Special

MmuINT0039778 @ mm10

Intron Retention

Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97990913-97991388:-
Coord C1 exon
chr15:97991344-97991388
Coord A exon
chr15:97990967-97991343
Coord C2 exon
chr15:97990913-97990966
Length
377 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
TGTCCCCTTCTTCTCCCCAGGGT
3' ss Score
11.8
Exon sequences
Seq C1 exon
GGTGCTCGGGGTAACGATGGCCAGCCAGGCCCCGCTGGACCTCCG
Seq A exon
GTAAGTTGCTGTCCTTCTTAAGCAGGTGACAGTAGCTGTGCAGCCCTGAAGTCTGTGGGGTTGCCCCTGTACTTTGTGGCAGGAAGGAGGTGGCTCATCCCGTGAGCATGCTGTTGACACTGCAGCCTGACATCCCCTGCTGCCCCTAGCAGTCTCCTCTTTTAAGGAGAGAGGTCAAAGCCCCGTGGCTTCTCACAGACTCAGAAACTCTCCAAGAGGAGCAGGGTGTCTCTCTGGAGGTCTTTGGGGAGAGCAGCCCTGGCAGTTTCTTCTAGCCACAGAGGTGGAAGGAGTGGGAGGTGGGGCGTCTCTCTTTGAGGCCTGGACAGAGTTCACTGACACCCAGCGCTCACCCTCTGTCCCCTTCTTCTCCCCAG
Seq C2 exon
GGTCCTGTGGGTCCCGCAGGTGGTCCTGGCTTCCCTGGTGCTCCTGGTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483:ENSMUST00000023123:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=FE(21.2=100),PF0139113=Collagen=PU(8.9=53.3)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(25.8=100),PF0139113=Collagen=FE(18.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000023123





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000085693
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr12:47989282-47989760 
LOW PSI
HsaINT0038819
(COL2A1)
Human
(hg19)
chr12:48383065-48383543 
LOW PSI
HsaINT0038819
(COL2A1)
Rat
(rn6)
chr7:139469961-139470343 
LOW PSI
RnoINT0039607
(Col2a1)
Cow
(bosTau6)
chr5:32465153-32465634 
ALTERNATIVE
BtaINT0041549
(COL2A1)
Chicken
(galGal4)
chr2:23714212-23716485 
LOW PSI
GgaINT0097663
(COL1A2)
Chicken
(galGal3)
chr2:23543134-23545407 
LOW PSI
GgaINT0097663
(COL1A2)
Zebrafish
(danRer10)
chr8:21173553-21173900 
LOW PSI
DreINT0049549
(col2a1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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
  • 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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