Special

MmuINT0036240 @ mm9

Intron Retention

Gene
ENSMUSG00000031491 | Chrna6
Description
cholinergic receptor, nicotinic, alpha polypeptide 6 [Source:MGI Symbol;Acc:MGI:106213]
Coordinates
chr8:28513684-28517945:-
Coord C1 exon
chr8:28516967-28517945
Coord A exon
chr8:28514995-28516966
Coord C2 exon
chr8:28513684-28514994
Length
1972 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
ATCCTTTGTTTGCATTTCAGGTA
3' ss Score
10.05
Exon sequences
Seq C1 exon
TGCTGTCGGCGACTTCCAGGTCGAAGGCAAGACCAAAGCTCTTCTCAAGTATGACGGTGTGATAACCTGGACCCCACCAGCCATCTTTAAGAGCTCCTGCCCAATGGACATCACCTTCTTCCCGTTTGACCATCAAAACTGCTCCCTGAAGTTTGGTTCCTGGACTTATGACAAGGCAGAAATCGACCTTCTCATCATTGGCTCTAAAGTAGACATGAACGACTTTTGGGAAAACAGTGAATGGGAAATTGTCGACGCCTCTGGCTATAAGCATGACATCAAGTACAACTGCTGTGAAGAGATTTACACGGACATAACCTACTCCTTCTACATCAGGAGGTTGCCCATGTTTTACACCATCAACCTCATCATCCCCTGCCTCTTCATTTCCTTCCTCACGGTGCTGGTTTTTTACCTTCCCTCCGACTGTGGCGAGAAAGTGACTCTTTGCATCTCCGTTCTGCTTTCTCTCACTGTCTTTTTGCTGGTGATTACAGAGACCATCCCATCCACATCTCTCGTGATCCCACTGGTGGGTGAGTATCTACTGTTCACCATGATCTTTGTCACGCTGTCCATTGTGGTGACCGTGTTCGTGCTGAACATACACTACAGGACCCCAGCAACGCATACCATGCCCAAGTGGGTGAAGACCATCTTCCTTCAGGCCTTCCCCTCGATTCTGATGATGAGGAAACCTCTGGACAAGACAAAGGAGGCAGGAGGTGTTAAGGACCCCAAAAGCCATACCAAGAGGCCTGCCAAGGTCAAATTTACTCATCGAGGAGAATCCAAACTTCTAAAGGAATGCCACCACTGCCAAAAATCAAGTGACATAGCACCTGGAAAGAGAAGATCAAGCCAGCAGCCTGCACGGTGGGTGGCAGAGAATTCAGAGCACTCGTCCGATGTTGAAGATGTCATCGAGAGTGTTCAATTCATAGCAGAAAACATGAAGAGCCACAATGAAACAAACGAG
Seq A exon
GTAAAAGTGGAGCCCTTTTCTCCAGCCAGCTGCACCCCTAGCAGGCCTACAGGCACTTTAGAGACTAGTCAGAGCGTCAGTGGGAGTTACATATGTGGAACAGTCAGGGACCGTCACCTAAGACCAGCTCTATTATCATGAAGCCTTGTGGGACCTGGGTTCAAGTTTAGGGAGCTATAGTGAGAGGATATATGTAGTCCTACAACAAATCTTCAGCCTGCATTTACTTACGGTGAGGTCTAGCCACAGTGCACATGCAGGACAAGCCTTCCTCAAGGAACAAGCCTCCAATGCATCGAACACTGACAAAGTGAGGGTGGGAAGGGAGACTGTAGAAATCATTATTAATAAAATCCCACCGGCGGGCTTGCTACCTGCTCTAATGGTTTGTGTTCCCAAATGAAACACACACACACACACACACACACACACACACACACACACAGTCTTTGTGTTTTAATATGCCGTATACAGCACAATAGCTGGGCCACTGCCTACCCTCCATGCTGTTACTATACCTCCCGCCAACAATCCCAAGTTATTACTTACTAATTCTATGTTCTATCTTGGTTGCCCTAGACCCAGTTGGGCAGCCTCTGGGCCATGTTTTCCCGGCTATTTCAAGTGGTGGCCATGTCTCTCTGTCCTGCAGTCTTCTCAGGCCTAGCATCTCACCTCTTCCTCCACACTCTCCCGGCATGGCAGGTCTCACTTCTCCTCCTCCTCCTCCTCCTCCTCCACTCCTCCTTCTCCTCCTCCTCCTCCTCCCTCTTCCCCTCCCCCTCCTCCCAGCCTGAGAACTCCTAAAATCCCACCTCTCCCTGTCCTTTCCAGCTTTGGCTGTTGGCATCTTTATTTACCAATAAGAACCAACTGCGGGCAGGTTCCCAGAAACTACAGGCAGACAGTCCCACGAAAACAGTTTTGTGGGGACCATAATTAGCATTCATAATACGTGCAGCTACAGAGACAGCCCAAGGAAAAGAAGAACTGTGGTACTGCCTGAAGCCCCAGTGGTGAAAGATGCCCCTTAGCAGTCAGCAGCTCCCATCACACTTCCTCTACTAGAGGGGGACCCAGACATGAGTTAAAGACATCTTGAAGATGTGCTCAGTATGCACACATTCCGTGCCTGTGTCCCACACTCTAATGCCTAGAGCTTGGCTCCTCCTACCCCAAGCAAGTGCTCAAGGATAGGGAGATCACCACTTGACTGAGGTTTCCCGCCAGGTGTCTGGAGATGCTTCATACTATAGCTCCTAACATCTGTAACTCATAGGGAAAGAATATCAGAACCACCACCACCCCCCAAAAAACACACTGAGAGACACTGAGAATGCCTGTCATAACATGTCACAGGAGAGCAATGGCCAGTGAGCTCACCTCCTGGCTGGCATCTTTTAGAATGTAGGCAATACAGTTACTGTTGATTTATCAGGCCAGGCAGGTCTCCTAATACACAACCCACAGAGACCATAGCAGAAGGCTAGAAGTTTGAAACTGGAAAGATTCCAGATATGCAATAAGCTCTCTTTGTTAGCATCCCTTAGCAGCCTAGAGGCTGCTTAGTCCTATGCAGGAGATCCTCCACCGTACCCCACATCCTCTGGCCTATCCTCTCACTTGCTTCACACTCAGATTCCCCCAAACAGCCAGGCACACGTGACAAGAGCTTGACTCTCAAGCAGATATTTTGTGGAGAGCGAAGAAAGGACCCTTATCACAGGCAAAGGGTCACAAAAGTCTTTGATACAGTTCATAGCCCAGTGATGTACATCTGCTCTCCTTAGACAATGAGTCCTACATAGGACATGCAGGCAGTCAGGCAGGCAAACATAATAGCAATAATTGGTTTTTTTGAAAGGATTGGAGAAAATGCTTTGGAGAAAAAAAAAAGTATTCATAAAACATAGCATGTTTTCTTATAGTCTTGGTTTTTAAAGCTAGCCTTGATCCTTTGTTTGCATTTCAG
Seq C2 exon
GTAGAAGACGACTGGAAATACATGGCTATGGTGGTGGACAGAGTCTTCCTTTGGGTATTTATAATTGTCTGTGTGTTTGGAACTGTGGGGCTATTTCTGCAGCCACTGCTTGGGAACACAGGAAAGTCTTAATTGGTATTGTCCCTTTACCTTCTGAATCTTTTAGATGTTGTGTTTTTTCCCGAGCTAGTCCCCACAAGAAAAAGCCAAGTACACAGACTCCTAAACCAAGACAAGAAGGGAGTGGGCATTGCTGCAGCCTTAGGAGCCTGAATACCTGTCTTCCTTACACTGGGTGTTTTATCACCTTGGAGCCCAGAGCTGGCAGTTGTCCTAGGCTAGGAGGACTGAGTCAGCTTCTCTATAATTTGCATTCTTTGTTTCAAGAAACACAAATGGTCCCTCGTAGAGCTAGGCCCCATAGTCAAGAGTCAGTCCACTCTGAAAGGTGATTGGCTTGTATCCGAAGCTCCTGCTGGTTATTGCAAGTGATGTGTATGGTTATCAAGAAACTCGGGAGCGCTGCTGACACTTGCAACACACCTGTCTGCTACTTTCTTGTGCATGTCCCTGTGATGTAGCTCACACTCATATCTGACATGTGCAATGGTCAAAGAAGAAAGCAGATAGCATCTCTCTTAGCAGACTATTCAATTCGTGGTGCAATGGGTTTTCTGTCCGTGTGAAAATCACTGAACTGATAGGCGTAAAAGGATGACGTTTATATGAGCTCATGGATTTGGAGGACTCTGCCCATGATCACTAGGTCCCATTGCCTCTGGGCCTTTGATGAGGCAAAGCATCATGCCTAGAAGAGGATGGCTGCCCACTTAAAGATAGCTACAAAGAAAGCAAACAGAGAGGAAGGCTCTGGAGTGCCAATATTCCTTTCACAGTCACAGCCCAATGACTTCATGTCTTCCTACAAGACCTTCCATCCTAGAAGCTCCACTACCTCCTGATAGCGTGGAGGAATCAGTCTCTAACACTTGTCCTTGGGGCTGATCCAAACCACAGCAGTATTGTCCTGGCAGGACATTTGGCTGGCTCCAGTACTGTGCTAGGTGCTACAAGGGGATACATAAGAGTCTTTCCCTTATAAAGTTACAGCCTTTTAGAAAAGCCGTATATGCAAAGAGCCACAGGATCAGGTAGTAGAGGATATAGCTAGAGCAACCCAAATGGGAGAAACTAATCGGACAAACCTAAACTCACTCTTGTGTTTCAAACAGATATCTGTGTAGCTTTTTCCCACGAGCCCTTCTCTAGCTCACTGCATGGAGATGAAATAAAATCGATATGAAATTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031491-Chrna6:NM_021369:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.069 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0293118=Neur_chan_LBD=PD(55.6=35.2),PF0293211=Neur_chan_memb=PU(86.1=62.4)

							
A:
NA

							
C2:
PF0293211=Neur_chan_memb=PD(13.1=70.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000033882





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000081033
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr8:42753311-42755845 
ALTERNATIVE
HsaINT0035200
(CHRNA6)
Human
(hg19)
chr8:42608454-42610988 
ALTERNATIVE
HsaINT0035200
(CHRNA6)
Rat
(rn6)
chr16:68865370-68866491 
LOW PSI
RnoINT0036303
(Chrna6)
Cow
(bosTau6)
chr27:37196045-37198338 
LOW PSI
BtaINT0038362
(CHRNA6)
Chicken
(galGal4)
chrZ:53431810-53434647 
ALTERNATIVE
GgaINT0065214
(CHRNA6)
Chicken
(galGal3)
chrZ:52492581-52495418 
ALTERNATIVE
GgaINT0065214
(F1NKI5_CHICK)
Zebrafish
(danRer10)
chr1:21794192-21799416 
LOW PSI
DreINT0046741
(chrna6)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGGTGGCAGAGAATTCAGAGC

				
R: 
GCCCACTCCCTTCTTGTCTTG

				
Band lengths: 
350-2322

			

		

	





	
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"