Special

MmuINT0177560 @ mm10

Intron Retention

Gene
ENSMUSG00000079173 | Zan
Description
zonadhesin [Source:MGI Symbol;Acc:MGI:106656]
Coordinates
chr5:137382073-137382505:-
Coord C1 exon
chr5:137382306-137382505
Coord A exon
chr5:137382212-137382305
Coord C2 exon
chr5:137382073-137382211
Length
94 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCGG
5' ss Score
3.7
3' ss Seq
CTTCACCTCCTCTCTTCCAGCTG
3' ss Score
10.27
Exon sequences
Seq C1 exon
CCATGACATGTCCTGCCAATACTGTGTACCAGCGCTGCATGACACCCTGCCCGGCGTCCTGTGCCAAATTTGTGACCCCCAAGGTCTGTGAAGGCCCCTGCGTGGAAGGCTGTGCCAGCCTCCCCGGCTACATTTACAGTGACACACAGAGCCTCCCAGTGACACACTGCGGCTGCACCGCCGATGGCATCTATTACAAG
Seq A exon
GTCCGGGTGGCATAGAGGCCTGGGAGCCCAGGTACAGAGAAGGGCACCTCGGGTGAATCTAGACCGGCTCCTGTCTTCACCTCCTCTCTTCCAG
Seq C2 exon
CTGGGTGACAGCTTTGTAACTAACGACTGCTCCCAGCACTGTACCTGTGCAAGCCAGGGGATCCTGCTGTGTGAGCCCTATGGCTGCAGAGCTGGGGAGTCCTGCATGGTGGCCAACTTTACTCGAGGCTGCTTCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079173:ENSMUST00000117564:83
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0182612=TIL=WD(100=80.6),PF127142=TILa=PU(16.4=13.4)

							
A:
NA

							
C2:
PF127142=TILa=PD(80.0=93.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000114068





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000132895
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr7:100794019-100794119 
HsaINT1047031
(ZAN)
Human
(hg19)
chr7:100391641-100391741 
HsaINT0184466
(ZAN)
Rat
(rn6)
chr12:22385295-22385388 
ALTERNATIVE
RnoINT0004133
(AABR07035782.1)
Cow
(bosTau6)
chr25:36368616-36368722 
BtaINT0163483
(ZAN)
Chicken
(galGal4)
chrUn_AADN03015180:4833-4927 
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGCCAAATTTGTGACCCCCAA

				
R: 
GCTGGGAGCAGTCGTTAGTTAC

				
Band lengths: 
176-270

			

		

	





	
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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