Special

MmuINT0023980 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr1:164638984-164639817:-
Coord C1 exon
chr1:164639660-164639817
Coord A exon
chr1:164639243-164639659
Coord C2 exon
chr1:164638984-164639242
Length
417 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
GTGTGATTTTGGTTTTCCAGGAG
3' ss Score
8.73
Exon sequences
Seq C1 exon
AAGAAGAACCAATTTTCACTAGGCAGGACAGCAATCGCAGTGAAAAGGAGACCACACAAGTGGTACAAGAAGCAGAACCTGAATCGGGGGCTCAACCTCGACCTGGCTATTTCAAACAGTTTCAGAAATCATTGCCACCACGATTTCAGCGTCAGCAG
Seq A exon
GTAATACTACTAAAACCAAAAATACTTTACCTCATATATGGGATTGGAAATAGATATCTTATCTTTCAGGATCTGATAATATAATATAAAACAAAATACATAAAGCATAGGAACTTACCTTAGTTCCTTTTTTCTTTGTAGTACACTTGTTGAGAATTGGTTGTTGAGAAGTTAGTTGACTTTCTCTATCATGTCTTTTTTGTCTTAAGCTTTACTCATAGACACATCTTCTACTTCTAGGAAATGATGAGATGCTTATGTGAATTATAAGAAATTACTGTAACTTATTTGGTCTTTTGCCAACTCTGTGCTGATTGTTTTTATCTTTAAATTTCCCAAACACCTTTGTTTTCAAATACGGTTACACTAATTAATTATAGAATAGAAATGTCAGTAAGTGTGATTTTGGTTTTCCAG
Seq C2 exon
GAGCAGATGAAACAGCAACAGTGGCAGCAGCAGCAGCAGCAGCAGCAGCAAGGTGTGCTTCCACAGACTGTGCCCTCACAGCCGTCTAATGGTTCAGTCCCTCCTCCACCACACAGACCCCTTTACCAGCCAATGCAACCCCACCCTCAACATCTGGCTTCTATGGGTTTTGACCCAAGGTGGCTCATGATGCAGTCCTATATGGATCCTCGAATGATATCAGGAAGGCCTGCTATGGACATTCCACCCATTCATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2l2:NM_001081290:13
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:
ENSMUSP00000028016





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028016f5784A, ENSMUSP00000038401, ENSMUSP00000038999
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:171535598-171536028 
ALTERNATIVE
HsaINT0016702
(PRRC2C)
Human
(hg19)
chr1:171504737-171505167 
ALTERNATIVE
HsaINT0016702
Rat
(rn6)
chr13:80580511-80580919 
Cow
(bosTau6)
chr16:39893748-39894175 
LOW PSI
BtaINT0118630
(PRRC2C)
Chicken
(galGal4)
chr8:4751667-4752303 
ALTERNATIVE
GgaINT0035899
(PRRC2C)
Chicken
(galGal3)
chr8:4893642-4894278 
LOW PSI
GgaINT0035899
([1])
Zebrafish
(danRer10)
chr20:15153640-15153807 
LOW PSI
DreINT0120732
(prrc2c)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CACTAGGCAGGACAGCAATCG

				
R: 
TAGGACTGCATCATGAGCCAC

				
Band lengths: 
342-759

			

		

	





	
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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