Special

MmuINT0092511 @ mm9

Intron Retention

Gene
ENSMUSG00000049252 | Lrp1b
Description
low density lipoprotein-related protein 1B (deleted in tumors) [Source:MGI Symbol;Acc:MGI:2151136]
Coordinates
chr2:41041390-41044458:-
Coord C1 exon
chr2:41044333-41044458
Coord A exon
chr2:41041522-41044332
Coord C2 exon
chr2:41041390-41041521
Length
2811 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAC
5' ss Score
7.56
3' ss Seq
GTTCTCTTTCCTCCATTTAGGTA
3' ss Score
11.59
Exon sequences
Seq C1 exon
GCAGCAATTCTTGCCAAGTAAACAATGGTGGGTGTTCTCAGCTTTGCTTACCAACATCGGAAACAACCAGGACTTGCATGTGTACAGTGGGATATTATCTCCAGAAGAACCGCATGTCATGCCAAG
Seq A exon
GTACACACTCACAAGAACTTGACTGTGCTATGCTTACTGAATCCATCAATAGACCCCCACAGATGTTAGTCAAGCACTTCCAGACAACCATCTTCTTAAGGCAATAGTTGCAGTGATACCTTATTGAAGACTGAACGGAGTCTCTCTCTTATAATAGTTTAGAGAAAGTGTGAGCCTAAATTTGAGTTTGCCATATGTTTTCTTATGTGTTCCTTTTATGAGTAATCTCTCTCTGTTTGGTTTGTGTGTGGGTACATGTTTGTCTGTGTCTGTCTGTGTGTCTATTTATCCATCTGCCCATCTGTTGTTCTGTCCATCCATTTGTCTGTGTGTTCCTAACAATGGGTTTTGTTCTGTACTTATTGAAGAGAACAGGAAACATATCACAGGAAAGGAATGAGGATTATTTTTGTTTTGTTTTGTTTTGTTTTACAGAATCTATTAAGAGTTTCAGAAGAAAGAAGTTAACTTGTTAATACCAGTTGACCTAGAACAGTAGTCACCCAGAAACCAATGTTTTCAACCTATATCTACTTGCTGCTTTTAACATTTAATTTTGACTAATAATTGTTTTCTTTAAGTTTACTTTAAAACTTCAAACTTGTTTAGCTGCTGCTTCTAGTAAATGATGGCAACAAGAAAAACAAGAACATGAACACACACACACACACACACACACGTTATTCTGGATAAGAGGCATATGGAAGAGTTCAATTTCAGACTAAAACTTATTATTTAGTTTATGTCTCAAATGCTGATTATCTGGGAAGGCCAAAGCAAAATAAGTTTGGTTACTTTTTTTCTTAAAAGTAGGTAAAACTAGTAAGTAAAAATGCTGAATTCACATTAAGGAAACATAGTTCAATGATATCAAGGTTTTTATTGACTTGGTTACAATTACTTTCAGAAAAATCAATTCCAGAAAATAGTATGGCACTTAACTGCACATACTGACATTTAATGGTTAGAAATATTTGAACTATCACTAAAAAAAAAAAAAAATCTTATTTTATTCCCTTCCTTCTTTCCTTCTTTGCTTCCTTCCTTTCTTCCACCCTCCCTCCCTCCTCCCTCTCTCTCAACCTCCCTCCCTTCCTTCCCCCCTCCCTCCCTTCCTTCCTTTCTTTCCTTTTTTCTTTGTTACTTTCTTCCTTTCTTTTTTTGTTATTGGGATGAACATGTTACAGCCTTGGTATAGAGGACAGCAGAGAGAGTCTGGGAGTGAATGCTTTCCATGTGGATCCAGGCAGGGAATTGAATTCAGTCAGATCTTCAGCCTTAGTAATAGCAAGTGCCTTTACTTACTGAGTTGTCTTGCCACCCTAAATGTTTGTAATTTTAAAAACTAATTTGACACACACACACACAAACCCCTCAATTCCAACTTACTACTTGCTTCTACACTCAACTCAAATTTGTTAATGTTGGAGTAAGCAGCCATGGTTGTTTAGGTGGGATATTTGCACAATTTGAAATCAGTCCTGTTCATTTCTTCCAGCTATTTAGACAAAACACCACTGATATCTGGAGCTTCAGATTTGCATATTCGAGGGACTAGAACACTTCTGGGAGAGAACTATGTACCACCTTAAAGATTCTATGCACTCTTTTTATTCCATATTCTATAGATATGTTATTTCACAAAATACTGCTTTTTGGTTTTTTTTTAGCTATATTGTACAGCCAATAATAAGAATTCAGTTTTGGGACTGGAAAGATGGCTCAGTGGTTAACAGGACGGGCTGCCCTTCCAGGGATCTTGAGTGCAATTCCCAGCAACCACGTGGTGGCTCACGACTATCTATAATGTGATCTGCTGCCCTCTTGAGGCAAGCAGTTGTATATGCAGATAGAATACTCATACATTAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAGAATAAACTCAAAAGAAAAACCTGTTTTATCTTAAACAATATCACTATACTACTTGAGAAATATATAAGTCATAATTATGACTTATTGTATTTAAAATAATATATGTAAGTGGCCATTATTCTATGTCAGTCCCTATTGAAAGGATCTTGGAACATTGTGACTTACTTTCACCCTTGTAAGTTGATGAGATGGATCACCTAATTTTCTAATCATAAAACTGAGGTACAAGGACATTAGCTAAGATCAAGTTTTGTGATTTACAAGTAATAGGCATATTTAAAGATAGATAATTTTATTTTAATAATATCTGTGCGTGTGGTGTGTATTTTCCAATATATTAGCAAATTGAACAAGTGTTAGTATATGAACTTCTGGTAGTAAGATTATATCTATATACTTACTTTACAATAACATCTTTATATTCACATGTTTTTATGATGTTCTAAAATGTATGAAGGGCAAAACTTAATACCTTATTAATTACCTAGCCCATTTGAATCTAAAGTAATTAAGAAGTACACTGTGTTCCCTTAAAACTCTGAATGTCAACTGTAACTAATAATGTAGTTGTGTAAATAAAAGCCACTACTTTCAGTAGCCAGTACATATTTTCTGTGAGGCCAGACATTCTGGAAATGATCTCATACCAAGGTCATTGCTGACAAGCCTTTTATTTTCCCCTTTTCTGGCTCCTGGGACCTGTGAGCTATGAAACCCTTTGAGAGAATGCAATGCACAACAGAGTTTCAGGGCCTTGGTTTACATATCTTTCAATCCTGGGATCTATACAACTATGTATATGAAGCTAAGAAACATTCACAAATATAAATTAATATTATAGAGATGATATGAATGTATTGTTATGTGAAGTATTCATTTTAAGTTCTCTTTCCTCCATTTAG
Seq C2 exon
GTATAGAATCTTTTCTTATGTACTCTGTTCATGAAGGAATCCGGGGGATCCCTCTTGAGCCACGTGACAAGGTGGATGCCCTGATGCCAATATCAGGAGCTGCTTTTGCTGTGGGGATAGACTTCCATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049252-Lrp1b:NM_053011:34
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:
NO

						

					

				








    
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)
chr2:140769345-140770880 
LOW PSI
HsaINT0096319
(LRP1B)
Human
(hg19)
chr2:141526914-141528449 
LOW PSI
HsaINT0096319
(LRP1B)
Rat
(rn6)
chr3:25815059-25816266 
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
chr7:31483020-31484655 
ALTERNATIVE
GgaINT0048795
(LRP1B)
Chicken
(galGal3)
chr7:33598401-33600036 
LOW PSI
GgaINT0048795
(LRP1B)
Zebrafish
(danRer10)
chr9:36717540-36717663 
LOW PSI
DreINT0090633
(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"