Special

MmuINT0023916 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:35295338-35296358:-
Coord C1 exon
chr17:35295881-35296358
Coord A exon
chr17:35295529-35295880
Coord C2 exon
chr17:35295338-35295528
Length
352 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
CACCCTGTTCTTCAATGCAGTGG
3' ss Score
7.38
Exon sequences
Seq C1 exon
GATCGAGGGGGTCCTCCCTGCAAACCCCCAGCACCTGAGGATGAGGATGAGGCATGGCGGCAGCGTCGGAAGCAATCTTCTTCAGAGATCTCCCTGGCAGTGGAACGAGCTCGAAGGCGCAGAGAAGAGGAAGAGCGACGCATGCAGGAGGAGCGCCGGGCAGCCTGTGCTGAGAAACTTAAGCGTCTTGATGAAAAGTTTGGGGCACCTGACAAGCGGCTCAAGGCAGAGCCTGCAGCCCCACCTGTTACCCCTGCTGCCCCAGCTCTACCACCTGTAGTCCCCAAAGAAATTCCTGCAGCTCCAGCTCTGCCACCAACACCTACCCCAACACCAGAGAAAGAACCTGAAGAGCCGGCACAAGCCCCTCCTGTGCAGGCCGCCCCCAGTCCAGGGGTGGCTCCAGTTCCCACTCTGGTGAGTGGGGGTGGTTGCACTGCCAACAGCAACAGCAGTGGCAGCTTCGAAGCCAGCCCAG
Seq A exon
GTATGAAGAAAGGGATGGGGCTTACTGGGTGTCAAGTCTGCTAGGCTTAAGGGGATAGTGGGTAGTAAAGATGGGTGTCAGTGGGAGAGAGTGCTAGGTTACGCTATTGAACTGTGAGTGGCGGGGTATGTGGGAGGAGAATCTAAGCATCTTGTAGAACAGAACTTCTGGTTCCTGTTTTGTGTTTTCTGGTGGTGTCACAGGAATACTTGACACTTTAAAGTATTTCTATGGTTCTTAAACAGGATGGCCACTTATTCAGTTCGTATTTTGTTAAATACTTAACTGGGGGTGGAATTTCTGGGATGTTTGACTGTTGTAATGGACCAAGTCACCCTGTTCTTCAATGCAG
Seq C2 exon
TGGAACCCCAACTGCCTTCAAAAGAGGGTCCTGAACCACCAGAAGAGGTTCCTCCACCTACCACACCCCCAGCCCCAAAGATGGAACCCAAAGGTGATGGGGTTGGTTCTACTCGCCAGCCCCCCAGTCAGGGCTTGGGCTACCCCAAATACCAGAAGTCATTGCCTCCTCGCTTCCAGCGGCAGCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2:NM_020027:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000025253





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000125893, ENSMUSP00000133550
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:31628240-31629143 
ALTERNATIVE
HsaINT1028150
(PRRC2A)
Human
(hg19)
chr6:31596017-31596920 
Rat
(rn6)
chr20:5149109-5149448 
LOW PSI
RnoINT0118574
(Prrc2a)
Cow
(bosTau6)
chr23:27483788-27484231 
LOW PSI
BtaINT0118572
(PRRC2A)
Chicken
(galGal4)
chr17:6195017-6195654 
LOW PSI
GgaINT0123920
(PRRC2B)
Chicken
(galGal3)
chr17:6821960-6822597 
LOW PSI
GgaINT0123920
(PRRC2B)
Zebrafish
(danRer10)
chr20:15153984-15154317 
LOW PSI
DreINT0120731
(prrc2c)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CACCAACACCTACCCCAACAC

				
R: 
GGAAGCGAGGAGGCAATGAC

				
Band lengths: 
342-694

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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