Special

MmuINT0140198 @ mm10

Intron Retention

Gene
ENSMUSG00000026927 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:MGI Symbol;Acc:MGI:1915362]
Coordinates
chr2:26384682-26385145:-
Coord C1 exon
chr2:26385083-26385145
Coord A exon
chr2:26384822-26385082
Coord C2 exon
chr2:26384682-26384821
Length
261 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
AACTTCGCCCTTCTCTCTAGGCC
3' ss Score
9.57
Exon sequences
Seq C1 exon
AAACGGGCTGTAAAAGCAGAAAATCATGTCTTGAAGCTGAAACAGGAAATAAATTTGCTTCAG
Seq A exon
GTAAGTAAAGAGAAAGGTTTGGCTGTCATACATGTGAGTTCAGGGAGGGAGAAAATAGTGTAAGCCAAGCACAGCGGTCGGAGCAGTCAGGAGGCTGAGGAAAAGGATAGTTGTACATTTAAGGCCAGCCTGGGCTACAGAGGCAAGAAGCACCTGTTTTGAACAGGCCAGGGCCAGGCTGGTCCCCGTGTCCAGATGTGTGCCCGTCGTGATGCAGAGGCTGAATTGCCTCGGGAGCACTAACTTCGCCCTTCTCTCTAG
Seq C2 exon
GCCCAGCTCTCAAACTTGAGGCGAGAAAATGAAGCCCTGCGGTCAGGCCAGGGTGCCAGCCTTTCTGTAGTGAAGCAGAACACCGACGTGGCCTTGCAGAACCTCCACCTTGTCATGAACAGTGCACACGCATCCATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026927:ENSMUST00000028293:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.085
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0026115=Tropomyosin=FE(10.8=100),PF131661=AAA_13=FE(16.7=100),PF0076914=ERM=FE(11.1=100)

							
A:
NA

							
C2:
PF0026115=Tropomyosin=FE(24.7=100),PF131661=AAA_13=PD(12.5=31.9),PF0076914=ERM=FE(25.6=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109737





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028293, ENSMUSP00000077133, ENSMUSP00000109735
  



Associated events







Other assemblies


mm9




Conservation


Human
(hg38)
chr9:136404195-136404630 
LOW PSI
HsaINT1041090
(SDCCAG3)
Human
(hg19)
chr9:139298647-139299082 
HsaINT0146373
(SDCCAG3)
Rat
(rn6)
chr3:3829747-3830019 
ALTERNATIVE
RnoINT0132059
(Sdccag3)
Cow
(bosTau6)
chr11:103912224-103912597 
LOW PSI
BtaINT0129895
(SDCCAG3)
Chicken
(galGal4)
chr17:7891251-7891359 
ALTERNATIVE
GgaINT0125718
(SDCCAG3)
Chicken
(galGal3)
chr17:8580350-8580458 
ALTERNATIVE
GgaINT0125718
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGCAGAAAATCATGTCTTGAAGCTG

				
R: 
GCGTGTGCACTGTTCATGACA

				
Band lengths: 
180-441

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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