Special

MmuINT0036210 @ mm9

Intron Retention

Gene
ENSMUSG00000027107 | Chrna1
Description
cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) [Source:MGI Symbol;Acc:MGI:87885]
Coordinates
chr2:73401338-73404998:-
Coord C1 exon
chr2:73404759-73404998
Coord A exon
chr2:73404365-73404758
Coord C2 exon
chr2:73401338-73404364
Length
394 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGC
5' ss Score
7.35
3' ss Seq
ACGCCCTCTGCTTCCCCCAGGCC
3' ss Score
9.5
Exon sequences
Seq C1 exon
GTTTTTATCGACACTATCCCAAACATCATGTTTTTCTCCACAATGAAAAGACCATCCAGAGATAAACAAGAGAAAAGGATTTTTACAGAAGACATAGATATATCTGACATCTCTGGGAAGCCGGGTCCTCCACCTATGGGCTTTCACTCTCCGCTGATCAAGCACCCTGAGGTGAAAAGCGCCATCGAGGGCGTGAAGTACATTGCAGAGACCATGAAGTCAGACCAGGAGTCCAATAAC
Seq A exon
GTAAGCTGTGTGGCTCCCAGTCCACACCTCCGGGTCTGTCTGTCTGTCTATCTATCTGCCTGCCTCTGCCTTCTGAGTGCTAAGACCAAAGGTTTGCGCCACAACCTCTAAGCTAACACACCTCTGGGTCTAAATGATTAAATGCATAAGTGTGACAGGGAGGTTGACCAATGAATTGGCTTCAAGCTCTAGTTACTAACTTCAGATGCACTGTGTTGACTATCTCTGGCAACTATAGTAAGTCATTTTGGCTTAATTATGCAAAAACTAAAGGTTGTAATATCAGGTGTTGAGGTTTGGAGGTTTACATATTGAAGGCCAGGCCAGTAGGGGGCGCTATGAGCCTGTGTCCCATCTCAGGGGATTCCTATCTAACGCCCTCTGCTTCCCCCAG
Seq C2 exon
GCCGCTGAGGAATGGAAGTATGTTGCCATGGTGATGGATCACATCCTCCTCGGAGTCTTTATGCTGGTGTGTCTCATCGGGACGCTGGCTGTGTTTGCAGGTCGGCTCATTGAGTTACATCAACAAGGATGAGCAGAGGCTGAGCTAAGCCTACCTCTGTCCCAGCCATAGCCATCGCTAGGAAAGATGGAAGAGAGGAAGGTCTGTCTCCTTGAATCCTTTCACACTTACCAAACATGCAGTGTTCTACATGTCCTACATGTTAATGAGAGTGATCTCTGCTCACACGGCTGTATTCTTGAAGTGTCTCCCCTTTGCTTCTGCTTTTAACACTATGGGCCTCCTTAAAGGGCGAACCCTTTGAAGTAAATAAAAGTGAGCCCTCAAAAGAAGTGTTTGCTTCTAAATGGCCCCTGGGAGAGTTTTGCTTGGATACTCAAGGTTTTCTGTTTGTATTGCCATGGCTAGTTGTTTTTGTTTTCTTTCCTTTAATAAATATAATTGTACTTATATGAGTGATCCGCCTACGTGTATGTCTCACATACACGCCTAGTGTCCATGAAGGTCAGAAGAAGGTATCCCATCTCCTAGAACTGGAACTACAAATGGTTGTGAGCGTCCACATGGAACCTGGGAATCAGGCCCTCTGGAAGAGCACCCAGTGTTCTTAACCACTGAACCACCCACCTATCGGGCTCAGTTAATTTTTATTTTTAAAGTGCTGAGAGTCCCTTACTTAAGACACACGGTTTCATACCTACTAGAAAAGTCGTGTCTACCAGATTCCCCAGATTTGATGTGGACACAAAGGAAGTGGTAGAAAGGAAATTAGGTAACTTTAAACTTAAAAAAAAATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATACTCGCACACATTGATGAAATTGGGGGACAACTTTTAGGAGTTAGTTCTCATCTTTTATCTCATTTGAGGCAAAGTATCTTGTGATTTCTGCCGCTGTGTTACATTCTCATGTAAAGCTTCCTGGGGCATTTTCCTTTCTATACTTCTCGGCCCATGAACAGAGTGCAGGGATTCCAGATGCATGCCGCCATCTCCAGCTTTTCATAGGTCCTAGGATAGAATTTAGGTCGTTAGGTTTGTCCAGCAAAAAACTACTTTTACCTGCTTAATCCATTTCACTGGCCCAAAGGTAATTTTAGGGCGATCACATACAAATAGTATCAAAACCTCATGGTTTAAAGTAGACTTCTGAAACCAGGAGAGGGAGAATGCTTTCTTAAGTGATTTCTGTTTGAGAGGCCTTCTTGAAAGGGCGCTTGGGATTCCTTGGGATTGTACCTAGAGCTTTGCACACAGAGCTATAACTGAGCCTCAGCTCTCCCAACTTAACGGAGCCCCTGGATTTTGTTCTCAGGACCCGAGGAAGGGCAGATCCCATCCTCATCAAGGGTGTGCCTCTGACCCCATGAGAATCGTCTCGCCCGCATGGGTTTATTTTATCCAAATTGTTTTACACAGTCTCCATAATGTCCCTAATTTACAAATGGAAAAAAAAATTTTTGGGGAAAGTTAAACTCTGCTCCATCTAGAAGTAGAAGAACTGAGATCTGAACCCAGACAGAACTTAAGATTCTAAAACAGGGGCTGGAGAGATGGCTCTATGGTTAAGATCATTCCCAGCAACCACAGGGTGCATGGTGGCTCACAACCATCTACAGTGGGATCTGATGCCCTCTGCTGGTGTGCAGGTGTGCATATACAAAGCACTCACACATAAATACATAAACAAACAAACAAATATTTTTTAAAGATTTATTTATTTATTATATGTAAATACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCATCAGATCTTGTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCAGAAGAACAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCAAATATTTTTTTTAAAAGTCAAAAAGAAAAGGGATTCTAAACCGACTTGCAGCTGATGGGGTCACCTGCTCCCTGCTCTCCCAGCATGCCTGGCGTGATCTAAGTAGTTCTGGTCTGTGTTGGTGGGGACTCTGTGATATCCTATTTCCTGCCTTCTCAATTAAAACCCCTGGCTTTTCCTTCAGTCCTTGGACGCAATCATGTTTGGAGTTCAGGCCCTATGAATGGAACCAGAAACGTATGCACACACCATCACCATTTCTGAAATCTGAAAAATAAATTCTCTGTGCCAAACTCTAGGCTCTAGTACAATTTACCCAGACCAAGAAGCCGTGTGGCTCTGGACGCAGAAAAGGCCTTTGAATCACAAACACATCTGATCCGTCATCTCCAGGGAGAGCTATAAACTGCATAACCAGGAGGCCAGTGCGAGCCCAGGTGGCTTCAATCTCCTGAGGGACTTCCCATCACCCCTGCACCAGTGCTGGGCTCTTTCATCTCAAATAGTTTGCACTTTAAAGTGGAAACAATTGGCAGTTTCTCAGAAAGTCACACTCGGGTCACCAAGTCACTCAGCAGTCCCATTCCCAGGTAGAGAGCCAAAGAAATCGAAAGAAAGACTTACACAATTTGTATGAGAACGCGCACAGAAGGCAAGAGCCAGAGAAAGCGGTCTAGGCTCCAACCCACAGACGACAAGCAAAAGGGATGTGGAGAATGGGTTTTGGGGTGTATGTGTGTAGGCCTGGGGGGCCATCGCCTTTTTGTTTTGTTGTTGTTTTTGAGATAGAGTTTCTCACTGGCCTGGAACTTGCCAAGTAGTTTAGGCTGGCTAGGCAGGCCATTCCGAGATCTGCCTGTCTCCTCTTTCTGCAAACAATTTAGTTGGCATGGGTTCTGGGGCTCTTACTCAGATCTAAAAACAAGCATTTTGTCAGTTGATCTAATTCTTTAGCTTTTTCTACTCACGACCACTTTTTGCTTGAGAAATGTTATGTAGAAATATAAAATATGTATAAAAATAAATAACAAAGAAATTTAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027107-Chrna1:NM_007389:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0293211=Neur_chan_memb=PD(31.9=57.5),PF0293211=Neur_chan_memb=PU(52.2=45.0)

							
A:
NA

							
C2:
PF0293211=Neur_chan_memb=PD(44.9=70.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028515





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:174748256-174748579 
LOW PSI
HsaINT0035169
(CHRNA1)
Human
(hg19)
chr2:175612984-175613307 
LOW PSI
HsaINT0035169
(CHRNA1)
Rat
(rn6)
chr3:60446204-60446805 
LOW PSI
RnoINT0036272
(Chrna1)
Cow
(bosTau6)
chr2:22137232-22137536 
ALTERNATIVE
BtaINT0038338
(CHRNA1)
Chicken
(galGal4)
chrUn_AADN03023691:2119-3366 
Chicken
(galGal3)
chr7:17988062-17989455 
ALTERNATIVE
GgaINT0046845
(E1BRV4_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGGGCGTGAAGTACATTGCAG

				
R: 
TACAGCCGTGTGAGCAGAGAT

				
Band lengths: 
348-742

			

		

	





	
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"