Special

MmuALTD1026547-3/3 @ mm10

Alternative 5'ss

Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130060874-130061380:+
Coord C1 exon
chr4:130060874-130060984
Coord A exon
chr4:130060985-130061223
Coord C2 exon
chr4:130061345-130061380
Length
239 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TCATATACCCTCTCTTTCAGGAG
3' ss Score
10.05
Exon sequences
Seq C1 exon
GGTGACCCCTGTGAAGTGTGCCCAACGCTGCCTGAAGGGTCCCAGAATTTTGTGGGGCTCCCTGGAAAACCAGGGCCTAAAGGGGAACCAGGTGATCCTGCTCCAGCCTGG
Seq A exon
GTGAGTGCCCAAGTGGCCACTGAGGAACATATGTACAAGACAGATGCAAGACAGCCAGAGGGACTGGCTGCTTCTCAGTACCACTGAGATTACTGAGTGTAGCCTAGATGGAATTTGAACCATAGAGCTTGGTGTGGGCTAGAGTGTCATCCCAGGTTTCCATGGCAACCTCCCAGAACTTTTCCCCAAGAGACTCTAGGGTATCCTTTGGGCAGGGTAGGGTGAAACCACATCTTACT
Seq C2 exon
GAGGGCCTAGGAACTGTGGGACTGAAAGGTGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-36-38,37-38,38-38-3/3
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=PD(14.3=21.6),PF0139113=Collagen=PU(41.3=70.3)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(17.5=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000035802





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000120339, ENSMUSP00000120384
  



Associated events







Conservation


Human
(hg38)
chr1:31689459-31689460 
Human
(hg19)
chr1:32155060-32155061 
Rat
(rn6)
chr5:148271084-148271425 
ALTERNATIVE
RnoALTD0007279-2/2
(Col16a1)
Cow
(bosTau6)
chr2:122570268-122570653 
ALTERNATIVE
BtaALTD0005682-3/3
(COL16A1)
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: 
GTGACCCCTGTGAAGTGTGC

				
R: 
GGTCACCTTTCAGTCCCACAG

				
Band lengths: 
144-383

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Ribosome-engaged transcriptomes of neuronal types
  • 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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