGAGCTTTGGTCCTGTGAAACATTTATTAGTCAGGTGAGTGCTAGGTCACGGTGTAAAGTACATTTATTCTTGTGAATAGTGAGCAAAGGGCTTGAAAACTCCAGTTTCGGAGACTCCGTTAATGGCTGAGAAGTTGGCTCAATGACCTCTAAAACTCGGGACGTCTCCATGTGGGAAATTTAAAACGAAAGCAACTCAGCCATGGAGAAATTCATCACAGGGGGGGTCACGGCTGCTCCCCTGCGTGTGGACATTTGTCAGATAAGAGTCAAGCATTTAGATCTGAGCCCACAGTGGGTTCGTCCAGGCGGGTGCTGCAAGATCACAGGCATCTATTGACATCTGAAAGATAAGAATGGCATCTGTCACCAACGTGAAAAATAACCAGGGGCCCCAACGCTGGCCAACACCCTCATGGCCTATTCTCTGCCTGTGAATGATTCTCCATCAACAGCTGACCTGTCTCCGTGGGCAGGGCACAGCCTGAGGCCTGTGCGCTCGGGGTAATTCTGATGCTGTTTGCACAGAAATCACTGGGAAATTGTAAGAGATCAGGTTCCAACACAACACCCGCAGCCTGCAGGAGGGAGCCTGTGTTGTTACTGGTGCACACCTTGAGGCTCTATGAGTTACTCGCTCCATTTTCTAAAATTCTGAACTATTCGTATGTCCTTGTTGGAGCACTGTGGACTGACAGAGACACTATTGTGCCTAGTTCGAGCCACCTTGGGTCAAACAAGCTATATGTGACAGCAGCTGTCCCCATGAGTGGCACTCAGCCCCTGCCCATACTTACCTTCGAAGCCTTCCCAGTCACGTAGACCCAGACCATGCCACTTGCACACTGGCTCTCTAAGATCAGAAGTCCAGGGACATCCCCCTGACCTGAAAGCAAGGAAGAGAGCTTCTTCCAAGCCGAGTCCAACAGACCCAGAGTGGCTTCCTGGTGCCCCGTGAGATGCTGAATCCAATGGAGGACAGAGGAGAAGATACCCGGGGCCTGGGGAAGAAATAAGGGGACTCAGCGCTTAAAGAGCATGTGTTTAGTAATACTTTTCTTTCTTGTCTCGTTGCAG
Seq C2 exon
GACACAATGGGCTGGTGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060224-Pyroxd2:NM_029011:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.047 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF134501=NAD_binding_8=PU(6.9=9.3)

							
A:
NA

							
C2:
PF134501=NAD_binding_8=FE(10.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000075825





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000075825f5152A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:98410959-98415008 
ALTERNATIVE
HsaINT1028623
(PYROXD2)
Human
(hg19)
chr10:100170716-100174765 
HsaINT0135638
(PYROXD2)
Rat
(rn6)
chr1:261983671-261986629 
LOW PSI
RnoINT0121125
(Pyroxd2)
Cow
(bosTau6)
chr26:19354968-19359201 
LOW PSI
BtaINT0120926
(PYROXD2)
Chicken
(galGal4)
chr6:21794813-21795082 
ALTERNATIVE
GgaINT0044273
(PYROXD2)
Chicken
(galGal3)
chr6:23674131-23674400 
ALTERNATIVE
GgaINT0044273
(PYROXD2)
Zebrafish
(danRer10)
No conservation detected
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"