Special

MmuINT0038879 @ mm9

Intron Retention

Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34176382-34179254:+
Coord C1 exon
chr17:34176382-34176681
Coord A exon
chr17:34176682-34179104
Coord C2 exon
chr17:34179105-34179254
Length
2423 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ACTAACCCTGCCCCTCCCAGGTG
3' ss Score
8.67
Exon sequences
Seq C1 exon
GCTGGGGTCTCTGAGCTGCCAGGGTGGCCAGGGGCACACAGTAGCGGCCACCGAAGAGCAAGCAGCACTGACAAGAAGAGGTGCCCCCACAACGGCACCTTGCTGCATGGAGCTGGGCCACTGAAAGCTGCTGACATCCCGGGGTCCTGGTTCCGAGGCTCAGCTGGCTTCTGTCTGCTGTCAGCACCAGGACTGCCTGGGATCTGGCATTCTGAGCCATGGAGCGGTGCAGCCGCTGCCACCGCCTCCTTCTGTTCCTACCTCTGGTGCTGGGTCTGAGCGCTGCCCCGGGATGGGCAG
Seq A exon
GTAAGAGGAGTCCTGCCTGGGTGTCAGTCAGTTGGAGGTTGTAGCATCTGCTTGGAAGGGACCTCTGATGCCTGGAGTAGGAGCATCTGAGCCTTAAGAAAGGGATTTTGGGCACCAGGATTTAGATGAAGGGCATGACACTTTTGGTTCCTTGGAGCCACTATAGGACTGTCTCCCTCTCTGAAATGACTGGCAGAGGGCAGGTGACGCCGGCCAACAGGAGCCACCGTCCAGAGGCTGAGTAGGCTGGATTCTTGGTTTGGATCCTTAGAAGAACTTGAGATGGCCAAAGCCAGTTTTGTCCAGGCTTTGCTGATGTCAGGGTAGTGAATACCAGGACTGATGGGTAGAGGAAATGGGGTGAACGTCTGTAGGTTGGAGCCTAGAAGGCTAGAGAAGAAAGCTACCTCCACTGTCCCGTCTTCTTTGGGTCCCCCAACCCCTCCCTGTGCCCTGGATGCTGCCACGCGGCTGGCTCTAGGGAGCCTGGGGGCTGGCTGCCAACAGGACGGCCGCTGGACAGGCCAGGATCAGGTGTCTGAGGCCAGAGCCAACTCTTTGCATTCCTGCCCCTCCCCTCTAGCCAGCAGGACTCCCGTGGGACCTTGGTGTCCACTGGCCCCATCTTTCCCCTTTTTACCTCCTAGAAGGGAAAGCCTCCTAGAAAAGAGGATTTGATAACTGGATCTAAGCAGAAAGGAACCAGTTCCTCTCTCCTGGAATACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGATTTTTGTATAGATATCCATTATTCATGTTTTCTCTGCTCAAGAGAGAAAATTGGCAGGATGACCGTGTAAAGGATCTAGGTTAGACTAAAGAAAGAGCAGATGAATGAAGTACACAGTGTTTACAGAGTTGAGGCAGGGGGATGACCAAGATAACTGTCTCCATTTGGGAACTGAGTGGAGGTGGGGGGAGGGACTCCAGGGAGATGGTTAGCTAAGAACTCCTGAGGGTATAGGACAGGGCATTTGGGGGCTCAAGGGGATAGGTGGAGTGGCAGTGGGTCTGAGACAGTGGGGTTAGTATGTGGCTTGAGGTGGGTGGGCTGTGAGCATGGCGTGGAACTGTCCTCCATCAGGATTTGGCGGAGGGTGGGGACCTCTCAGGTCTCCTTTGCCCGGGGTCTCTGTGAGTCTCTGTGTCTCTGTCTCCCTCACCGTACTCTCTCAAAGCTGCCCTTGTGTGTCAGTGTTTGCAAAGCTGCTACACTTTGGGGCCAGGCTCCTCAGGGGCGGGGGGAAGGTCGCGGTTTCCTCAGCTCCTGGACTCAAAGGGCCTTTTCTCTCCTGCCTGCCCCACCTCATCCACCCCACCAGGCTCTGCTCTCCTGACTGCCCTGGCCTCTGCCCCGCCCCACACTTCTACCAACACTTTTGCAAGCACTCTCTGTGGGAGTTCTCTGCTGTGGAGATGGTGTGGGAAGTGTGGGAGCAAACTTTCTCGTTCCATCATCGAGTTTGGGCCCGGGAAGCTGAAACCTAAGGAGACCTGGCTGATGGCCTGAGACTTGAATCTTGGGATTCAGGTGGTGGGGGATGGCAGGGCAGGACTGAGGTTCCAGGTGTCCGGAGCTTGCCTGGGCTTTGGGCAAGAACTCTGATAGCATTTACAGATGTGTGGCTTGGGGCCCTGGACCTGCTCCTGGTCTGTGTGGCAGCTTCAGTTTCCCCTTCCCCCTCTTCGAACCCATTCGCCAAGTCTGAGGGCACAGGCTTCTGGGCCACCTTATTCTTATATGCCCTTCCTTAGCACAGGCAGAGTTGCCCCTGCCCCCACCTCAACCCAGTCTCTGTGGCAACTGGAAGACCTCTCTTCTACAGCTGCCTCTCGGCCTCCCCTGTGCCCAGGATGATCGATTGCCCAGATGTTGTTTGTGCTAGAGACCAAGCAGATGCCAGGAAGCCAAAGACTGGGAGATAAGGAAAGAGAGGAAGAGGGAGAAAGAGGGAGAGAAAAGGGTGAACAGTGTGTCAGAGAGATGGGAAAACTGAAAAGAGGGTGTGGGAGGGTCCAGCAGGTGCACAGGCGGGGGAGCAGGGGGCAGAGGGCAGGAGAGATGGATGGAGCAGGGAGTCAGAGTGTGAGCCTAGCAGACTCACAGCAGAAAGACAGAGACAGCGAGTCTGAGACACAGATGCTGACAGAGGGAGGCAGAGAGAGTGTGGAGTTGCATGCCAGCCGGCTAGGTGCACCTCCCCTCTGTATCACTTTGCTTCCTATATGGAAATATAGGTCCCTTTAGGAGAATGTCAGGGAGACTGAGATCTGGGTGTTCCCTGGTTAGACCCCCCCTTGAGACATGTTCTCACTCCTAACTAACCCTGCCCCTCCCAG
Seq C2 exon
GTGCTCCCTCTGTGGATGTGCTTCGTGCCCTGAGGTTCCCCTCCCTTCCCGATGGTGTTCGGAGATCAAAAGGGGTCTGTCCGGGTGATGTGGCTTACCGTGTGGCACGGCCTGCCCAGCTCAGCGCACCCACGCGCCAGCTCTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330-Col11a2:NM_009926:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000076193f1530A





     
      









    
Other Inclusion Isoforms:
NA
          









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



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:33189470-33192158 
ALTERNATIVE
HsaINT1008046
(COL11A2)
Human
(hg19)
chr6:33157247-33159935 
Rat
(rn6)
chr20:3830458-3832873 
ALTERNATIVE
RnoINT0038862
(Col11a2)
Cow
(bosTau6)
chr23:7316024-7318758 
LOW PSI
BtaINT0040765
(COL11A2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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
  • 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"