Special

MmuINT0039780 @ mm10

Intron Retention

Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97988948-97989384:-
Coord C1 exon
chr15:97989286-97989384
Coord A exon
chr15:97988993-97989285
Coord C2 exon
chr15:97988948-97988992
Length
293 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
CTATACCATCTTCTTGTCAGGGT
3' ss Score
5.66
Exon sequences
Seq C1 exon
GGCGAAGCTGGTCCCACTGGTGCTCGCGGTCCTGAAGGTGCTCAAGGTTCTCGTGGCGAGCCTGGCAATCCTGGGTCCCCTGGGCCTGCAGGTGCTTCT
Seq A exon
GTAAGTTCATCTCTTTGGCCTGGAAGGCATGGCATGTGTGGCCTTGTCACAAATGTACATGTCACCTGGAGTCCCAGTCACTGGGACCACTAAATGGTCATGCTGGCCAAACACCTCCCCCTGACATCCACGACTGTCTCCCTTCACCCGTAGTCCACCCCATGAGACAGGCAGGAGGGATGCCCCTGAAGCAGACAGCACTTGTCCCTGACCCCTAGACTGGGGCCCAATGGGCCGAATGGTTGGGTTGTTTCTTTGCTGTTTATTTTATCGCTATACCATCTTCTTGTCAG
Seq C2 exon
GGTAACCCAGGGACTGATGGTATTCCTGGAGCCAAAGGATCCGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483:ENSMUST00000023123:19
Average complexity
IR
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(2.5=6.1),PF0139113=Collagen=FE(36.8=100),PF0139113=Collagen=PU(15.2=36.4)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(16.1=100),PF0139113=Collagen=FE(17.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000023123





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000085693
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr12:47987314-47987610 
LOW PSI
HsaINT0038821
(COL2A1)
Human
(hg19)
chr12:48381097-48381393 
ALTERNATIVE
HsaINT0038821
(COL2A1)
Rat
(rn6)
chr7:139468197-139468441 
LOW PSI
RnoINT0039609
(Col2a1)
Cow
(bosTau6)
chr5:32467200-32467476 
ALTERNATIVE
BtaINT0041551
(COL2A1)
Chicken
(galGal4)
chr7:526045-526496 
LOW PSI
GgaINT0045575
(COL5A2)
Chicken
(galGal3)
chr7:530644-531095 
LOW PSI
GgaINT0045575
(COL5A2)
Zebrafish
(danRer10)
chr8:21174159-21174243 
LOW PSI
DreINT0049551
(col2a1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGAAGCTGGTCCCACTGGT

				
R: 
CGGATCCTTTGGCTCCAGGAA

				
Band lengths: 
140-433

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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