Special

MmuINT0092531 @ mm9

Intron Retention

Gene
ENSMUSG00000049252 | Lrp1b
Description
low density lipoprotein-related protein 1B (deleted in tumors) [Source:MGI Symbol;Acc:MGI:2151136]
Coordinates
chr2:40734985-40737788:-
Coord C1 exon
chr2:40737660-40737788
Coord A exon
chr2:40735108-40737659
Coord C2 exon
chr2:40734985-40735107
Length
2552 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGA
5' ss Score
5.27
3' ss Seq
GTCTTGCAATTTTTTTTTAGCAC
3' ss Score
7.15
Exon sequences
Seq C1 exon
GTGCAGTCACTTGTGCTGCTGACATGTTCAGCTGCCAGGGCTCCCATGCCTGTGTGCCCCAACACTGGCTGTGTGATGGTGAGAGAGACTGTCCCGACGGGAGTGATGAGCTATCCAGTGCAGGCTGTG
Seq A exon
GTATGAACATTGTCTGAAGTTGTGTGTCAAAGAATTCAGTGGCAGCATTCAGGGGAATTGTTTTATCATATCATAATATACTTTCTTTCACTTTTCCCATCCTTGGGATGAGTATGTAATAGTAGTAGTTTATCAAGATGCAATTCTGTAATAATAGTAGTTTTTCAAGCCTTATACATTCAAAGTGTCATAAAAATATTTAATATTAGCACCAATTTTAAAACTATTCCACTGGCTGCAATTTTACTACTTGAACTCCAAAAAAGCATAACTTGATTATATACAGATTGTTGGTTGTTCTAGTCTTTTCTTATTTAACAATTATCCCTTTCAAATTGTTTTTGAATGCCTATTACACTCACCCTATAAATTGCTGCTATTAAGTAAGTACTGATCCGGAAGTCAGCGGACAATTACTAAGTCTAGAAGTGAGGAATTAAACCTTGGGTCATGAATAAATGAAACTGAAGGATCAAGAAGACACCTTTAAGGTCAATTTACAAAGTTTCTAACTCAAGATTATATTAAGGAGTCACTCAAGAGAAAATGGTTAGATAATCCTTTTCCATGATCAGGAGGATAAAAGAACTCCTCATGTGACTGTCAATACCAAAGATCAACTTGTGATCTGTTGAACTGGGCTGCTTATCAGAATGGGTTTGTTTGTCAGATTCAGTCTATTGAATGAAATCTGACAATGTCATGATTTACTTTTAAATGCATAAATCATTACATCCTTAAAATATTCTATATGACCTTTTGGGCACACATGTATGTCAACAGAATAAAACCCCACAGAAAAATATTTGCTCACAACTCATCCTATTGTAGAATATGATCTTGAAACTGATATATTTTCTATGAAGGTCAGTGTTGCTACTGATGGTGGAATAACAAATGATAATTAATTAATTTAAAAAAATGCACATAATCCTACATGCTTTTGCTATTGTAGTTAGCATTCTGGGAGGTATGTTAACACTTGTGAGCCACATGGGTATTATTCAATAAATTATGCTAAATACAACAAATCGCCCTCTGGTGATCTAAAAGTGATGCAAAATAAGTCACTGCTGCTGTGTTTTAGAGAAGAACGGATATATCAGTGTGAGTATAATTCATTCGAGGAATAGCAACTGTCATAGCTCAGTGACCTGAGTTATTAGCCACTCTTGAGTTTTAATTTTATTAAAATATGCAAAGTTAATGTTGCTGCTCTCTGGCCTCTCTATAGTGGTTCAAAATAAATTTATTGAAAGTAAATTATACTGGGCTACCTGCCCCCCCTCCCTCACACACCCAGATGTCCTTTCTGTTTTGTCTATTCATAGTTCTATGTAGACAAATACTTGGAGGATAGTGGAGGTTTCTTCAAGAGGTATGGGGACAGCTGGATGCAGTAGACTGAAAGGGGTATGTGAGACAATATTTGTAAATTCCCAAGTCTCACGGTAATGTACATAAAGGATACTAGATTACCACAAAGAAATGGGCCAGTACTTTTGTGTTGACTTTTTTGAAAACTGACCATATTACTTCATCTTGAAGGACCAAAAAAAGAGTTGCTCTCCATGAGGACAGCATTTCTTATAGCCCTCCATGCCCATTGTATGTTAATCAATGCAGTAATAGGTTTTTCAGTTAAGACATGTTTGTTTACATTATTGAGTACTGTGAACAATGTCATAAAGTGTTTTTAGAAAACCTGTAAAGCATAATAATATAGAAATAAGAATTCTGAGAGTGCTCATAAATTGTTGAATACCTAAGTTGAAAGATCATTTCTACATCCCTTACATGCCCATGGAAATATTGTCAGAGAGATTTAAATCCCTTCATTAAATAGGGAAAAACAAATGAACAAAGAAGGTGCAAGCTTTCTCAAGCATGGAAATATAAGGATCAGAGCCAATTATGGGACTAGTGTGGTGGCATTTGCCTATAGCAGATCAGCCACTAAGGATTCACTATGACCCAAACCCTAATTACTACAGCAGTTACACTTTTAGTTGACTATAAAGGGCGCTGTAAATTATTTTGGTTCTATGAATATAATATCAAAGTGGATTTTATTGCAAATTTGATCAACCATCACTTAGGCTCTTGCTGGAACACTACTTTCATGGGGCTATGTTCCTAAAGGATCAATACTCCATTACAAGGGTCAGTATTCATGGTATTGGTGGAGTTATGGAAGGGCTTATTACTCTGTAGACTTTAACTTTGCTTGAATTAAGATGCTGTTTCTGCAGGTTTCTGAAAGATTTTTTTCTTAAAGAACAATATTCTCAGTCTTCTTAATGTTCCTTCCATGTCTCTTATGAACATTAAATTTCTATTCAGTGAATCAACCTTTGAATCATACATGTATCTATTAGCATTTTAATATACATGAGATCATTCTTTTGCCTAATACACTGAATAAAAATACATTAGCATTTTCTCTGAGTATCTACACACTGATAGAAAAAAGCCTCGTACTTTACACTTCAAGTATGAGAGAAGATGAAATATGTGCTTATGTAATTTTATGTCTTGCAATTTTTTTTTAG
Seq C2 exon
CACCCAACAATACATGTGACGAAAATGCTTTCATGTGCCATAATAAGGTGTGCATTCCCAAGCAGTTTGTCTGTGACCATGACGATGACTGTGGAGATGGGTCAGATGAATTCCTACAGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049252-Lrp1b:NM_053011:52
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:
PF0005713=Ldl_recept_a=WD(100=93.2)

							
A:
NA

							
C2:
PF0005713=Ldl_recept_a=WD(100=90.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000054275f4696A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000054275, ENSMUSP00000129192
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:140506919-140509927 
LOW PSI
HsaINT0096339
(LRP1B)
Human
(hg19)
chr2:141264488-141267496 
LOW PSI
HsaINT0096339
(LRP1B)
Rat
(rn6)
chr3:25494565-25497104 
Cow
(bosTau6)
chr2:56704776-56707940 
Chicken
(galGal4)
chr7:31445231-31446170 
ALTERNATIVE
GgaINT0048813
(LRP1B)
Chicken
(galGal3)
chr7:33559119-33560058 
LOW PSI
GgaINT0048813
(LRP1B)
Zebrafish
(danRer10)
chr9:36773143-36776128 
LOW PSI
DreINT0090652
(lrp1bb)
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"