Special

MmuINT0121143 @ mm9

Intron Retention

Gene
ENSMUSG00000054580 | Pla2r1
Description
phospholipase A2 receptor 1 [Source:MGI Symbol;Acc:MGI:102468]
Coordinates
chr2:60282188-60285597:-
Coord C1 exon
chr2:60285440-60285597
Coord A exon
chr2:60282253-60285439
Coord C2 exon
chr2:60282188-60282252
Length
3187 bp
Sequences
Splice sites
5' ss Seq
GGGGTACAC
5' ss Score
0.38
3' ss Seq
CTCTCCCTTCCCTTCAATAGCTG
3' ss Score
8.56
Exon sequences
Seq C1 exon
ATGCGCCGTGGCTCTTCTATCAGAACGCCGAGTACCTCTTCCACACCCACCCAGCGGAGTGGGCCACCTTTGAGTTTGTCTGCGGCTGGCTGCGAAGTGACTTCCTCACAATTTATTCTGCTCAGGAGCAAGAATTCATCCACAGCAAAATCAAAGGG
Seq A exon
GTACACGAACACAAATCACTTCACAGAATTCATAGTTTACACCTTCCGTCCTTGGGGGAGGCGATATTTTTAAAATTTGACTCTACACATTCATTTAAGTTTCCGTAAAAGTCCTGGCTTTCTTTTTTTTCAGACTCTTTTCCCTCTGACTATACAGATTCATAGAAAATTATGGGGACGTGGGTTGGTTATGCCCCTTTGACTTCTGTTTCTTCTGTAATAGCAAGGGTATTAAGTGAGAGTCATTCTTCACTCTCTGGGCCACTCTCGCCACTCGTGAGGGCTTCCTGATCTAATCACTTTCCAGAGGCTCACACTTCCCAGCATGTCATCTTGTGAGTTAGGATTTCAATATTAAGGACTGGGAAGGGAGGAGACATCTACATTCGGTGTGGCTGTAGATTTCCAAGCAGTATTTATTTCTACCCACGATTGGTACTTTTGGTTGTCAGTAGTACGGTGGTATTTATGGTGAGCATTAGTGTTTCACACGTAAGATGTCTCATGTCTACCAATATGCTTGCCAAGTTGGTGGATGCAGGGGAAATTACTGACTCTAGGATGAGGAATCAAACTCAGCAAAGGTGATATGGCTCACTTTTGACCCATACCTGGCCAAAAAAAAACATCAAAAAAGTTAGAATAAATAATTATTTTGAAATAGCACGGTTTCATATCACTTTTCTATGAAGAATAGTCACTAAGACTGTGAAAGGCAAAAATAACATTTATTTGGAGTGTAGAAGAATTTAATATGAGATAGAAAGCTGGGTAGAGTTTTTCTAACAAAAACAATTTTTCTTTTGAAGGATGCTTATGTTTTCTCTGAATCTCTGATAATAGACCATGGGGTGTTAGAGTGAGCTTTGAATATTTTTCTTTTCTCTAATCTTCTCTTTCTGATCAACGATGAAAACATTAAAAGCTACAGCACTTGAGAGTCAGAGGACTTGATTGGCTTACCAATCAATCACTTGTATCTGTCATATACAGTATTTGCACTTTAAAACTGCAATTCACTCTTTTAAGTTTTGTGTTTGTAAGCATTTCTAAAACTGTATATCAAATCTATTACTTCTTAAAATCTGGCTGTTTAAACCCTTAAACTAACGCCCTTGATCACTTTGGTAGAAACCTAAGAGATGACAGATTGCCTTTGCTGAAGAAAGTTGAGTAGATGATTATGTTGGCTTGTGTGTCTAGCTCACTGGGAAATGACCTTTCCTGTCAGTTAACCATAAGGCTACTTGAGCATAACAAAATATAACTGATTTGTGAAATGCATGCTCATATTACATTTCTTCTTTCAAACACCTATTATTAGGTTTCAGTTGTTATGGCTGTATATACCTAGCTAACATTTAAAATATTCACTTTTCCATACCAGGCTGTTTTGTCATCTTTCAGCTTGTCCTGTAAAGTTCTCTACCACATATGTCACAGCTGGGATGCACTATGTGGCAGATGATCATATCTTAAATCAGGTGGCAATAAATATACCACTTAAGATATAAATGTCATAGAAACAACAATATGAACTAACCAGTACCCCCCAGAGCTCCCTGGGACTAAACCACCAACCAAAGAAAACACATGGTGGGACTCATGGCTCCAGCTGCATATGTAGCAGAGGATGGCCTAGTCGGTCATCAATGGGAGGAGAGGACCTTGGTCCTGTGAAGGCTCTATGTCCCAGTATAGGGGGATGCTGGGGCCAGGAAGCAGGTGTGGGTGGGCTGGTGAGCAGGGGGAGGGGGAAGGGGGAGGAGATTTTCAGAGGGGAAACCAAGAAAGGGGATAACATTTGAAATGTAAATAAAGAAAATATCTAATTAAAAAAAAAAAAGAAAAAGAAGATATAAATGTTATAACTTCCCCTTAAAGGTCCTAAACTGGGAGAGTGAGTGGTCAGGCTATGATTTTGACTGCTGTTGCCCATGTGCCTTCCTTAGATGCAATTAAGTTGTAGTCTTCCTGCCGTATCCATGCCAATCTCAACGGAAGCACTCCAAAGTATGAAAATGGGGCTCTGAATTCAGCATGTGGGAACACGCCCACGGAACAGTGCCTCAGGGATCTCAAATTATAGTGGCTCCCCCTTTGCAATATTCTCAAATTGCTGCTCTGGCAGACAGCCATGCTGGCTAAGAAGTAAAAGCACACTTGTTTCAAAATAAGAATGTTAGCAAGCTATCAGGTTCTGTGGTAGTGACTTGCAATTCATATGGAAATAAATAATGTATCTTAAAAATGTATCCCCAAGCCCTCCCAAAAGGAAATAAGAGTACAAATTTAAATACATAAGGCCTTAACCTTAATAGGGTTTGGGCATATAAAAGTTAATTTGAATTTTGATACACATACAGAGGGAGCAGATACGCCGTAAAGCACACTGCTCGAGAGGGCTCAGTGAAAGCTCATCTGTCCCTTCCTCTTTTGTGATTAAGGAGAAGGCTTCAATTTCCTGGACCATAAGTCCAGCATGATATCTGCAGTGCAGTGTGTACGTGAGTGTGCGCCTGCATGTCCATGCTTCTCCACTTGATACTTCACTGTGCTTAGACTGGGTGATTAATAATTGACTGTAGACTAATAAAATGGATAATTTGCTAGCTTTCAGACATTGGAATTCTGTAGGGTTGTTTTGTCCTATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCTCTCTCTCTCTCTCTCAGTGTGGACACTGTCTAAAGGTTCACAGACTAATATGCTTAGACTCTAAATCTTTATTCTGTTAATGTCTTTGTACCTTGTTTGTCAAATAAATGTGACATCTGCAGGGAGCTTCCATAAATCACTGAGAGAAGAAGCCACTAATTATAGTCAGAAGAGGTACCCGTCTCTCTTTTATGTCACGTGACTTCTCACAGAGTTAGAAGCCTTGCCTTTCAAGTTGAATGAAACAGAAATATTTTCAGTGGTTCACTATCATTCTCTTTCATAATGAACAGGGAATGCTTTAGAATAATTCAATTTCACGACTTCTCTAGACACTAGCCCTTAGCTCGTTACTCTTCTTTACATAACCTGGTAACATTGTAGTAATTAAAAAACCAATAGCAACCCCATTGATCCAAATAGTAGAACAATGTAAACAAGAACATCAAACACTGACATGTTCTCTCTCCCTTCCCTTCAATAG
Seq C2 exon
CTGACAAAGTATGGTGTGAAGTGGTGGATCGGACTTGAAGAAGGAGGAGCCAGAGATCAAATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054580-Pla2r1:NM_008867:17
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:
PF0005916=Lectin_C=PU(32.4=67.9)

							
A:
NA

							
C2:
PF0005916=Lectin_C=FE(18.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000108144





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000065205
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:159970213-159976067 
LOW PSI
HsaINT0126450
(PLA2R1)
Human
(hg19)
chr2:160826724-160832578 
LOW PSI
HsaINT0126450
(PLA2R1)
Rat
(rn6)
chr3:46513778-46516740 
ALTERNATIVE
RnoINT0112547
(Pla2r1)
Cow
(bosTau6)
chr2:36471583-36480685 
BtaINT0112887
(PLA2R1)
Chicken
(galGal4)
chr7:21351817-21353130 
ALTERNATIVE
GgaINT0050860
(PLA2R1)
Chicken
(galGal3)
chr7:23440391-23441704 
LOW PSI
GgaINT0050860
(PLA2R1)
Zebrafish
(danRer10)
No conservation detected
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"