Special

MmuINT0036235 @ mm9

Intron Retention

Gene
ENSMUSG00000035594 | Chrna5
Description
cholinergic receptor, nicotinic, alpha polypeptide 5 [Source:MGI Symbol;Acc:MGI:87889]
Coordinates
chr9:54852138-54855586:+
Coord C1 exon
chr9:54852138-54852966
Coord A exon
chr9:54852967-54854220
Coord C2 exon
chr9:54854221-54855586
Length
1254 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTGT
5' ss Score
6.36
3' ss Seq
GTATTTATTTTTTTTAACAGGTT
3' ss Score
10.47
Exon sequences
Seq C1 exon
TGCAGACGGACGTTTCGAAGGGGCCAGTACGAAAACAGTTGTCAGGTACAATGGCACTGTCACTTGGACGCAGCCAGCAAACTACAAAAGTTCTTGCACTATAGATGTGACCTTTTTCCCATTTGATCTCCAAAATTGCTCCATGAAATTCGGCTCATGGACGTATGATGGATCCCAGGTCGATATAATCCTAGAGGACCAAGATGTCGACAGAACAGACTTTTTTGACAATGGAGAATGGGAAATCATGAGCGCAATGGGGAGCAAGGGGAACCGGACGGACAGCTGCTGCTGGTACCCCTGCATCACCTACTCCTTCGTGATCAAACGGCTGCCTCTCTTCTACACCCTGTTTCTTATCATACCCTGCATCGGGCTCTCGTTTCTGACTGTGGTTGTCTTCTATCTCCCTTCAAACGAAGGTGAAAAGATTAGCCTGTGCACTTCCGTGCTGGTCTCTCTGACTGTCTTCCTGCTGGTGATTGAGGAAATTATACCGTCATCTTCCAAAGTCATACCTCTGATCGGGGAGTACTTGGTGTTCACCATGATCTTCGTGACCCTATCCATTATGGTGACTGTCTTTGCCATCAACATCCACCACCGCTCTTCTTCCACACACAATGCTATGGCGCCGTGGGTTCGTAAGATATTTCTCCACAAGCTTCCCAAACTGCTCTGCATGAGAAGTCATGCCGATAGGTACTTCACTCAGAGAGAAGAAGCCGAGAAAGACGGTGGACCTAAATCTCGGAATACTTTGGAGGCCGCGCTCGATTGCATTCGCTACATCACGAGACACGTAGTGAAAGAGAACGACGTCCGCGAG
Seq A exon
GTTTGTGGCGAGCATAAACACCCCCGCAAAGTGGGGTATCTACATGAATCTCACCCTCCATTTCCCCAGAGCATCTTGAATGACCCTGAAGAAAGTTTAGTAGTATGCATTTGAAGGGATAGTAATATTGACTTAGTTCTTTGGCTCTGGAATAGTTTACTGATTTAGATTTATCTTCCATAACTTTGTTTCTGAATTTTTACATTATAGTTTATCAAAAATTACCTTTTTTGAAGAATGAGTCTAATATAAACCTTAAGATACTTTGCATAGAGATATCTTTTGTAGCTTGTTTACAAATGAATATTAGTAAAATTGAAAAGAGCAAGGTGCATGGCTATAATTCTACCATTCAGGGGCTGAGGCGGGAGGATTGAAAGTTAGAGTCTATATTGATGTACTTTAGGAAGTTCATGGTTAGCATGGGCTACATAGGGAGATTATGTCTAATAAAAGCAAAGTGAAATAAATAGCCATAAAAATAAAGAAAAGGAATAAGGTGTGCCCATGTGTTATTTTATACTTTAGAGTTTTCAGGAAAGCAGTAATAGTATCCCTGCCTTCCTCCCTCCCTTCCCCTCTTCATCCCCTTCTCTCCTCCTTCCTTCCTTCCTTCCTTCTTTCCTTTTTTTTTTTTTTTTTGAGACAGTCACTTTATAGTCCTGGCTAGACTGGAATTTGGTATGTAGACCAGGCTGGCTTCAGACTTACAGAAATTCCCCCTTTTGGATTAAAGTCGTGTTCCATTATGCCAAAGCCCCCACCGTTCACTTTTTAAAGAAAATTTCACTATGTAGCTCAGGTTAGCCTTGAACTGTCAATCCTTTTACTCCAGCCTCCTGAATGCTGAGATTTCAGCAAATACTGCCATGTGCAGGTTATGACTTTGAACTAACTCTTTGTTATTGTTCCAAGGTGCTGGCCTTGAACTTCTGATCCTCCTGCCTCAGTCTTCCAAGTAGCTGGTACTACATGCTCCTACCACTGTGGCCAGTTTACTTTTAACAAATTAGTACTTGTTAACTGTAGTATTCTATGGCAGTATAATTGAATTATTGTAGGGTTTAAGATATTGATGGAATCTTAAAAGGTAAGAATTTATTGAATATAAATTCCAAATTTAAATTTAGAATGGGATTTAATAAATTATACTAGTCTGTCTTAGAGATCTGGGCATAGGAGACAGCAAATGATTATCTCTCTGTTTTTTATCCTAAAATACAGCTTTATATATGTATTTATTTTTTTTAACAG
Seq C2 exon
GTTGTTGAAGATTGGAAATTCATAGCCCAAGTTCTCGATCGGATGTTTCTATGGACGTTTCTTCTGGTTTCAATCATTGGGACGCTAGGGCTTTTTGTTCCTGTTATTTATAAATGGGCCAATATAATAGTCCCAGTTCACATTGGAAACACAATTAAGTGAAACCAAGAAATTACACTGGACTTAGTGAGCAGTCAAGCAGCTCTTAGGACACGTATGCCATTATGAAAATATTTACAATTTGATATAGGCAGTAACAGATTAGCAGTTTCTGACATTGGCTTAATGTTGTCCATTAGAACTGTAGTAATAGCCTTGAGTACCAACACTGTCCGCCTGCACTAGTGAAGGCCTACCATCGCATCCTGGCAAATCCTACTAACTTGCAACCAGTGACGAAGGGCATCTTTGGAGTACTGGAAAATGCAACTATATTTGAAGACTGTTTAAAGCTTTTCTCCCCACATTTAGTAAAAGCATATATTTGTGTGGTTTTGAATTTTCAGAATGGGTCTTGTTAAATTGTCCAGGCTGGCCCTAAACCTCCTGAGTAGCTAGGACTATGGGTGTGCTCCATTTTGCCCTGTTCTGTATTCATGGATATAAAACACATCATACTTTTATAGGAGATAAGCCGATTACTTGGTTTAATAATAACTATTTTTGTGAAGAGACACCATGATCAACAACTCTTATAAAGGAAAACATTTAATTGGGGCTGGCTTACTGGTTCTGAGGTTTAGTCCATTATTGTCATGGCAGAAGCATGGCAGCATACAGGCAGACATAATGTTGAAGACAAGAGTTTTCTACATCTGGATTGGCTGGCAGCAAGAAGAGAGAGTGACCCACTGGACATGACTTGAGCTTCTGAAACCTCAGAACCCACCTCCTGTGACACACTTTCTTCAACAAGGCCACACCTCCTCATAGTGCTACTCCTTGGTGATCAAGCATTCAATCTATGGGTCTATGAGAACCATTTCTATTCACACCACCCTTGATAGGATGCTATTCTTACTGACATTTTTAATATGTGAAAAATGGTAACTAGAAACTCCTTAAGTCTACTTTATTCTTCATATGGCAATATGGAATGGCTTTTGTGCTAACTAACTTTGCAGCTTACTGTCCACTGAAAACATATAACAGGCATCTCCTGCAGACATTCTTTGTAATGACTTTATAATCCTGCAGTGACACATTTTTTGTAATGACTTCAGTCGCCTTGTCCATATTCTTTGGTTAGGAGAGCTACTTATTTATCTCTGATTTCAGAATAATACTGCAGTTGTACAGATTCCCGTCTCAAAACGGGATGTTATGTCTCTGTCTTGGTAGTTCTGTGGAAAAAATCATTCTGGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035594-Chrna5:NM_176844:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
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)

							
A:
NA

							
C2:
PF0293211=Neur_chan_memb=PD(43.1=57.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000082923





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000091364, ENSMUSP00000091365
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:78590637-78593091 
ALTERNATIVE
HsaINT1007686
(CHRNA5)
Human
(hg19)
chr15:78882979-78885433 
Rat
(rn6)
chr8:59587056-59588464 
ALTERNATIVE
RnoINT0036298
(Chrna5)
Cow
(bosTau6)
chr21:31492594-31495753 
BtaINT0038357
(CHRNA5)
Chicken
(galGal4)
chr10:3130571-3132178 
ALTERNATIVE
GgaINT0030250
(CHRNA5)
Chicken
(galGal3)
chr10:4572201-4573808 
ALTERNATIVE
GgaINT0030250
(F1NIT6_CHICK)
Zebrafish
(danRer10)
chr18:40496627-40499316 
LOW PSI
DreINT0046736
(chrna5)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TTGCCATCAACATCCACCACC

				
R: 
CAAAAAGCCCTAGCGTCCCAA

				
Band lengths: 
342-1596

			

		

	





	
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"