Special

MmuINT0106854 @ mm9

Intron Retention

Gene
ENSMUSG00000006471 | Ndor1
Description
NADPH dependent diflavin oxidoreductase 1 [Source:MGI Symbol;Acc:MGI:1926047]
Coordinates
chr2:25100339-25103574:-
Coord C1 exon
chr2:25103480-25103574
Coord A exon
chr2:25103375-25103479
Coord C2 exon
chr2:25100339-25103374
Length
105 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
TCTGAGGCCTGCCTTTCCAGCAA
3' ss Score
4.59
Exon sequences
Seq C1 exon
GAGCAGAAGGTATATGTGCAGCACCGGCTTCGAGAGCTGGGGCCACTTGTCTGGGAGCTGCTGGATGGCCAAGGTGCCTACTTCTACCTAGCAGG
Seq A exon
GTGAGCAAACTTGGGAATGTCGGGGGGTGGACCAGCCTTTAGGGAAGGGTAGTAGTAAGGGTTGGGAATCGGGATCACTGAGCTTTCTGAGGCCTGCCTTTCCAG
Seq C2 exon
CAATGCTAAATATTTGCCTACGGATGTTTCGGAAGCCCTTATGTCCATTTTTCAAGAAGAAGGACGACTCTCCACTGCAGATGCATCTGCCTACCTTGCTAGGCTCCAGCAGACACTGCGCTTCCAGACTGAAACCTGGGCCTGAGGAGCCACTTGCTAGCTCACACTCACATTAACAGCTGCATTGGGTAGCCTGCTGGAGTCTAGAAGGCCCATTGTTACCTCTTGCCTTCTAATCCCAGAACACTGGGTAGACCCACAGTTTCGCTTTTTTGGTCCAGCTGACCAGGAGGGCAGTCCTTGCGTACAGCCAAACTCAGTGGAACCCAGTGTCCCATACGTAGGCCCAGCCCCGGTGCAGCTAGAACTCCTGGTTTTCTCTCAGACCCCTTCATTCTGCCCCAAATCTGCATTTATAGTCCCTACCACCAAGGGCCTGCTAAGCCCTCCAAAGGACATAGAGCTGTGCGGGCTGCACTGCCCGTCTGACCCCGTGCTATTCCCATTAGTCCCATAACACCTGTGCAGCTCAGCTCAGTTGAAAAGCCACCAGGGACCAAGTCTCCTGAGCATTGGGAATGGGCAAATCTGTCTGTCTGCAGGTCCATAAACATGAGTTAACTGCCTGGGTAGCCGCTCACTTCTCTTTTATTGCTTCTAGATTTGAGAGTGGTGGTTGGGACATGGATTATCTGCATCTGCTAGTGGTGGGCAAAGAGCCCTCCAGGGCATGAGCACAGGCTTGTACTGACAGTTTAGCCAAGCTAGTCCCCTTCTCTGATGGCCACACAACTCAGCCAAGCTCATATACCCTTCTCTCATGGCCAAGCAGAGAGGGCTTAGAGAGCTATTTATTTGGAAGTCCCAGCCAAGAGCCAGCATGCACTATTCTTTCCAAAGAACTGAAAGAATGATCAGGTGGAGGGGGTGTGATTTGTGTTGGCCCGCCCATGGGCAGGGCCTCCACTGCTGGGAAGGAAACCCTGTTGGAGCAGTCAGACAGGTCCAAGGGCAGCTGGGCGCTAAGGAACCTCGGTTCTGTCTGTCAGCTTGTGGAAAACAGGGACCAGACCAACACCACTCTTAGGCCTCAGATACCAAGAGTTGACATGCTGCGGGGACCCAAGTGAAGCTTACTTCCAGTGAGGTCAGCAAGCCGAAAGGGTTATCTAGAGGTTAGTGCTCAGGTGGATGGGTGGAGGCCAAGCTCTGCCTGGCTCCTGAGGGCCACACCTTCATATCTACAACAATCCCTGCAGTCATCCTGGAGTCTCCGTCTACGCATCCTGACCTCTGTTCTAGTGGTAACCTGGGACCTAATGACACCAGCTCTGTGTCTACTAGTTCACCCGGTGCTTCTCTGGGTCCTGAGCTCTTGGACCCACTGTGCCAGCTACCAGCAGATGGAGAGGATGATCTCAGGGCCCCTCTGGGTGCCAGAACTCCAGACAGTAAACCGGAACTGGAGGCCAGAGACCCATCCGCTGCCAGGGCCCTGGAGTCAACTGTGGAAGAGCAGGAAGGTGAGGGGCAGGTTGTGGAGGAGGAGGAATGTCCCATCTGTGCTGAGCCTTATGGGCCTAGTGAGCACCACCTGACCCTGCTAAACTGTGGTCACAGCCTGTGTGTGGGCTGCCTACACCAGCTGTTAGGCATGACCCCCAGAGCTGACCTGGGCCGTGTGTGCTGTCCACTGTGTCGTCAGAAGACACCTATGCTAGAGTGGGAGATCTGTCAGCTGCAGGAGGAACTGCTTCGAGCTGATGGACCCCAGCGCCCAATGCGGACTGCATCCGTCACAGCCCTGCATCCTGGCCCTTGGCCCTGGGGTCCCTTAGAGCACCGCTACCAGCTGCGCTTCCTGGCAGGGCCTGTGGGAGGGCGAAGCTGTCTCCCCTTCCTGCCCTGCCCTCCCAGCCTAGGCACCTGGTTGTGGGCACTACGGGAACGTGGCCCCTGTGCCCGCCGCTTGTCACTGCTGAGCCTACTGGTCCTTGAACTGCTCGGGCTGGTGGTCATCTTCATGCCGCTCCTTTTACTAGGGGTGCTCTTCATGCTGCTAGACCGTTCCACCCACTAAGCAGAGCCCAGAATGCTGGCCAAGCTTTGAAGTCCATGCACGCTTGGATTCTGGTAATCAGCAAAGACTTGTTATCACCAATACCAAGACTATACATGCCTAAGAGCCTACGCCAGCCAGAGTGCTTACACACCCTTGCAGCCTAGATATTAGCTAAAGCCAAGGACACAAGGACAGCCTCTGAAGGAGCTTGGCCTGGCAGAAAGAGTTGTGAAAAGAACCCTATGTGCTTGCCATGGGCGGTCATCTCACTGGCCACAGGCAGAAGCTGGGCTATACCGCCAGCTCGTAGTCCAGCTGGTGAGAGTGGACACAAATGTGTGATTCCAACAGTGATTCTGTTTATCCTGAGATCTGTTCATTGGAGAAGGCAAGGGCTGCAGACTCTCACCTGCACCAGACAGAAGCTGGTGTGTGTCCTGAAGGCAACAGCAGCAGCCACAGTAACTACCAGGAGAGGCCTGCACTGCACAAGCCAGCCTTCAAAAGCTCCCACCCAACCTAAGCTACTCTCACCAGAGAAGGTAGCCCAGAGGAGCTGGGATCAATATTGCCTTTGTTTTGCAAGGGCCCATCCAGACCCTGAAGCCTCCAAATGCCCAAGGTCTAGCTCTGTTCCTAGTTGACTCTGCAATTCATGTCACTGGACCAGGAGCCCTCACTTGGGAGATGCAGACAAATCTAAGCTCACTTCATGGCTCATTGGTGACACAATGTAAGGTGTAACATTTCAGGCTGAGTCCTATATAACAAGCATAAGAAAGGCTCTCAGACCAGGCAGTGGTGGCGCACACCTTTGATCGCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCCAGGCCAGCCTGGTCTACAGAGCGAGTTCCAGGAGGACAGCCAGGGCTACACAGAGACACCCTGTCTCCCAAAAAAAAAAAAAAGTTCTCAATAAACAGTTGTTACTGATTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006471-Ndor1:NM_001082476:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0017516=NAD_binding_1=WD(100=53.3)

							
A:
NA

							
C2:
PF0017516=NAD_binding_1=PD(10.3=22.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109989





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000006640, ENSMUSP00000097903
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:137216189-137216271 
ALTERNATIVE
HsaINT0111729
(NDOR1)
Human
(hg19)
chr9:140110641-140110723 
ALTERNATIVE
HsaINT0111729
(NDOR1)
Rat
(rn6)
chr3:2467320-2467423 
LOW PSI
RnoINT0099541
(Ndor1)
Cow
(bosTau6)
chr11:105884458-105884540 
LOW PSI
BtaINT0100313
(NDOR1)
Chicken
(galGal4)
chr17:967934-967997 
Chicken
(galGal3)
chr17:1356528-1359639 
ALTERNATIVE
GgaINT0126439
(NDOR1)
Zebrafish
(danRer10)
chr5:31898105-31898237 
LOW PSI
DreINT0103032
(ndor1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GATGGCCAAGGTGCCTACTTC

				
R: 
CCTTCTAGACTCCAGCAGGCT

				
Band lengths: 
243-348

			

		

	





	
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"