Special

MmuINT0023979 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr1:164639660-164640960:-
Coord C1 exon
chr1:164640414-164640960
Coord A exon
chr1:164639818-164640413
Coord C2 exon
chr1:164639660-164639817
Length
596 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
TTTACTGTTTCTTTGAGCAGAAG
3' ss Score
5.84
Exon sequences
Seq C1 exon
CATCCCCCACCTCCAGATCGACAAATACCTGGAAGACAAGGCCCCTTTCCCTCCAAGCCTCCAGTACCTGATAACGATGAAATATGGAAGCAAAGACGAAAACAACAGTCTGAAATATCTGCAGCAGTAGAGCGTGCTCGTAAACGCCGTGAGGAGGAAGAGCGAAGGATGGAGGAACAGAGGAAGGCAGCGTGCGCAGAGAAATTGAAGCAGCTGGATGAGAAGCTCGGGATCATAGAAAAGCAGCCATCTCCAGAGGAACTTAGAGAAAGGGAGAGAGAGAAGGAGCGGGAGAGAGAACTTGAAAAAGAGAAAGAGCGGGAGCTTGAGAAAGAGCAGGAAAAGCAGAGGGAAATGGAGAGGGCAAGACAGCAAGAGAAAGAGTTAGAACAACAGAGAGAAAAGGAGCAGGAACTACAAAGGCTGAGAGAACAGGAAAAGGAGGGCGAGCCAAAGGAACAGGAAAAAGAGGAAAAAGTTGAACCCCAAGAGCCTGTTGTAGAGCCTGCGACAGAAAACCAAGAAAGTGAAAACAACTGCAAGAAAG
Seq A exon
GTATGGTGCCCCACCCACATTTCATAGTTAATTATGCATTCTCCTTAGTTGTTAATGGTGGAGAGGTGAAGGCAGGGCCTTGCATGTATACTTGTGATGCATCATCCTCTAGGACAGATGGACAGATGGAACAAGTTTTCCTCAGGATAAAAACAGTAAACAGGTCCTTGACATAGCCCTGACTGGCCTGAAATTGCACTGTAGAGCAGGCCGGCCTCAAACTCAGAAATCTGACTGCCTCTGCCTCCCGAGGTGCTGGGGTTAAAGGCGTGTGCAGCTACACTTGATTGTCCTCTTCCCAGGTATAGATCATATCATGTAAATACTGAGTGTTAACATAAATATTTATTGAAATAAATGAGAAGTATTAGGACCTTGGGTTTTTGTCAAGTAAATACATATGTGTGTAAGTGAAGGATTTGGATCTGTGTTCTCCTTAGAGTCCAGGTTTATAAGAATCTGTTGATAGTTTAGTGATATGTTATTGATGTTTTTCATATTGGGTTACAAAGTGATGATTTGGAGTATTATGGAGATCCTTTTTCCTCTTTAACAGCATGTTTGATAGGATTATTTTTTACTGTTTCTTTGAGCAG
Seq C2 exon
AAGAAGAACCAATTTTCACTAGGCAGGACAGCAATCGCAGTGAAAAGGAGACCACACAAGTGGTACAAGAAGCAGAACCTGAATCGGGGGCTCAACCTCGACCTGGCTATTTCAAACAGTTTCAGAAATCATTGCCACCACGATTTCAGCGTCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2l2:NM_001081290:12
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
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:171532962-171535427 
LOW PSI
HsaINT0016701
(PRRC2C)
Human
(hg19)
chr1:171502101-171504566 
LOW PSI
HsaINT0016701
Rat
(rn6)
chr13:80581090-80581869 
Cow
(bosTau6)
chr16:39887397-39893577 
LOW PSI
BtaINT0118629
(PRRC2C)
Chicken
(galGal4)
chr8:4752472-4753260 
LOW PSI
GgaINT0035898
(PRRC2C)
Chicken
(galGal3)
chr8:4894449-4895224 
LOW PSI
GgaINT0035898
([1])
Zebrafish
(danRer10)
chr20:15153984-15154317 
LOW PSI
DreINT0120731
(prrc2c)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAAGGAGCGGGAGAGAGAACT

				
R: 
CCCCGATTCAGGTTCTGCTTC

				
Band lengths: 
355-951

			

		

	





	
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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