Special

MmuINT0069482 @ mm10

Intron Retention

Gene
ENSMUSG00000032649 | Colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:MGI Symbol;Acc:MGI:2138232]
Coordinates
chr1:152468449-152471805:+
Coord C1 exon
chr1:152468449-152468559
Coord A exon
chr1:152468560-152471687
Coord C2 exon
chr1:152471688-152471805
Length
3128 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
GCTGTAAATTCTTCTTTCAGGTC
3' ss Score
9.79
Exon sequences
Seq C1 exon
GGCAGCCACTGATCACAATGTGGACAATACAACGGAAATACTCAGGGAGTGGCTGAAAAGTGTGCAGCGTTTGTATCACTATGTGGAGTGGAGGCCTATGAACGAGCCAGA
Seq A exon
GTGAGTAACTCGGAGAGATGCAAAAACTCTTCCTCCTCCTGCGCTCCTTCTCATCTGAGCTTCAGATCTCCTGGGGGTGCGCATGGATTTTCATTGCTATCCTTTCTGCATCTGACTTGCAAATGTGGCCTTTTCTTCTATTAATAGATTCGCACAACTCCCTGCTCTTCTGTGCTCCTGGGCTGCCAGCCAGGCTGTTCTCAACAGCGTATAAATTATAATGGTGTTGTATGTTTTAAATATTGATTCTATTTATTGGTTTTTTTTTAGGATGAACTGGCCTATTTTCATAAAATCATGGTGAAATTTTATAAATCTTCCGCACATACCTTACTTTTAAGTTATGTCTTGAAGGTTATCGCAAAGCAATCATTGAAGGCGCTAACTCACTTTGAACTGCATAGTATCTGTCATATACTGCGATTATTTAGTCAATATTCTAGTGATGAACATATAGGCTATTTCACTCTTGACATAGAAATTTCTTAGTCATTTCCAGCTCCATGTCAGATCATATATTTATATTAGTCTTGATTCTCTTGAGAAAGAGCAATAGGAAATATATAACATTATATACAGAGAATGTTATATATCGGTGATTTTTTAAGACTGGTTTATGTACTGGAGAATAGATAATCCAACAATATCTGTCTGCCTGCATGCTAGACAGCCAGAGAAACCAGGAGCTTCTGAGTCCAGGAAGCTGTAAGCCTTAGGACAAGAAAAATAAACTTACAGCCCCACGTGAAGGCCTGGGGACACATGGAGGGTTATTTAGTTGCAGCTCCATTGGAAGATTGAAGGAGCCCATGGTGTGGTGAAGGGAGTCAGCGCATGCTCAGTCAGCAAGCCTGCTTGTGTGGTCTTCTCCTCTTTCTACCTTTGTACCTAGTCCCCCATGTATTACAGTACCACCCACATTTAGGGCGGTCGTCCCCATCACTGGAGGTTCCCCATGCCAATCATCTCTGGAAATGTACACACAAACACACCTGCAATTTATTAATCCCCTTAGTATCTCTCAAACCAATCAAGTTGGTCATCCAGATCAACAACCACAGTGTCATACCACCAGAGAAGTCTTCCTAAGATACAAACTTCATTTCTTTATATTACAAAGGTTCAAATAGATCTCATGTGCACACAGAACAAAGTCCAAACCCCTGAGACAAACAAAGATTTCCATATTTCCTGCTCTTTCGCAAAAAAAAAAAAAAAAAAAAAAAAACCATATACTTTATCCAGAATGTCAAGTTTATTTCCAATGCCCAAGTCTGAAGCACACCCTGGAAGTGTTTTCTTCATTGTAGCCAGCTATCATCCTAACTCACAGACAATAGAGAAAGGGGTCATTTTATTCACCTGTAAAGAACTTTTTACTTCAATTGCTTATTTTCTATGCTGTCCTTTTGACAAGATTCATTGAGTTAGCCTTAATTAACTGGAATGTATTCAAACTTTTTGAAATTATCCATGAGCTTTTGGCAAGGCATACAATATACAAATGCTGTCTATTTCCCCCATCTCTGTATTTTTAGAAGGCACCAAATCAAAACGTGCTGGAAAAACAAATTAGTGAATAAAATAAAAAATAAATGTATTTGGTTCCCAAGGCAACTATGATTCCAGTTTCAAGATTTATAGACATTGAATGAATAAGTAGCCTGCATTTCTGCACAAGAAAAGCCATTTATTAAAAGCCAAATGTATAGAGTAATAATATCAACAAATGTCATTGCAGAACAAATATATTCTTCTAGACTCTGCCATATACATATATAAGCACTCATAATAGTTGAATACATACAAGTATATATAATATCTAAAATCCAAGTCTATGGTCTACATATTAAGCAAATTTGACAATTAAGTTTGAACACTATAAAAGATTGTAAATAGCTCTTGGGTATTTCTTGGATGCAATTTAGCCTACTCTTAAAAATGTTACACAGGAAGACTCTGTAGCTCTACTTTGCTTCCCAGATATGTCCTCTGTAGCCAGGTTTTTACTTTATATATTATATGCCAAGGTCAGTGTGAAAAACATTTCATAAGGCATTAATTTTTGGCAATATAGTCAGAAAAGCAGGAATTCCAGTAATTCCCACTGAAACAGTAATTGAGAAAGATATTGCAGAGAGTTCCTGGGTTGCATGTGTTTCATTTGTATAGTTACAGTCTCAATGTTTTGTGACTTTTCATGTGTTAAGGCAAACATACTGCGCATGCACCTCCAAGACCGTGACGTGGCAGCCAGCTAGAGTGACGTTCATATCCACCTCTGAGATACAAGCTGAGAGCTTGCAGAAGGACCTAGAGCACGCACTGAATCATTTGCCTTTGTGGCCATTCACGAGTCTAGCTATCTCATGATGTCAGCAGAAATCTCTAGACCATTATGTGTCTGCTCCATCATTTCACAAGACAGGTCAATGTGTTAAACTTTATTGAATCATTTACTGAGAGCTTAACAAGTAATCTAAGCCTTTGATTTTTGTAAGACACTCATGCCTTTAACCTGTACTTTCACATTTATCTGATAAGGTATATTAAGTATCTAAGAATATAAGCTTTGGGGAGTAACTGCCTGGATATGAATTCTGGTGGTATCACTTAATATAATACTAATTATTCTATACCAGTATTGTTGTCTCTGAATCCGAGAAAAATAGTAGGATTACTTCATAAGACACATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGAGCTTGCTGAAGAAAAGCCAGGCACAGTGGCTATTATATACTTTATAATTACAAGGCTGGTGCAGGGGGATACTTAAATCTAGGAATTCAAGATCACTCTCAGCAACACAGTGAGACGTCTCTCATCTCAAAGAAGGAAGAGGAGGAGGACAAAGAGGAAGAGGAGGAAAACCCACTGATGTATTTTATATACTGTTATGTTCAGTGGGAAACAAATTTCTAAATCTCTCATTGTTTCCGTTTGCCTATCTATGATATAGAGTTGATGTTTTCTGGTCTCTTGTGCCTTGTCCCTAGAGTGGCGGAGGAGTCATTGCATACAAACACCAAGGGCCCAGCTACATCCATGCAGACACTCAGTGGCTGTAAATTCTTCTTTCAG
Seq C2 exon
GTCTTACCCTGATGAAATCGGACCAAAGCACTGGCCAAACTCCCGGTTTTCTCACGTCATGAAACTGCGACAAGCAGCCCTTCGAACTGCGAGGGAAAAATGGTCAGATTACATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032649:ENSMUST00000044311:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.075
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF137041=Glyco_tranf_2_4=FE(30.6=100)

							
A:
NA

							
C2:
PF137041=Glyco_tranf_2_4=FE(32.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037532





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000119210
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr1:183975215-183978409 
LOW PSI
HsaINT0069713
(COLGALT2)
Human
(hg19)
chr1:183944349-183947543 
LOW PSI
HsaINT0069713
(GLT25D2)
Rat
(rn6)
chr13:69862574-69865715 
LOW PSI
RnoINT0040556
(Colgalt2)
Cow
(bosTau6)
chr16:66494532-66497427 
LOW PSI
BtaINT0067231
(GLT25D2)
Chicken
(galGal4)
chr8:7718869-7719562 
ALTERNATIVE
GgaINT0039806
([1])
Chicken
(galGal3)
chr8:8058719-8059412 
LOW PSI
GgaINT0039806
(GLT25D2)
Zebrafish
(danRer10)
chr1:57286523-57288176 
LOW PSI
DreINT0007395
(COLGALT1 (1 of 2))
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
  • 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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