Plant Circular RNA Database

Detail information of Os04g0641000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0641000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025569
					
						Alias
						Os_ciR9609
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 32611615-32614659  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0641000						
					
						Parent gene annotation
						
							Similar to DNA-directed RNA polymerase. (Os04t0641000-01);Simila
r to DNA-directed RNA polymerase. (Os04t0641000-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os04t0641000-01:3

General Information
CircRNA Name	Os04g0641000_circ_g.1
ID in PlantcircBase	osa_circ_025569
Alias	Os_ciR9609
Organism	Oryza sativa
Position	chr4: 32611615-32614659 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0641000
Parent gene annotation	Similar to DNA-directed RNA polymerase. (Os04t0641000-01);Simila r to DNA-directed RNA polymerase. (Os04t0641000-02)
Parent gene strand	+
Alternative splicing	NA
Support reads	2/1
Tissues	root/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	Os04t0641000-01:3

			
						 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  
						
							CGACACTAAGGAGAACAAATCCGCTTCAGATGATCTCGGACTTGAGGAAAACTCGCCAACGAGT
TGCTTATGCTGGGAAAGCCGGTGATGCAAGATATCCgctattccctcgaagttatggaagagcc
atcaaaggacaatgggcaatcatcctgtgttgttgatcctgagctggaacctatgatgctggat
gatgctag

									
								

					

						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
						
							GCTATTCCCTCGAAGTTATGGAAGAGCCATCAAAGGACAATGGGCAATCATCCTGTGTTGTTGA
TCCTGAGCTGGAACCTATGATGCTGGATGATGCTAGAGAGGGAGTATCCCATACATTGGATGAT
GCAAATGGGCATTCTTCTATGGATGTTGACAGAGGATGCCATTCTATGGACACCACGAGATCAT
CTCTGGGTGATGATGGTAAAGGAAAGCGCGACTCATATGCCCAAATTCCAGTCGACATGAGTAT
TCCAAGCCTAGAAAAGTTCTGCAAAGAAGCATCAAGGTCCTTCTTTGATGAGATTGGTCTGATC
AGCCATCAGATAAATTCTTATAACGAGTTTGTCTCACATGGGCTCCAGGAACTTTTTGATTCTC
TGGGGGAAGTGACTGTGGAGCCTAGTTATGATCCTTCAAATAGAGGACCAGGTGGCTGGAGACA
TGCTATCATCAAGTTTGGAAGAGTGCAACTAGAAGAACCAGTATTTTGGTCTCATGGATGTGAT
ATTGATGAACAATCGCTCAAACTGAAGCCAAGGCATGCTCGCCTACAGAATATGACATATTCTT
CCAAAATGAAAGTGGAAGTTCATTTCCAGGTCAGGGTTCTTATTGTTATTTTCTACACTAAATA
TTTACTTTTATGCCATAATTTGTTGAATGCCATGAGCACAAACGGTATAAGCAATGCAAAAAAA
AGGTAGCTGTAAATGCTTATATGTGCTCAGCATAATTCCTTTTTCTACTTTTTGAGCGCTGTGT
ACAACACACAATCAATTCCTGTTCTCCTACGCTTAGCTTGTAAAAGTGTGAACATCACGTGACA
ATTTGTCCATCCACCGAACATCACCTGAAGAATATAGAATAAAATAGTCCACTTATAAGCGTAT
AACATGAAATGGAGCAGTCAAGGATCAGATGGGTGATTAGTGTTTCTTGAGCTGCTCCACAGTC
AGCAGCATGCGCTGTTGAATAATGTATGGTACTGTTTCAGTCATGCCTGATCCTATTATCTTAA
TTGAACTATTATGCCAATATATTTGCCTGTTCCTAGTATTATTGTGCGCTGATTTGTCTCCCTG
ATGCAAAACAAAGCTATGACGTGTTGGTGTTCCTTAGTTTTCTTTGGTGTTACTATAATCTGGT
TTACTGAAATGTTCTTAACCGTGTCAGGTTTACTCTATGGAGAAGAGTGACAAGGCTAAAACAG
GGAATGATAAATTTGGTTACAAGCGAAACATTATTAATGAAACATATTATATAAATATTGGCCG
CCTTCCAGTTATGGTTATGTCAAATTTATGTTGGCTCCACAAACTCAAGGAAAGTGATTGCCAA
TTTGATTCTGGTGGATACTTTTTGATCAAGGGAATGGAGAAGGTAATACTGTATATTCATGTTT
CTCCTTGCCTTATCATTCAGTGATTATGTATTGTGCCTGGTCTCCATTCTTTCATTATCATGTG
TTCAAGCGTTTATTTTTGTATGCTAGGATGAACTGCAAGGTTGTGGGGGGAAATTATATAGTAG
AAACCTCTGCCTAAATGGAAAGTTGGAAACTCCTACTCAAAAAGTAAAAAAAAAAGAGAGAGGA
AAAACTCACATGTAGATATGGTAATTGTTATCCATGCAAAATATCAACATCAAACCCAACATAG
TTTGTGAGATATGAAACTGGCAAATAATGAAGGAAAAGTACTTGTCCTGATTTTTTTTTTCTTT
TTCTTCGCTATTGTCAATTTCATATCTCATAGATAGTCAAAATTTGATCTTGAGATTTCGTATG
GTTGCCTAATATGACCTTTCCTTTATGTGAGTTTCTCTCCCTTTTTGAAATTTTTGGATAACCT
CGTGGTTTCCTCCAAAGTTTGGAGGAAAACCACTACTTTATAGGAAACCACCAAGTCATCCAAA
GTAGTGGTTTTCACTACAGATTTTCCTCCAAATTAGTTCTGTAGAATCATTTCATTTTTTTTTT
GTTTGGCGTTTTAGTATAGTGTGTGGACAGCTGACCATAGCCCTAATTATTCGTAGTGATCTGT
TGGAGAGTGATTCTCAATGTTTAAACCCTCTGCTGGAAAGAAAGTTTTTGTACCATATATGGCG
TTTTTATTTTATATCACTATGTTTCATACTATATAAATTTTAAATGCTGCAGGTATTCATTGCG
CAAGAGCAAAAATGTCTGACCAGGATTTGGGTTGAGGACCGTCCTTGCTGGATGGTCTCTTTCT
TGTCTCCAATCAGAAGAAGGCGCATATATATAAAACTAATTGATTCTGCAAATAATGAAGATGC
CAGTGGGGGGAAGATCATTTCCATCTCCTTTTTGTATGCAAATATGCCAATATGGTTGATGTTT
TTTGCACTAGGCATATCATCAGATAAGGATATCTTTGATGTTATAAATATGGAAGACTGTGATG
CTTGTGTTATCAACACAATTACCGCAACTATTAAAGAATCAGATGAATTGTGTGAAGGCTTCCG
TAAATCAGATAAAGCCCGGCAGTATGTTGACGAATTGATTAAGAATTCAAAATTTCCTCCTGCA
GAGCCATTTGATGATTATATTGCTAAATACCTCTTCCCCAGCATAAGTGGGAACCGGAACAAAG
CACTTTTCTTAGGTTACATGGTCAAATGCCTTTTAATGGCTTTCACTGGGAAGCGCAAATGTGA
CAACAAGGATGATTTCCGGAACAAGAGGTTGGACCTAGCTGGTGAATTGCTTGGAAGAGAACTC
CGTGCGCATATTAGGCATGCAGAGAGACTCATGGTTAAGGCCTTGCAGAGAGATTTAAATAGTG
AGCGTGAGTTACAAGAATTTGATCATTATCTGGATGCTTCAATTATTACCAATGGTCTAAACCG
TGCCTTCTCTACTGGTTCTTGGTGCCATCCTTACAAAAGAAATGAAAGATGCGCAGGAATTGTT
GCGACACTAAGGAGAACAAATCCGCTTCAGATGATCTCGGACTTGAGGAAAACTCGCCAACGAG
TTGCTTATGCTGGGAAAGCCGGTGATGCAAGATATCC
						
					

			
		

Sequences
Splice junction sequence	CGACACTAAGGAGAACAAATCCGCTTCAGATGATCTCGGACTTGAGGAAAACTCGCCAACGAGT TGCTTATGCTGGGAAAGCCGGTGATGCAAGATATCCgctattccctcgaagttatggaagagcc atcaaaggacaatgggcaatcatcctgtgttgttgatcctgagctggaacctatgatgctggat gatgctag
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	GCTATTCCCTCGAAGTTATGGAAGAGCCATCAAAGGACAATGGGCAATCATCCTGTGTTGTTGA TCCTGAGCTGGAACCTATGATGCTGGATGATGCTAGAGAGGGAGTATCCCATACATTGGATGAT GCAAATGGGCATTCTTCTATGGATGTTGACAGAGGATGCCATTCTATGGACACCACGAGATCAT CTCTGGGTGATGATGGTAAAGGAAAGCGCGACTCATATGCCCAAATTCCAGTCGACATGAGTAT TCCAAGCCTAGAAAAGTTCTGCAAAGAAGCATCAAGGTCCTTCTTTGATGAGATTGGTCTGATC AGCCATCAGATAAATTCTTATAACGAGTTTGTCTCACATGGGCTCCAGGAACTTTTTGATTCTC TGGGGGAAGTGACTGTGGAGCCTAGTTATGATCCTTCAAATAGAGGACCAGGTGGCTGGAGACA TGCTATCATCAAGTTTGGAAGAGTGCAACTAGAAGAACCAGTATTTTGGTCTCATGGATGTGAT ATTGATGAACAATCGCTCAAACTGAAGCCAAGGCATGCTCGCCTACAGAATATGACATATTCTT CCAAAATGAAAGTGGAAGTTCATTTCCAGGTCAGGGTTCTTATTGTTATTTTCTACACTAAATA TTTACTTTTATGCCATAATTTGTTGAATGCCATGAGCACAAACGGTATAAGCAATGCAAAAAAA AGGTAGCTGTAAATGCTTATATGTGCTCAGCATAATTCCTTTTTCTACTTTTTGAGCGCTGTGT ACAACACACAATCAATTCCTGTTCTCCTACGCTTAGCTTGTAAAAGTGTGAACATCACGTGACA ATTTGTCCATCCACCGAACATCACCTGAAGAATATAGAATAAAATAGTCCACTTATAAGCGTAT AACATGAAATGGAGCAGTCAAGGATCAGATGGGTGATTAGTGTTTCTTGAGCTGCTCCACAGTC AGCAGCATGCGCTGTTGAATAATGTATGGTACTGTTTCAGTCATGCCTGATCCTATTATCTTAA TTGAACTATTATGCCAATATATTTGCCTGTTCCTAGTATTATTGTGCGCTGATTTGTCTCCCTG ATGCAAAACAAAGCTATGACGTGTTGGTGTTCCTTAGTTTTCTTTGGTGTTACTATAATCTGGT TTACTGAAATGTTCTTAACCGTGTCAGGTTTACTCTATGGAGAAGAGTGACAAGGCTAAAACAG GGAATGATAAATTTGGTTACAAGCGAAACATTATTAATGAAACATATTATATAAATATTGGCCG CCTTCCAGTTATGGTTATGTCAAATTTATGTTGGCTCCACAAACTCAAGGAAAGTGATTGCCAA TTTGATTCTGGTGGATACTTTTTGATCAAGGGAATGGAGAAGGTAATACTGTATATTCATGTTT CTCCTTGCCTTATCATTCAGTGATTATGTATTGTGCCTGGTCTCCATTCTTTCATTATCATGTG TTCAAGCGTTTATTTTTGTATGCTAGGATGAACTGCAAGGTTGTGGGGGGAAATTATATAGTAG AAACCTCTGCCTAAATGGAAAGTTGGAAACTCCTACTCAAAAAGTAAAAAAAAAAGAGAGAGGA AAAACTCACATGTAGATATGGTAATTGTTATCCATGCAAAATATCAACATCAAACCCAACATAG TTTGTGAGATATGAAACTGGCAAATAATGAAGGAAAAGTACTTGTCCTGATTTTTTTTTTCTTT TTCTTCGCTATTGTCAATTTCATATCTCATAGATAGTCAAAATTTGATCTTGAGATTTCGTATG GTTGCCTAATATGACCTTTCCTTTATGTGAGTTTCTCTCCCTTTTTGAAATTTTTGGATAACCT CGTGGTTTCCTCCAAAGTTTGGAGGAAAACCACTACTTTATAGGAAACCACCAAGTCATCCAAA GTAGTGGTTTTCACTACAGATTTTCCTCCAAATTAGTTCTGTAGAATCATTTCATTTTTTTTTT GTTTGGCGTTTTAGTATAGTGTGTGGACAGCTGACCATAGCCCTAATTATTCGTAGTGATCTGT TGGAGAGTGATTCTCAATGTTTAAACCCTCTGCTGGAAAGAAAGTTTTTGTACCATATATGGCG TTTTTATTTTATATCACTATGTTTCATACTATATAAATTTTAAATGCTGCAGGTATTCATTGCG CAAGAGCAAAAATGTCTGACCAGGATTTGGGTTGAGGACCGTCCTTGCTGGATGGTCTCTTTCT TGTCTCCAATCAGAAGAAGGCGCATATATATAAAACTAATTGATTCTGCAAATAATGAAGATGC CAGTGGGGGGAAGATCATTTCCATCTCCTTTTTGTATGCAAATATGCCAATATGGTTGATGTTT TTTGCACTAGGCATATCATCAGATAAGGATATCTTTGATGTTATAAATATGGAAGACTGTGATG CTTGTGTTATCAACACAATTACCGCAACTATTAAAGAATCAGATGAATTGTGTGAAGGCTTCCG TAAATCAGATAAAGCCCGGCAGTATGTTGACGAATTGATTAAGAATTCAAAATTTCCTCCTGCA GAGCCATTTGATGATTATATTGCTAAATACCTCTTCCCCAGCATAAGTGGGAACCGGAACAAAG CACTTTTCTTAGGTTACATGGTCAAATGCCTTTTAATGGCTTTCACTGGGAAGCGCAAATGTGA CAACAAGGATGATTTCCGGAACAAGAGGTTGGACCTAGCTGGTGAATTGCTTGGAAGAGAACTC CGTGCGCATATTAGGCATGCAGAGAGACTCATGGTTAAGGCCTTGCAGAGAGATTTAAATAGTG AGCGTGAGTTACAAGAATTTGATCATTATCTGGATGCTTCAATTATTACCAATGGTCTAAACCG TGCCTTCTCTACTGGTTCTTGGTGCCATCCTTACAAAAGAAATGAAAGATGCGCAGGAATTGTT GCGACACTAAGGAGAACAAATCCGCTTCAGATGATCTCGGACTTGAGGAAAACTCGCCAACGAG TTGCTTATGCTGGGAAAGCCGGTGATGCAAGATATCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.150553336

Conservation Information
Conserved circRNAs	NA
PMCS	0.150553336

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							32614630-32611675(+)
32611633-32611675(+)
						
						Potential amino acid sequence
						
							MLGKPVMQDIRYSLEVMEEPSKDNGQSSCVVDPELEPMMLDDAREGVSHTLDDANGHSSMDVDR
GCHSMDTTRSSLGDDGKGKRDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFV
SHGLQELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPR
HARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMSNLC
WLHKLKESDCQFDSGGYFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRRRIYIKLI
DSANNEDASGGKIISISFLYANMPIWLMFFALGISSDKDIFDVINMEDCDACVINTITATIKES
DELCEGFRKSDKARQYVDELIKNSKFPPAEPFDDYIAKYLFPSISGNRNKALFLGYMVKCLLMA
FTGKRKCDNKDDFRNKRLDLAGELLGRELRAHIRHAERLMVKALQRDLNSERELQEFDHYLDAS
IITNGLNRAFSTGSWCHPYKRNERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPL
FPRSYGRAIKGQWAIILCC*(+)
MEEPSKDNGQSSCVVDPELEPMMLDDAREGVSHTLDDANGHSSMDVDRGCHSMDTTRSSLGDDG
KGKRDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVSHGLQELFDSLGEVTV
EPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRHARLQNMTYSSKMKVE
VHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMSNLCWLHKLKESDCQFDSGG
YFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRRRIYIKLIDSANNEDASGGKIISI
SFLYANMPIWLMFFALGISSDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDKARQY
VDELIKNSKFPPAEPFDDYIAKYLFPSISGNRNKALFLGYMVKCLLMAFTGKRKCDNKDDFRNK
RLDLAGELLGRELRAHIRHAERLMVKALQRDLNSERELQEFDHYLDASIITNGLNRAFSTGSWC
HPYKRNERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPLFPRSYGRAIKGQWAII
LCC*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	32614630-32611675(+) 32611633-32611675(+)
Potential amino acid sequence	MLGKPVMQDIRYSLEVMEEPSKDNGQSSCVVDPELEPMMLDDAREGVSHTLDDANGHSSMDVDR GCHSMDTTRSSLGDDGKGKRDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFV SHGLQELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPR HARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMSNLC WLHKLKESDCQFDSGGYFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRRRIYIKLI DSANNEDASGGKIISISFLYANMPIWLMFFALGISSDKDIFDVINMEDCDACVINTITATIKES DELCEGFRKSDKARQYVDELIKNSKFPPAEPFDDYIAKYLFPSISGNRNKALFLGYMVKCLLMA FTGKRKCDNKDDFRNKRLDLAGELLGRELRAHIRHAERLMVKALQRDLNSERELQEFDHYLDAS IITNGLNRAFSTGSWCHPYKRNERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPL FPRSYGRAIKGQWAIILCC(+) MEEPSKDNGQSSCVVDPELEPMMLDDAREGVSHTLDDANGHSSMDVDRGCHSMDTTRSSLGDDG KGKRDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVSHGLQELFDSLGEVTV EPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRHARLQNMTYSSKMKVE VHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMSNLCWLHKLKESDCQFDSGG YFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRRRIYIKLIDSANNEDASGGKIISI SFLYANMPIWLMFFALGISSDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDKARQY VDELIKNSKFPPAEPFDDYIAKYLFPSISGNRNKALFLGYMVKCLLMAFTGKRKCDNKDDFRNK RLDLAGELLGRELRAHIRHAERLMVKALQRDLNSERELQEFDHYLDASIITNGLNRAFSTGSWC HPYKRNERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPLFPRSYGRAIKGQWAII LCC(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0641000_circ_g.1

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