Special

MmuALTA0017686-2/4 @ mm9

Alternative 3'ss

Gene
ENSMUSG00000067629 | Syngap1
Description
synaptic Ras GTPase activating protein 1 homolog (rat) [Source:MGI Symbol;Acc:MGI:3039785]
Coordinates
chr17:27095022-27096790:+
Coord C1 exon
chr17:27095022-27095166
Coord A exon
chr17:27096383-27096553
Coord C2 exon
chr17:27096554-27096790
Length
171 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
GTGGCCCTCTTCTTCAGCAGCCT
3' ss Score
4.9
Exon sequences
Seq C1 exon
GGGAGTTCATTCGTGCTCTGTATGAATCTGAGGAGAACTGTGAAGTAGACCCCATCAAGTGCACAGCGTCCAGTCTGGCAGAGCACCAGGCCAACCTGCGGATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCATTG
Seq A exon
CCTCCTGTCTTTCTCCTGCAGTCCCTCCCTCCCGGTCTCTCTCACCTGTCTCCACACCCTCACCTTCTACCACCCCCTCAGCATGTTCCCTGAAAGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTTTCTCTCTTTCTCTCTCTGTCTCCCCACCCCTTCCCCCCAG
Seq C2 exon
CGTGTTCCCGAGGGAGCTGAAGGAGGTGTTTGCATCTTGGCGGCTGCGCTGCGCAGAGCGGGGCCGAGAGGACATTGCTGACAGGCTGATCAGCGCCTCGCTCTTCCTGCGCTTCCTCTGCCCGGCCATTATGTCGCCCAGTCTATTTGGGCTTATGCAGGAGTACCCAGATGAGCAGACCTCACGAACCCTCACCCTCATCGCCAAGGTCATCCAGAACCTGGCCAACTTTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067629-5-9,5-8,5-7,5-6-2/4
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption when splice site is used (sequence inclusion)





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF083377=Plexin_cytopl=FE(34.3=100),PF0061614=RasGAP=FE(27.9=100),PF067666=Hydrophobin_2=PU(51.9=57.1)

							
A:
NA

							
C2:
PF083377=Plexin_cytopl=PD(6.4=11.2),PF0061614=RasGAP=PD(44.2=95.0),PF067666=Hydrophobin_2=PD(46.3=31.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000080038f5343A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000080038, ENSMUSP00000080038f5342A
  



Associated events






Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:33408328-33408329 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:7556440-7556824 
LOW PSI
BtaALTA0029322-2/3
(SYNGAP1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAAGGTGGTCAACTCCCATT

				
R: 
CAGGTTCTGGATGACCTTGGC

				
Band lengths: 
245-416

			

		

	





	
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
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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