Special

MmuINT0117744 @ mm9

Intron Retention

Gene
ENSMUSG00000028073 | Pear1
Description
platelet endothelial aggregation receptor 1 [Source:MGI Symbol;Acc:MGI:1920432]
Coordinates
chr3:87561066-87562092:-
Coord C1 exon
chr3:87561849-87562092
Coord A exon
chr3:87561187-87561848
Coord C2 exon
chr3:87561066-87561186
Length
662 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
CCTCACCCCCTATTCCACAGCTG
3' ss Score
7.86
Exon sequences
Seq C1 exon
AGTGTGCCCCGGGAATGTGGGGACCACAGTGTGACAAGTTCTGCCACTGTGGCAACAACAGTTCCTGTGATCCCAAGAGTGGGACGTGCTTTTGCCCCTCTGGCCTGCAGCCCCCCAACTGCCTTCAGCCCTGCCCTGCCGGCCACTATGGTCCTGCCTGCCAGTTTGATTGCCAGTGCTATGGGGCATCCTGTGACCCCCAGGATGGAGCCTGTTTCTGCCCTCCAGGGAGAGCAGGACCCAG
Seq A exon
GTGTGTTATGAGGCCATAAACATATGACCATAAATGAGGACATGATGGCGTGGAGAGACTGAGATCTTAGTTCAGCTCTGCTGGGTACCAGCCAAGCAGCTTTGAGCAGCCACCAATTCCTTTTGAAGGATTCCCTAGGCCAGCTGCCACTGTCATAGCATTAGAAAGTAAGCACATGTGTGCACGCGCATGTGTGTGTGCACGTGTGCAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGGAGTGTCATTAAGTGAGACTGAGATGTAGACCTAGGCAGAATCCAGGGCCACGTGCAGAGGGGCCTGGGGTGTTGAGTTCTCCAGGATGCAAGAGCTGACTAGGAGAAGGTTATCAAGAGGGGACCACCTGAGCAGGGGAGGAGATGCACAGGGCCCTGCATGCTGGAGGAACAGACCTGCAACACACTCTTGCTCTCCCCACCTGCTGATGCTGGGGTGTCCTTGCCAGCTACTTGCCTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTGAGAGAGAGCCCCTTCTGTGCAGAGGGCAGCCTTGGGGAGCAAAGAGGGCCCCTGAAGTTTCTTCCTCATGACCCTCTGACCTCACCCCCTATTCCACAG
Seq C2 exon
CTGTAATGTGCCCTGTTCACAGGGCACTGATGGCTTCTTCTGCCCCAGAACCTATCCTTGCCAAAATGGAGGTGTTCCTCAGGGCTCCCAAGGCTCCTGCAGCTGCCCACCGGGCTGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028073-Pear1:NM_152799:8
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:
NO

							
A:
NA

							
C2:
PF126612=hEGF=PU(61.5=19.5)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000133988





     
                   









    
Main Skipping Isoform:
ENSMUSP00000029714





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000103213
          









    
Other Skipping Isoforms:
ENSMUSP00000078090, ENSMUSP00000088503, ENSMUSP00000133323, ENSMUSP00000133474
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:156906881-156907609 
ALTERNATIVE
HsaINT0122928
(PEAR1)
Human
(hg19)
chr1:156876673-156877401 
ALTERNATIVE
HsaINT0122928
(PEAR1)
Rat
(rn6)
chr2:187122379-187123212 
ALTERNATIVE
RnoINT0109569
(Pear1)
Cow
(bosTau6)
chr3:13994302-13995038 
LOW PSI
BtaINT0109850
(PEAR1)
Chicken
(galGal4)
chr25:409240-409312 
LOW PSI
GgaINT1021191
(PEAR1)
Chicken
(galGal3)
chrZ:55270423-55270710 
GgaINT0060905
(MEGF10)
Zebrafish
(danRer10)
chr10:16151103-16151236 
LOW PSI
DreINT0094993
(megf10)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTGTGCCCCGGGAATGTG

				
R: 
CTGCAGGAGCCTTGGGAGC

				
Band lengths: 
345-1007

			

		

	





	
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"