Special

MmuINT0092532 @ mm9

Intron Retention

Gene
ENSMUSG00000049252 | Lrp1b
Description
low density lipoprotein-related protein 1B (deleted in tumors) [Source:MGI Symbol;Acc:MGI:2151136]
Coordinates
chr2:40732062-40735107:-
Coord C1 exon
chr2:40734985-40735107
Coord A exon
chr2:40732203-40734984
Coord C2 exon
chr2:40732062-40732202
Length
2782 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TGTTGCATCCTCTTCTCTAGGAT
3' ss Score
10.33
Exon sequences
Seq C1 exon
CACCCAACAATACATGTGACGAAAATGCTTTCATGTGCCATAATAAGGTGTGCATTCCCAAGCAGTTTGTCTGTGACCATGACGATGACTGTGGAGATGGGTCAGATGAATTCCTACAGTGTG
Seq A exon
GTGAGTAAGGCATCTTATAGGATAAATCAGTTGAAGGTCTATCAAAGGGACTCCAAGACACAGAAGTAACCAAAACAAACAGACATTTATTAGTGAATTCAGTAAATTCAGTGCTAAACAATGGAGTATGGGAGTTTGTCAGGTTCTGAGCACATTCATTTCTAAAACATTCCCTTCTTTCATGAATTCTGAGCAACCACCAGTCAAACTGGGAAATGTCTAGAAAAGGCCTTTGCATAGAAGTAGTTAGAATTGCTTTGAACTTTGAAGACGAGACATGACAGGCTTATCTAACCTTAAATGTACATCAAACAATGATATACAAACAAACAAACAAACAAAGAAACCAAAAATGCCAAAAGATTACACTTTTAAAATCTTCTGTACATTTAAAATATCAAAGAATGAAGTTAGCGTTTTCCTTAATATTTTACGTTGACACATGCACTACCTAATGTTTAAATTATCATTATGATCATCAATCGTGTCTCAGAATTATGTTGTTTATCTAATTATAACATTTATTTCTTCCAGAATAGGATTTTTAGTAGAACTAGTTATATATTAAAATTCAGTTTAGAGTGTTCTGTAAGCATAGATTCTTTGTGAATACTAAAATGCTAGGAATGCGTTAATTTACTTAACACATGTGCAAGGGTGATTCATGTGCTTAGGTAGCGTCCGCACCACATGACTATCCTTTATGGAAACTCACTGAAACCTGACGACCACCTTGGATTGCAGACCCAGGGCCTATATTTGACCTCCTTTGTCACGGATTTAGTGCTCTGCAGACTCTTCCCCATGGACTGCATTCAGTGTGTTCTGCTGTTCTCCATGTGAGGTTGACTAAGAGCCATATTTCATTCTTTTGTGATATTTCTATCTTTAGTCTTAGATGGGATCTCTGAGAAATCTTTTATTTATAATTATTTCATATTTTAGCCTTCAGTCAATATATTTTAAGTAGTATATCATAATTAACATATAATGGTTTTATATTGGTCATTTACTTACTTGTCTATTTGAGATAAATGACTGGCATAGTATTTGCTATGTAGATTAGCCTGTACTCAAATCCATAGATATCCCATGTCCTCGAATTAAAAATATGTACTACAAGGAAATAGGATATCACAATAAAATTTAACTTTAAGAACTCTCTCTTTTATCATAGTTCAAGAAATACTGCATACATGAGTCTAATCTGTTTAGGAAATTACTAGAACATTTTAAAAGTGAACAGTGTGGATCTAAACCATATCAGTAATGGTGCCATAGAAGAAAACAGAAAACTTATAGCTTACTCATGGACTTTTAGCTGGGAATGGGCAAGATAAAGACATTTCCAATTGATATGAATTGGAGAATGGCAGTACTGCTGGTAAGCTTAGGTACACAGTAATGTGATGGATAGTTTTTGTGACGTGCGAAAGAAATGAAATACATGGTTGAAGATTTGAAATTGTTTTAAATAAATAAATAAATAAATAAATAAATAAATAAATAAGCAAAACAACAACAGCACAAACAGTATTCTGGAGTCAAAATGCTGTAAGTTGTATCAGAAAAGGCTTTTTTACAGGAAGATGGAAAAAAAAAAAAAAAACCCTGGAGAGTAGATTATGAATACTTAACCAGGAAGAGTGTGCAATCAAGAGCAACAAAAATGCTGCCAAAAAACCAGTCAGTTAGAATCCTGGGAGACTTAAATTTGACAGCTTTGCTTAGTATTTTTTTCTTTAATCTCTAAGAGGAATTTCTAAAGAAGATGTTACAGGAAATGATGTTCAATTAATTAATGGGAAATGGAAGTTGGTAAGTAGAAACAAGATTTTGCATAAAAGTAAAGCAAAGAATTGTGCTTAGGGAGATGAAGGTGGATTTGTGGCTGATTGGACCAGACAGGATTTGTATGCTCACTAACAGGGACAACCTGCTCTTGCGGGGACAGGCTATAAACAGGATGCAGCAGCAGATTCCACTTTCACCATTCAGTATGACGAATTCTTCGGTAAGATTTGCAGTGAATTGTCTTTGCCACTTTAGAATGACTTAATAAAATTCTACCTCTAAAAGAAGAATTTTCCAGTTTTATCACTACTTACTAAGAATGTCTGTCTATAATTTACATGAAGGAAAATGTCATTATAAAACCTAATTTACAAAGTCAAGCATAAATATAATTCAAATAAAACAAACAGATGTTAATCTCAACAAATCATGGTTTATTATATAACTCGACTTTTAATGAATTGGCATACTTGACAGTTACAAACAATTTTATACTCATTCTTTTATAAATAGGATTTTATTCTTATTAAACAATTTCTTTCTGCACTGAATAATGTTTGTCAAGCATAAGTATAATATTACAACTTCTAAAAATAGTTCTTAGAGCTCAGAATCCATTTGCCTGTAAGTTCTAATGCTGCACATAACCACGCAACCAAGTCTGTGAATAGATTATAGTAGTGACCATTCTGCTTCACATCCTAAGAGAAATGGGTCGGATATAGACAATCACAGAATAGAAACAGTTGCATGTGTGGTAGTCATCTATCCTTACCTGGTATGTTATTTCCAAGATTATATTTGACCTTTTATTATGCTTTCACAAACACAAAAATATTGCTTATAGAAGTAATGGAGAAATGAGACGTATTTTCCAAAGAGGTCCATTCTGCCTACTTGTTAAATAGGGGTGCTGCGCACTGAGAGGGTGAAGTGCTGATTAATTTTTATGACAAGAGCTTAGTGAATGTTGCATCCTCTTCTCTAG
Seq C2 exon
GATACCGGCAGTGTGGTCCAGAAGAGTTCCGCTGTGCTGATGGGCGCTGCCTCGTGAATACTCTGTGGCAGTGTGATGGTGACTTTGACTGTCCTGACAGTTCCGATGAGGCTCCAATCAACCCAAGGTGCAGGAGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049252-Lrp1b:NM_053011:53
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=90.5)

							
A:
NA

							
C2:
PF0005713=Ldl_recept_a=WD(100=87.5)

						

					

				








    
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)
chr2:140503104-140506795 
LOW PSI
HsaINT0096340
(LRP1B)
Human
(hg19)
chr2:141260673-141264364 
LOW PSI
HsaINT0096340
(LRP1B)
Rat
(rn6)
chr3:25491448-25494441 
Cow
(bosTau6)
chr2:56708064-56711603 
Chicken
(galGal4)
chr7:31444485-31445107 
ALTERNATIVE
GgaINT0048814
(LRP1B)
Chicken
(galGal3)
chr7:33558373-33558995 
LOW PSI
GgaINT0048814
(LRP1B)
Zebrafish
(danRer10)
chr9:36776252-36778396 
LOW PSI
DreINT0090654
(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"