Plant Circular RNA Database

Detail information of Os12g0540800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os12g0540800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_011898
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 21620278-21622450  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0540800						
					
						Parent gene annotation
						
							Galactose oxidase/kelch, beta-propeller domain containing protei
n. (Os12t0540800-01);Hypothetical conserved gene. (Os12t0540800-
02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0540800_circ_g.2 Os12g0540800_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						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
						Os12t0540800-01:9

General Information
CircRNA Name	Os12g0540800_circ_g.1
ID in PlantcircBase	osa_circ_011898
Alias	NA
Organism	Oryza sativa
Position	chr12: 21620278-21622450 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0540800
Parent gene annotation	Galactose oxidase/kelch, beta-propeller domain containing protei n. (Os12t0540800-01);Hypothetical conserved gene. (Os12t0540800- 02)
Parent gene strand	+
Alternative splicing	Os12g0540800_circ_g.2 Os12g0540800_circ_g.3
Support reads	1
Tissues	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	Os12t0540800-01:9

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							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   
						
							NA							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	NA 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	NA 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  
						
							ATGCACTGCAGGTGTCCCAGAAACACTTGTACTTAACATGTCAACATTTGTATGGTCAGTCGTT
ACTGGTCTTGAAGGCCGTGCACCCCCAACAAGTGAGagtgcaaaagtgtcgcaccccgttaaat
cggcctccgaggagtccaaagtactcgtggtggagaatgggaagatggttgatgttcaggacaa
ggaaatca

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							AGTGCAAAAGTGTCGCACCCCGTTAAATCGGCCTCCGAGGAGTCCAAAGTACTCGTGGTGGAGA
ATGGGAAGATGGTTGATGTTCAGGACAAGGAAATCACCATGGAAGGCCTCTGTTCCATAAGTTC
TTATGACCAGTGGGCACGGATCCCTGTTTCTGGACCGCTTCCGAAACCTCGCTACAAGGTCCTC
CTTTTTTTACTTGCATGATCTCTAAATTCCGTCTAGTCTGTTGTGCTGCCATCGTCTTCTCTTG
GTGGTTTTGACATGCTGCACTTATCTTCTACAGCATGCAGCTGCTGTGGTTCAGGAAAAGATGT
ATGTTTTTGGTGGAAATCACAATGGCCGTTACCTTGGTGACATGCAGGTATATTAGTCGGTCAT
TATACTTAATATGTTTTTTTCTTGTGATGGATTCTTGGTATAAACTTTAAAATAGACTCAAAAT
TCCTTATTTGCTTATTAATAGAGGTTAATTGTGCAAGTTCCTAACTTTACTCTCGAGCGTTGAG
AATGATATGCATCTCAACAATAGTATCTTCCTTTGGTTGAAGGTTCTGGATTTCAAATGTTTAT
CATGGTCGAAGCTAGAAGCTAAAATACAATCAGAAGAACCTTCAGACTTGACTGGAACAGCTTC
GCTTCCTCCTTGTGCTGGTCATGCACTGGTAATCACCAGATACTCTTTATAGTCAAGTTGAGCG
GAACTGGATTTTCTCCCAGATAGATATAACTGTGTAGCGTATTTCCTTCTGGCATTTAATCTCC
GCAGGTTCCATGGGGAAACAAGATCCTCTGTCTTGCAGGACACACAAGGGAACCTACAGAAAGT
CTCAGTGGTTAGCCTAATATTTTGCTCCTTTTTTTCTAATCTTATTTTTTTTGTGCGAGTTATA
TTTCTTATATAAAATAACATATTTATGTCAGTTAAGGAGTTTGATCCACAAACTTGCACCTGGT
CAACCTTGCGCACTTATGGCAGATCACCGGTACCTTTTTTTTAATCTATTTATATTGTCAGAAA
GCTTCTAAAGTACTCGCTGCTTTTTTTTTTTTTGTCTAAGAATATGTGGCGGTAATCTTCCTTT
TGCTTTAGAGCTCATGCGGTGGCCAATCAGTGACTCTTGTTGGAGGCACATTAGTAGTGTTTGG
AGGTGAAGGTGATGGGAGATCCCTTCTGAATGACCTGCACGTTCTTGATCTCGAGACCATGACT
TGGGATGAATTTGAGACCACGTAAGTTTTGTGATTGAAGCATGTTTTTCAGTTGTTGTAAAGTG
AACAAATGACAATATATTTTTTTAAAAAAAAAAGTGATCAAAATGTTTATGGTCCTTAATATTA
GGATTCTGCTGAATGACCTGAATTTTGTAACTCGTGTGAAAATGCTATTGCAGGCGTACTCCAC
AAGTTATATATTTTTAGGCATTAATTATGAAATCATTCTTCTAGTAAATTCATTACCAAGTTCC
TTGAGGTGCAGAGCTGATATCTGACTATTTTAAACTGTACTGTAATTTTCCAGAGGCACACCCC
CTTCTCCAAGGTCAGAGCATGCTGCTGCGTGCTATGCTGATCGTTATCTCTTGATATTTGGCGG
GGGTTCTCATTCTACATGTTTCAGTGATCTACATCTCCTTGACATGCAGACGGTGAGAATTGAA
TCTTTTCTTTAGAGCTGGTATTCACTACTTTAGGAAGTCCAAATAAATGGTTATCTGCTAATTG
CAGATGGAATGGTCAAGACCAGAACATCAGGGTATTACTCCCGAACCAAGAGCAGGGCATGCAG
GTGTTACGGTTGGTGAGAACTGGTTTATTACTGGAGGTGGTAATAACAAGAAAGGTAAGGATGA
AAATCCAGCACCTACCTTATACTACGATTATGACTTCCAAAACAATTGAGCTTATTCAATTTCC
ATGGTTTTATCACCCTTGAGTGTAGCTCCTTATCCATTTACAGATGATATATTTGTTATATCTT
TTCTTGATAGTTTTTGAGCTTTTCTTTAGAAAAAGAAAAGTAGCTCACGAAACAGTTTTCGCTC
ACATGTGCTTAATCGGCTAATCATGATGCACTGCAGGTGTCCCAGAAACACTTGTACTTAACAT
GTCAACATTTGTATGGTCAGTCGTTACTGGTCTTGAAGGCCGTGCACCCCCAACAAGTGAG
						
					

			
		

Sequences
Splice junction sequence	ATGCACTGCAGGTGTCCCAGAAACACTTGTACTTAACATGTCAACATTTGTATGGTCAGTCGTT ACTGGTCTTGAAGGCCGTGCACCCCCAACAAGTGAGagtgcaaaagtgtcgcaccccgttaaat cggcctccgaggagtccaaagtactcgtggtggagaatgggaagatggttgatgttcaggacaa ggaaatca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AGTGCAAAAGTGTCGCACCCCGTTAAATCGGCCTCCGAGGAGTCCAAAGTACTCGTGGTGGAGA ATGGGAAGATGGTTGATGTTCAGGACAAGGAAATCACCATGGAAGGCCTCTGTTCCATAAGTTC TTATGACCAGTGGGCACGGATCCCTGTTTCTGGACCGCTTCCGAAACCTCGCTACAAGGTCCTC CTTTTTTTACTTGCATGATCTCTAAATTCCGTCTAGTCTGTTGTGCTGCCATCGTCTTCTCTTG GTGGTTTTGACATGCTGCACTTATCTTCTACAGCATGCAGCTGCTGTGGTTCAGGAAAAGATGT ATGTTTTTGGTGGAAATCACAATGGCCGTTACCTTGGTGACATGCAGGTATATTAGTCGGTCAT TATACTTAATATGTTTTTTTCTTGTGATGGATTCTTGGTATAAACTTTAAAATAGACTCAAAAT TCCTTATTTGCTTATTAATAGAGGTTAATTGTGCAAGTTCCTAACTTTACTCTCGAGCGTTGAG AATGATATGCATCTCAACAATAGTATCTTCCTTTGGTTGAAGGTTCTGGATTTCAAATGTTTAT CATGGTCGAAGCTAGAAGCTAAAATACAATCAGAAGAACCTTCAGACTTGACTGGAACAGCTTC GCTTCCTCCTTGTGCTGGTCATGCACTGGTAATCACCAGATACTCTTTATAGTCAAGTTGAGCG GAACTGGATTTTCTCCCAGATAGATATAACTGTGTAGCGTATTTCCTTCTGGCATTTAATCTCC GCAGGTTCCATGGGGAAACAAGATCCTCTGTCTTGCAGGACACACAAGGGAACCTACAGAAAGT CTCAGTGGTTAGCCTAATATTTTGCTCCTTTTTTTCTAATCTTATTTTTTTTGTGCGAGTTATA TTTCTTATATAAAATAACATATTTATGTCAGTTAAGGAGTTTGATCCACAAACTTGCACCTGGT CAACCTTGCGCACTTATGGCAGATCACCGGTACCTTTTTTTTAATCTATTTATATTGTCAGAAA GCTTCTAAAGTACTCGCTGCTTTTTTTTTTTTTGTCTAAGAATATGTGGCGGTAATCTTCCTTT TGCTTTAGAGCTCATGCGGTGGCCAATCAGTGACTCTTGTTGGAGGCACATTAGTAGTGTTTGG AGGTGAAGGTGATGGGAGATCCCTTCTGAATGACCTGCACGTTCTTGATCTCGAGACCATGACT TGGGATGAATTTGAGACCACGTAAGTTTTGTGATTGAAGCATGTTTTTCAGTTGTTGTAAAGTG AACAAATGACAATATATTTTTTTAAAAAAAAAAGTGATCAAAATGTTTATGGTCCTTAATATTA GGATTCTGCTGAATGACCTGAATTTTGTAACTCGTGTGAAAATGCTATTGCAGGCGTACTCCAC AAGTTATATATTTTTAGGCATTAATTATGAAATCATTCTTCTAGTAAATTCATTACCAAGTTCC TTGAGGTGCAGAGCTGATATCTGACTATTTTAAACTGTACTGTAATTTTCCAGAGGCACACCCC CTTCTCCAAGGTCAGAGCATGCTGCTGCGTGCTATGCTGATCGTTATCTCTTGATATTTGGCGG GGGTTCTCATTCTACATGTTTCAGTGATCTACATCTCCTTGACATGCAGACGGTGAGAATTGAA TCTTTTCTTTAGAGCTGGTATTCACTACTTTAGGAAGTCCAAATAAATGGTTATCTGCTAATTG CAGATGGAATGGTCAAGACCAGAACATCAGGGTATTACTCCCGAACCAAGAGCAGGGCATGCAG GTGTTACGGTTGGTGAGAACTGGTTTATTACTGGAGGTGGTAATAACAAGAAAGGTAAGGATGA AAATCCAGCACCTACCTTATACTACGATTATGACTTCCAAAACAATTGAGCTTATTCAATTTCC ATGGTTTTATCACCCTTGAGTGTAGCTCCTTATCCATTTACAGATGATATATTTGTTATATCTT TTCTTGATAGTTTTTGAGCTTTTCTTTAGAAAAAGAAAAGTAGCTCACGAAACAGTTTTCGCTC ACATGTGCTTAATCGGCTAATCATGATGCACTGCAGGTGTCCCAGAAACACTTGTACTTAACAT GTCAACATTTGTATGGTCAGTCGTTACTGGTCTTGAAGGCCGTGCACCCCCAACAAGTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.133690819

Conservation Information
Conserved circRNAs	NA
PMCS	0.133690819

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							21620351-21622447(+)
21622065-21620398(+)
21620571-21622408(-)
						
					

						Potential amino acid sequence
						
							MVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQEKMYVFGGNHNGRYLGDMQ
VLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKILCLAGHTREPTESLSVKEF
DPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLNDLHVLDLETMTWDEFETT
GTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWSRPEHQGITPEPRAGHAGV
TVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSESAKVSHPVKSASEESKVL
VVENGKMVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQEKMYVFGGNHNGR
YLGDMQVLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKILCLAGHTREPTES
LSVKEFDPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLNDLHVLDLETMTW
DEFETTGTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWSRPEHQGITPEPR
AGHAGVTVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSESAKVSHPVKSAS
EESKVLVVENGKMVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQEKMYVFG
GNHNGRYLGDMQVLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKILCLAGHT
REPTESLSVKEFDPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLNDLHVLD
LETMTWDEFETTGTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWSRPEHQG
ITPEPRAGHAGVTVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSESAKVSH
PVKSASEESKVLVVENGKMVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQE
KMYVFGGNHNGRYLGDMQVLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKIL
CLAGHTREPTESLSVKEFDPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLN
DLHVLDLETMTWDEFETTGTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWS
RPEHQGITPEPRAGHAGVTVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSE
(+)
MQVLRLVRTGLLLEVVITRKVSQKHLYLTCQHLYGQSLLVLKAVHPQQVRVQKCRTPLNRPPRS
PKYSWWRMGRWLMFRTRKSPWKASVP*(+)
MLVARFRKRSRNRDPCPLVIRTYGTEAFHGDFLVLNINHLPILHHEYFGLLGGRFNGVRHFCTL
TCWGCTAFKTSND*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	21620351-21622447(+) 21622065-21620398(+) 21620571-21622408(-)
Potential amino acid sequence	MVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQEKMYVFGGNHNGRYLGDMQ VLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKILCLAGHTREPTESLSVKEF DPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLNDLHVLDLETMTWDEFETT GTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWSRPEHQGITPEPRAGHAGV TVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSESAKVSHPVKSASEESKVL VVENGKMVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQEKMYVFGGNHNGR YLGDMQVLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKILCLAGHTREPTES LSVKEFDPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLNDLHVLDLETMTW DEFETTGTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWSRPEHQGITPEPR AGHAGVTVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSESAKVSHPVKSAS EESKVLVVENGKMVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQEKMYVFG GNHNGRYLGDMQVLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKILCLAGHT REPTESLSVKEFDPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLNDLHVLD LETMTWDEFETTGTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWSRPEHQG ITPEPRAGHAGVTVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSESAKVSH PVKSASEESKVLVVENGKMVDVQDKEITMEGLCSISSYDQWARIPVSGPLPKPRYKHAAAVVQE KMYVFGGNHNGRYLGDMQVLDFKCLSWSKLEAKIQSEEPSDLTGTASLPPCAGHALVPWGNKIL CLAGHTREPTESLSVKEFDPQTCTWSTLRTYGRSPSSCGGQSVTLVGGTLVVFGGEGDGRSLLN DLHVLDLETMTWDEFETTGTPPSPRSEHAAACYADRYLLIFGGGSHSTCFSDLHLLDMQTMEWS RPEHQGITPEPRAGHAGVTVGENWFITGGGNNKKGVPETLVLNMSTFVWSVVTGLEGRAPPTSE (+) MQVLRLVRTGLLLEVVITRKVSQKHLYLTCQHLYGQSLLVLKAVHPQQVRVQKCRTPLNRPPRS PKYSWWRMGRWLMFRTRKSPWKASVP(+) MLVARFRKRSRNRDPCPLVIRTYGTEAFHGDFLVLNINHLPILHHEYFGLLGGRFNGVRHFCTL TCWGCTAFKTSND(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0540800_circ_g.1

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