Special

MmuEX0031224 @ mm10

Exon Skipping

Gene
ENSMUSG00000022678 | Nde1
Description
nudE neurodevelopment protein 1 [Source:MGI Symbol;Acc:MGI:1914453]
Coordinates
chr16:14175291-14185873:+
Coord C1 exon
chr16:14175291-14175439
Coord A exon
chr16:14183476-14183612
Coord C2 exon
chr16:14185694-14185873
Length
137 bp
Sequences
Splice sites
3' ss Seq
TGTGTGCTTCTTCTACCCAGAGC
3' ss Score
8.06
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
Exon sequences
Seq C1 exon
GAGAAGTTTGAGATGCAGCACTCAGAGGGTTACCGGCAGATCTCAGCCTTGGAGGATGACCTGGCGCAGACGAAAGCCATTAAAGACCAACTGCAGAAATACATTAGGGAACTGGAACAAGCCAATGATGACCTGGAAAGAGCCAAACG
Seq A exon
AGCCACAATCATGTCCCTGGAAGACTTTGAGCAGCGTTTGAATCAAGCCATTGAAAGAAATGCCTTCCTAGAGAGTGAGCTGGATGAGAAGGAGAATCTTCTAGAATCTGTGCAGAGGCTGAAGGATGAAGCCCGAG
Seq C2 exon
ATCTGCGGCAGGAATTGGCTGTGCAACAGAAGCAAGACAAGCCCCGGACACCCATGCCAGGCTCAGGGCAAGCCAAGAGGACAGACATGGCTGTGCAGGCCACAGGCTCTGTACCGTCTACTCCAGTAGCTCACCGAGGACCTAGCTCTGGTTTGAACACACCAGGAATGTTCAGACGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022678_MULTIEX1-4/5=2-5
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref, Alt. Stop)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.492 A=0.478 C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF088265=DMPK_coil=PD(1.8=2.0)

							
A:
PF079267=TPR_MLP1_2=PD(3.8=30.0),PF040127=PspA_IM30=PD(11.6=80.0),PF088265=DMPK_coil=PD(1.8=10.0),PF0017016=bZIP_1=PD(6.4=30.0)

							
C2:
PF057016=WEMBL=PD(10.4=32.8),PF048808=NUDE_C=FE(30.5=100)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000023359





     
                   









    
Main Skipping Isoform:
ENSMUST00000023359fB13468





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000111461, ENSMUSP00000112817, ENSMUSP00000119355
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr16:15687375-15687511 
ALTERNATIVE
HsaEX0042206
(NDE1)
Human
(hg19)
chr16:15781232-15781368 
HIGH PSI
HsaEX0042206
(NDE1)
Rat
(rn6)
chr10:878473-878609 
HIGH PSI
RnoEX0058756
(Nde1)
Cow
(bosTau6)
chr25:14209637-14209773 
HIGH PSI
BtaEX6108682
(NDE1)
Chicken
(galGal4)
chr14:7550589-7550725 
HIGH PSI
GgaEX1039136
(NDE1)
Chicken
(galGal3)
chr14:7616206-7616342 
HIGH PSI
GgaEX1039136
(NDE1_CHICK)
Zebrafish
(danRer10)
chr3:36538413-36538549 
HIGH PSI
DreEX0049750
(nde1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGAGGGTTACCGGCAGATCTC

				
R: 
TAGACGGTACAGAGCCTGTGG

				
Band lengths: 
246-383

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • 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"