Special

DreEX0023077 @ danRer10

Exon Skipping

Gene
ENSDARG00000012405 | col1a1a
Description
collagen, type I, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9102]
Coordinates
chr3:23101374-23104136:+
Coord C1 exon
chr3:23101374-23101481
Coord A exon
chr3:23101589-23101642
Coord C2 exon
chr3:23104029-23104136
Length
54 bp
Sequences
Splice sites
3' ss Seq
ATATTTGTTTGTAAACATAGGGA
3' ss Score
4.17
5' ss Seq
CCTGTAAGC
5' ss Score
3.69
Exon sequences
Seq C1 exon
GGTGACCAAGGTGCCAAGGGTGCTGATGGTGCTGCTGGTAAAGATGGCATTCGTGGTATGACCGGACCAATTGGACCCCCCGGACCTGCTGGAGCTCCTGGTGACAAG
Seq A exon
GGAGAATCTGGTGCTCAAGGACTTGTTGGACCTACTGGTGCCCGTGGACCACCT
Seq C2 exon
GGACCCGCTGGAGCTCGTGGAGACAAGGGTGAGACTGGTGAGGCTGGTGAGAGAGGCATGAAGGGACACAGAGGATTCACTGGAATGCCAGGACCCCCTGGTCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012405_MULTIEX1-27/40=26-38
Average complexity
C2
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=FE(44.9=100),PF0139113=Collagen=PU(23.7=50.0)

							
A:
PF0139113=Collagen=PD(7.7=33.3),PF0139113=Collagen=FE(22.4=100)

							
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)
chr17:50190327-50190380 
HIGH PSI
HsaEX0016396
(COL1A1)
Human
(hg19)
chr17:48267688-48267741 
HIGH PSI
HsaEX0016396
(COL1A1)
Mouse
(mm10)
chr11:94946574-94946627 
HIGH PSI
MmuEX0012189
(Col1a1)
Mouse
(mm9)
chr11:94807888-94807941 
HIGH PSI
MmuEX0012189
(Col1a1)
Rat
(rn6)
chr10:82756445-82756498 
HIGH PSI
RnoEX0022987
(Col1a1)
Rat
(rn6)
chr10:82756623-82756676 
HIGH PSI
RnoEX0022988
(Col1a1)
Cow
(bosTau6)
chr19:37099557-37099610 
HIGH PSI
BtaEX0009626
(COL1A1)
Chicken
(galGal4)
chrUn_JH375554:80501-80554 
Chicken
(galGal3)
chrUn_random:31478624-31478677 
HIGH PSI
GgaEX6047837
(COL2A1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ATGGCATTCGTGGTATGACCG

				
R: 
TGTGTCCCTTCATGCCTCTCT

				
Band lengths: 
135-189

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]











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