Special

MmuINT0152946 @ mm9

Intron Retention

Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48427770-48428397:+
Coord C1 exon
chr6:48427770-48427940
Coord A exon
chr6:48427941-48428265
Coord C2 exon
chr6:48428266-48428397
Length
325 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
GACCTGAATGTTACCCATAGGCC
3' ss Score
7.14
Exon sequences
Seq C1 exon
TGGCCTGTGGCTGGAGCCCCTGGACTCCATGGAGCCCTTGCAGCCAAAGCTGTAATGTGGGCATTCGACGGCGCTTTAGAGCAGGCACTGAACCACCTGCTGCCTTTGGGGGTGCTGAGTGCCAAGGTCCCAATCTAGATGCTGAATTCTGCAGTTTGAGGCCATGCCGAG
Seq A exon
GTAAGAGTGGGAACCTAGAGTCTGAGACTTCCTTGGAGAACCTATCTAGGGTTCCTTCCAGAAAGAAACCAACAATACCCCCCAGGACCCCATTAGTGATATAAGGATCCTAAGAGGTGGGTTCCCAGAGGCCTTGCGAGTCCATTCCCTTAGAAAGACCCTCCCTAGAGGCCAGTCCACTTCCTCTCTGAAGGCACCAGTTCTCCTAGGGTAGAGGTGACCCTGCAGATGAAGTTACACAAGATGAGAAGGAAGGGGTGCGTTTGGATATCTGGGTTTGGGAGGGAGGTGTGCCGGGTATGGAAGACCTGAATGTTACCCATAG
Seq C2 exon
GCCCTGGTGCAGCATGGAGTTCCTGGACCCCATGCTCAGTGCCCTGTGGTGGTGGCTACCGAAACCGCACTCAAGGCAGTGGCCCGCACAGCCCTATCGAGTTCTCTACCTGCAGCCTGCAGCCCTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797-Sspo:NM_173428:59
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=0.022
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009313=VWC=PD(39.3=41.4),PF053758=Pacifastin_I=PD(3.3=1.7),PF0009014=TSP_1=WD(100=87.9)

							
A:
NA

							
C2:
PF0009014=TSP_1=WD(100=88.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000131401





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047991
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:149808655-149809041 
HsaINT0159525
(SSPO)
Human
(hg19)
chr7:149505743-149506129 
ALTERNATIVE
HsaINT0159525
(SSPO)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr4:113469228-113469517 
BtaINT0141464
(SSPO)
Chicken
(galGal4)
chr2:427632-428017 
GgaINT0095202
(SSPO)
Chicken
(galGal3)
chr2:334514-334915 
GgaINT0095202
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGAGCCCCTGGACTCCATG

				
R: 
CAGGCTGCAGGTAGAGAACTC

				
Band lengths: 
278-603

			

		

	





	
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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