Special

MmuINT0023942 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:35296725-35297132:-
Coord C1 exon
chr17:35297042-35297132
Coord A exon
chr17:35296936-35297041
Coord C2 exon
chr17:35296725-35296935
Length
106 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
ACACTGTGATCTGCCCACAGCAA
3' ss Score
8.09
Exon sequences
Seq C1 exon
GGGCCCATGAAGAGGTTGACTATACTGAAAAGCTCAAATTCAGCGATGAGGAAGATGGACGAGACTCCGACGAGGAGGGAGCTGAGGGCCA
Seq A exon
GTGAGTTAGGGCCCAGGGGAGGGAGGCACTGTTTTTCTTGTGGTGCGCTAGCCTCATAGAAGGGTTGCTTATAGCAGAGCTTAGTTACACTGTGATCTGCCCACAG
Seq C2 exon
CAAGGATTCCCAGTCAGCTGCTGCTGAGGAACCTGAGACAGATGGCAAAAAGGGCACCTCCCCTGGCAGCGAATTGCCCCCTCCCAAGACAGCCTGGACAGAGAATGCTCGGCCTTCAGAGACAGAGCCAGCTCCTCCTACCCCAAAGCCTCCCCCACCTCCACCTCACCGGGGGCCAGTCGGGAACTGGGGGCCCCCTGGGGACTACCCA
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2:NM_020027:9
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)
chr6:31626863-31626981 
LOW PSI
HsaINT1028148
(PRRC2A)
Human
(hg19)
chr6:31594640-31594758 
HsaINT0016664
(BAT2)
Rat
(rn6)
chr20:5150504-5150606 
LOW PSI
RnoINT0118600
(Prrc2a)
Cow
(bosTau6)
chr23:27485334-27485443 
LOW PSI
BtaINT0118597
(PRRC2A)
Chicken
(galGal4)
chr8:4756048-4756065 
Chicken
(galGal3)
chr8:4897751-4898029 
GgaINT0035895
([1])
Zebrafish
(danRer10)
chr19:27164369-27164445 
LOW PSI
DreINT0120715
(prrc2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGGCCCATGAAGAGGTTGACT

				
R: 
GAGGCTTTGGGGTAGGAGGAG

				
Band lengths: 
243-349

			

		

	





	
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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