Special

MmuINT0113730 @ mm9

Intron Retention

Gene
ENSMUSG00000042359 | Osbpl6
Description
oxysterol binding protein-like 6 [Source:MGI Symbol;Acc:MGI:2139014]
Coordinates
chr2:76390175-76393174:+
Coord C1 exon
chr2:76390175-76390307
Coord A exon
chr2:76390308-76393070
Coord C2 exon
chr2:76393071-76393174
Length
2763 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGT
5' ss Score
8.54
3' ss Seq
AACATTTTTGTCTTCGTTAGATC
3' ss Score
7.58
Exon sequences
Seq C1 exon
ATGCAGCCCAACAGCTTTCCATGGCAGTCGCCATTACCATGCAGTAACAGCCTCCCTGCGACCTGCACAACTGGGCAGAGTAAAGTGGCAGCCTGGCTGCAGGACTCAGAAGAAATGGACAGGTGTGCAGAAG
Seq A exon
GTTAGTTCCGGCCCCTGTGGGGTCTCAGGATGAGCCCTGCACCCAGAGGTGATGGTGCAAGGAAAACACTACAGCTTCCAGTCTCACCTCCCAAGGGACCGGGCCTTTCTTCTTAGTTATACACTTCTAGATCCTTGTCTGCTCTGTAACCCACGCTTCTCAGCTGCCAGTTCTCCCACCTCCTCACAAGTGGCTCTGAGCTTCTCCCCTGCCTTGGCTTCTACATCTTCAACCTTTTCATCTCTTTACAAATTCCATCTCACTACCTTCACCTGTCCATTTGGGGCCTGATGAACCTTCCAGTCTTGTACCTGCACTCTGCACTGCCCTACTCTCTGGTGCCCTCCATGCTTCCTTCTGCTGTTGTGTTGATATCCTGTTGCTATGTTCTCGATAGCACAGAAGTAAACAGAAGGATCCAGGGTGGCATGTCCGGAGTTCCGTGTGACTGGGGTTTCGCTTTGGATAGGCCTTTCAGGACTAGTCCATCCTTCTTTGGGCTGCTTAATCTACTACTTTCTCCTCCCCCACCAAAGCCCTTTGGTCCACTCTTTATCCATTGGCCATTTCCATTCTGAAACAGTTTTCATTTGACCCACAAACCTGACAAAAAGCAAGGGCAAATAGAGAGTATTTAATAAGTCTCACCTGATTTTTTAGATGCTCTTGAGATACTGTAAGCATTAATTTTGCTCTTTTATGATACTATTATAAAAACAGATGTTATGTAACCTTTTAATGCTTTCACTTAGACAAAATAAATTAATGATCTGTGTTAATCCTCCTATACCCTCACCATTGGGTTAACTCCAAATTTGCATTTTCCAGACACCAAGCTCCCAAACTTAATCCACATGGGAAACTATGATTTAAAGGGGATTTTCATATTCATAATCATGTCCATTTGACATCCAACTAGAGTGTTTGCCTAGGCTGTATTCACCACATACAGCTTCCAGTTGTGGAAGGAGACGGATGACTTTCAGACAGCACTGTAGCTTCCTGCCATATTTGGAGACCACCCAGGCTCTCCTGTCTGAAGGCCAGCTACAGAGGTGCTTCCTCCCTTAGTCCAGCCTCTATTGCTAGAAAAGAGGAGCCAGGATTCAAATTCAGACACTCTCACAATAGAGCACAGATCTGAATATAGTGCCCTGCCAGTTCTCCTGGGTTCCCCCTTGAGGCTATATGAGCACCCAGACTTTATGTTCGCCAGTGCTTATCAGGCCTAGCTTGACTCCCTATTCACACAGTCTTGTCCTATCCTTACCAGCCTTTCATGCATGATCCATTCCTGTCCTCTTGTTTCTGGTGGTCACATAGTCTCCTAACTGCATGACCCACTCTCCTGCACAGTTAGTTCATCCTTCTCAGAGGCTCATGGATAATGACCACCTGTGAGCCGGTTTGCAGGCCCATGCCAGTACACGGAGCATATTCTGTTGTTTTCAGCCATGAGGCATAGGTACTGGTTAACTGTCTGTACTTTGTGGGTAGAGAGAATGAAATCCATAAAGGTTTAGACATTTGGCCAAAATTCTAGAGTTGCCCTGGTGGAGGGGATGGGATTGCAGCCAGCTCACAACTGACTAGTCCCCAGAGCTTTGTTCACTACAGAATGCCCCAAGACTGGTAATTCTTAAGATAACTCTGTAATCACCCCCCAGTGGCTCTTCCCTGGCTCCAAGGTGTTTCCCCAAAGTGCTTATCCCAGCATTTAGCAGCCAATGTGTTCAGCAGTCTGGCCATATCTAGCCTTTCAACCTTGCACACTTCTGAAGACTCAAGCAACTGTTGTTCTATGCATTTACATATGCCCATCTCTGTGCCTTTGGACAGACTCTGCCCAACCTGAAGTTCCCTCTGTGTCCTTCTCCACCTTTCTGTCTGGCTAAAACATTTCTGTCAATTGTCTAGACCCTGTGGGGGTGTGGTGGGGTCACTCTTGTAAATCTGTTCTCAAACCATGAAGCAAGGAACACTCTCTTTTCTCCTAATCTCTTGCTGCACTTAAAAAAAAAAAAACCACTATACTGATTATTTTCATAGAGCATGGCTACTACTGAGATGGGGTTCAGTTGTTTTAAAGGAATATTTCATATTTATTTCATTGGTTGAATTTCAAAAGATGTAATGTTTTATGGAACCCCCTTATATGTCTGATTGACAGTTCCACCAGTTGTCTGTTTCAGACTTGCATGAAACCAGGCCTTAGATATATGGATCAATTGCTTGGCTCTTAGGGCATATTTTTTTTCCATAGAGATTAAATTTAAATTACTAAGACTCTACAGTAGATTTTACAGGAGTCATGCCTTGACACACAGTTAGTGGGCTGGAGGACAGATGTGTTCCACTGGATTTTCCTCTTCTGTTTCTCTGAACTTGACTTTGCCTCCACCCAAATTCCAGGCGGCTCCCTAGTAAATCGTTTTAGAGGAGCTAGGCTCCTAGGAATAAAACCACAAGCCTACCAAACTCCCCAGAGTGCCCATGAGATGAAATCCGTGAGGGCGGAACCATGATCACACACAATGGGAAGTGTTAATGGTATCTACTCTCTGAGTCATAGTTGGTAAGAAACCATCTCATTGCCAGCAGCGCCCATGATTCAGGCCCAGAGCGAGGTATGCTCTGTTACCTGTCCGTATCACCATCATGTAAATGTGGGTATCCTGTCTCATATACCACATTGTGGACTAGGTCCCCTTTATTATTGTCACCTGCATTTCTACCCAGTTCGAACATTTTTGTCTTCGTTAG
Seq C2 exon
ATCTTGCACACTGCCAGTCAAACCTTGTGGAACTTAGCAAGCTCCTGCAAAACTTGGAGATCCTTCAGAGAACTCAGTCGGCGCCTAACTTCACTGACATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042359-Osbpl6:NM_145525:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.053 A=NA C2=0.157
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000077123





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000077123f4373A, ENSMUSP00000088290, ENSMUSP00000107560, ENSMUSP00000107561
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:178336434-178338990 
ALTERNATIVE
HsaINT0118696
(OSBPL6)
Human
(hg19)
chr2:179201161-179203717 
ALTERNATIVE
HsaINT0118696
(OSBPL6)
Rat
(rn6)
chr3:63409130-63411343 
LOW PSI
RnoINT0105825
(Osbpl6)
Cow
(bosTau6)
chr2:18524602-18530499 
LOW PSI
BtaINT0106017
(OSBPL6)
Chicken
(galGal4)
chr7:14958941-14959401 
ALTERNATIVE
GgaINT0047051
(OSBPL6)
Chicken
(galGal3)
chr7:16556370-16556830 
LOW PSI
GgaINT0047051
(E1BQU1_CHICK)
Zebrafish
(danRer10)
chr9:1422197-1423253 
DreINT0108880
(osbpl6)
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"