Plant Circular RNA Database

Detail information of Os01g0259200_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0259200_circ_g.2
					
						ID in PlantcircBase
						osa_circ_001187
					
						Alias
						Os01circ08024
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 8684014-8686010  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os01g0259200						
					
						Parent gene annotation
						
							Similar to serine/threonine protein kinase PBS1. (Os01t0259200-0
1);Similar to Protein kinase. (Os01t0259200-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0259200_circ_g.3 						
					
						Support reads
						3/4
					
						Tissues
						leaf/shoot, root
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os01t0259200-01:3
Os01t0259200-02:3

General Information
CircRNA Name	Os01g0259200_circ_g.2
ID in PlantcircBase	osa_circ_001187
Alias	Os01circ08024
Organism	Oryza sativa
Position	chr1: 8684014-8686010 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os01g0259200
Parent gene annotation	Similar to serine/threonine protein kinase PBS1. (Os01t0259200-0 1);Similar to Protein kinase. (Os01t0259200-02)
Parent gene strand	+
Alternative splicing	Os01g0259200_circ_g.3
Support reads	3/4
Tissues	leaf/shoot, root
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os01t0259200-01:3 Os01t0259200-02:3

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							F: GCCAAGAACCACTAGATTGGAC
 R: TGCTTTATACACACTGCCGAAT
PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	Yes Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	F: GCCAAGAACCACTAGATTGGAC R: TGCTTTATACACACTGCCGAAT PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							TGACATTTATAGTTTTGGTGTGGTCTTTCTTGAGCTAATTACTGGACGAAGAGCGCTTGACAGC
AATCGGCCACCTGATGAACAAGACTTGGTTGCATGGtggaatattcaaagtcgtcagagagttg
cccactgaagactgaagggtcgatagatatggttggaattcggcgaaataaggggcatggtgaa
gcaacgat

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 791
Transcript exons: 8684014-8684222,8684468-8684657,8685619-8686010
TGGAATATTCAAAGTCGTCAGAGAGTTGCCCACTGAAGACTGAAGGGTCGATAGATATGGTTGG
AATTCGGCGAAATAAGGGGCATGGTGAAGCAACGATCTTCACTTTGCGCGAGCTTGCTGATGCT
ACCAACAACTTCAGCACGGAGTGCCTTTTGGGCCGAGGAGGATTCGGCAGTGTGTATAAAGCAT
TTCTCAATGATAGACAGGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAG
AGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAGTCAAGTTGTTT
GGTTACTGTGTGGATGGAGATCAGCGCCTGCTTATTTATGAATATATGCCATTGGGATCACTAG
AAGACCGCCTTCACGATCTCAGACCCGGCCAAGAACCACTAGATTGGACAACACGGATGAAGAT
TGCTGCTGATGCAGCTGCTGGTTTGGAGTATCTGCATGATGAGGCCATTCCAGCAGTTATTTAC
CGGGATATTAAACCGTCAAACATTCTTCTTGGCGAAGGGTATAATGCAAAGTTGTCTGACTTTG
GACTTGCTAAACTTGGTCCTGTTGGTGATAAGACTCATGTGACAACTCGTGTCATGGGGACACA
TGGTTATTGTGCTCCTGAGTACCTCTCGACTGGAAAGCTTACGATCAAATCTGACATTTATAGT
TTTGGTGTGGTCTTTCTTGAGCTAATTACTGGACGAAGAGCGCTTGACAGCAATCGGCCACCTG
ATGAACAAGACTTGGTTGCATGG
						
					

						Genomic sequence
						
							TGGAATATTCAAAGTCGTCAGAGAGTTGCCCACTGAAGACTGAAGGGTCGATAGATATGGTTGG
AATTCGGCGAAATAAGGGGCATGGTGAAGCAACGATCTTCACTTTGCGCGAGCTTGCTGATGCT
ACCAACAACTTCAGCACGGAGTGCCTTTTGGGCCGAGGAGGATTCGGCAGTGTGTATAAAGCAT
TTCTCAATGATAGACAGGTTTGTATTTTCTACTCAAGCACCCAACTCCTTATGCACTTCGAGTC
CCAAGCTATGCCGCGAGCATGAAACAAGCTTTTTCAACAACACTGCTTTGAATACTTTGTGATA
TTGATAAAAGAAACTGTTCCTTTGGTCAAAATTGATGGGAATGCTTAGACTATTGATGTTAACA
GAAAGTATTGTTATGCTATATACCCTTTGTATAAATTTCTAATTTGGTTCCAGCATTTGCTGCA
TCGCAGGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTG
TGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAGTCAAGTTGTTTGGTTACTGTGT
GGATGGAGATCAGCGCCTGCTTATTTATGAATATATGCCATTGGGATCACTAGAAGACCGCCTT
CACGGTTAGTATTTTATTGGAAATTGTATAATATCCTCTGTTAGCTCCTAGAAAAACCTGAAAG
TTCCCTAAGAATCTGTAGTTGTGTTAGAAAACATTTTATATTTTTCATTGTTACATCATCGTGA
TTTAAAGCACATCTAACCACTTGAACATGGTGAAAAGAACTGTCTTCTAGGTGAGAAGAAATAA
AAAAAAATAAAGAGCTGATAATTTGGCACCTCTTTCAGCATTTTAAAGATCAGTAGCTGATAGT
ACATAATAACTTCAATATAGAAAGAGTTCACAACTTCTGTACTTTTGGATTTCCCTGAATTCGA
AGTGTGTTTTCTGCATTCTATCTTGGCAAAGAAAACAATTGGTTTTCTTCAATGTTCCATCCAT
CATATTTTCTAAATTTGAATTTCTATTATAATCTGTTGTATCTGAAGATGGCTTGAAGTAATTC
CTTTAAATGATAAACATCGCAACCTTTTACCTTCAAATGGCTATTACTATGCCTTGCTAAAACA
TCATTTGACCTTTTTATTATGTATGATGAAGGTGCTATTGTTTTTGGCATTGAAAATTATTATC
CAGTATTTTGGTAGACCTGTCTAGGATCCAGATTAGTTTTGTTTCCATTGTCTTATGCATCTGA
TCAAAAGCTAAAGCTAGCATGGAATGTTCAACTTTAGGCAGATCTGTCTAGAATTCAGTGAGGA
TTCGAGGGCATAACTTTTCATAACCATCCATAACCACTTTTTTTTTTTTGGTTTGACGAGAGGA
CCCTGCAGTGTATATTCAATAATAAAGAGATAGATTCAGCATGTCGCTGTTTATCACCCTTCAT
GTCCGTTTCTACCATTAGACCACATGGTTCAAAAAGAATTAAATTGTTCTTTACATTCCAGTAA
GCTACTTAATTTCCTTAAGTATTATTACTGGATACCCTGTTAAAAATTTGCTGCCGATGCTTTT
TACAGATCTCAGACCCGGCCAAGAACCACTAGATTGGACAACACGGATGAAGATTGCTGCTGAT
GCAGCTGCTGGTTTGGAGTATCTGCATGATGAGGCCATTCCAGCAGTTATTTACCGGGATATTA
AACCGTCAAACATTCTTCTTGGCGAAGGGTATAATGCAAAGTTGTCTGACTTTGGACTTGCTAA
ACTTGGTCCTGTTGGTGATAAGACTCATGTGACAACTCGTGTCATGGGGACACATGGTTATTGT
GCTCCTGAGTACCTCTCGACTGGAAAGCTTACGATCAAATCTGACATTTATAGTTTTGGTGTGG
TCTTTCTTGAGCTAATTACTGGACGAAGAGCGCTTGACAGCAATCGGCCACCTGATGAACAAGA
CTTGGTTGCATGG
						
					

			
		

Sequences
Splice junction sequence	TGACATTTATAGTTTTGGTGTGGTCTTTCTTGAGCTAATTACTGGACGAAGAGCGCTTGACAGC AATCGGCCACCTGATGAACAAGACTTGGTTGCATGGtggaatattcaaagtcgtcagagagttg cccactgaagactgaagggtcgatagatatggttggaattcggcgaaataaggggcatggtgaa gcaacgat
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 791 Transcript exons: 8684014-8684222,8684468-8684657,8685619-8686010 TGGAATATTCAAAGTCGTCAGAGAGTTGCCCACTGAAGACTGAAGGGTCGATAGATATGGTTGG AATTCGGCGAAATAAGGGGCATGGTGAAGCAACGATCTTCACTTTGCGCGAGCTTGCTGATGCT ACCAACAACTTCAGCACGGAGTGCCTTTTGGGCCGAGGAGGATTCGGCAGTGTGTATAAAGCAT TTCTCAATGATAGACAGGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAG AGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAGTCAAGTTGTTT GGTTACTGTGTGGATGGAGATCAGCGCCTGCTTATTTATGAATATATGCCATTGGGATCACTAG AAGACCGCCTTCACGATCTCAGACCCGGCCAAGAACCACTAGATTGGACAACACGGATGAAGAT TGCTGCTGATGCAGCTGCTGGTTTGGAGTATCTGCATGATGAGGCCATTCCAGCAGTTATTTAC CGGGATATTAAACCGTCAAACATTCTTCTTGGCGAAGGGTATAATGCAAAGTTGTCTGACTTTG GACTTGCTAAACTTGGTCCTGTTGGTGATAAGACTCATGTGACAACTCGTGTCATGGGGACACA TGGTTATTGTGCTCCTGAGTACCTCTCGACTGGAAAGCTTACGATCAAATCTGACATTTATAGT TTTGGTGTGGTCTTTCTTGAGCTAATTACTGGACGAAGAGCGCTTGACAGCAATCGGCCACCTG ATGAACAAGACTTGGTTGCATGG
Genomic sequence	TGGAATATTCAAAGTCGTCAGAGAGTTGCCCACTGAAGACTGAAGGGTCGATAGATATGGTTGG AATTCGGCGAAATAAGGGGCATGGTGAAGCAACGATCTTCACTTTGCGCGAGCTTGCTGATGCT ACCAACAACTTCAGCACGGAGTGCCTTTTGGGCCGAGGAGGATTCGGCAGTGTGTATAAAGCAT TTCTCAATGATAGACAGGTTTGTATTTTCTACTCAAGCACCCAACTCCTTATGCACTTCGAGTC CCAAGCTATGCCGCGAGCATGAAACAAGCTTTTTCAACAACACTGCTTTGAATACTTTGTGATA TTGATAAAAGAAACTGTTCCTTTGGTCAAAATTGATGGGAATGCTTAGACTATTGATGTTAACA GAAAGTATTGTTATGCTATATACCCTTTGTATAAATTTCTAATTTGGTTCCAGCATTTGCTGCA TCGCAGGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTG TGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAGTCAAGTTGTTTGGTTACTGTGT GGATGGAGATCAGCGCCTGCTTATTTATGAATATATGCCATTGGGATCACTAGAAGACCGCCTT CACGGTTAGTATTTTATTGGAAATTGTATAATATCCTCTGTTAGCTCCTAGAAAAACCTGAAAG TTCCCTAAGAATCTGTAGTTGTGTTAGAAAACATTTTATATTTTTCATTGTTACATCATCGTGA TTTAAAGCACATCTAACCACTTGAACATGGTGAAAAGAACTGTCTTCTAGGTGAGAAGAAATAA AAAAAAATAAAGAGCTGATAATTTGGCACCTCTTTCAGCATTTTAAAGATCAGTAGCTGATAGT ACATAATAACTTCAATATAGAAAGAGTTCACAACTTCTGTACTTTTGGATTTCCCTGAATTCGA AGTGTGTTTTCTGCATTCTATCTTGGCAAAGAAAACAATTGGTTTTCTTCAATGTTCCATCCAT CATATTTTCTAAATTTGAATTTCTATTATAATCTGTTGTATCTGAAGATGGCTTGAAGTAATTC CTTTAAATGATAAACATCGCAACCTTTTACCTTCAAATGGCTATTACTATGCCTTGCTAAAACA TCATTTGACCTTTTTATTATGTATGATGAAGGTGCTATTGTTTTTGGCATTGAAAATTATTATC CAGTATTTTGGTAGACCTGTCTAGGATCCAGATTAGTTTTGTTTCCATTGTCTTATGCATCTGA TCAAAAGCTAAAGCTAGCATGGAATGTTCAACTTTAGGCAGATCTGTCTAGAATTCAGTGAGGA TTCGAGGGCATAACTTTTCATAACCATCCATAACCACTTTTTTTTTTTTGGTTTGACGAGAGGA CCCTGCAGTGTATATTCAATAATAAAGAGATAGATTCAGCATGTCGCTGTTTATCACCCTTCAT GTCCGTTTCTACCATTAGACCACATGGTTCAAAAAGAATTAAATTGTTCTTTACATTCCAGTAA GCTACTTAATTTCCTTAAGTATTATTACTGGATACCCTGTTAAAAATTTGCTGCCGATGCTTTT TACAGATCTCAGACCCGGCCAAGAACCACTAGATTGGACAACACGGATGAAGATTGCTGCTGAT GCAGCTGCTGGTTTGGAGTATCTGCATGATGAGGCCATTCCAGCAGTTATTTACCGGGATATTA AACCGTCAAACATTCTTCTTGGCGAAGGGTATAATGCAAAGTTGTCTGACTTTGGACTTGCTAA ACTTGGTCCTGTTGGTGATAAGACTCATGTGACAACTCGTGTCATGGGGACACATGGTTATTGT GCTCCTGAGTACCTCTCGACTGGAAAGCTTACGATCAAATCTGACATTTATAGTTTTGGTGTGG TCTTTCTTGAGCTAATTACTGGACGAAGAGCGCTTGACAGCAATCGGCCACCTGATGAACAAGA CTTGGTTGCATGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_001953* 						
					
						PMCS
						0.383961726

Conservation Information
Conserved circRNAs	osi_circ_001953*
PMCS	0.383961726

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8685989-8684053(+)
8686008-8684046(+)
8684071-8684046(+)
						
						Potential amino acid sequence
						
							MNKTWLHGGIFKVVRELPTED*(+)
MVEYSKSSESCPLKTEGSIDMVGIRRNKGHGEATIFTLRELADATNNFSTECLLGRGGFGSVYK
AFLNDRQVVAVKQLDLNGLQGNREFLVEVLMLSLLHHPNLVKLFGYCVDGDQRLLIYEYMPLGS
LEDRLHDLRPGQEPLDWTTRMKIAADAAAGLEYLHDEAIPAVIYRDIKPSNILLGEGYNAKLSD
FGLAKLGPVGDKTHVTTRVMGTHGYCAPEYLSTGKLTIKSDIYSFGVVFLELITGRRALDSNRP
PDEQDLVAWWNIQSRQRVAH*(+)
MVGIRRNKGHGEATIFTLRELADATNNFSTECLLGRGGFGSVYKAFLNDRQVVAVKQLDLNGLQ
GNREFLVEVLMLSLLHHPNLVKLFGYCVDGDQRLLIYEYMPLGSLEDRLHDLRPGQEPLDWTTR
MKIAADAAAGLEYLHDEAIPAVIYRDIKPSNILLGEGYNAKLSDFGLAKLGPVGDKTHVTTRVM
GTHGYCAPEYLSTGKLTIKSDIYSFGVVFLELITGRRALDSNRPPDEQDLVAWWNIQSRQRVAH
*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8685989-8684053(+) 8686008-8684046(+) 8684071-8684046(+)
Potential amino acid sequence	MNKTWLHGGIFKVVRELPTED(+) MVEYSKSSESCPLKTEGSIDMVGIRRNKGHGEATIFTLRELADATNNFSTECLLGRGGFGSVYK AFLNDRQVVAVKQLDLNGLQGNREFLVEVLMLSLLHHPNLVKLFGYCVDGDQRLLIYEYMPLGS LEDRLHDLRPGQEPLDWTTRMKIAADAAAGLEYLHDEAIPAVIYRDIKPSNILLGEGYNAKLSD FGLAKLGPVGDKTHVTTRVMGTHGYCAPEYLSTGKLTIKSDIYSFGVVFLELITGRRALDSNRP PDEQDLVAWWNIQSRQRVAH(+) MVGIRRNKGHGEATIFTLRELADATNNFSTECLLGRGGFGSVYKAFLNDRQVVAVKQLDLNGLQ GNREFLVEVLMLSLLHHPNLVKLFGYCVDGDQRLLIYEYMPLGSLEDRLHDLRPGQEPLDWTTR MKIAADAAAGLEYLHDEAIPAVIYRDIKPSNILLGEGYNAKLSDFGLAKLGPVGDKTHVTTRVM GTHGYCAPEYLSTGKLTIKSDIYSFGVVFLELITGRRALDSNRPPDEQDLVAWWNIQSRQRVAH *(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Chu et al., 2017

circRNA

Detail information of Os01g0259200_circ_g.2

Address

Any questions?

Supported by