Special

MmuINT0038910 @ mm9

Intron Retention

Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34195223-34195554:+
Coord C1 exon
chr17:34195223-34195312
Coord A exon
chr17:34195313-34195500
Coord C2 exon
chr17:34195501-34195554
Length
188 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
ACCCTAAATCTGGTTCATAGGGT
3' ss Score
6.37
Exon sequences
Seq C1 exon
GGTGACCCTGGTCCTCCTGGGGCCCCAGGGAAGGATGGTCCTGCTGGTCTGAGAGGCTTCCCAGGAGAGCGAGGCCTTCCAGGCACTGCT
Seq A exon
GTGAGTGTGACCCCCAAAGCTAACAGCCTATGAATATGGTCACTCATCACCTGGTCCCCTTGATATTATACCCCGCTTTGGGGGCCTACATCTCCCCAAAGCCCACACTTCCCAGGATGTCTTTTGGGGCCCCATGCCTGTGAAGGCTTGCCTTCTCACTCACCACTTACCCTAAATCTGGTTCATAG
Seq C2 exon
GGTGGACCCGGCTTGAAAGGAAATGAAGGTCCAGCTGGCCCTCCTGGCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330-Col11a2:NM_009926:38
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=PU(46.0=96.7),PF0139113=Collagen=PU(10.3=26.7)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(26.6=100),PF0139113=Collagen=FE(24.6=100),PF0139113=Collagen=PU(12.8=61.1)

						

					

				








    
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)
chr6:33172104-33172288 
LOW PSI
HsaINT1008077
(COL11A2)
Human
(hg19)
chr6:33139881-33140065 
Rat
(rn6)
chr20:3850732-3850904 
LOW PSI
RnoINT0038872
(Col11a2)
Cow
(bosTau6)
chr23:7299334-7299509 
LOW PSI
BtaINT0040799
(COL11A2)
Chicken
(galGal4)
chr17:7541344-7541419 
LOW PSI
GgaINT0125296
(COL5A1)
Chicken
(galGal3)
chr17:8223043-8223118 
LOW PSI
GgaINT0125296
(Q90689_CHICK)
Zebrafish
(danRer10)
chr19:7271163-7271333 
LOW PSI
DreINT0048999
(col11a2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGTGACCCTGGTCCTCCTG

				
R: 
GGCCAGCTGGACCTTCATTTC

				
Band lengths: 
130-318

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"