Special

MmuINT0038934 @ mm9

Intron Retention

Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34183385-34186623:+
Coord C1 exon
chr17:34183385-34183447
Coord A exon
chr17:34183448-34186563
Coord C2 exon
chr17:34186564-34186623
Length
3116 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACT
5' ss Score
8.77
3' ss Seq
TACATGTATGTCTCCCTCAGGTT
3' ss Score
8.85
Exon sequences
Seq C1 exon
TACCCCACCCCAGGTGAAGAGGAAGGAGTCCTGGAGTCCAGTCCCTTGCCATTCCTTGAAGAG
Seq A exon
GTAACTTCATCCCCAGCCTCATCCCAGCCAAGGGCCCCAAACCCCATAGCATCTTGAGGAGCCGTGCCTCCTTGGCCGGAGGGCTCTTCATTTTCCTACTTAAGACTTTTCCAGTCACTCTAGACCTCTATCTGCTTGTCTAAGTATGGTCAATTCTTCTGATGTCATGGCCGCCTCATTGTCTTTTGACTCTAAAGTACACTCTCCATGTTGGTGTTCAGTGAGTTCCTCCTGTGCCACAGTGCCATTCTTGGGTCCCTTTTCTGTCCAGCACTCTCACTTTCTTCTCTCTGTCTTTGGTTTTGGATTCCTCATCTATCATTATGTCTATGGACTGTCCTGTGTCCAGCCCTCCGGCCATCCTAGTTTTCTACTGTTTCCTCTAACCACACCCATTTCCAAACATCCACTTTGTGGTCAGTAGTCATCCCGTTTCCATTCAGTCTCCCCTTGATCCCTTGGGGAAGAACACCCCAGACCCAGCGACCCTCAGGATCCTTTGGGCTAGAAGTTTTCAAACCCTGGGACCCATAGGACATCTGCTCTCAGGTCTAATGCCTCCATCTATCCTTCCTCCCTCCTGGTCCTTGGGAAGGAGCAGACAGATCTTCAGGTCTCCCCAACAGCTGACAGTTTCCAGGCAGAGGAATATGGGGAGGGAGGCACAGACTCCCCAGCAGGGTTCTACGATTACACCTATGGCTATGGGGATGATTATCGTGAGGAGACCGAGCTTGGCCCTGCCCTCTCTGCGGAGACAGCTCACTCAGGAGCCGTAAGTGGAAGCAGCTCCTGGTCCATCCTTTGCCATCAGGAGATGCGATGTGGATTGCTTCCTGTTTGATCCTTGTTGGCTGTGGGCTACTTCCTATTTGATCCTTGTTGGCTGTGGGCTACTTCCTGTTTGGTCCTTGTTGGCTGTGGGCTACTTCCTGTTTGGTCCTTGTTGGCTGTGGGCTACTTCCTGTTTGGTCCTTGTTGGCTGTGGGCTACTTCCTGTTTGGTCCTTGTTGGCTGTGGGCTACTTCCTGTTTGGTCCTTGTTGGCTATGGGCTACTTCCTGTTGGTTTGTCACATTCCCGTCACATGAGATGTCTGTGTTGCTTGAGAAGATCACTTTCTGCTTTCTCTTGCCCGTGTCTTAACCCGTGGTTCCCTGTAGATCCTCTGTCTGTGGCAAGTGGACTTTTTTCAATCCCACGGCTACTTCCTTCCTTTTTTGGCCACTCTTTGTCTAAATCAAGATGGATGTTACAAACCTGTTCAGTCAATAAGAAGCTTGTGCCCAGTGCCCATCTGTCTCACTCATCTCTTCTTGGTCAAAACAACTTTGTGTCCATGGTGACGGCAGAGTTTCTAGCTTCCCCTGTGGCATCTTGCAACCTTTGCAGCCACTTCTGGTCTGTGTTTCTCTGTCTTCTGTAGCCTTAATGTCCCTCTTGGTGACTGTGTGAGGCTGAACTAAAGGGATTGTTTGTGTTCTGATCTTCTTGATGTCTTGTGTCTGTTTTCTTTGACAATAAGCCACTCCTGGGTACTTCAGATTATCAGAGTTAGAAGGCTATCCGTTGTGGACCTAGATATTTATCATGGCCATTTCCTGTGTGTCCTCACCTTGCTGTCGGTGTGTTTTCTGGACCCTGCCTTTCATTGTCTTAATTCTCTTTTCGAGAGTCACTTTCTATTTGTTTTTCTGAATTTCTTTTCTCTCTTGGTCATGATAGCCATGCTGTTTTTGAAGATCCACTTCCTCGATTCTTTTTTTCTTGGCTGCTTCCTGTCTCTCTGAGCATTTCCTGTCTGTTCACTGTGTTTTCTAGCCATCTTGGCCATGTTTAATTTTTCTTGGCTCTGGCATAAGTGGGTGTCCCTTTATTTGCCTCCTCAGTGATTTTCCCAGGTCTTCAAACACCCCTGGCTGTTGGACTGCTACCCCTTGGCTCCGCTCTGTCCTTTGCCTGCCTTGCTGCCACAGCTGTCCCCTTGCTGCTGCTGCTGCTGCTGCCTAATGCTGTGCCCTGCCCATCCCTTATGGCCACCCTTGCTGCTTTTGCCTTGTGCCTCTTTCTGAGTACTTGGGGTTGAGCTGGAATTTGGGAACTGATCATGCCTAACTGGCCAAGGTAGGGGTGGAGGGGAGGATGCTAACGGTCTTCGTTGGGGGTGGGGGGGTGGAGTGGTAGCAAATGACCTTGTTCCTCTCTGTCGCTATCTTTGGTCTGGCCTAGAGCTTAGAGTGAGAATTGGGGTGGAAGAGTGGGAGGGAGGGACTGGTCGACGTAAGGGGAGGTGTATATCATAAGGGAGGAGAAGGGAGGCACAGAACTCTTGCTGGGAAGGGAGCTAGGGAATTATGGGAGTTACTTCTGAAGTTTAGTTAACTGACCCCAAGAGCTGTATTCTTCCAAAATCCAGTCAGAAGGCTAGAATCTGGGATATCAGTGACAAGGGTTTTCTAGATCTCCTTTGTGTGTGTGTTTTGACTACACACACATAAACATAAACACACAAACACGTATATGTCTATATGTATGTGCATACCACATGCATACTCGATGCCTATGGAGGTCAGAAGATCAGGGTGTTGGATCCTCTAGAACTGGAGTTAAAGATGGTGTGAATCACCGTGTAGGTGCTGGGAACCAAATCTGGATCCTTTTCGAGTACAACAAAGTGCTCTTAACTGCTGAGCCATCTTTCCAGCCCCTCTGGGCAATTTTACCTTGTCTATACATTAGGGCACACACTTTTTATTTTCCGGAGATAAACCCATGGCTTTTAAAATCAGATTGTCATGTGGTTCCCTGCCTTACACCCAAGAAATAAACCTACCCACTTCTTAACAAGCAGGGTAAGGATGGAGAAGGATCTGAGAATTCCTGGGGTTAGAAGGAGCCTTTGGTGACAGGGTGGGGTCCCCCATAAGAGGAATGCTAGGGTTTGGAATCCAAAGGGGCAAGACTTTCGGGGTGGCAGCATGACCAGGGACCAGGGCTTAGGTTTTGGAGGTGGTGTGCAGGAGTTCCTGCAAGTGAAGGCTGGAGTTGGGGTGGATCAATCCTGGTGTCCTGGCTGTTCACAGGCCCCACTGGGGGTTACATGTATGTCTCCCTCAG
Seq C2 exon
GTTGCCCACGGACCCCGGGGGCTAAAGGGAGAGAAGGGAGAGCCTGCAGTGCTGGAGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330-Col11a2:NM_009926:6
Average complexity
IR-C
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(1.7=5.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084772





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000076193, ENSMUSP00000076193f1530A, ENSMUSP00000109895, ENSMUSP00000122082
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr6:33181171-33184991 
ALTERNATIVE
HsaINT1008101
(COL11A2)
Human
(hg19)
chr6:33148948-33152768 
Rat
(rn6)
chr20:5322035-5324175 
ALTERNATIVE
RnoINT0081792
(LOC100911886)
Cow
(bosTau6)
chr23:7308125-7310223 
LOW PSI
BtaINT0040828
(COL11A2)
Chicken
(galGal4)
chr23:4931623-4931874 
LOW PSI
GgaINT1009861
(COL16A1)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr12:329760-330497 
DreINT0049029
(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
  • 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"