Special

MmuINT0152924 @ mm9

Intron Retention

Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48416288-48416868:+
Coord C1 exon
chr6:48416288-48416398
Coord A exon
chr6:48416399-48416673
Coord C2 exon
chr6:48416674-48416868
Length
275 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TCTTTCTCTCCTGTACCCAGATG
3' ss Score
9.91
Exon sequences
Seq C1 exon
AAAAGAACCAGACAGTGATCCACATGACCACTCCTGCCCCTGCCCCTGCCTCTGCCCCCAGCCCTCAGATTGGAGCCCATCTAGTCACCTATGTTCTGCCTCCCACGGCAG
Seq A exon
GTAAGTCATGCACGTGCTGTTTCAGATGCTGAGAGGGACTGCCCTAGTGGTTACCAGACCTCTAGAGAAACAGGATCTCTGGCCCAGTCCCCTGCCTTACACACACTGCCGGTGGTGAAGTCACCCTTCCCAAGTTGCACTGCCCAGCTCTGCCCCACCCTTGTTCAATTTTTCTGTCCTCTGTACTGCATCTCCCCTGTGGTTCCCTGATTGTCCTTGCCACCCTCTCTTTTGCCTTACTCGAGCCTACCTCTCTCTTTCTCTCCTGTACCCAG
Seq C2 exon
ATGCCTGCTATTCTCCCCTGGGCCTGGCTGGATTGCCCATGTGGGCACCATCCCAGCACTGGGAACACATCACCAGGGCTGACCCTGTGGAAGCTCCCATGGCAGGGCCTGGCCCCAGAGAGGGGGCTTCTGCTGAGTGGCACACCCAGCCACTCTATCTACAGCTGGACCTTCGTCGGCCTCGGAACCTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797-Sspo:NM_173428:39
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.342 A=NA C2=0.303
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0075420=F5_F8_type_C=PU(26.0=48.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000131401





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047991
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:149794899-149795210 
HsaINT1043036
(SSPO)
Human
(hg19)
chr7:149491987-149492298 
HsaINT0159503
(SSPO)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr4:113457174-113457463 
BtaINT0141441
(SSPO)
Chicken
(galGal4)
chr2:421175-421440 
GgaINT1026460
(SSPO)
Chicken
(galGal3)
chr2:327707-327893 
GgaINT0095187
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGTGATCCACATGACCACTCCT

				
R: 
AGTGAGGTTCCGAGGCCG

				
Band lengths: 
292-567

			

		

	





	
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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