Special

MmuINT0038907 @ mm9

Intron Retention

Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34194345-34194618:+
Coord C1 exon
chr17:34194345-34194398
Coord A exon
chr17:34194399-34194564
Coord C2 exon
chr17:34194565-34194618
Length
166 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CACTCTGGCTTTCCCCTCAGGGA
3' ss Score
10.97
Exon sequences
Seq C1 exon
GGCCCTGCAGGGAAGGATGGGCTGCCGGGACACCCCGGCCAGAGAGGAGAAGTG
Seq A exon
GTGAGTGATCCAGGGGTGTGTGTGTGGGGGGGGGGGGGGCTTGGATCTTGCTGAGTCAGCCGCCTTGGTGCTGTGCTTCCTCTGGGAGCCTAGAACTTGGGGCCTGCCCCACTGTCTCCCACACTTGTCCTATCTGGCTGTGACGTCACTCTGGCTTTCCCCTCAG
Seq C2 exon
GGATTCCAAGGAAAGACCGGCCCACCAGGCCCGCCCGGAGTGGTGGGACCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330-Col11a2:NM_009926:35
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:
PF0139113=Collagen=PD(6.9=27.8),PF0139113=Collagen=FE(23.3=100)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(16.4=66.7),PF0139113=Collagen=FE(24.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000076193f1530A





     
      









    
Other Inclusion Isoforms:
NA
          









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



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:33173114-33173347 
LOW PSI
HsaINT1008074
(COL11A2)
Human
(hg19)
chr6:33140891-33141124 
Rat
(rn6)
chr20:3849890-3850004 
LOW PSI
RnoINT0038869
(Col11a2)
Cow
(bosTau6)
chr23:7300312-7300521 
LOW PSI
BtaINT0040795
(COL11A2)
Chicken
(galGal4)
chr17:7536427-7539903 
ALTERNATIVE
GgaINT0125293
(COL5A1)
Chicken
(galGal3)
chr17:8218126-8221602 
ALTERNATIVE
GgaINT0125293
(Q90689_CHICK)
Zebrafish
(danRer10)
chr19:7272389-7272466 
LOW PSI
DreINT0048997
(col11a2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTGCAGGGAAGGATGGGCT

				
R: 
CTGAGGTCCCACCACTCCG

				
Band lengths: 
104-270

			

		

	





	
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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