Special

MmuINT0152674 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr16:90243117-90243454:-
Coord C1 exon
chr16:90243289-90243454
Coord A exon
chr16:90243204-90243288
Coord C2 exon
chr16:90243117-90243203
Length
85 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
CATGGTTTTTCTTACTCTAGGTT
3' ss Score
10.05
Exon sequences
Seq C1 exon
GTCCCGCCCCATCAGCCGGGCCCTCCTGTTGTCGGTGCTCTCCAGCCGCCCGCTTTCACCCCTCCCTTAGGAATGCCCCCTCCAGGCTTTGGCCCTGGCGTTCCTCCTCCCCCTCCTCCTCCACCATTTTTGCGCCCAGGATTCAACCCAATGCATTTACCACCAG
Seq A exon
GTACACTGGCTTGCTTGAGAATACCCTTTTTAGGCTCTGAGATGAAGTCACGGAGCAGGAGTTGACATGGTTTTTCTTACTCTAG
Seq C2 exon
GTTTCCTTCCTCCTGGACCCCCACCTCCTATAACTCCACCAGTATCCATTCCTCCACCTCACACTCCACCAATAAGCATCCCAAACT
VastDB Features
Vast-tools module Information
Secondary ID
-Srsf15:NM_178923:17
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:
ENSMUSP00000044472





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000131974, ENSMUSP00000132250
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr21:31685485-31685567 
ALTERNATIVE
HsaINT0148707
(SCAF4)
Human
(hg19)
chr21:33057798-33057880 
LOW PSI
HsaINT0148707
(SFRS15)
Rat
(rn6)
chr11:30385888-30385971 
LOW PSI
RnoINT0131065
(Scaf4)
Cow
(bosTau6)
chr1:3095592-3095680 
ALTERNATIVE
BtaINT0128915
(SCAF4)
Chicken
(galGal4)
chr1:103997589-103997712 
ALTERNATIVE
GgaINT0115192
(SCAF4)
Chicken
(galGal3)
chr1:108129680-108129803 
LOW PSI
GgaINT0115192
(SFRS15)
Zebrafish
(danRer10)
chr10:25742267-25742345 
LOW PSI
DreINT0131059
(scaf4a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCCCTTAGGAATGCCCCCTC

				
R: 
ATTGGTGGAGTGTGAGGTGGA

				
Band lengths: 
178-263

			

		

	





	
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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