Special

MmuINT0153249 @ mm9

Intron Retention

Gene
ENSMUSG00000079442 | St6galnac4
Description
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 [Source:MGI Symbol;Acc:MGI:1341894]
Coordinates
chr2:32451214-32455994:+
Coord C1 exon
chr2:32451214-32451321
Coord A exon
chr2:32451322-32452533
Coord C2 exon
chr2:32452534-32455994
Length
1212 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGA
5' ss Score
5.94
3' ss Seq
ACCCTGTTCCCTCCTAACAGCGA
3' ss Score
11.1
Exon sequences
Seq C1 exon
GAGACAATCAGGCTCCTTTCTCAGCACCGGTTGGTTCACCATGATTCTGGCCCTGGAGCTGTGCGAGGAGATCGTGGTCTACGGGATGGTCAGCGATAGTTACTGCAG
Seq A exon
GTTAGACCGGCGCCCAGGCTGGGGGTAGGGGACAGGGAAGGAGGGGGAGGTGTGAAGTCTTGAGCCAGAGGGTCTGTGAGCCGTGAGGGCTTCATGATGGGTGACCCGGGCACAGACAGCCCCCAAGGGCAGGCCTTTGGGAAAAAGACCAACATTTAGCTGGGCATAGTGATCCTGCTCAGGAGGTGGAGACAGGAGAATGAGAATCAAAGCTAACCTTGGCTCCAGATCAAGTTCAAGGCTACCCCGCCCCACACCTTCTGAGAGCCCCTCTGAAAAACTCAAACCAAAACAAAGCCTTGTACACCTCTCAGGTTGGTGAACCGTCTATGTAACTATGAGACTTTGCTACGTGACATCATCTAATACAGAGGTCATACTTAAGAACCAGGAGGTGGTGCACACAGCTCTAATCCCAGCACTCAGGAGGCAGAGTTCAGGGCCAGCCTGGTCTACAGAGGGAGTTCCAGGGCAGCCCAGAGAATCCTTGTGTCAAACAAAACAAAACATCTTAGGATCCACGTGGTGGAAAGAGACCCTGCTCTCAAAATGTCTTTTGACCTCCACATGCACTTTGTGGCAGCTTCTTACCCCCCACCCCCCAAATAATGAATAGATGCAAAAAAAAGTTAAGTTGCCAAAAAGATTTGGCAAAGTGAGCCTTGGGTTAGACCCACCTGATGGAGTGCTCACCCCCTGGACCCTATATCTATTTTAATGAAACATTACAGATAGATTTAGTTGACTTAAATACTGTGAGTTCAGATATGGATATGGAATTCTATTATAAGCATGTTATATTCTTATATTTCAGTATTACTATAACTAAGGAGTCTGGGAAAGGCCCCAGATTTTCACCCTTTCCCTTCAGAACCTATGTCTCGGGTGTATGAGAGAAATGGTCACAGCAGCCTAGGCGCACACTACTTCCTAGCAGGAGGGCGTGCCGCTGGCCCTGGCTACAGGAGTTAGGCATGGGCCGCTCCTGCCTAGAGTTTATCCATTGACTCCATTTCCAGATGGCCTGTTGTAGGGGTGTTTTTCAGATCCAAGGTCACCCAGCTTGCAAGGAGCAATTTCTGAATCCTGGCCAATGGGCTCCTCGCCTGCCCGGTCTCTGCCATCTGTCTCCCTCCTGCGCAGCTGAGGCCTAGTCCCAGAGGCTGGCAGCTTTGAGGCCTTGTTCCACCTGACCCTGTTCCCTCCTAACAG
Seq C2 exon
CGAGAAGAGTCCCCGCTCCGTGCCCTACCACTACTTTGAGAAGGGCCGGCTAGATGAGTGTCAGATGTACCGTTTGCATGAGCAGGCTCCAAGGAGCGCCCATCGCTTCATTACCGAGAAGGCTGTGTTCTCCCGCTGGGCCAAGAAGCGACCCATCGTGTTCGCCCACCCGTCCTGGAGGGCCAAGTAGTTCCTGTTGCCAGTGACTGCCAGGCCTCAGCCAGGCCTGTGACCCATTCCAGGCCAACACGGCTCTAATGTGAGCATTTATGACTCACCTTCTACCTGACACCAGGTAGAACATGAAGTCTCTATTACCCAACACTGGGTACACTCGGAGGAACCTCAGGCCTTGTGACTTGAAGAGGAGTCGAGAAGATGCCATTTACACCACCCCTGCTTCCAGAAGAATCCACATCTTCATCTTGGGGTTTGTCCCACTGCCAGGTTGTTTAAGTGACCTTTGCCCTGGGTCCGTCGATGGCCCCACCTCACCAGCATTATGGCTTTATACCAGTCTTGAACCTTTCCTCTACCTGGCTCCAGCCACATGGTGCCACATTCTCAGGCTGGTGGCCCTGGTTGGTGCACCCTGGAACTTGGGATTTGATGGATGTGAGGGCCTTTGAGCCTCAGCCTCTCAGGACTGACTGTCTTGGGAGTGTGCTGGTAAAGGCAGATTTTCTGGACACTGTGTCTCTGTGGTAACGGATGTGGGATGGGGGTTAGTTAGGACAAGGCCTGTAGCCTGTTCCCTGGAGGGCTGACTGAGCCTTCCAGCCCTTCTCTAGGCCCACAACTGTCCTGCTCTTCCCGCATTGTCTGGACATCAGCCCTACAGTCTCCTGCCCCAGCATCCCACAAGCCTGACCTTCTGATGGTCTGACCACAGGACTGTGCTGGCCCAGGACAGCCACCCTGCCCTCACTCAACAGGCACAGAGCGGGGCCTGGGAGGACTCGGGGTGAGGAAGAAATTCCACCCAACGCCACTTTCCTGCCTCATGAGTCAGATTCCAAAGTCTTTGCCAGTCAGGCTGTCTCTTAACTGTGGGACATGATTCCTTTGTAAAACAGAGGGCAGAACGAACTCAGCGCGGGGAGGGTGCTGACCAGAAAGGAGTGGTCTCGGGGCCAGCCCTTTCTCTGAGTTTTGCTTTTCAGTACTAAAACACAGCCACCACCTAGCTGTTAAGGAGGGTGTGAGGCCACCCTGCGGAGGGAGCTGGTGCTCATTACAGATGATATAGCCCAGGCTAGCTTTCAGGAGGTGTCTGAACTAGGATGCTGGCAGCCTTGAGAGCTCACTACCCAGGCTCTGCCTCCTTCCCCCTTTGGAAGACTGAAGAATGGCACCCTGGGCTTTAGCTCTCTGCTTCAGAGTTCGGGACCCTCTGGGTGTAACCTGCGCGGTCCCCAGAGTCCCGTGCTTAGTTTAACCTCTCCTGCTACAAACTTGAAATTCCTTATTTTAGGTCTTGGTTTGAAACAAGGAACCTCTCAGTTTCCTTACCGGATCCCACAAAGGGCAGAACCCGTCATGCTAAGGGCTCTGGTGGCCTAGCCCACTCTCCCTCCTACCCATTTTCCCAGGAGTGACTAGAGACCTGGCACCTGGCCCACAACACTGCCCTTGTCCCTGTCCAGTGCCAGGTGGACCGGAAGCCTCATATGTGGGAGGGGAAGCAGAGAGGGAAATCTCTGAGCCAGGGTTACAGGCGGGAAGCCAAACCGTTTCCGCAGGCCTGGAGGGGCTGAGGGGCTGAGTGTAGGGATAGGCCATGAGTGGGTCGTGGGTGAGACGAAGGGTCCTGGCATCAGGCCTGACCCCATGTTCCCAGGCAATAAAGACAGTAGAGTAGTTCCTGCCTCACCAGATTGTATGAGCTCAGAGATGCTGGGGTGCCCCTTGGGGCTTACTTAGAACACACTTGGCTCTCAGTATTCAGAAGCCACCATTTAAATAGGGTGGCCCTCTGCCTGACTGATCCTGTTCCACCCTGGCATAGGTGGCATCAGTGCAAAATAATAATAATAATAATGATGATGTTCTCATCCTAATGAGAATAGTGTCTTCTGGTGCCATTTTGAGTGACTGTGACTCAGGAACAGAGATGTATGTTACCCCGAATTCCATGTTCCGTTGCGGAAACAGTTTCATGAAGTTTTATAGTTTTGCGGAACATAAAGTCCTAAGTCCAGGCAAGTCTAAAATACATTGGTGGGGACATCAGAAAGGTGGGTACGGCAAGCTGGGGAGGACTTTCCTATAAGGTCTGAGAGGTTGAGAGCTTTGGGTTGGTAGAAGCTATGTTCTGACAAAGGTAGTCAGGAAATGGCTGTGTGAAGCTACAGCTAGCCCAAGATCTGCTGATTTTGGCCTCTGGGCCATCTCCGGAGGCCTGGTTTCTTTCTAGGACTTTTTGCTCATGGTAGAGAGCTGGCTCTCCATCCCATTAGAAGTCTCCGCACCTGTGCCCTTCTCCGTGCATGTCCAGGGTCAAGAGACTCCCTGGTCCTGGTGGGATCTAGACTACTCCTTTCTGAGAGTCAGTCTTCCTGCTTTCAGCCATAAGGAAATGCTGACCCAACCCTTAGACAAGGCACACAGAGATGCTTCTGTCCTGGCTTCTGGGTGAGGTGTTTACTGCTGGGTTGGCCTGAATAAATTGTATTTCTCAGGGAAGCTGTCAACCACTTCCTCCAAGCACACAAAGATGCCCACTGACAGGTCTGGCTGTTGGCACAGCGTCTACTGAAGACTCCCATGATGAAACTCAGGGGCCCCCTCCTTGGACACTGTGGGTCCGGTACCTGCTGGAAGGTGAGAAGGGGGTAGAAGCCATGTATAGTCTTGAGGTGTTGTGGGGGCCACTGGGGTTTACAGACTCTGGCCTCTTGTGTTCCTTTTCCTCCTCCGGTTCTTTTGTCTCAGCCAGTTCTGCCTAAGCCCGGGGAGGAAGGGAGGCAGGTCCTACAGACACGGGTGGCTTAGGACTCCTTCATCAGGAATCTCGGCTGGGGTATGAGCGTCTCTATGGTGTCTATTGCGGGAGGAATGGAACTCCACGATTACGGGGAACAGTTGAGCACTCCTGTCTAGCCCCTGTCTGTGGAGACCCAGGTACTTCCCAGTTCATGTCCACGGCACCAGGCTCAGAGCGCGGCTTAAGTCTCCATCTCCGCTCACTGTAGAGGTTGAAAGTTGGAGTCCCCAGGCCTGGCTTCAGCTGAGCTTGGCACAAATCTGTCTGCTGAACAGAACTGTTGCTATAAGTTGGGAGCTGAGGGGCTGGAGAGATGGCTTAGCGGTTAAGAACACTGACTGTTCTTCCAGAGGACTGGGCTTTGAATCCCAGCAGCCTGATGGCAGCTCAAAACTGTAACTCCAAGATCTGACATTCTCACATGGACATACATGCAGGCAAAACACCAATACATACAAAATAAAATTTTAATTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079442-St6galnac4:NM_011373:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0077713=Glyco_transf_29=FE(14.3=100)

							
A:
NA

							
C2:
PF0077713=Glyco_transf_29=PD(22.3=87.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099882





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000092655, ENSMUSP00000115430
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:127908582-127909950 
LOW PSI
HsaINT0159872
(ST6GALNAC4)
Human
(hg19)
chr9:130670861-130672229 
LOW PSI
HsaINT0159872
(ST6GALNAC4)
Rat
(rn6)
chr3:11616310-11617592 
LOW PSI
RnoINT0144222
(St6galnac4)
Cow
(bosTau6)
chr11:98586350-98589665 
ALTERNATIVE
BtaINT0133007
(SIAT7B)
Chicken
(galGal4)
chr17:4871019-4871089 
LOW PSI
GgaINT1026492
(ST6GALNAC4)
Chicken
(galGal3)
chr17:5507087-5507157 
LOW PSI
GgaINT0124772
(ST6GALNAC4)
Zebrafish
(danRer10)
chr21:3689999-3691239 
LOW PSI
DreINT0156609
(st6galnac4)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCCTTTCTCAGCACCGGTTG

				
R: 
GTTGGCCTGGAATGGGTCAC

				
Band lengths: 
344-1556

			

		

	





	
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"