Special

MmuINT0146352 @ mm9

Intron Retention

Gene
ENSMUSG00000017664 | Slc35c2
Description
solute carrier family 35, member C2 [Source:MGI Symbol;Acc:MGI:2385166]
Coordinates
chr2:165107581-165108433:-
Coord C1 exon
chr2:165108283-165108433
Coord A exon
chr2:165107645-165108282
Coord C2 exon
chr2:165107581-165107644
Length
638 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
GGGTGTCCCTGTCCCCACAGCAC
3' ss Score
9.52
Exon sequences
Seq C1 exon
AGCTTCCACTTTCCGCTCTTCATGACCATGCTGCACCTGGCCGTCATCTTCCTCTTCTCCGCCCTGTCCAGGGCACTGGTTCAATGCTCCAGCCACAAGGCCCGGGTGGTGCTGAGCTGGACGGACTACCTCAGAAGAGTGGCCCCCACAG
Seq A exon
GTAGGTCCAGTGTGGGGAGGGCTGCTGGAGAGCCTAGGATAGAAAGCAGAGGCCCTTGTGGCCACACGCTACCTACCTCCTCTCCTCCCCACCTCTCTCCCACGGCCAGGTCTCAGCAAAGCCGGCAGTTGCCCTTGTCTGGCAGTTGCCCTTGTCCGTGCTGGCTCACATGGGCCTCAAGCGGGCTCCACCAGACGCAGAATGGGGGAGCCTCACCCTGTAACCATGCTAAGTTGGGCTAAAAGATTTCCTAGGACTAGTGTTGAGTGGGCAGGACTTGAAGAGTGGATGGGGACCTCTGACCCTGGGGATGTGAGGTCGGAAAGGGAGCTGAGAGCTCGGCTGGAGGGGGAAAGGAAGAAGGAGGGTTAGCAGGCTGGGCCAGTGGAGGGCCAGGTGCCCCTCGAGCCATTTGGCAGGATCGGGTTAATCCTCTTGCATGGAACTGTTTAGATTCTCTCGCAGAGGAGACTAACAGGCCTAGCCAGTCAGGATGGGCTCCAGCGCTAAGCAGGACAGCCTTTGGCTAGGGGTTGGCCTTGAATTGCTTAGTGGAAGGGAAGACAAACAGGGCCTTAGGTGTCTAAGCCTTATGCTTGCCAACTGGCTGCCCTGCCTGGGTGTCCCTGTCCCCACAG
Seq C2 exon
CACTGGCAACAGCACTTGACGTGGGCCTGTCCAACTGGAGCTTCCTCTACATCACTGTGTCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017664-Slc35c2:NM_144893:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.021 A=NA C2=0.047
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0089215=EamA=FE(35.2=100)

							
A:
NA

							
C2:
PF0089215=EamA=FE(14.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000017808





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000104921, ENSMUSP00000104922, ENSMUSP00000104923, ENSMUSP00000116288, ENSMUSP00000118227, ENSMUSP00000118605, ENSMUSP00000119071, ENSMUSP00000120036, ENSMUSP00000123299, ENSMUSP00000123450, ENSMUSP00000123757, ENSMUSP00000125708
  



Associated events






Conservation


Human
(hg38)
chr20:46356638-46357622 
ALTERNATIVE
HsaINT0152592
(SLC35C2)
Human
(hg19)
chr20:44985277-44986261 
ALTERNATIVE
HsaINT0152592
(SLC35C2)
Rat
(rn6)
chr3:161806940-161807421 
LOW PSI
RnoINT0137691
(Slc35c2)
Cow
(bosTau6)
chr13:75805667-75805764 
BtaINT0135359
(SLC35C2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr20:10679730-10680884 
ALTERNATIVE
GgaINT0011632
(SLC35C2)
Zebrafish
(danRer10)
chr23:20506087-20507728 
LOW PSI
DreINT0150760
(slc35c2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCTTCCACTTTCCGCTCTTCA

				
R: 
AGGGACACAGTGATGTAGAGGA

				
Band lengths: 
214-852

			

		

	





	
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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