Special

MmuINT0117740 @ mm9

Intron Retention

Gene
ENSMUSG00000028073 | Pear1
Description
platelet endothelial aggregation receptor 1 [Source:MGI Symbol;Acc:MGI:1920432]
Coordinates
chr3:87563399-87564307:-
Coord C1 exon
chr3:87564146-87564307
Coord A exon
chr3:87563504-87564145
Coord C2 exon
chr3:87563399-87563503
Length
642 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GACCTCTTCTCAACCCACAGCTT
3' ss Score
8.31
Exon sequences
Seq C1 exon
ATGTGTCCTTCCGGCTGCTGGCTGCAGTGCTGTTTTGTTACCGTGTGCCCTATCGCAGGCCTCTGCAATGCCACTTTGTCCCCTCCTCCTCCTGGCCCTAGGCCTGCGTCTGACTGGGACACTCAACTCCAATGATCCCAATGTCTGTACCTTTTGGGAAAG
Seq A exon
GTGAGAGGGGCCAAGCTTGATGTTCGTCCCACAGGGTGGCTCCTCCCGGGAATCTGTTTCTGGTCTCTTTGCACTCTCTGTGGTGTTTGACCTTCCCCACCTCTGCCCTTGTCTCATCTCTGTCCTGTCTTTGTCCCCAGGTTCCTCTGGGAGGGAGCCATTCATTGTAGATGAAGCAGAGGGGCTGGCTGTGGGTAGGTAGGGACAGGACAGGAAAACAGGGCCCTGGGTAGAGAAGCCAAAAGTCTTCAATGCCAACTGGGTCCAGACAAGTTCAATCTTCCCGTGTGCATGTGTGCATACGTGTGCATGTGTGTGTCCCCGTATCCGTGTGTGTGTGTGTGTGTGTGTGTGCATGCATGTGCGTGCCTGTGTCTGTGTGCGTGTGTCTGTGTGTGTCCGTGTGTGTCTGTGTGTAAGGCTTTGGCCCCTAGGATGAGAAAATAGCTCTGGTAGGAGGAGTTCTAGAACGTTCCAGCTCTAGAAGCCTCTACACAGGACAGATAGGGAAGGGTAGGAGGAGGAAGCCCAAATATTGAGTACTGATTCTCTCCATGGTGAAGCCTGGCCTTGGCGTTCTGCTGCGCGGTGCCAGCTCCAGTTTCAGGCTGGCCTTGCCCCTGACCTCTTCTCAACCCACAG
Seq C2 exon
CTTCACCACGACCACTAAGGAGTCCCACCTGCGCCCCTTCAGCCTGCTCCCAGCTGAGTCCTGCCACAGGCCCTGGGAGGACCCCCACACCTGTGCCCAGCCTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028073-Pear1:NM_152799:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF075468=EMI=PU(12.2=28.1)

							
A:
NA

							
C2:
PF075468=EMI=FE(47.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000029714





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000078090, ENSMUSP00000088503, ENSMUSP00000103213, ENSMUSP00000133323, ENSMUSP00000133474, ENSMUSP00000133626, ENSMUSP00000133749, ENSMUSP00000133988, ENSMUSP00000134100, ENSMUSP00000134215, ENSMUSP00000134387
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:156904028-156904747 
ALTERNATIVE
HsaINT0122921
(PEAR1)
Human
(hg19)
chr1:156873820-156874539 
ALTERNATIVE
HsaINT0122921
(PEAR1)
Rat
(rn6)
chr2:187124800-187125344 
ALTERNATIVE
RnoINT0109565
(Pear1)
Cow
(bosTau6)
chr3:13996753-13997414 
LOW PSI
BtaINT0109846
(PEAR1)
Chicken
(galGal4)
chr25:410572-410648 
LOW PSI
GgaINT1021184
(PEAR1)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr16:30520788-30525598 
LOW PSI
DreINT0112345
(pear1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ATGTGTCCTTCCGGCTGCT

				
R: 
GTAGGCTGGGCACAGGTGT

				
Band lengths: 
267-909

			

		

	





	
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






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