Special

MmuINT0036234 @ mm9

Intron Retention

Gene
ENSMUSG00000035594 | Chrna5
Description
cholinergic receptor, nicotinic, alpha polypeptide 5 [Source:MGI Symbol;Acc:MGI:87889]
Coordinates
chr9:54850207-54852966:+
Coord C1 exon
chr9:54850207-54850316
Coord A exon
chr9:54850317-54852137
Coord C2 exon
chr9:54852138-54852966
Length
1821 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TATTATTTTGTTTCTTCTAGTGC
3' ss Score
9.45
Exon sequences
Seq C1 exon
GAATGGATAGATGTAAAGTTAAGATGGAATCCTGATGACTATGGTGGAATAAAAATTATACGTGTTCCTTCAGACTCTCTGTGGATCCCAGACATCGTTTTGTTTGATAA
Seq A exon
GTAAGTCATATTCTAAGTATTATTTCCTATTTCCAAAAGAAAACTTGCATTGCTACTAGGCACCAGTAATTTTTTTTCCTCTTGTCTGCAAATTGTTTAGCTATGAAATCAAATGACTTGACTTTGTGTCTCTTTGTTGCATGTGTGCTGTGGATCCTTTGCCTTTTTTGGTGTGTTTTTTTTTTTTCATCATAAAAGTGTTATCTGATTTCTGAAATAAGAAAAAGGACATGGCCAATGTGGAGTAAAGAAAAGTGGTATGCATTATCTGATAGAGATAATGGCTGTGGTTCATTTACACATACAGTAAACTCATGTGCTTGGCAGTGTGTTCACGGCGAGCTTCCGTGCTGGGCGCCACCCATTGTACTTTGCCTAAGGTAGTTACACTTGTCTATGATCACAAAGCTCTCTCTCTCTCTTTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGGCCAGGCTGGCCTCAAACTCAAAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCAGGTACAGTAAGGTTTCACCCCAAGACCCTGGCATATCCACCTACCCCTTATTCAAGTGAGACTTCCAGGTTTCAGGGGATTTTTTTTTTAGTTGAGGTTACAATTTATGGTCAACCTTGTTTTCTAATATTACATAAATACATTGTCATGATGGCACAACCCATTTTTCCACGGTGAGGAGTTTGGGGTTCATTTTTGATGGTAATGTCAGTTACCAGCTGTATTCCCCCTCCCCTCCCCTCCCAGGGCCATCTCAGAGTAAATGTGAGAGTTTGCATGTATCGTAAAGCACCCTGTCTCATTTGCAAAAGGCTTTTAGAGCAAACACTATGCAAAAAATGATCTTTTGAAGCCTTTACTTCTGTGTTCCCTGATATGGAAGGATGGAGAAGGCTCGTAAGGTAACACGAGGCAGCTTCTGGCACATTCTCTCAGTAACCACAAGCACCTTGTCCTGTTTGCACAAAAGCTTTGGCATGCAGACAGATCAAATGCTGTGCAAAAGCAATCTTTTGAAACCTTTTGCTTCCACATTAATATGAAAGCATGAACAAAGCTTGCAAGGTAGCACGATGCAGCACCATGAGCCTCAGCTGCTCTCTGTATGAAAACATTGTTATGACTCAGCATAGATAGATTGCACGGCACGGTGAAAAGCCCACAGGACTTGAAGATACAGAGCAAGACTATGAAGGAATCCGGTGCTTCTGCCTGCAGCTGTGCCTGCCCAGCACAGGAGCATCCCAGGTGTGCCCTGCATGGTGCAGATACTCCTTCCTCTTAGGGTAGAAAGCATCTATTATTTTGGTGGAGGAGAAAGTCTAGGGATGTGGATTCGGGCTCTGCCTTTCTGTGTGCCCAGTATATAAACAGCCCGATCCTGTTTGTATGTAAAGTGGCATCTTTTCAATGACTAAAATCTCAACATTTTGAGAAACTTGGATTTGCCCGGCTCACAATACAAAGGGAGGAATAGGCTCAGTCCCAGCAGAATTCTTACATGATAGACAGATGTGACCCCGTGGGTGGAGCAGGCATTGGGGCAGACAGTAATTTCAAACTCATTTCACACTATTACCCCCAGGATCCTTTTAAATTAGGCTTATCAAATGTGTCCTCGGGCTGTTTGACTTCGGCGCTATTATTTTGTTTCTTCTAG
Seq C2 exon
TGCAGACGGACGTTTCGAAGGGGCCAGTACGAAAACAGTTGTCAGGTACAATGGCACTGTCACTTGGACGCAGCCAGCAAACTACAAAAGTTCTTGCACTATAGATGTGACCTTTTTCCCATTTGATCTCCAAAATTGCTCCATGAAATTCGGCTCATGGACGTATGATGGATCCCAGGTCGATATAATCCTAGAGGACCAAGATGTCGACAGAACAGACTTTTTTGACAATGGAGAATGGGAAATCATGAGCGCAATGGGGAGCAAGGGGAACCGGACGGACAGCTGCTGCTGGTACCCCTGCATCACCTACTCCTTCGTGATCAAACGGCTGCCTCTCTTCTACACCCTGTTTCTTATCATACCCTGCATCGGGCTCTCGTTTCTGACTGTGGTTGTCTTCTATCTCCCTTCAAACGAAGGTGAAAAGATTAGCCTGTGCACTTCCGTGCTGGTCTCTCTGACTGTCTTCCTGCTGGTGATTGAGGAAATTATACCGTCATCTTCCAAAGTCATACCTCTGATCGGGGAGTACTTGGTGTTCACCATGATCTTCGTGACCCTATCCATTATGGTGACTGTCTTTGCCATCAACATCCACCACCGCTCTTCTTCCACACACAATGCTATGGCGCCGTGGGTTCGTAAGATATTTCTCCACAAGCTTCCCAAACTGCTCTGCATGAGAAGTCATGCCGATAGGTACTTCACTCAGAGAGAAGAAGCCGAGAAAGACGGTGGACCTAAATCTCGGAATACTTTGGAGGCCGCGCTCGATTGCATTCGCTACATCACGAGACACGTAGTGAAAGAGAACGACGTCCGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035594-Chrna5:NM_176844:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)

							
A:
NA

							
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:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000082923





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000091365
  



Associated events






Conservation


Human
(hg38)
chr15:78588424-78589804 
LOW PSI
HsaINT0035195
(CHRNA5)
Human
(hg19)
chr15:78880766-78882146 
LOW PSI
HsaINT0035195
(CHRNA5)
Rat
(rn6)
chr8:59584681-59586226 
ALTERNATIVE
RnoINT0036297
(Chrna5)
Cow
(bosTau6)
chr21:31489848-31491761 
BtaINT0038356
(CHRNA5)
Chicken
(galGal4)
chr10:3133011-3133983 
ALTERNATIVE
GgaINT0030249
(CHRNA5)
Chicken
(galGal3)
chr10:4574641-4575613 
ALTERNATIVE
GgaINT0030249
(F1NIT6_CHICK)
Zebrafish
(danRer10)
chr18:40502909-40503603 
LOW PSI
DreINT0046733
(chrna5)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCTGTGGATCCCAGACATCGT

				
R: 
AAGGAGTAGGTGATGCAGGGG

				
Band lengths: 
351-2172

			

		

	





	
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"