Special

DreEX0023087 @ danRer10

Exon Skipping

Gene
ENSDARG00000012405 | col1a1a
Description
collagen, type I, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9102]
Coordinates
chr3:23103677-23104136:+
Coord C1 exon
chr3:23103677-23103784
Coord A exon
chr3:23103874-23103927
Coord C2 exon
chr3:23104029-23104136
Length
54 bp
Sequences
Splice sites
3' ss Seq
TTGTTTTTTTTACTTGTTAGGGC
3' ss Score
7.75
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
Exon sequences
Seq C1 exon
GGTGACCGTGGTGAGACTGGCCCATCTGGCACTCCTGGAGCCCCTGGACCTCCTGGTGCTGCTGGACCTATTGGCCCTGCTGGAAAGACTGGTGATCGTGGAGAGACC
Seq A exon
GGCCCTGCTGGTGTCCCCGGCCCTGCTGGCCCCTCTGGTCCCCGCGGACCCTCT
Seq C2 exon
GGACCCGCTGGAGCTCGTGGAGACAAGGGTGAGACTGGTGAGGCTGGTGAGAGAGGCATGAAGGGACACAGAGGATTCACTGGAATGCCAGGACCCCCTGGTCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012405_MULTIEX1-37/40=36-38
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=1.000 C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(8.1=19.4),PF0139113=Collagen=FE(41.2=100)

							
A:
PF0139113=Collagen=FE(20.0=100),PF0139113=Collagen=PU(24.6=94.4)

							
C2:
PF0139113=Collagen=PD(17.6=41.7),PF0139113=Collagen=FE(50.7=100)

						

					

				








    
Main Inclusion Isoform:
ENSDARP00000003177





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSDARP00000047009
          









    
Other Skipping Isoforms:
NA
  



Associated events







Conservation


Human
(hg38)
chr17:50188096-50188149 
HIGH PSI
HsaEX0016382
(COL1A1)
Human
(hg19)
chr17:48265457-48265510 
HIGH PSI
HsaEX0016382
(COL1A1)
Mouse
(mm10)
chr11:94949181-94949234 
HIGH PSI
MmuEX6088965
(Col1a1)
Mouse
(mm9)
chr11:94810495-94810548 
HIGH PSI
MmuEX6088965
(Col1a1)
Rat
(rn6)
chr10:82759014-82759067 
HIGH PSI
RnoEX0022998
(Col1a1)
Cow
(bosTau6)
chr19:37101905-37101958 
HIGH PSI
BtaEX0009631
(COL1A1)
Chicken
(galGal4)
chrUn_JH375554:82815-82868 
Chicken
(galGal3)
chrUn_random:31475777-31475830 
HIGH PSI
GgaEX6047844
(COL2A1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGGTGAGACTGGCCCATCTG

				
R: 
CCAGTCTCACCCTTGTCTCCA

				
Band lengths: 
138-192

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]











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