Special

MmuINT0113670 @ mm9

Intron Retention

Gene
ENSMUSG00000029822 | Osbpl3
Description
oxysterol binding protein-like 3 [Source:MGI Symbol;Acc:MGI:1918970]
Coordinates
chr6:50259312-50262694:-
Coord C1 exon
chr6:50262631-50262694
Coord A exon
chr6:50259391-50262630
Coord C2 exon
chr6:50259312-50259390
Length
3240 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
AATTTGATATTTCATTTCAGATG
3' ss Score
7.89
Exon sequences
Seq C1 exon
GTCAGCCACCACCCACCTATCTCCGCCTGCCACGCTGAGTCCGGAAACTTTGTTTTCTGGCAAG
Seq A exon
GTAATGTGCTGATCCGTTTGACTGCCACCTTCATAGCACTAAAGGTTTTGTTTGCTCCAGGGATCCTCTGTCCCCATCGTTCCATCTCAGAGCTTTTTCTCTCTCTTTCCCTGTAACTTCTCTCGGAGTGCCTCACTTGTTGAAGGATTTACAAGGTTCCCAGCTTTTTAGCAGAGGGTAGGCAGCAAATGGGTTTCTTGCTTTTTAAAAATTTAAGTCTTAGCCGGGCGTGGTGGTGCACACCTTTGATCCCTGCCTCGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCAAGGCCAGCTTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAAAAAAAACAAAAACAAAAAACAAAACAAAAATATGTCTTGTTTCTAAAATTACAGTTGACACCTGACTTCTATTCATCTTTTTTTTTTAATAATATCTTTTATCCACTGAACTTTTCCCCATTTATTTGGTGTCTGTGTGTCTGCACATGCACACATATGTGTGTGCGTGCGTGCGTGCGTGCGCAGGTCAGATGATAACTAGCAGGTCTGGGCTTTTACCTTCTGTCATGGTTTGGAAGGATGGAACTCATGGCATAAGTGACAAGCACCTTTTCCTGCTGAACCATCTCACTGGCCAGTTTGTTTGTTTGTTTGATTGGTTGGTTGGTTTTGTTGTTGTTTTGAGTGCTGTTTGGAGGAGGTTTTCGTCTAAGTTTTGTGGTTGTTGTCATCTTGCTTTGTGTTTATAGTTTTTGTCTGGCTTTGTCTTTGCTGTTCTCAAGAACATAAGCTAAAAGGTTTGGGAAAGGCAAGCAGGGTGGTGGTTTTGGTATTGATGTTCCTAAACCTTACATTTGGAGATGGAGGGAGATGGAAAGTTGTTCACAAAAATAATGCTTCAGATTTTTCCAAAATGAGTTAGTTCTGTAAAATGTTTATTTATTCAGAAGGTTGGGGTACAGTAAGAGAAGCTGAGCGTCCCAGGTTTTGTTTGTTGGGGACGGAGGCTCACGTAGTCCAGGCTAGCCTCAGATTCGCTTTATAGACTAGGATGGCCTGGAACTTCTTATCCTCTGGCTTTACCTCCTGCAGTGCTGGCTTCCCGGCATGCACTACCACACCTGGTTTACACAGTGCCAAGGACTGAACTTCAGGCCTTGTGCATGCTACTACGCAATTACCAACTGAGTTACAGCCTCAGCTCCTAATCAGCTTTTAAAACATTTTCTTTACCAGCACTGTCATTTGGTTCCTGTGCACTCTTTATACACACTGACATGGGCACATATCGTTGTGATACTTGAAACTACAACAGCACACTGTAACACTTCCCACTCACTCTGCCTGGAGGCTGGCAGTATTACTGGTTGAAAAGTACAAGTTAATTGTTTCTTTTCTTTAATCTTTTCTATCGATGCTTGATATTAGATATTGAAGCTTCACCTAAGATCTGTCTACTTTTCACTAAAACCCTCTGGAAATGTTTCTCATAAGGCTCCCAAGCTTCCACCTGATAAATCTCGTGGGCCCTGTAAGTGCTTCCACTTGGTTTTCATAAAGTCTGCATTTTTGTTTTTAACAAGAGAGCCTTTTCCAGATAGTCCCTGGAGGCCCCTGTGTTACTTTCCTCCTCACTCTTTCCTGGGTGGTTCCACCTGTTTCCTGGATATAAGATCCTCAAGTCTTCCCCATCTCGTCTCACATTTCTCTGCCCTTTAACTGGGTTGTTTAGATGTTTGTTGTGATTATAGATGTAAGTGATTAAAGTGTGCCTTGCTTTTATTTGTCAAATCTGTTCCTTGTTCCCCCTTTCCTCTTTTTATGCCTACTTTTGAATTAGTTAAATATTGTCTCTATGTCCATTTGTCTCTTCTGTTGTATTATACCTATAGCTCTTTGTTTTATGCCTTAGTTGTTACTTCAAGATTCATGTTATGTATCTTTAAGGTTTTGCAGTCTGCCATCAACTGGCATTATTATATACCAGTTTAGATGCATTAAGAAACATAGCAAAGTAAACCTGCCCTTTGTAAGATTGTGTGTGTTATAAGTTGGCAGTGTGTTAATGTCTTTGCTCAAATCCAAATCTCCATTTTCCAGTTTTCATACCAATTTTATTGAAAAATACTCACACACTGTATCATTTACCCACTTAAAGTTTATAAATTTGCGATTTTTTTTAACTTAGCACAACTAATTTTAAAATAGTTTCATCACCTCAAAAACAATTTCTTTGGCAAACACACTCTCCCAGCCTCCTTTAAATCCACCATTTGCAGGATTTCTTTGGAGGAATCCACTCACCTGCCTCACCTGGACCACAGGCACGCATCTCCTAGCTGCTCTGCTTCTGCCTCTCCCTACATTTCTTCTGTCTCAATGCGGTGAACAGTCAGGGCCTGCTTCACATTCTCAGTCTCCCTTCTCCTTCTCAGTGTCAGCATCCGCAAATTAGGACGACTGACATTGCTTCTAAATATTCCCTCCTTTTCTCAGCCTGTGCCTGTTTGCCCCTCCATTCTCCATTTTTGCTGCTTCCCTTAAGAATCTGCTGCACCACAGCTGGGGGCTGGACTCACTCCTGCTTGTCCCCTGAGCAGCCACAGTAGCCACTTCTCTTGCCACCTCACTCTTAACCCCTCCTGCCCATGTCCCGTTCTCCGTATGGCTTTGATTTTTTTTTGCAATTTTTTGTCTCTTCACACTGGTTCCCTGAATGTTTTCAAAGAGGACTTATTAGCCAGGCTTGCAGAACCAAGTGTTTCCTCAATCTGACCTTCTGCTCTAACCCTCAGATAATCTCAGACCTTCAGGACACAGCCACAGTCGACTCTCTTATACCTCTAACCCTGTAAATACTGTTTTCCCAACACCGATTTCTCTATGCTTCATGAACTCATTTGGATTCTACAAAACCCTGTTCACATGGCCCCTTCTGAAAAGCCTCATTCAAGGCTTTTGGTAGACATACAGCCATCCCCCCCACCCCCACTCCATCTCATGCTACAGCACACTAGAATGGCCTGTGTTTGTGTGACCGCAACTTTTTTCACCCCACTTTCATGCCATTGACTCTTTCAAGAGGACTTTGTATTACAGCTTTGCTTTCCTGGTTCTGTTTTTGGGGTGCCCAGTTGGCATTTCTAGCACAATATGGAATGAACAGTGTCTATCTAGCTGTCTTGTTCAATACTTGATAATTTGATATTTCATTTCAG
Seq C2 exon
ATGTGAGATGGAAAAATAAATTCTGGGGTAAATCCATGGAAATTGTCCCGATTGGCACAACCCACGTGACTCTGCCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029822-Osbpl3:NM_027881:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0123713=Oxysterol_BP=FE(6.1=100)

							
A:
NA

							
C2:
PF0123713=Oxysterol_BP=PD(0.1=0.0),PF0123713=Oxysterol_BP=FE(14.5=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000087473





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000071643, ENSMUSP00000110110, ENSMUSP00000110112
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:24816689-24820174 
LOW PSI
HsaINT0118635
(OSBPL3)
Human
(hg19)
chr7:24856308-24859793 
LOW PSI
HsaINT0118635
(OSBPL3)
Rat
(rn6)
chr4:80041810-80045074 
ALTERNATIVE
RnoINT0105771
(Osbpl3)
Cow
(bosTau6)
chr4:71471228-71474745 
LOW PSI
BtaINT0105965
(OSBPL3)
Chicken
(galGal4)
chr2:31786173-31788523 
ALTERNATIVE
GgaINT0097805
(OSBPL3)
Chicken
(galGal3)
chr2:31581887-31584237 
LOW PSI
GgaINT0097805
(F1NN81_CHICK)
Zebrafish
(danRer10)
chr16:21578159-21578253 
LOW PSI
DreINT0108826
(osbpl3b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"