Special

MmuINT0152679 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr16:90258956-90260547:-
Coord C1 exon
chr16:90260386-90260547
Coord A exon
chr16:90259092-90260385
Coord C2 exon
chr16:90258956-90259091
Length
1294 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
CATTTTCTTACATATAACAGAGT
3' ss Score
4.22
Exon sequences
Seq C1 exon
TGTAAGCCAGAATATAAGGTTCCAGGCCTGTATGTCATCGACTCCATCGTGAGACAGTCTCGGCACCAGTTTGGAACTGATAAAGATGTTTTTGGGCCAAGATTCTCTAAAAATATAACTGCTACATTCCAGTATTTATATCTTTGTCCATCTGAAGATAAG
Seq A exon
GTATGGTTAAAACGTAACAAGCTAACATTTTGCATTTTGTCCAGCTTATTTCCTCTTTATATTTCTCACACAATGCTTACGTTCACGTTGTTGACACTTGTTATTTATGTTACTGGGTGATATCTTCATGTACTGATCTTGAATTGTAAGGTCAGTTTTTTCTACGGTGGTCATTTCCTATTCTTGCTTATATGTGAAATGGAGAAGTCACTTGGCCTCTGTACAAGGACTTTTATAATGTTGAATCATAGAAGGAGCCAGAGTTATAGATCCTGAGCAGAGCAGAGCAGAGCTTGCTGGCGAGTGAGGAGTGCCTTACCTCTGTGCATGGGAAGCCTCTTCTAAACGGCGTGGTAACAACAGCCAACAGCTAGGCGCTGTACACTACACATTTCATGTTACATATCCTGCAGTTAAAAGAAACTAGCAAAGGTTGTTCAGGAAGCATTATCTTTCCTTAAAGAACATATTGCTAGTGGGCATGGAGACACATATCCTTTGATCTCAGCACTTAGTGGGCAGATTGCTAATAACAGCAAGCTGAAGCTACAGAAGGAAGACAGACAACAACTCTGTGTGAGAGAAAATACTCACCAGGGTTTTGCATACTCTAGAAGACCCAGATTTGTTCTTCCCCAACATTCACACATGCAAGTGATTAATCTGCAGTAAGACTGCAACACACACATACATACACACACACACCACACACACATATACACCACACACACACATACACACACCACACACACACCACACACACACACCACACACACACCACACACCATACACACACACACACCACACACACAGTTTCACTGAAAGAAAGAAGGAACGAACATGAACGATACATGCATTCTAAATAGGTGGGAATTCACAGTAAACATCACTAACACTAACTTAACCTGCTGCTTTAGTTTCTCTTAATTCTTAAAGAAGTTATGTAACAGAAAAGGGAACTTGGTTTGGTCAAACCAGAGAGAGAGGGAAAGTGCCCGTGTCTGAGAGTAGCGACATTTGCATGAGGAGAGGCGTTGTGGGTTTGCAGAGTCTGTATAAGAGCATTAGAAATGGTTCTTGACGTGTTTACCTTCCTTTGTATTTGCTAGCTGTGTATTCTGTTTATATTCCTTTTCATTGGATCATACCACCGAGAAAAGGTTAATTTGAGTTTAACTGGGTAATAGTTCTGGTGGATTTTTTCCCTTATGAAACAGTAATTCTCTTTAAAATCAGATATGATACATTATTTCTATAAATATTTATTGTATGTTCATTTTCTTACATATAACAG
Seq C2 exon
AGTAAAATAGTTCGTGTGCTAAATCTTTGGCAAAAAAATGGAGTGTTCAAAATTGAAATTATTCAGCCTCTTTTGGACATGGCAGCAGGAACCAGTAATGCTGCTCCAGTAGCAGAAAATGTCACCAACAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
-Srsf15:NM_178923:4
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:
ENSMUSP00000044472f1382A, ENSMUSP00000131974, ENSMUSP00000132250
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr21:31702380-31703764 
ALTERNATIVE
HsaINT1040924
(SCAF4)
Human
(hg19)
chr21:33074693-33076077 
HsaINT0148710
(SFRS15)
Rat
(rn6)
chr11:30402402-30403768 
LOW PSI
RnoINT0131072
(Scaf4)
Cow
(bosTau6)
chr1:3075169-3076712 
LOW PSI
BtaINT0128920
(SCAF4)
Chicken
(galGal4)
chr1:104017840-104018948 
ALTERNATIVE
GgaINT0115178
(SCAF4)
Chicken
(galGal3)
chr1:108149931-108151039 
LOW PSI
GgaINT0115178
(SFRS15)
Zebrafish
(danRer10)
chr10:25750764-25750857 
LOW PSI
DreINT0131064
(scaf4a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGCCAGAATATAAGGTTCCAGGC

				
R: 
CTTCATTGTTGGTGACATTTTCTGCT

				
Band lengths: 
294-1588

			

		

	





	
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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