Special

MmuINT0038881 @ mm9

Intron Retention

Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34187902-34188263:+
Coord C1 exon
chr17:34187902-34187988
Coord A exon
chr17:34187989-34188206
Coord C2 exon
chr17:34188207-34188263
Length
218 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
TGTCCCTCCTGCTCCTCTAGCTG
3' ss Score
10.08
Exon sequences
Seq C1 exon
TTCCGGTTTGGCAGTAGTGGGGGTGACAAGGGCCCCGTGGTGGCAGCCCAGGAGGCCCAGGCCCAGGCGATTCTGCAGCAGGCACGG
Seq A exon
GTGAGCAGGGGCAGGGCAGGGGTGCGGACTGGTAGAGGGAGGTATGTGGTGGAAAGGGAAGACCGGTGTGGAAAGAGAGTGGGTTTTCTGAGGCCGAGGGGAGATGGAGGAGAGTAAAGGTTACAGGGAGATTAGAGCGAGGATGGGCAAATCTGGGGTTGTTGGGATTCTGTCACATTGCCTCCCTCTCACCCCTTCTGTCCCTCCTGCTCCTCTAG
Seq C2 exon
CTGGCACTCCGTGGGCCCCCTGGCCCCATGGGTTACACGGGCCGCCCTGGACCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330-Col11a2:NM_009926:11
Average complexity
IR-S
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:
NO

							
A:
NA

							
C2:
PF0139113=Collagen=PU(25.8=84.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000076193f1530A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000076193, ENSMUSP00000084772, ENSMUSP00000109888, ENSMUSP00000109890, ENSMUSP00000109893, ENSMUSP00000109895, ENSMUSP00000109896, ENSMUSP00000115026, ENSMUSP00000122082
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:33179488-33179718 
LOW PSI
HsaINT1008048
(COL11A2)
Human
(hg19)
chr6:33147265-33147495 
Rat
(rn6)
chr20:5320425-5320674 
Cow
(bosTau6)
chr23:7306516-7306778 
LOW PSI
BtaINT0040769
(COL11A2)
Chicken
(galGal4)
chr23:4928090-4928189 
LOW PSI
GgaINT1009884
(COL16A1)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr19:7278907-7279605 
LOW PSI
DreINT0048971
(col11a2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TTCCGGTTTGGCAGTAGTGGG

				
R: 
GCGGCCCGTGTAACCCAT

				
Band lengths: 
132-350

			

		

	





	
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
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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