Special

MmuALTD0003406-2/2 @ mm9

Alternative 5'ss

Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:129758679-129760419:+
Coord C1 exon
chr4:129758679-129758723
Coord A exon
chr4:129758724-129758765
Coord C2 exon
chr4:129760366-129760419
Length
42 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTCT
5' ss Score
1.07
3' ss Seq
TCATGGTTTCTCTCTCTAAGGGG
3' ss Score
7.32
Exon sequences
Seq C1 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCC
Seq A exon
GTAAGAACCTAGCAGCACTCCACCCCCCTTCCTGCCAGCCAG
Seq C2 exon
GGGCTTCAAGGGGAGCGAGGCCTCACGGGCCTGACTGGAGACAAAGGAGAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-57-65,59-65-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption when splice site is used (sequence inclusion)





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=FE(23.0=100),PF0139113=Collagen=PU(13.2=60.0)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(3.2=11.1),PF0139113=Collagen=FE(23.3=100)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000120384





     
                   









    
Main Skipping Isoform:
ENSMUSP00000095479





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000095479f4145A, ENSMUSP00000120339
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr1:32136155-32136156 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr2:122592730-122592818 
ALTERNATIVE
BtaALTD0005684-2/2
(COL16A1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chrUn_random:12603897-12603898 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTTTTCCTGGTGCTGTTGGCT

				
R: 
CTCCTTTGTCTCCAGTCAGGC

				
Band lengths: 
84-126

			

		

	





	
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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