Special

MmuINT0146355 @ mm9

Intron Retention

Gene
ENSMUSG00000017664 | Slc35c2
Description
solute carrier family 35, member C2 [Source:MGI Symbol;Acc:MGI:2385166]
Coordinates
chr2:165106117-165106454:-
Coord C1 exon
chr2:165106286-165106454
Coord A exon
chr2:165106201-165106285
Coord C2 exon
chr2:165106117-165106200
Length
85 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGC
5' ss Score
7.43
3' ss Seq
TGCCATGTCCTGTCCTGCAGGCC
3' ss Score
10.92
Exon sequences
Seq C1 exon
CGTGCAGCCCTGGTCCTGGTGGTCCTGCTCATTGCTGGGGGCCTCTTCATGTTTACCTATAAGTCCACGCAGTTCAATGTGGAGGGCTTTGCCTTGGTGCTGGGGGCTTCGTTCATCGGTGGCATCCGCTGGACCCTTACACAAATACTCCTGCAGAAAGCCGATCTTG
Seq A exon
GTGAGCCTCTGGGGAGGACTTGGGGCCGGGTAAACACAAAGCAACAGGCTCAGCCTGACAAAACTTGCCATGTCCTGTCCTGCAG
Seq C2 exon
GCCTCCAGAATCCCATTGACACCATGTTCCACCTGCAGCCACTCATGTTTCTGGGCCTCTTCCCTCTCTTTGCCATATTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017664-Slc35c2:NM_144893:7
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0089215=EamA=PD(13.4=33.3),PF0315111=TPT=PU(18.5=49.1)

							
A:
NA

							
C2:
PF0315111=TPT=PD(48.2=93.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000017808





     
      









    
Other Inclusion Isoforms:
NA
          









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



Associated events






Conservation


Human
(hg38)
chr20:46354966-46355072 
ALTERNATIVE
HsaINT0152594
(SLC35C2)
Human
(hg19)
chr20:44983605-44983711 
ALTERNATIVE
HsaINT0152594
(SLC35C2)
Rat
(rn6)
chr3:161805511-161805596 
LOW PSI
RnoINT0137694
(Slc35c2)
Cow
(bosTau6)
chr13:75801917-75804317 
ALTERNATIVE
BtaINT0135362
(SLC35C2)
Chicken
(galGal4)
chr20:11074152-11074436 
ALTERNATIVE
GgaINT0011635
(SLC35C2)
Chicken
(galGal3)
chr20:10678748-10679032 
ALTERNATIVE
GgaINT0011635
(SLC35C2)
Zebrafish
(danRer10)
chr23:20512754-20512871 
LOW PSI
DreINT0150783
(slc35c2)
Zebrafish
(danRer10)
chr23:20512956-20513814 
LOW PSI
DreINT0150784
(slc35c2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGGGGCCTCTTCATGTTTACC

				
R: 
GCAGGTGGAACATGGTGTCAA

				
Band lengths: 
169-254

			

		

	





	
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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