Special

MmuEX0011368 @ mm9

Exon Skipping

Gene
ENSMUSG00000035594 | Chrna5
Description
cholinergic receptor, nicotinic, alpha polypeptide 5 [Source:MGI Symbol;Acc:MGI:87889]
Coordinates
chr9:54848259-54852966:+
Coord C1 exon
chr9:54848259-54848303
Coord A exon
chr9:54850207-54850316
Coord C2 exon
chr9:54852138-54852966
Length
110 bp
Sequences
Splice sites
3' ss Seq
GTGACTTTCTCATTTTAAAGGAA
3' ss Score
8.92
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
Exon sequences
Seq C1 exon
GATGAGAAAAACCAGCTAATGACCACCAACGTCTGGTTGAAGCAG
Seq A exon
GAATGGATAGATGTAAAGTTAAGATGGAATCCTGATGACTATGGTGGAATAAAAATTATACGTGTTCCTTCAGACTCTCTGTGGATCCCAGACATCGTTTTGTTTGATAA
Seq C2 exon
TGCAGACGGACGTTTCGAAGGGGCCAGTACGAAAACAGTTGTCAGGTACAATGGCACTGTCACTTGGACGCAGCCAGCAAACTACAAAAGTTCTTGCACTATAGATGTGACCTTTTTCCCATTTGATCTCCAAAATTGCTCCATGAAATTCGGCTCATGGACGTATGATGGATCCCAGGTCGATATAATCCTAGAGGACCAAGATGTCGACAGAACAGACTTTTTTGACAATGGAGAATGGGAAATCATGAGCGCAATGGGGAGCAAGGGGAACCGGACGGACAGCTGCTGCTGGTACCCCTGCATCACCTACTCCTTCGTGATCAAACGGCTGCCTCTCTTCTACACCCTGTTTCTTATCATACCCTGCATCGGGCTCTCGTTTCTGACTGTGGTTGTCTTCTATCTCCCTTCAAACGAAGGTGAAAAGATTAGCCTGTGCACTTCCGTGCTGGTCTCTCTGACTGTCTTCCTGCTGGTGATTGAGGAAATTATACCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035594-'3-5,'3-4,4-5
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
ORF disruption upon sequence exclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=0.000 C2=0.022
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0293118=Neur_chan_LBD=FE(6.9=100)

							
A:
PF0293118=Neur_chan_LBD=FE(17.6=100)

							
C2:
PF0293118=Neur_chan_LBD=PD(54.9=40.4),PF0293211=Neur_chan_memb=WD(100=47.7),PF0293211=Neur_chan_memb=PU(54.2=14.1)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000082923





     
                   









    
Main Skipping Isoform:
ENSMUSP00000091364





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000091365
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:78588314-78588423 
ALTERNATIVE
HsaEX0015311
(CHRNA5)
Human
(hg19)
chr15:78880656-78880765 
HIGH PSI
HsaEX0015311
(CHRNA5)
Rat
(rn6)
chr8:59584571-59584680 
ALTERNATIVE
RnoEX0021206
(Chrna5)
Cow
(bosTau6)
chr21:31489738-31489847 
BtaEX6077431
(CHRNA5)
Chicken
(galGal4)
chr10:3133984-3134093 
HIGH PSI
GgaEX6007416
(CHRNA5)
Chicken
(galGal3)
chr10:4575614-4575723 
HIGH PSI
GgaEX6007416
(F1NIT6_CHICK)
Zebrafish
(danRer10)
chr18:40503604-40503713 
HIGH PSI
DreEX6066459
(chrna5)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCAGCTAATGACCACCAACGT

				
R: 
TCTGTCGACATCTTGGTCCTCT

				
Band lengths: 
248-358

			

		

	





	
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
  • 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"