Special

MmuINT0092733 @ mm9

Intron Retention

Gene
ENSMUSG00000030201 | Lrp6
Description
low density lipoprotein receptor-related protein 6 [Source:MGI Symbol;Acc:MGI:1298218]
Coordinates
chr6:134409250-134412679:-
Coord C1 exon
chr6:134412554-134412679
Coord A exon
chr6:134409487-134412553
Coord C2 exon
chr6:134409250-134409486
Length
3067 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACG
5' ss Score
9.65
3' ss Seq
CCGTCTCTCCTCACATGCAGAGC
3' ss Score
9.08
Exon sequences
Seq C1 exon
GACAGCACCCTTGTGCCCAGGATAATGGTGGCTGTTCACATATCTGCCTTGTAAAAGGAGATGGTACGACAAGATGCTCCTGCCCCATGCACTTAGTTCTGCTTCAGGATGAGCTGTCCTGTGGAG
Seq A exon
GTAACGATGTTAAACTCTTTCATCTATTGCTAGTCTGCAAAGCTGCTATTTCTCCTGACTTAATTTGTTTGTCTCCCAGGCTTGCCTTTCCCCCACTTGCTCCCCAGACATTCCCTACTGCTCCAGACTCCAGTGACCACTGTTTTAACAAACTCTGTTTCTGTATGGGTTTTACACATTCCACATAAAAGTGTAATTATTAGATGGTTACCATTCTTATTTCATTTAACATGTATTCTCTAGGCTCATTTCTTTGTAGCAAGCACATGATAGGAGTTCCCTTTTTAAAAGTCAAATAGTATTTTATTATTATATATGTCTTATGGTATTTTCAACCTATGAATTATATTTCCAGAACAAATGAAACAAAATCAAACCTTGTAAGCATATTTAATGCTATTGAATTATATACCCTTTAATGATTCAACTGATAAAATGTTGTTACATATGTTTTATCATAGTTAAAAGAAATTGTGTTTCCATATAGAGTGCTAGACTTGCTTTAAAAAGCAAATCCTGAAGAAATTTAAGAGATAAAACTGAGCCAGTATCCCATCTTCAGTTAGAAAATATCTTTTAAAGGGACTCAATTTTTTTGCTTATAAAGTAATTTTTTATTTGTATATAAAATTAATAGCAAGTTTTAGAAAATTAACACAAATGTCACCTGACTCAAGATGTAGAATGTTGCTTTAAGAAAGTACTCTTGAAGATCGTGTACTCGAGAGATGGAGGCAGTTCAAGATCATGCTGGGCAAGGAAACCCTTTCTCCAAGAAACAAAAAATGAGCTAACAAACAGGGAGGGGAAAAGAAAGATGGTGGCAATCACAAAAGAGAATGCCATGACCCTGTGATGCCAGCGCTGGACCACAGGGTGGATTAGAATCTGGCCTGGGCATTTAGTGGGACCTGTTCAGTCCATCACCACGTGAGAGAGGAGGGAGAGGAGGGCACAGAGGAGAGGGAAGGAGAGAAACAGAAAGCAAGGAGCCTCGGTTCTTTCTGGGCAGTTTTCTAGAAGCAGCGCCTACTCTGCAGACTCTGCCAGTCAGAGTTGGTTTGAACATTACCAGTGGGGCTGTGGCATGTAACCTTTCGGGTGTTAGCTTCTCTGACATAATTCTCTTACATAATGTCTTTTTAACTACTGAGTCACAGTTCATTATGTAACACTACAGTTACTCTGCTGTGAGGAACCATTGTGTTTCATTTTTAATAAAACTTCTGTGCATGTTCTGGACAGTCATTGTAACGTACAGTGACTCCACAGCATAAGTAAGTAGTGACGTCTGGGAACTAAACGCCACTGTACAGCTCTCACTTGAACTTGCCTCATTTACCATGTGAGGCTGTGTTTCTTTCCAGCTTGCTCTCTGCTTTTATCTGACTTAAGAATTTGGTTGATGTCCGCTCTGGCGAGGTCTGTTTCCATGTGCTTCTGTGTACTTGTGTCATTACAAATGTGTCTTTCTCCTCTTTTGTAATATCTTACGTATTCATCAAGTGCCTGTGAGGTCCCGTGCTCTGAGAGGTCTGTAGTAGCTGCTTGGATCTCCCGCATGTTGTGCAGTGTAAACTACAACTCCTTCAGATTTACCATGTAAACTGTTCAGCTGTGATCTGCATTAGTCTGTTTTAAAGATAATGCTTTTCTGATCAGCATATGATAAACTCATGTGTTTCTTAGAGGATTTATTAGCACATGTTTTAATGAAATAAGTTTAGTAAGATAAATTAAATAATATTAATAATAACAATACAGGATTACACACTATAATCCAGCATTCAGAAGGCTGAGGCAAGATTTTCTCCAACTCAAGACTAGCCCGGGGTGTACAGTAAGACTTTGCTCATGTAGACAAACACAAGTTGACAAAATAATGAAGGCTTTAATGACGTCCCTAGTTGTTCTACTCTTGTCCTTTTAAGGATGACCATCCCTTGTTTGTCACACAGTCAGCTGTGTGTCCTTGAACATCACTTAGCCTCCGGGCTAGATTGCTGTGTGTCATGGCTTGTGTCTGTAGTATCAGTTTAAGTTACATGGATGGTTGTGAATTATTTGAGCCCAGAGTTCAGCATGAAAACAGGATGAGACCTTGACTCTTAAAATTACAGAAAGGGTAGGGTATGGACACACAAGGAGGAGCCGTGTGCTTGAGGTGGTGAGAGCATTCGCTGCACAAGCAGGAGGGCCCTACTCACAACTCCAAACACCATGGAAAAATAAATAAAGCCAGGCATGGCTGTGCGTACTGTGGCCCTAGCCCTGTGCTGAATTAGGAGGGTCGGTGTGGCTCTCTGGCCACCAGTGTAGCTCCAGGTTTAGTGAGAGACCTCGTCTTGCCTTAAATGGAGAGCAGTAAAGCGGGACACCCAGTATCCTCCTCTGACCTGTACCTGTATACACAAGACAGACAGGGAAGGAATATAAGGAAAAATGAGAGAAGAAGAGTGCATGTGGTGGGTTGTGTCCAGGCCTCACATGGAAGGCGAGCTACACATGGCAGAAGCATGTTTTTCCATAGACATATAAACAAGTAACAATAGCCAGTTCTAATGAGTAACCTGGAAGTATACTCACTTCTGTCCACTAGACTTGGAAGGAGCATGAAAACACATTCCAAGATGTTTTTTAAGACACTGAGGTCACAAAACTCGTGTCTTGTTTCTTGGACTTTTCTCACAAGCACTCGGGATTTCTCTCCCAGGACTCCATTCTTGGGCTATGTTCGACCACTCACACAGTAAACCCAGTGACAAGAAGGAGTAGGGTCTTCAGGGGTGTGAGCACCTCAGCGCTATGTTCATTCTAAGCTAACTTTAAAAAAACATGGAAATTGGCAGTCATAGTGGTGTTTCCTGGGTGGGTTGCAGACGTTTTCGTCCTAATCAGGCTGTAATGCTAAGACTGCCTGTGTTTTTAACTGGTTACTGCATCTGGATGTCTGTGAGCAGATGAAGTATGTATTGTAACATGTTGCCTGTGTAGTTTGCCTAGGCCCCCTTGGCTCTCGTGTTGTCTCTGTGTGACCACTGCTCTTTCCGTCTCTCCTCACATGCAG
Seq C2 exon
AGCCTCCAACGTGTTCTCCTCAGCAGTTTACCTGCTTCACTGGGGACATTGACTGCATCCCTGTGGCTTGGCGGTGTGATGGGTTCACTGAGTGCGAAGACCACAGCGATGAACTCAATTGTCCCGTGTGCTCAGAGTCTCAGTTCCAGTGTGCCAGCGGGCAGTGCATTGATGGTGCCCTTCGATGCAATGGCGATGCGAACTGCCAGGACAAATCAGATGAGAAGAACTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030201-Lrp6:NM_008514:17
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:
PF146701=FXa_inhibition=WD(100=86.0)

							
A:
NA

							
C2:
PF0005713=Ldl_recept_a=WD(100=48.8),PF0005713=Ldl_recept_a=WD(100=46.2),PF0005713=Ldl_recept_a=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000032322





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000107581
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:12132058-12135174 
ALTERNATIVE
HsaINT0096543
(LRP6)
Human
(hg19)
chr12:12284992-12288108 
ALTERNATIVE
HsaINT0096543
(LRP6)
Rat
(rn6)
chr4:168205386-168213381 
ALTERNATIVE
RnoINT0086712
(Lrp6)
Cow
(bosTau6)
chr5:98150984-98158731 
LOW PSI
BtaINT0087033
(LRP6)
Chicken
(galGal4)
chr1:71843751-71845137 
ALTERNATIVE
GgaINT1016982
(LRP6)
Chicken
(galGal3)
chr1:73982014-73983400 
GgaINT0121430
(LRP6)
Zebrafish
(danRer10)
chr25:10553408-10554909 
LOW PSI
DreINT0090866
(lrp5)
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"