Plant Circular RNA Database

Detail information of Os04g0531300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0531300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_024663
					
						Alias
						Os_ciR9477
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 26566506-26569175  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os04g0531300						
					
						Parent gene annotation
						
							tRNA-dihydrouridine synthase domain containing protein. (Os04t05
31300-01);tRNA-dihydrouridine synthase domain containing protein
. (Os04t0531300-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0531300_circ_g.1 Os04g0531300_circ_g.3 Os04g0531300_circ_g.4 Os04g0531300_circ_g.5 						
					
						Support reads
						2
					
						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
						Os04t0531300-02:7
Os04t0531300-01:7

General Information
CircRNA Name	Os04g0531300_circ_g.2
ID in PlantcircBase	osa_circ_024663
Alias	Os_ciR9477
Organism	Oryza sativa
Position	chr4: 26566506-26569175 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os04g0531300
Parent gene annotation	tRNA-dihydrouridine synthase domain containing protein. (Os04t05 31300-01);tRNA-dihydrouridine synthase domain containing protein . (Os04t0531300-02)
Parent gene strand	+
Alternative splicing	Os04g0531300_circ_g.1 Os04g0531300_circ_g.3 Os04g0531300_circ_g.4 Os04g0531300_circ_g.5
Support reads	2
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	Os04t0531300-02:7 Os04t0531300-01:7

			
						 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  
						
							GCACAAAACAAACCATAAAAGAAATGATAATGCACTATTCTTGCCTTGAATTCCCTGAAGGAAA
AGGTGTGAACAAGTGTGATACAATAGCTGATTTAGCggtaccctgccgtttaggctactggctg
ctgaatatggtgctgatatcacttacggagaagaaataatagatcataagtttttgaagtgtga
acgtgtta

									
								

					

						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: 863
Transcript exons: 26566506-26566611,26567030-26567168,26567402-26567510,26
567595-26567731,26568175-26568311,26568749-26568855,2656
9048-26569175
GGTACCCTGCCGTTTAGGCTACTGGCTGCTGAATATGGTGCTGATATCACTTACGGAGAAGAAA
TAATAGATCATAAGTTTTTGAAGTGTGAACGTGTTACAAATGAATCTCTTGGTACTACTGATTT
TTTGGAGAGAGGGACTGATACTGTAGTATTCCGTACTTGCCCACAAGAAAGGGATAGGGTTGTA
TTCCAAATGGGAACATCTGATGCTGTGAGGGCACTGAAAGCTGCTCAGCTTGTGTGTAACGATG
TTGCTGCTATAGATATCAACATGGGTTGTCCCAAATCTTTCTCTCTTAGTGGTGGAATGGGAGC
CGCATTACTCTCCAAACCTGAGCTTATTCATGATATTTTGACCACATTGCGGAGGAACTTGGAC
ACTACCGTGACATGTAAAATCCGTCTTCTGAACACACGCCAGGACACTGTGGAGTTGGCTCGCC
GAGTTGAGAAGATTGGTGTTCCAGCCCTTGCTGTCCATGGAAGAAAGGTCAAAGACAGACCAAG
AGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGTCTGCACTGTCAATTCCAGTTATAGCT
AATGGAGATGTATTTGAATATGAGGATTTTAAAAGAATTAAAGATGCTACAGGTGCCGCTTCTG
TAATGGTTGCCAGAGGTGCCATGTGGAATGCCTCAATTTTTTGTCCCAAAGGAAAAACACCTTG
GGAGGATGTCAAAAGAGAGTACGTGAGAAAGAGTATTTTGTGGGACAATGATTTGAAGAGCACA
AAACAAACCATAAAAGAAATGATAATGCACTATTCTTGCCTTGAATTCCCTGAAGGAAAAGGTG
TGAACAAGTGTGATACAATAGCTGATTTAGC
						
					

						Genomic sequence
						
							GGTACCCTGCCGTTTAGGCTACTGGCTGCTGAATATGGTGCTGATATCACTTACGGAGAAGAAA
TAATAGATCATAAGTTTTTGAAGTGTGAACGTGTTACAAATGGTATTGTAGTTCAATTGGTGTT
TGGCATTTTATTATGATCTCGCATGCAACTGTATTAACAGTTAAGTTCTTCTCAGAAAATTTGT
TAAGCAGTTGGCATAATGTTATCTTTTTTGGGATGACCTGACTCCTATAATATTGCCTTTGAAG
TACATGATTGAAAATGTTCATCTTAAAATCTTAAATTACTATTGATGGTACATGGTTGTTATTG
AAGATCATGAAAAATATATGTTTTGATAACAAATTTAGAGTTAGATGCCTTTAAGAAGTAAGCT
TCTTGATTTTTTCCTATGAAATTGGGGAACTTTTAACAGTTCCATTTATTTGATCTCTATTATC
TCCACTACTGTCTAGATTTGTTCTTTCTGTGTCGTATAATCCTTCCATGCTAATAAATTTTATC
AATGCTACTCAGAATCTCTTGGTACTACTGATTTTTTGGAGAGAGGGACTGATACTGTAGTATT
CCGTACTTGCCCACAAGAAAGGGATAGGGTTGTATTCCAAATGGGAACATCTGATGCTGTGAGG
GCACTGAAAGCTGCTCAGCTTGTGTAAGTCTTATTTCTGAAAATATTTACGGTTGAAGTTCTGA
AGTAAAATAATATAGGTTCCAATGAGTGGATAAATCCATATTTCCTTTTTCCATGAAAAATTCC
TAGGTGCATTGGGTTACTTATACCATGGTTGCTGTTTGAATTGTTTCAATTAATCAAGGAATCG
GATCAATTGTTTTAACCGCCCCTGCTTTAGATATTTTCTTTGATCACAGTTTCATCCTTACCAG
GTGTAACGATGTTGCTGCTATAGATATCAACATGGGTTGTCCCAAATCTTTCTCTCTTAGTGGT
GGAATGGGAGCCGCATTACTCTCCAAACCTGAGCTTATTCATGATGTACTCAAATTTACTGTTT
TGTTTTATTACTTAAATATTCTAGAAATTCATTCACTTATCAAGTATGCAAATCACATCATGTA
GATTTTGACCACATTGCGGAGGAACTTGGACACTACCGTGACATGTAAAATCCGTCTTCTGAAC
ACACGCCAGGACACTGTGGAGTTGGCTCGCCGAGTTGAGAAGATTGGTGTTCCAGCCCTTGCTG
TCCATGGAAGGTTAGTTACGCTTCATACTTTTGAGTTCTGATAGAAAATTGTACTCATCCACTC
TACTTTATAATGTGCAATTTACCATCTTTCTCTCTCCAATTGTCCATTTAGTTGAAATCCCTAT
GTTTAAGAATCCAAGGTGAAAATAGTATTGATATTCACAGCTATTTGGCTTGTTTACTATATTT
ATAGGATCCATCCTAAATGATGCTGCTAAAATCCATGAACTGTTCAAATGAATGGTTGGCATTT
TTCCATGTTCCTTTCCGAAACACCTGAGCCTTCAATTGACTACATTTGAGATATATTTTATAAG
TTCTTTTTTGCAACCATTAAAATGAATATGCTGCAGAATAATGTCATATATCAACTCTCCATTT
TCAATCTTCCCTAATATGTCTTTTTTTGTTAATTGATTTCCCTGATGTTGGATTCCTTTACACA
TGCAGAAAGGTCAAAGACAGACCAAGAGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGT
CTGCACTGTCAATTCCAGTTATAGCTAATGGAGATGTATTTGAATATGAGGATTTTAAAAGAAT
TAAAGATGCTACAGGTTTGTATGCTCAGTTAACATTTCTCAATTTTCTTTGTTTAGTAAAGTAG
CTGTCTGTTCAGTTTTACTATAAATCTATAATTTGGCAGAGTATAGCAAACAGAGGGAGATATA
GAAATGAATCTAAAATTTGTCCCATTTGTGTTTCTTCCTTTACCAGTTATCAATATTGAGCTTA
CTTTTCTACTACCCAAAGCAATCTATATGTACTGCGAGTGTTTCCTAAATACCATAGGAAACCG
AACATCTGAAAAATTCAGTGACTACAATATTCATTTATGAGCAACCATGAGTATCATAGCATTT
CTTGGAAACTAGAGATTGTTAGCGGTTGTCAGAATTGCTACTGTTGTTACTTGGAGAGTTCATT
GCATTGCCAGATATTATTTTTTGTGTTTCTTTTTATTGGTTTGTATCTTGATTTCTGCAACTGC
CAGGTGCCGCTTCTGTAATGGTTGCCAGAGGTGCCATGTGGAATGCCTCAATTTTTTGTCCCAA
AGGAAAAACACCTTGGGAGGATGTCAAAAGAGAGTACGTGAGAAAGGTATTTGATTGTTCTTCC
CACACCATTCCTATTTCAGTGTCAAAGTTTTATTATGTTAGCATCTCCTCTCTCAGTTGTCCTA
TTTTTCATGGGGCTAAAACAGGTTTCTTTGCCCTAACATCTAAATTAATAATAATTTTATGCTT
TATTTCCTTCATTGACATCACATTACATTGTAATTCTTTTCCGCAGAGTATTTTGTGGGACAAT
GATTTGAAGAGCACAAAACAAACCATAAAAGAAATGATAATGCACTATTCTTGCCTTGAATTCC
CTGAAGGAAAAGGTGTGAACAAGTGTGATACAATAGCTGATTTAGC
						
					

			
		

Sequences
Splice junction sequence	GCACAAAACAAACCATAAAAGAAATGATAATGCACTATTCTTGCCTTGAATTCCCTGAAGGAAA AGGTGTGAACAAGTGTGATACAATAGCTGATTTAGCggtaccctgccgtttaggctactggctg ctgaatatggtgctgatatcacttacggagaagaaataatagatcataagtttttgaagtgtga acgtgtta
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: 863 Transcript exons: 26566506-26566611,26567030-26567168,26567402-26567510,26 567595-26567731,26568175-26568311,26568749-26568855,2656 9048-26569175 GGTACCCTGCCGTTTAGGCTACTGGCTGCTGAATATGGTGCTGATATCACTTACGGAGAAGAAA TAATAGATCATAAGTTTTTGAAGTGTGAACGTGTTACAAATGAATCTCTTGGTACTACTGATTT TTTGGAGAGAGGGACTGATACTGTAGTATTCCGTACTTGCCCACAAGAAAGGGATAGGGTTGTA TTCCAAATGGGAACATCTGATGCTGTGAGGGCACTGAAAGCTGCTCAGCTTGTGTGTAACGATG TTGCTGCTATAGATATCAACATGGGTTGTCCCAAATCTTTCTCTCTTAGTGGTGGAATGGGAGC CGCATTACTCTCCAAACCTGAGCTTATTCATGATATTTTGACCACATTGCGGAGGAACTTGGAC ACTACCGTGACATGTAAAATCCGTCTTCTGAACACACGCCAGGACACTGTGGAGTTGGCTCGCC GAGTTGAGAAGATTGGTGTTCCAGCCCTTGCTGTCCATGGAAGAAAGGTCAAAGACAGACCAAG AGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGTCTGCACTGTCAATTCCAGTTATAGCT AATGGAGATGTATTTGAATATGAGGATTTTAAAAGAATTAAAGATGCTACAGGTGCCGCTTCTG TAATGGTTGCCAGAGGTGCCATGTGGAATGCCTCAATTTTTTGTCCCAAAGGAAAAACACCTTG GGAGGATGTCAAAAGAGAGTACGTGAGAAAGAGTATTTTGTGGGACAATGATTTGAAGAGCACA AAACAAACCATAAAAGAAATGATAATGCACTATTCTTGCCTTGAATTCCCTGAAGGAAAAGGTG TGAACAAGTGTGATACAATAGCTGATTTAGC
Genomic sequence	GGTACCCTGCCGTTTAGGCTACTGGCTGCTGAATATGGTGCTGATATCACTTACGGAGAAGAAA TAATAGATCATAAGTTTTTGAAGTGTGAACGTGTTACAAATGGTATTGTAGTTCAATTGGTGTT TGGCATTTTATTATGATCTCGCATGCAACTGTATTAACAGTTAAGTTCTTCTCAGAAAATTTGT TAAGCAGTTGGCATAATGTTATCTTTTTTGGGATGACCTGACTCCTATAATATTGCCTTTGAAG TACATGATTGAAAATGTTCATCTTAAAATCTTAAATTACTATTGATGGTACATGGTTGTTATTG AAGATCATGAAAAATATATGTTTTGATAACAAATTTAGAGTTAGATGCCTTTAAGAAGTAAGCT TCTTGATTTTTTCCTATGAAATTGGGGAACTTTTAACAGTTCCATTTATTTGATCTCTATTATC TCCACTACTGTCTAGATTTGTTCTTTCTGTGTCGTATAATCCTTCCATGCTAATAAATTTTATC AATGCTACTCAGAATCTCTTGGTACTACTGATTTTTTGGAGAGAGGGACTGATACTGTAGTATT CCGTACTTGCCCACAAGAAAGGGATAGGGTTGTATTCCAAATGGGAACATCTGATGCTGTGAGG GCACTGAAAGCTGCTCAGCTTGTGTAAGTCTTATTTCTGAAAATATTTACGGTTGAAGTTCTGA AGTAAAATAATATAGGTTCCAATGAGTGGATAAATCCATATTTCCTTTTTCCATGAAAAATTCC TAGGTGCATTGGGTTACTTATACCATGGTTGCTGTTTGAATTGTTTCAATTAATCAAGGAATCG GATCAATTGTTTTAACCGCCCCTGCTTTAGATATTTTCTTTGATCACAGTTTCATCCTTACCAG GTGTAACGATGTTGCTGCTATAGATATCAACATGGGTTGTCCCAAATCTTTCTCTCTTAGTGGT GGAATGGGAGCCGCATTACTCTCCAAACCTGAGCTTATTCATGATGTACTCAAATTTACTGTTT TGTTTTATTACTTAAATATTCTAGAAATTCATTCACTTATCAAGTATGCAAATCACATCATGTA GATTTTGACCACATTGCGGAGGAACTTGGACACTACCGTGACATGTAAAATCCGTCTTCTGAAC ACACGCCAGGACACTGTGGAGTTGGCTCGCCGAGTTGAGAAGATTGGTGTTCCAGCCCTTGCTG TCCATGGAAGGTTAGTTACGCTTCATACTTTTGAGTTCTGATAGAAAATTGTACTCATCCACTC TACTTTATAATGTGCAATTTACCATCTTTCTCTCTCCAATTGTCCATTTAGTTGAAATCCCTAT GTTTAAGAATCCAAGGTGAAAATAGTATTGATATTCACAGCTATTTGGCTTGTTTACTATATTT ATAGGATCCATCCTAAATGATGCTGCTAAAATCCATGAACTGTTCAAATGAATGGTTGGCATTT TTCCATGTTCCTTTCCGAAACACCTGAGCCTTCAATTGACTACATTTGAGATATATTTTATAAG TTCTTTTTTGCAACCATTAAAATGAATATGCTGCAGAATAATGTCATATATCAACTCTCCATTT TCAATCTTCCCTAATATGTCTTTTTTTGTTAATTGATTTCCCTGATGTTGGATTCCTTTACACA TGCAGAAAGGTCAAAGACAGACCAAGAGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGT CTGCACTGTCAATTCCAGTTATAGCTAATGGAGATGTATTTGAATATGAGGATTTTAAAAGAAT TAAAGATGCTACAGGTTTGTATGCTCAGTTAACATTTCTCAATTTTCTTTGTTTAGTAAAGTAG CTGTCTGTTCAGTTTTACTATAAATCTATAATTTGGCAGAGTATAGCAAACAGAGGGAGATATA GAAATGAATCTAAAATTTGTCCCATTTGTGTTTCTTCCTTTACCAGTTATCAATATTGAGCTTA CTTTTCTACTACCCAAAGCAATCTATATGTACTGCGAGTGTTTCCTAAATACCATAGGAAACCG AACATCTGAAAAATTCAGTGACTACAATATTCATTTATGAGCAACCATGAGTATCATAGCATTT CTTGGAAACTAGAGATTGTTAGCGGTTGTCAGAATTGCTACTGTTGTTACTTGGAGAGTTCATT GCATTGCCAGATATTATTTTTTGTGTTTCTTTTTATTGGTTTGTATCTTGATTTCTGCAACTGC CAGGTGCCGCTTCTGTAATGGTTGCCAGAGGTGCCATGTGGAATGCCTCAATTTTTTGTCCCAA AGGAAAAACACCTTGGGAGGATGTCAAAAGAGAGTACGTGAGAAAGGTATTTGATTGTTCTTCC CACACCATTCCTATTTCAGTGTCAAAGTTTTATTATGTTAGCATCTCCTCTCTCAGTTGTCCTA TTTTTCATGGGGCTAAAACAGGTTTCTTTGCCCTAACATCTAAATTAATAATAATTTTATGCTT TATTTCCTTCATTGACATCACATTACATTGTAATTCTTTTCCGCAGAGTATTTTGTGGGACAAT GATTTGAAGAGCACAAAACAAACCATAAAAGAAATGATAATGCACTATTCTTGCCTTGAATTCC CTGAAGGAAAAGGTGTGAACAAGTGTGATACAATAGCTGATTTAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.22638495

Conservation Information
Conserved circRNAs	NA
PMCS	0.22638495

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26567123-26566569(+)
						
						Potential amino acid sequence
						
							MGTSDAVRALKAAQLVCNDVAAIDINMGCPKSFSLSGGMGAALLSKPELIHDILTTLRRNLDTT
VTCKIRLLNTRQDTVELARRVEKIGVPALAVHGRKVKDRPRDPAKWDEIADVVSALSIPVIANG
DVFEYEDFKRIKDATGAASVMVARGAMWNASIFCPKGKTPWEDVKREYVRKSILWDNDLKSTKQ
TIKEMIMHYSCLEFPEGKGVNKCDTIADLAVPCRLGYWLLNMVLISLTEKK*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	26567123-26566569(+)
Potential amino acid sequence	MGTSDAVRALKAAQLVCNDVAAIDINMGCPKSFSLSGGMGAALLSKPELIHDILTTLRRNLDTT VTCKIRLLNTRQDTVELARRVEKIGVPALAVHGRKVKDRPRDPAKWDEIADVVSALSIPVIANG DVFEYEDFKRIKDATGAASVMVARGAMWNASIFCPKGKTPWEDVKREYVRKSILWDNDLKSTKQ TIKEMIMHYSCLEFPEGKGVNKCDTIADLAVPCRLGYWLLNMVLISLTEKK*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os04g0531300_circ_g.2

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