Special

MmuALTA0015154-1/2 @ mm9

Alternative 3'ss

Gene
ENSMUSG00000039316 | Rftn1
Description
raftlin lipid raft linker 1 [Source:MGI Symbol;Acc:MGI:1923688]
Coordinates
chr17:50308328-50329999:-
Coord C1 exon
chr17:50329546-50329999
Coord A exon
NA
Coord C2 exon
chr17:50308328-50308480
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TCTTTCCACGTTGTAGACAGCTG
3' ss Score
1.43
Exon sequences
Seq C1 exon
GAGGGAGAGCCCGGTTGCGCGGCGCTGGCGACGCACGGGGCGGACGGGTCTCTCGTGCGGGGCTGCCAGGGGCCGCTCGGCTTCCCCCAAGAAGATGCAGCACAGCATATTTTGCACATGAGTTCAGAGGAAGAGGAAGTGTAGCGGGCGGACGCGCGGCGGAGGCGGCGGCGGCGGCGCGGGGTGGAGTGGGGGCGGCGGGGCTGGAATCAGAGCGCGCAGGGCGCAGAGCGCAGCGAGCGGGAGCGCGGCGGCCACTGGCTCTGGAGAGGTACCTGTGCGGCCAGCGCCGGAGGGACAGACGACAAGCGAGCGGCCGCGCCCCGCGCTCTGCCCCCACCCCCGGGGTCGCGTCGTCCGCGCGCCGCCCTGCTCTGCATGGCACAAACTTTCATCCCGGGACACAGCACGCTGTCTCCGCCCGCGCCACGGTCACCGCTGCTGGTCCCCTAAG
Seq A exon
NA
Seq C2 exon
CTGTCAAGATGGGTTGCAGTTTGAACAAGCTGGAGAAACGTGAAGAAAAGCGGCCTGGGAACATTTATTCAACTCTGAAGAGACCTCAGGTGGAGACCAAAGTAGATGTGACCTATGAGTACTGCTTTCTAGAGTTCACCACACTGACTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039316-0-1,0-0-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact





	

	
5' UTR





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=NA A=NA C2=0.184
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
PF152501=Raftlin=PU(9.9=98.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000046524





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:16493878-16493879 
ALTERNATIVE
HsaALTA0007125-1/2
(RFTN1)
Human
(hg19)
chr3:16535232-16535384 
ALTERNATIVE
HsaALTA0007125-1/2
(RFTN1)
Rat
(rn6)
chr9:12761412-12761564 
ALTERNATIVE
RnoALTA0033655-1/2
(Rftn1)
Cow
(bosTau6)
chr1:155283671-155283672 
Chicken
(galGal4)
chr2:34915581-34915582 
Chicken
(galGal3)
chr2:34360079-34360080 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCACAAACTTTCATCCCGGGA

				
R: 
GCTTGTTCAAACTGCAACCCA

				
Band lengths: 
103-107

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"