Special

MmuINT0153258 @ mm9

Intron Retention

Gene
ENSMUSG00000026811 | St6galnac6
Description
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 [Source:MGI Symbol;Acc:MGI:1355316]
Coordinates
chr2:32467744-32470707:+
Coord C1 exon
chr2:32467744-32467923
Coord A exon
chr2:32467924-32470300
Coord C2 exon
chr2:32470301-32470707
Length
2377 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
TGTCCCTCCTTGCTCCACAGACG
3' ss Score
11.43
Exon sequences
Seq C1 exon
GAGCAGCGGTCAGCAGTGTTTGTGATCCTCTTTGCCCTCATCACCATCCTCATCCTCTACAGCTCCAACAGTGCCAACGAGGTCTTCCACTACGGCTCCCTGCGGGGCCGCACGCGTCGGCCAGTCAACCTCAAGAAGTGGAGTTTCTCCAGCGCCTACTTCCCTATCCTCGGCAACAAG
Seq A exon
GTAGAGCAGCTCCTGAGGGGCGTTCCCTGACCTCTGCTAGCCCCGCCCCAAACTCTCGGGGCGTTCCCTGACCGCTGATAGCCCCGCCTCCCAACTCTCGGGGCGTTCCCCGAACACTGATAGCCCCGCCTCCCAAGTCTCGGGGCGTTCCCTGACCGCTGATAGCCCCGCCTCCCAACTCTTCTTTCCAATACCCGTATGCCTCCTCTTAGAGGCGAGGACGGATGAGGCCCATGAGTTAAGATCATGGCTCTTTGCTCAGGATGGGATCTTGGACAAGTGTTCTGTAGCAGGCCTTAGTTCTCTCTAGGATCCTACCCTTAGTGTTAAAAAGTTTCATTTTAGCCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGAGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGCTCCAGGACAGCCAGGGCTACAGAGAGAAACCCTGTCTCGAAAAAACCTAAAAAAAAAAGTTTCATTTTTTTTGGTCCAGTGAGATAGTTCAGTAGGTAAAGGTGTTTGTTGCCAAGCATTGCCTGAGTTAGGTCAATCTCTGGAACCTAATAGTGGAAGGAAAAGACTGACTGCAGCAAGCTGTCCTCTGGCCTCCACACGTGTGTGTTGTGGCATGCCTCCCCCTCAAACACACATGCACATGTAATTCTGAAAAATAAAATCTTCTGGCTGGACATGGTGGTGCGTGTCCTTTAATTCCAGCACTCGGGAGGCAGAGGCAGGCGAATCTTTGTGAGTTCGAGGCCAGCCTGGTCTACGAGTAAGTTTCAGATAGCCAGAGCTACACAGATTCCCTGTCTCAAAACAATATTCATCTTCTGAGTTGGACTTCTGGTTTTCATGGCTCTCTGGGGACACACCCCATAAGCTTGGGGGGAGAACGCTAAGGTTCTGGAGAAACAAAATCAGGAACAATACTGGGTACCTTGTGTCGAGTGACAGCTGAGCCATGCTGCTTTCTCTGTAGAAGCGATGAGGTGATCACGGCTAAAACCACAGGCATGGGAGGGTCCAAGTCTCCTAGCCCATGCTGAAGTGCAGCTACTGAGAAAGGTCGAACGACTAGAGTCTAATAGGATTCAGCACTCTGACCTCTATGGACATGGTCAATGTCATGGCCAATGTCATCTCTGGGGATCTCTCTTTGCCCGAGGTACCTGTGAGATTCACACATGCAGGCTGCCCTCCCTTGCTAGATTTTCTTCAGAGGCTTTGTGTATTTAGTGGAGGACCGTTGGCTCTGGGCACACCCTCCCTGGCAAAGGACCCGTAATAGGTGTTACGAGAGATGGGAGAGAAGGGGAGAAAGTTGAACCGCTGAGTGTAGGAGGTTTGAAGGTGAGGACGTCTGAGTCTGGCTTGTCACTTCTCCCAGCCTGATGGTTAGAAGACGAGGTAGAGGAGCTGTGTCTCCAGTGTTGGACCTTGTTAGAGGCTATGGAGAATTTGTATGGAGGCTTGGTGCGTTTGGAGGAAGCGTTCTCTGCACAGGGCTGGGTTCCAGCCCGTCTGTCTCCTGTTTCTCAGTGTGCTACCCCATGTCTTTGTGCTTGCTGGTCTGGTAACTTGTTCTTCAGATGTGACTCTACAGACAGTTCTGAAGACGTCCCAACTCTTCATTCCCCCCACCATGTTTTTTCCTAGTGTATATTACATTGTCTGTTTCCCCAACTTAAGCCTCTTTCTTGTTTTGTTTTTTAGTTTTTTATTAGCATATAATAATTAATGGGTTTCTTTTTTTTCTTTTTTTAAGTTATTTACTTAACAGATTGATCTCAGCTTCTCTTGCTACCTCTCCCCCATCCCTCCCTGTCACCTCCCCTCCCCCATCCACTCCTATAATGGCTTTCTTACGACTTTTTTTTTCTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTGGGTTTCTGAGACAGGGTTTCTCCGTGGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCCGGCTACAACATTTTTATGATACATATAATATGTAGTTCGATGATCTCACTCCTCCCTTGCCTTCTCTTCCTCAGTCTCTCCCTCCTTCAGCCACTCCCCCAGCGTCCATAACTGCCTCAAGAAGGGGTGGAACCTCTAGAGCCTCTGCTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCCTTAGCTCTGTTCCTAGCTAGTTAGGAATATCTGCAGAACCTAAATTAATGTGTTTTGAAAGATTGCAACGGCCGCACAGGACCCTGCATAGAGCATCCCTGATAGTGTCCCTCCTTGCTCCACAG
Seq C2 exon
ACGCTGCCGTCCAGGTGCAACCAGTGTGTGATCATCACCAGCTCCAGCCACCTGCTGGGCACCAAACTGGGCCCTGAGATTGAGCGGGCTGAGTGCACCATCCGCATGAACGATGCTCCCACCTCTGGCTACTCGGCTGACGTCGGAAACAAAACCACCTTCCGCGTAGTGGCCCATTCCAGTGTATTCCGTGTGCTGCGGAAGCCCCAGGAATTTGTCAACCGGACCCCTGAGACGGTGTTCATCTTCTGGGGACCCCCAAACAAGATGCAGAAGCCCCAGGGCAGCCTCCTGCGCGTCATCCAGCGGGCGGGCCTCATGTTCCCGAACATGGAGGCCTATGCCGTCTCTCCCGCCCGCATGCAGCAGTTTGACGACCTCTTCCGGGGTGAGACGGGCAAGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026811-St6galnac6:NM_016973:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.048
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0077713=Glyco_transf_29=PU(16.1=73.3)

							
A:
NA

							
C2:
PF0077713=Glyco_transf_29=PD(48.9=95.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000080555





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000071983, ENSMUSP00000092654, ENSMUSP00000092655, ENSMUSP00000108914, ENSMUSP00000108915, ENSMUSP00000114934, ENSMUSP00000115430, ENSMUSP00000118893, ENSMUSP00000121833
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:130653323-130656790 
LOW PSI
HsaINT0159880
(ST6GALNAC6)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:98572651-98575104 
LOW PSI
BtaINT0141694
(ST6GALNAC6)
Chicken
(galGal4)
chr17:4873515-4873671 
ALTERNATIVE
GgaINT1026495
(ST6GALNAC6)
Chicken
(galGal3)
chrUn_random:7559118-7559274 
ALTERNATIVE
GgaINT0004882
(ST6GALNAC6)
Zebrafish
(danRer10)
chr21:3671543-3673504 
LOW PSI
DreINT0156617
(st6galnac6)
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"