Special

MmuINT0150790 @ mm9

Intron Retention

Gene
ENSMUSG00000037617 | Spag1
Description
sperm associated antigen 1 [Source:MGI Symbol;Acc:MGI:1349387]
Coordinates
chr15:36151161-36153996:+
Coord C1 exon
chr15:36151161-36151321
Coord A exon
chr15:36151322-36153863
Coord C2 exon
chr15:36153864-36153996
Length
2542 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TTATTTTCTTGGTCCTATAGATG
3' ss Score
9.16
Exon sequences
Seq C1 exon
AATAGCACGAATCTTAACAGAGCTAGATGGATCAAAATGGCGGGAGAGACTGCCACCCATCCCAGCTGTACCCACATCTGAGCCACTGCGAGTTTGGCTCCCTGCTGCAGAGACCCCAGACCAAGATCCCTGTCCCAACAACTGCATGCCGAGCATCACAG
Seq A exon
GTATGGAGGACTACCCATGTCTCCTCACGAGGGAGCAGAAGCTGAACTATGGTGTCAGACGTGGGCTTAGGCTTTTCTCCCTCCTAACACGATTTCGGAAGCTGCTTCTCATCTACGTCCTTGTGAAAGGCAGGCAGGGAGGGAGTAACCAAGCCAGTGGCCATGTCTTAATGTGGAGCTGGCATTATTGAGAGGGGGAAGGAGGAAGAGGAAGAAAGGAAGGAAGGAAGCAAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGAAGGGAGGGGAAAGAGGAAGAAGAGGAGGAAGAAAAGGAGGAGGAAGAAATTATTAAGCTTTCCAGGAAACCACGTGACAACTTAACAGGAGTAAGAAAGAGTGCTGTGTTAAAAATAAACCAGAAAGCTGATTCAGGGGTGCTTGCTGTGCAAACCTGAAGACCTGTGCTCAGTGTCTAGGACCCATGGTGGAAGGGGAGAGCAAACAGCCTGAGATGCCTCTGAGTTCCACATGCCTGCTGTGGGACATGCCTGTCCATAGTCATACACACACCGCATGTACAGATAATCAGTTCTGAGGTAATAACATGCAGATATGGAGTAGGGAAACTTGGATGCTGAGTAAATATCACACCTAGCTTTAAGGTTTGTTGCTACTCATTGAATCTTTTGTTTTTGAACATTTGTTTTCTGTGTATGAGTACTTTACCTGCATGTATGTATGTGTACCACATATATGCCTGGTGTCAGAAGAGGGTACAGGTAGTTGTGAGCCTCCATGTAGGCACTAGGAATTGAACCCAGGTCCTCTGTAAGAGCAGCAAGTACTCTTAACCACTGAGCTGTCGTCTTTCCAGTCCCCAGGTTTTAAACATTGTGTGTATGTGGGTGTGTGCATTGGCACAGGTGCTCACAGAGGTCTGAAGGGTCAGCCATGCGTGCTGCATGCCAAGCTTGCGTGCTCTACAAGAGCGTAGTGCTCCTAACTACTGAGCCATGCTTCCAGTGCCCAGCTTTGCGGGTTTTGAGTAAGGGTTTTCCCATGGTCCAGACTGGCCTCTAACATGATGTAGAACCACGAATAACCCTGAGTGCTGGTCCTCCCACTTCTCCCTCCCAAGTGCTAGGACCTCAGGCATGTACCACAATGCCCACTCCCTGATGGTATTTGTAACCATTTCATAGACTTATTCTGCCATAATTCCAGCTTCATGAAATGTCTAAAGTACTAATACCCAAGAGTATTAAGTACTAATATTAGTACTTAGTATAAAGTACTAATACTTAGAGACAGTGTGCTTTATAATTACTGGAAACTGTGGGCTAGCGGGTTCACTGGAGTGGGCATGTGTGAGACTCAACCTCATATCATCTAGTTACCTGTGTCTTGGTATATGGATGACTACTGCTGTCTCTAACACAGTTCTTGTTCCTGTTAGTGTTTCCAGATTGCCAGAGGGGAAGAGAAGACATGGCAATGTGTGTAACACAGTGGGACACAGTGGCACTGCACTCTGCAGCATGTGGAACACAGTGTGGCACTACACTCTCAAACATGTGTAACACAGTGGCACTGCACTCTCCAGCATGTGGAACACAGTGGCACTGCACTCTGCAGCATGTGGAACACAGTGTGGCACTGCACTCTCCAGTGTGTATAACACAGTGGCACTGCACTCTCTAGCATGTGCAACACAGTGGCTCTGCACTCTCTAGCATGTGTAACACAGTGGCACTGCACTCTGAAGCATGTGTAACACAGTGGCACTGCACTCTGCAGTGTGTGTAACAGTGGCACTGCACTCTATAGCGTGTGTAACATAGTGTGGCACTGCATTCTCCAGCATGTGTAACACAGTGGTGCTGCACTCTCCAGCATGTGTAACACAGTGTGACACTGCACTCTCTAGTGTGTGTAACAGTGGCACTGCACTCTGCAGCATGTGGAACACAGTGTGGCACTGCACTCTCCAGCATGTGTAAAACAGTGGTACTGCACTCTGCAGCGTGTGTAACACAGTGGCACTGCACTCTGCAGCATGTGTAACACAGTGGCACTGCACTCTGCAGCGTGTGTAACACAGTGGCACTGCACTATGAAGCGTATGTAACAGTGTCACTGCACTCTGCAGCGTGTGTAACACAGTGACACTGCACTCTCCAGCGTGTGTAACAGTGGCACTGCACTGCAGCGTGTGTAACACAGTGGCACTGCACTCTGAAGCATGTGTAACAGTGGCACTGCACTCTGCAGCATGTGTAACACAGTGGCACTGCACTCTGAAGCATGTGTAACACAGTAGCACCTCACTCTCTTATGTGTGTAACATGGTAGCACTGTACTCTATTCTCATAATTTGAAAGCAACAGCATCATAACTATTCATACATTCAGCAGCTTCTCCTCTTTAATTTTATGTTTTGTTCTGTTTAGCCGAGCACCTCATGTGTGAGGGTGCAGCTCTGCAATGGAGAGTTTGCTGATAATTGTTCTTAAGATTTTATAGACGTATTTACATGAATGTTTTCTCTATGTGTTTATTTTCTTGGTCCTATAG
Seq C2 exon
ATGAAAAAATGTTTCAAGCCCTCAAGGAAGAAGGAAATCAACTTGTAAAGGACAAAAATTATAAAGATGCCATTAGTAAATACAATGAATGCTTAAAGATTAACAGCAAGGCATGTGCCATCTATACAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037617-Spag1:NM_012031:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.152 A=NA C2=0.022
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF134141=TPR_11=PU(61.8=93.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047335





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000047335f3702A
          









    
Other Skipping Isoforms:
ENSMUSP00000132233
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr8:100225340-100231155 
ALTERNATIVE
HsaINT0157140
(SPAG1)
Human
(hg19)
chr8:101237568-101243383 
ALTERNATIVE
HsaINT0157140
(SPAG1)
Rat
(rn6)
chr7:75043803-75046169 
ALTERNATIVE
RnoINT0141949
(Spag1)
Cow
(bosTau6)
chr14:66331006-66334532 
LOW PSI
BtaINT0139369
(SPAG1)
Chicken
(galGal4)
chr2:128200219-128202725 
ALTERNATIVE
GgaINT0096250
(SPAG1)
Chicken
(galGal3)
chr2:134066962-134069468 
ALTERNATIVE
GgaINT0096250
(SPAG1)
Zebrafish
(danRer10)
chr6:52227881-52227956 
LOW PSI
DreINT0166350
(tomm34)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"