Special

MmuINT0036225 @ mm9

Intron Retention

Gene
ENSMUSG00000032303 | Chrna3
Description
cholinergic receptor, nicotinic, alpha polypeptide 3 [Source:MGI Symbol;Acc:MGI:87887]
Coordinates
chr9:54859150-54863955:-
Coord C1 exon
chr9:54862944-54863955
Coord A exon
chr9:54860737-54862943
Coord C2 exon
chr9:54859150-54860736
Length
2207 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
TCTTATTTTTTGTTTTCCAGATT
3' ss Score
11.05
Exon sequences
Seq C1 exon
CGCCGATGGGGATTTCCAAGTGGATGACAAAACCAAAGCTCTACTCAAGTACACAGGAGAAGTGACTTGGATCCCTCCGGCCATCTTTAAGAGCTCATGCAAAATCGATGTGACCTACTTCCCGTTTGACTACCAAAACTGCACCATGAAGTTCGGCTCCTGGTCCTACGACAAGGCAAAGATCGACCTGGTCCTCATTGGCTCCTCCATGAACCTCAAGGACTATTGGGAAAGTGGCGAGTGGGCCATCATTAAAGCCCCGGGCTACAAACATGAAATCAAGTACAACTGCTGTGAGGAGATCTACCAAGACATCACGTACTCGCTATACATTCGCCGCCTGCCGCTGTTCTACACCATCAACCTCATCATTCCGTGCCTGCTCATCTCCTTCCTCACTGTGCTCGTCTTCTACCTGCCCTCCGACTGTGGGGAGAAGGTGACGCTCTGCATCTCCGTGCTCCTCTCCCTGACGGTCTTTCTCCTCGTGATCACCGAGACCATCCCTTCCACCTCACTGGTCATCCCCTTGATCGGGGAGTACCTCCTCTTCACTATGATTTTTGTCACCTTGTCCATCGTCATCACAGTCTTTGTGCTCAACGTGCACTACAGAACTCCGACCACACACACGATGCCCACTTGGGTCAAGGCTGTGTTTTTGAACCTTCTCCCCAGGGTCATGTTTATGACTAGGCCAACCAGCACCGAGGAAGACGCCCCAAAGACGAGGAACTTCTACGGTGCTGAGCTCTCAAACCTGAACTGCTTCAGCCGTGCAGACTCCAAAAGCTGCAAGGAAGGCTACCCCTGCCAAGATGGGACATGTGGCTATTGCCACCACCGTAGGGTAAAAATCTCAAATTTCAGTGCCAACCTCACAAGAAGCTCCAGTTCTGAGTCTGTTGATGCTGTGTTGTCCCTGTCTGCTCTGTCACCAGAAATCAAAGAAGCCATCCAAAGTGTGAAGTATATTGCTGAAAATATGAAAGCACAGAATGTAGCCAAAGAG
Seq A exon
GTAAATATGGTTTTTATTATGGCTTCCTTGTGCAGTGATGCATAGGGCAGAGGTTAGAAAATTAGACTCTTGTGGGGTGGGGCAGATTGCCCAGCAATTAAGGGGACTTGCTGCTCTTGGTAAGGATACAAACTTGGTTTCTAGCACCCACATCAGGTGGCCCACAATGCCCATAACTCTACTTCTGGGGAATCCAACACCCTCCTTTGGTCTCCTCAAATGAACACACACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTAGCCTTGAGTCAGAAGCTGTGTTCAGACCAGTTAGATGCCCTTGGGTAGATTAGTTACCTCACTTGTAGTCCAGGCTGGCCTTGAACTCACAATTATACTGTCTCAGCTTCCTCTGTAGTGGGATTCCAGGACTGTGTCATTGTATCTTGTCTCAGATTTACACAGGGATAAGGGTCATTTCTTAAATCAGCATTGATATTAAAAGTATTGACATCAAGGAGTCTGCTGAAGCAACCCTGAGACTGCACTGTCTTTACCCCCATTTTTCAGATGAGGACATTGATACCAAGGGAGATGAAATTTGCTCAGACTAGAAAGGAGCAGGGCTTGATTAAAACTAAAGTTTGTCACCTTTTTCTACAGGCTGTCTCCTATAGCCCAGGGGATGTTGTTATTTGTCCTATAGAGGGATGTGTAAGACTCAGGTTGTGGACCTGAGTGCTTATAGACACATCTCATGAATTCAAATAGAGTCACTATGTCAAACAGGGCATTAGGATTCTAACTTGGCCACAACTGTGACTTCATGGTGTCACCAAAAGGACACATTTACTCAAGCTTATAATGGTGAAATAAAAACCACATCTCCCAGGCCATTTCAGTGTGCTTAATTGAATCACAGAATTACACGCTGCTTCTTCATTATGTGATCATTGCTTCAGATCAGTTGACTCCTGGGCTCTCTCTCAGCGCAATTGTGGTTTCTTTGCTTTCTGAATTGTCTGGGAGTTTAATTACCATAGATTCTCCTTCCTGTGTCAAGCCTAAATTGAAGCTCATTATATACAATTATTCTTGCTCTTTCTTCCATCTTTGGCTGTACCATCAGCCATTATGTCTGCTGTTCAGCCTGTCTGGCTGTACAACTGAGGATGTCATTTGGTAAGGTGGGCAGTTTAAAGGGAAGTAGGGACGAAGAAAAATGTTAGGCTTGCCCGATGGGCTTATTTCACGTTTGGAACAGATGTTACACGGAAATTAGAATCTAAAACAAGCATTAGTACTTTGAAACAATGTTAAATGATGTTGAATTAAAGTCATCATTCTAACAAAGGCTCCAGATCTTCCTGTAGAGGTATATTAGCTTTAATAACTGGACTTCAATTTAGAGAAAAATAGATTTTACACACACACTTCTGAGTGGTGGTACATACTTGTAATCACAGCTCTCAGGAGGCTGCGACAGGGTGATGAACAATTTGAGCCCTACCTAAACTGTGTAGACATGAAGACCAGACCTTGCCTTGAAAGAAAAATGTGTTCTCATTAGAAACAGAGCTAACATAGCACATATTTTTCTCCTGTTTCTCCACTACATGAAACTTGAAGTTAGTAGATATATTAGTACTTTTCTTATTGCTGTGACCATTTGCCTGATAAGAAGCAACCTAAGGGAGGGTTTATTTGGACTTACTGCTCCAGGGAAAATGGTCCATCATGCAGTCATGGTGGCAGGAGTGTGAGGCAGCTGGTCACAGTGCACCCAAGGCCATGAAGCAGAGAGATGAAGGCCACCATTCAATTTACTCTTCAATCTGTACTCTTCTAGGACCCTAGCACAGGGAAGGATGCCGACCATGGTTAGGGTAGGTCTTTCCACCTTCATCAGTCTAATCTAGATAGTCCCTCATGGTCACCTCCAGAGGCAAACCTAATTAGATAATCTCCCCTGAGTACGCCCAGTGGCTTGTCTCCTAGGTGATTGTAGATCCTGTCAAGATGACAAATCTATGGTATTAACCATCACCATAGATTTCCTCAGATCATATCAATAAGTAAAAAATATTTCTTATATATTAAATAAAATGGATTCTTTACCTTATAAGACTTAATACTGAAAACTGACCCTTCTCCTTCATGTTCCATTTTCTCTTATTTTTTGTTTTCCAG
Seq C2 exon
ATTCAAGATGATTGGAAGTATGTTGCCATGGTGATTGATCGCATTTTTCTCTGGGTTTTCATCCTGGTGTGCATTTTAGGAACTGCAGGATTATTTCTGCAACCCTTGATGGCCAGAGATGACACATAAACTGTGACCTGTTCGCCAAGGCTCGCTCACCTGTGCTGATGCAAGGGCACTTTCTCAATAGCCCCACACTTTATCCGATCACTGCTTGGAGTTTGCTATTTCAAGGGTTATTTTCCACTCATCTTGATCTTTTTTTGTTGTTGTTGTTAAAAAGAAATGTGGGAGAAAAACATCTAGTTATTTACTAAGGATAAATGAACATTTCACTATCCCCATGATTGAAAACTAGATAGAAATTTTTTCTGTTCATAAATATTAAATCCATTAGCTCAGAATCTCTATAGAACTCATTTGTTCAGCCCATAAACTACTTGAAGTTATAAAGTATTCCAGCAGCACCCCATCACTTCCATTCTTTACTATTTTTTCAAAGGCTTCCACCTCAATTTTGTTGCTGCTAAACCCCACATATCATACCCTGAGATGTGACGCCTGGTCTCACACTCATTGTTAGTAAACTACCATAGTCTGTTCAAGTTGCTAATTTAGAAAAACATCCCATAGAGCCCTGAAAGACTTTTTAATCCCAGCACTCAAGAGGTAGAGTCAGAGGCAGGTTGGATCTCTGTGAATTCCAGGCCAGCCTGGTTTAGTTAGTGAGCCCCAGCCCAACCATGGCTGCAGAGTGAAACACTGTCTCAAAACCACAAGACCACAAACACTGGACAACTAAACGCAAAGTTATTTCTCATAGTTTAGGAGCTTGAGACGTCTAGGATCAAGGTGCCAGCAAGACTATCTGGGGAGGAGTCTTCTTCATAAAGCATACCTTCCAGTGCGTCACCACGTGGCTGAAAGGGCGAGTGTTTCTGGAATCTTGGTTCCCTTTGTCAAGGCATGCCCTCATGACCTCATGACCTCCCAAACAGCATTGCACGGTAGGTTCACACGCGAGCTGCAGGGAGTCATCCAGACCCTAGGATGTCAGGGTAAGGCTTCACTATTATAGCACTAGGGTTTGTGCTCCCGACTCGAGTTGGGATGAGAGATGTGTGGACTTCGGCAGCCGATGGTTCCTGCCCACTAGGATGCCAATAACAGGCCTGTGTGCCTCGGTTGTCAGAGCACCCAGAATGCAGGACGTTGTCAAAATTAGTTATGCTTGAGAAGCTATTTGAACGAATTGAGTTTCCCATATTACATTTCCAAATCTAAACCACAACTCCTAGAGTCCACAGAGACCATTTTGAGTATTCTCACTAGTTTTTTTTTTTTTTTCTGTGCAAAAATAAAACCTGACAATTGCAATTCACTGTGGCTCATATTTCACTAAGTCAAAAGGAAGTGTGTTCTATGAAGTTTGTTGGCTTACAAATATCTCAACAGTGATTGAGATATAAGAGATGAGGGATATACACAAACTAAGATAGCTAACAGCAATTTACATTAAACTAGTTTTTATTAGTGTTTCCTCATATTGTTAAGCACCTGAGATAATAAATTTTAAAGGAGGAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032303-Chrna3:NM_145129:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.005 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0293118=Neur_chan_LBD=PD(55.6=34.0),PF0293211=Neur_chan_memb=PU(86.7=63.6)

							
A:
NA

							
C2:
PF0293211=Neur_chan_memb=PD(12.5=72.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000034851





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000109955
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:78596733-78601252 
ALTERNATIVE
HsaINT1007685
(CHRNA3)
Human
(hg19)
chr15:78889075-78893594 
HsaINT0035182
(CHRNA3)
Rat
(rn6)
chr8:59594136-59596363 
LOW PSI
RnoINT0036287
(Chrna3)
Cow
(bosTau6)
chr21:31500235-31505330 
LOW PSI
BtaINT0038347
(CHRNA3)
Chicken
(galGal4)
chr10:3127130-3127749 
ALTERNATIVE
GgaINT0030095
(CHRNA3)
Chicken
(galGal3)
chr10:4568760-4569379 
ALTERNATIVE
GgaINT0030095
(F1NWY0_CHICK)
Zebrafish
(danRer10)
chr1:21794192-21799416 
LOW PSI
DreINT0046741
(chrna6)
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"