Special

MmuINT0036314 @ mm9

Intron Retention

Gene
ENSMUSG00000027221 | Chst1
Description
carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 [Source:MGI Symbol;Acc:MGI:1924219]
Coordinates
chr2:92451851-92455409:+
Coord C1 exon
chr2:92451851-92451980
Coord A exon
chr2:92451981-92453299
Coord C2 exon
chr2:92453300-92455409
Length
1319 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGCCTGTCTCCTGTCCACAGACC
3' ss Score
12.54
Exon sequences
Seq C1 exon
GTAACTGCTGTGTGTGCTGCATATGGTTGGAAGAAGACCCCTGTCCCCAGCTGTCCCTTTGGAGCTACCTTCTCCACCTGAAGGCCTGAGGTGACTCACTTCCATCACAGGACCAGTTGAATTCCAGAAG
Seq A exon
GTGAGGCTTGTTTCCACGACTTTCTAATACAGGACCCACGTGGGCTTCTCGCCTGAGACACTTGGGCGCACATGCTAGCCGGCTCCTGCCCACAGGAGCCCTGGGATGGTCAGAAGGAGCATGGCTTGTTAAGGGTGGGATATGCAAGCTGTAGCTTGAAAGTTAGGGCTTCACGGCTCAGGGGTGAGGATAGGTCGGCTGGAGCGCCCGAGACAGTGTCAATGTGGAGAGCAGGCAAAGTCACGTGTCATAGCCTGGGGGCAGACTGTGGGACACAGAAGAAGGGCAAGGAGAGAGGAACTGGTGCCCAAGCCAACCTGCCTGCTGCCTCCACAGCCTGTTGGCCTCGGGGCTGTGCAGATCACTGGTCCGCCTTACAGCAGTCCTTCTTTGGGAGGTGTTGAGGTCCTTGGCACTGAGTCTGGAAGCAGCCCTGGCATCTCTCGGGACCTGGTGGCTGAGGCAGCATCCCCTGGCCTACCTTGTGACAAGCTTGGGACTTGCTTGTTGTGAGCCCATGGGATAGGCTTTCCTTTTCTATTTTCCTGTGGTTCCTCCCTCCCCCTCCTCCACTTTTGTGGACTGAAGGGCTGGGGGAGTAGCTTGGGGCCAGAAACAAGCCCTGAGTCCTATGCAGAGAGATCCATCCCAGTAGCCTCTGGGCCCTGCCCTTGCGCTAGGCCATTTGACTTATAACACTGCAGGTGCCTAGGTAACTGGGCATCTGGAGGCAGCTGGGTGCCCTCATTTGCAAGGTAGCAAGGCCATGGTCTACCCACCGTGGACAGTTCCTGGCCCAGCTGGATTCTGCTGTCAAGTCAGAATTCATGGAGCACAGGGGTCTCTGCTCTCCCGGATTTGTGTTTGGGGAGGGGAATTTGGTGTGCATCTTTCCTTTAAGGGTTAGAGGAAGACAGAGAAAAAGATCATTGTCTGGGGTGGGGGGTGGGTGAGTATCAGCCTGTGGGACTAGAAGATGCTGGCAGGGATCGCAGGCAGTGTCGGGGTGTGGCATGAGCCATCCTCTGGCCCCACCAAGTGTGGAAGCTGGGAGAGTTGGGTTTTGACACAGTAAGCAGGCTGGGCTAGGAAAACCAGAGCTCAACAGGGAGGCCTCTGCAACCACAACTCTCTTAGCTCTTGGGGTCCAGGGAGTCGGTCTGTTTAGCTCTCTGAAGCTCCCGGGAGTCACCAAGAAAATGACAAGTGCCTAGGTATTGTAGGTCTCACGGGATGTGTGAACACTGGGTGTTTTCCTGGACCCCGTGGTGGCTCTTGGCTGTGTGAAGCACCTACCCTTGCCTGTCTCCTGTCCACAG
Seq C2 exon
ACCCGGTGCCTTGGAGCAACAGCCCCATGACGGTGCCCAGCCATGCAATGTTCTTGGAAGGCTGTCCTCCTCCTCGCCCTGGCCTCCATTGCCATCCAGTACACAGCCATCCGCACTTTCACCGCCAAGTCTTTCCACACTTGCCCTGGGCTGACAGATACTGGCTTGGCAGAGCGGCTGTGTGAGGAGGGCCCTACCTTCTCCTACAACCTCTCCAGGAAGACCCACGTCCTGATCCTGGCCACCACACGCAGTGGCTCTTCCTTTGTGGGCCAGCTCTTCAACCAGCACATGGATGTCTTCTACCTGTTCGAGCCGCTCTATCACGTCCAAAACACGCTCATCCCCCGGTTCACCCAGGGCAAGAGCCCCGCAGATCGCAGGGTCATGCTAGGTGCCAGCCGGGACCTGCTGAGGAGCCTTTATGATTGTGATCTCTACTTTCTGGAGAACTACATCAAGCCACCTCCAGTCAACCACACCACCAACAGGGTCTTCCGCAGAGGGGCCAGCAGGGTCCTTTGCTCCCGTCCAGTGTGTGACCCTCCAGGGTCCTCTGACCTGATCCTGGAGGAGGGGGACTGTGTGCGCATGTGTGGCTTGCTGAACCTGACCTTGGCAGCCGAGGCTTGTCGTGAGCGCAGTCATGTGGCCATCAAGACTGTGCGGGTGCCCGAGGTGAATGACTTGCGGGCTCTAGTGGAAGACCCCAGGCTGAACCTCAAGGTCATCCAGCTGGTGCGAGACCCTCGTGGCATCTTGGCTTCTCGCAGTGAGACCTTCCGGGACACCTACCGGCTCTGGCGGCTTTGGTACGGCACAGGGAGGAAGCCCTACAACCTGGATGTGACACAGCTGACCACTGTGTGTGAGGATTTCTCTAGCTCTGTGTCTACTGGCCTCATGCGGCCCTCCTGGCTCAAGGGCAAGTACATGCTGGTACGTTATGAGGACCTGGCCAGAAATCCAATGAAGAAGACAGAAGAGATCTACGAATTCCTGGGTATCCCCCTGGACAGTCACGTGGCACACTGGATCCAGAACAATACGAGGGGCGACCCCACTTTGGGCAAGCACAAATACAGCACAGTGCGCAACTCTGCAGCCACAGCTGAGAAGTGGCGCTTCCGCCTCTCCTATGACATCGTGGCCTTTGCCCAGAATGCCTGCCAGCAGGTGTTGGCTCAGCTGGGCTACAAGATGGCCAACTCAGAGGAGGAACTGAAGAATCCGGCCATCAGCCTAGTGGAGGAGCGTGACTTCCGCCCTTTTTTGTGACCTGGGTGTGGTGGGGGTGGGAGGCAGGTGGCTCTGGTTTTGCTGACGCGGACCTACTATGGGCCGTCTTTAACTGTTGCCTTATCTCCCTCCTCCCTCTCCCACCCTGTCTGTGTATCCATTCCAGCCCCTGCCCACTCTCCCCTTTCCTTCGCCTCTCCCACACCATCTGTGTGTCCTTCTTGACCTTGCCCACTTCCTTTTCTCCTGCCTCTTTTTGCCCCTGAAATTTGCACTATGTCTCTGGAGGGGAACACTGGGCAGAGGGCGTATGATGTGGGGTTACTCCCCCCACCCCATTTAGACACAAGGATGTTGGGTCTCTGTGAGGATGGGGACGATGTTTACAGGCACCCAATCGCACATTCATTCACACGTGCACACAGGCACACGATGAGAGGCACCCCAGCACACAACTGGTAGTTTTGCAATTGTCTTCTCAAGGTAAGAGGATGGACACAAAGGGGCCGTACCTCCCCAGTTTAAGGAAAGGGTCCATCCCCGCCCCCTTCCTGCTCCCTCCCCTGGAGTAGGGCACCCGTCCCTCCTGCACACCCTTGCCTGGTGGTGAGCAGGGTTTTACTGTGAGGTGAATTGGGACTACTTTCTATTTGGTTTGTGGTGAGCTTGTCTGTCTGAGTCTTGTGGCTACCCCTAGACCAGTAATGGCTAATGAATCTTAGAAGTTTCTGATTGATCTTGGGGTCCCTCTGTGCTATTTCTTTGTGCCAAAAAAAAAAAAAAAAGACAAAAAAAATGTGGATCAGTTTGCAGAGTGAAAATTGAAATGCTTTATTTGTGTTTTCTGTAAATAAAAATGTGCAGTACTGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027221-Chst1:NM_023850:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
5' UTR





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
PF0068522=Sulfotransfer_1=WD(100=78.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000064246
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:45650966-45651992 
ALTERNATIVE
HsaINT0035272
(CHST1)
Human
(hg19)
chr11:45672516-45673542 
ALTERNATIVE
HsaINT0035272
(CHST1)
Rat
(rn6)
chr3:81509515-81510703 
LOW PSI
RnoINT0036366
(Chst1)
Cow
(bosTau6)
chr15:76575890-76577334 
LOW PSI
BtaINT0038430
(CHST1)
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: 
TGGTTGGAAGAAGACCCCTGT

				
R: 
GATCAGGACGTGGGTCTTCCT

				
Band lengths: 
344-1663

			

		

	





	
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






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