Special

MmuEX0008481 @ mm9

Exon Skipping

Gene
ENSMUSG00000042507 | C130039O16Rik
Description
RIKEN cDNA C130039O16 gene [Source:MGI Symbol;Acc:MGI:2685106]
Coordinates
chr12:85493785-85497526:-
Coord C1 exon
chr12:85497377-85497526
Coord A exon
chr12:85495845-85496057
Coord C2 exon
chr12:85493785-85493981
Length
213 bp
Sequences
Splice sites
3' ss Seq
TTCATTCTTGTCCCCCATAGACT
3' ss Score
9.8
5' ss Seq
GCGGTAAGT
5' ss Score
11.37
Exon sequences
Seq C1 exon
ATCCAGACCAAGACTGTGGCCCAGTGCGTGGAATTCTACTACACCTACAAGAAACAGGTGAAAATCGGCCGCAACGGGACGCTCACCTTCGGCGACCTGGATATCGGTGACGAGAAGTCAGGCCAAGAGGAGGTTGAGGTGGACGTTAAG
Seq A exon
ACTTCTCAGAAGTTCCCAAGGGTGCCTCCTCCCAGAAGAGAGTCCCCAAGTGAAGAGAGGCTGGAGCCTAAGAGAGAAGTGACAGAACCCAGGAAGGAGGGGGAGGAGGAGGTGCCAGACACCCAGGAGAAGGGAGAGCAGGAGGAGGGGCGTGAGCGCTGCCGGCGGGCCGCTGCCGTCAAAGCTACACAGACACTACAGGCCAATGAGGCG
Seq C2 exon
GCCAATGACGTTCTCATTCTCCGGAGCCATGAGCCCAACGCCCCGGGGTCTGCAGGTATCCAGACCTCAGAGAAGCCGAGGGAGGGGCCGGGGAAGTCCCGAAGGGCACTGCCTTTCACAGAGAAGAAGAAAAAAGCCGAGGCATTTAATAAAACCCAGAACCAGGAGAACACCTTCCCTTGTAAAAAGTGCGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042507_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.300 A=1.000 C2=0.864
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0024926=Myb_DNA-binding=PD(34.8=32.0)

							
A:
NO

							
C2:
PF0214814=zf-UBP=PU(31.0=27.3)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000048120





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000105923
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr14:73721297-73721509 
ALTERNATIVE
HsaEX0009490
(ELMSAN1)
Human
(hg19)
chr14:74188000-74188212 
ALTERNATIVE
HsaEX0009490
(C14orf43)
Rat
(rn6)
chr6:107639050-107639262 
ALTERNATIVE
RnoEX0031751
(Elmsan1)
Cow
(bosTau6)
chr10:85520346-85520558 
HIGH PSI
BtaEX0012732
(ELMSAN1)
Chicken
(galGal4)
chr5:25432385-25432523 
HIGH PSI
GgaEX0013629
(ELMSAN1)
Chicken
(galGal3)
chr5:28317999-28318172 
HIGH PSI
GgaEX0013629
(C14orf43)
Zebrafish
(danRer10)
chr17:37403043-37403165 
HIGH PSI
DreEX0029742
(elmsan1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAAACAGGTGAAAATCGGCCG

				
R: 
TGCCGCACTTTTTACAAGGGA

				
Band lengths: 
296-509

			

		

	





	
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
  • 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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