Special

MmuINT0109920 @ mm9

Intron Retention

Gene
ENSMUSG00000036805 | Noxa1
Description
NADPH oxidase activator 1 [Source:MGI Symbol;Acc:MGI:2449980]
Coordinates
chr2:24948062-24950725:-
Coord C1 exon
chr2:24950268-24950725
Coord A exon
chr2:24948145-24950267
Coord C2 exon
chr2:24948062-24948144
Length
2123 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
ACACACATTTTTGTCCCTAGGCA
3' ss Score
10.13
Exon sequences
Seq C1 exon
GGCTATGTGATCATAGACCCTCTCCTCAGTGCTAGGGACTTGTTTAAGTAGTTCTAGGCGGGGCGTGAGAGAGGGGCCTAAGCCTTGGGCCATCTACTCAGTTTCAAGGACCGACTGTCACAACTCCAGTTGTCTTGCTACCAGCTGCTTCTCATTGCTGTCCCGGTCCCCTTGGCCCTGGCCTACGGCCTCCCAGCTTCTGTGGGGCACCCTCCTCCTGTCCCACGCGCTCCAGCTAGAATCGCTAACTTCCTTCGCCTCAAAGCAGGCGTCCCCGCTCCATGAGCTCTCTAGGGGATCAGATACGGGACTGGCACCGGGGTGTGCTGGCCGTGGCACGCGAAGACTGGGACTCTGCGCTGTGCTTCTTCTCAGATGTCCGAGAGCCGCTGGCTAGGATGTACTTTAACAGGGGCTGTGTGCATCTGATGGCAGGGGATCCCGAGGCTGCGCTGCGG
Seq A exon
GTAAGCACCCCAGGACTGGATAACAGATTCCCCTCTCACATCCCTGGTGGAGGCTTTAGGGGAATGCAGATGAAGATGTGACTGCGAACATAAAACCTTATCTTCCAATGGGCATCCTGGAAAAAGACGCTCTTCCGCACCTTATAGTCAACATAGAAGAAGGGGAGGAATCCCTGCCCTTTACCCTGTCATTTACGTAGAGATTGTTCAACTAATGTCCTCTCTTAGTGCCTGCCTGAGGCAGGTTGGAGCTTTGTGGTTAGAAGACCCCTCTTTTTGTTGAGACCAGAATGGGAAGCAGGGCGCCTTCAGTCTCTATAGCCATATAAGCCAAATGCGGCAACTGTACCAGACCTGGCCTGCCCAGGCTCTCTGGTGCTCAGGACTGAGGAAGGAGCATACCCGAAGGCAGGCTGGTGGCTGGGTCAGAGCAGTCAGGGGCTCTGCACGTCCTCTGATAGTGTGCATTTCAGCAGATGCTTGTGATGGGATGGTGGCACACAGTCTGTCATTCCGGTTCTGAGTGAGCACTCACATGAATCTCCACCTGCTTCTCAAAGCAGACCTACTCAGGGGAGCACACTGTAGAGTGAGCATCAGGGCATCCCCCCTTCATGTTCACCATTCCTGGGTGTATGATAGAAGCCCTCAGCACTCTGCCTACAACGCAGACCTACCTGGACACCACAGATGGAAAGCAAAGACACCCAAGACCAAGGGTGAGAGCAGAAACCTGGGCTGTGTGGAGATGGTCTCTTTATTATTTCTTTCTGGAAGCCTTAATTATTTATTTATTTACATGTGTGTATAAATCAGGAGGAAACTTGTGGGAGTCAGTTTTCTCTTTCCCATGTGGAACCTAGTGATCAAACGCAGGTCATTAGGCATGGTGGCAAGTATCCTTACCCACTGAGCCATCTTGCCAGCTCTCTTCTATTACGTCTTACATATTTATCTGTACCTATTGTTTCTTCATTAGAAGGGTTTTGTTTGAGCCACGAATAGTGATGCCTGCCTTTAATCCCTCTGGAGACAGAGGTAGGCTCTGCACATCTGAAGTTTGAAGCCAACAGAGGCAAACAGGTCTCTGAGTTTGAGGCTAGCCTAGTCTACAAAGTGAGTTCCAGGAAAGTTCCAGTTCCAGGGCTACACAGAGAAATTCAGTCTTAAAAACCAAAACCAAGCCAAACCAAAAAACAAAAAGGTTATTGTTCAGGAAAGGGAACGTAATGATCTGTTACCAGCTGGTTCAACAGTGAGTAAGTCCCACGCTCCCCTCCTCACACTGTAACTAGAGAGTTTGAAATGCTCTATCATAAGAAGAAGAAGAGGCACTGCCTTGAGTCAATAAAACTTACTTGTGTACAAGCACAGGCACACTGGCCAGACCTGGAAACGTTGAGAAGTGGGTGGTATAACTGACTGCAATAAGGAAATCTAAGTGTACAGGTCTCACGAGGTTGCACTTGAACGTGTCGGTGTGAAGCTGTAGTGTTGGATGGATCTGTGAGCAGCCATGCCATTTCCTGGACATGAGAAAGCTTCAAAGTCAGACCCAGCTCACAGTCAGCCCTCGCCTGGCCAGGCAAGGTGGTAGGAAACCGCAGCAGGTGCCTGTGTACAGAAGACTTCTGTGTTCTGATTCTAATCCACACACTTGTGTGCCGTTTCGTGGGAACTACCAAAGGAGATTTAAAAACAGTTATTAATGGATTTTATGTATGTGAGTTCTTCCATTACAGATGGTTCTGAAACACCATGAGCTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGCCCTCTCTAGCTCCTGCAAAGAGATTTTTTAAAGTCCAAAATTTACACAGTCCTGTCTCCCAGAGATGACTTTTATTGATACTGGGGGGCGTTTTCTTCTAGCTCTGTGCTCCTTGTGGAAGAATTGGGTTTCTATGCCATGGGGCTGTGCCCTGAGTCTGTTGTGAGGTGCTTGGGGCAGCTGAGAAATCTATGCAGTAACACACTTTCCAGGCTTTAACTGGACAGTGGTCCTCAGCTGTTGATACATTTCCATGTATGTTTGTGGCTTTGGGTTCCTCAGTTACTGAGTTTAGTGTTCCACACACATTTTTGTCCCTAG
Seq C2 exon
GCATTTGACCAAGCAGTGACTAAGGACACCTGCATGGCTGTTGGCTTCCTCCAGCGGGGAGTGGCCAATTTCCAGCTGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036805-Noxa1:NM_001163626:1
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=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF134141=TPR_11=PU(35.7=42.4)

							
A:
NA

							
C2:
PF134141=TPR_11=FE(38.6=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037423





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000110014
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:137423707-137426247 
ALTERNATIVE
HsaINT0115003
(NOXA1)
Human
(hg19)
chr9:140318159-140320699 
ALTERNATIVE
HsaINT0115003
(NOXA1)
Rat
(rn6)
chr3:2306876-2309002 
ALTERNATIVE
RnoINT0102394
(Noxa1)
Cow
(bosTau6)
chr11:105709256-105711109 
ALTERNATIVE
BtaINT0103030
(NOXA1)
Chicken
(galGal4)
chr17:902848-904092 
LOW PSI
GgaINT0125101
(noxa1)
Chicken
(galGal3)
chr17:1294387-1295631 
LOW PSI
GgaINT0125101
(NOXA1)
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"