Special

MmuINT0003812 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr8:113636402-113636750:+
Coord C1 exon
chr8:113636402-113636483
Coord A exon
chr8:113636484-113636586
Coord C2 exon
chr8:113636587-113636750
Length
103 bp
Sequences
Splice sites
5' ss Seq
GAAGTACGT
5' ss Score
7.46
3' ss Seq
TCCCCTGTGTTCTATGGCAGTGT
3' ss Score
8.23
Exon sequences
Seq C1 exon
GTTACTTAAGGACAGGCTCAATCTCTCTGGCCCAGACTCAGGACCGGTTGATCTCTCTGAAGCGTATCAACTCAAGGCTGAA
Seq A exon
GTACGTAAGAGTTCTATATACTCTTAGACTAAGGACTACACACCCCTCCTGACTTTGCCACAGAGCCCATAACAGTAGAATTTTCCCCTGTGTTCTATGGCAG
Seq C2 exon
TGTTGTAGGTATCCCTTCTGAGATCATCTCCCCGAAGAAAGTGGCTGAACTTCACCCTCTCCTCAATGTGCATGATCTGGTCGGGGCCATGTACGTTCCTGAGGATGCAGTAGTGTCCTCTGCTGATGTGGCTCTGGCCCTGGCAAGTGCTGCCTCCCAGAATG
VastDB Features
Vast-tools module Information
Secondary ID
-4930402E16Rik:NM_198308:4
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:
ENSMUSP00000046639





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000117570, ENSMUSP00000121325
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr16:70128866-70128958 
ALTERNATIVE
HsaINT1026587
(PDPR)
Human
(hg19)
chr16:70162769-70162861 
HsaINT0122644
(PDPR)
Rat
(rn6)
chr19:43132123-43132352 
LOW PSI
RnoINT0109335
(Pdpr)
Cow
(bosTau6)
chr18:1935539-1935629 
LOW PSI
BtaINT0109632
(PDPR)
Chicken
(galGal4)
chr11:1788810-1788899 
ALTERNATIVE
GgaINT0025822
(PDPR)
Chicken
(galGal3)
chr11:1769870-1769959 
LOW PSI
GgaINT0025822
(F1NG59_CHICK)
Zebrafish
(danRer10)
chr18:50957138-50957362 
LOW PSI
DreINT0016269
(PDPR)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACTTAAGGACAGGCTCAATCTCTCT

				
R: 
CATTCTGGGAGGCAGCACTTG

				
Band lengths: 
243-346

			

		

	





	
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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