Special

MmuINT0038889 @ mm10

Intron Retention

Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34052464-34052985:+
Coord C1 exon
chr17:34052464-34052517
Coord A exon
chr17:34052518-34052940
Coord C2 exon
chr17:34052941-34052985
Length
423 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TACCCAGCCTTGTGTTTCAGGGA
3' ss Score
7.59
Exon sequences
Seq C1 exon
GGACCTAGAGGACTCCTTGGCCCTAAAGGCCCGCCTGGTATTCCTGGGCCGCCG
Seq A exon
GTGAGTGACACCGGGGCTTCCAGCCCTGACCTTACCCCTGCTCTCTCCAGTTCCCCACCCTTCCTGATACTTTGTTTCTTCCTCCCAGTCTGTGATGGTTCCCACTCCCTCCCCCGTTATTTCTGCTCTAGCTTCCCCCCAAGAAGCACTTGGTGGACCGCATGGTGCAGTGCACAAGGGCTCTGACTATAGCCAAACACAACAAAAATCTTCAAGAAAAACAAAACAAGCCCTCAAACCCACAGACCCACACCCTGCAGATCCACACGCGCTGGCTGGTTGGGCCAGTCTGGATTTGAGATGAATGCGCGGTCTGATCGGGCATCTGCTGTCCACCCTCTGGGGTGACCAGGCTTCCCGGAAACCACAGTGCTCCTGGCCTGGCCCCAGCTTCCAGCCTGCTTACCCAGCCTTGTGTTTCAG
Seq C2 exon
GGAGTCCGAGGCATGGACGGTCCCCACGGCCCCAAAGGGAGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:19
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(22.7=100),PF0139113=Collagen=FE(23.0=100)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(18.7=100),PF0139113=Collagen=FE(18.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084772





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000109890, ENSMUSP00000109893, ENSMUSP00000115026, ENSMUSP00000122082
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr6:33177707-33178131 
LOW PSI
HsaINT1008056
(COL11A2)
Human
(hg19)
chr6:33145484-33145908 
Rat
(rn6)
chr20:5318632-5319169 
Cow
(bosTau6)
chr23:7304844-7305178 
LOW PSI
BtaINT0040778
(COL11A2)
Chicken
(galGal4)
chr12:9073459-9073546 
LOW PSI
GgaINT1010142
(COL7A1)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr19:7276957-7277435 
LOW PSI
DreINT0048980
(col11a2)
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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