Plant Circular RNA Database

Detail information of Os05g0594700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os05g0594700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029221
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 29610291-29612438  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os05g0594700						
					
						Parent gene annotation
						
							Similar to Hv711N16.16 (Fragment). (Os05t0594700-01);Similar to 
Hv711N16.16 (Fragment). (Os05t0594700-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0594700_circ_g.4 Os05g0594700_circ_g.5 Os05g0594700_circ_g.6 Os05g0594700_circ_g.7 Os05g0594700_circ_g.8 Os05g0594700_circ_g.9 						
					
						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
						Os05t0594700-02:5
Os05t0594700-01:5

General Information
CircRNA Name	Os05g0594700_circ_g.3
ID in PlantcircBase	osa_circ_029221
Alias	NA
Organism	Oryza sativa
Position	chr5: 29610291-29612438 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os05g0594700
Parent gene annotation	Similar to Hv711N16.16 (Fragment). (Os05t0594700-01);Similar to Hv711N16.16 (Fragment). (Os05t0594700-02)
Parent gene strand	+
Alternative splicing	Os05g0594700_circ_g.4 Os05g0594700_circ_g.5 Os05g0594700_circ_g.6 Os05g0594700_circ_g.7 Os05g0594700_circ_g.8 Os05g0594700_circ_g.9
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	Os05t0594700-02:5 Os05t0594700-01:5

			
						 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  
						
							TGTTGGATTTTTGTTCCAGACTGGCTTTCTTGGCTGTTTTGGTTCCGAGGTGGATGCCATTGAA
TACTACAAAGCAGAGATTGAGAAGATTGGGAAAGAAgatcaagatattcgttccaatatcaatt
ttagcttcgcttgttctgttccctgtgaactggacaaatgacaccctagacagcatgaaggtag
tccacagt

									
								

					

						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: 586
Transcript exons: 29610291-29610437,29610979-29611114,29611423-29611524,29
612126-29612245,29612358-29612438
GATCAAGATATTCGTTCCAATATCAATTTTAGCTTCGCTTGTTCTGTTCCCTGTGAACTGGACA
AATGACACCCTAGACAGCATGAAGGTAGTCCACAGTAAAATTGACAAACTTTCAATATCAAACA
TACCTTATGGGTCAAACAGGTTTGTTACTCACTTGGTTATGGCTTATGCTGTCACGTTTTGGAC
CTGCTATGTACTGTTCCGAGAGTATGAGATAATTACAACGATGAGATTGCGGTTTCTTGCTTCA
GAGAAACGGCGACCAGACCAGTTTACAGTTCTTGTGCGGAATATACCTCCAGATCCTGATGAAT
CAATTAGTGAGCTCGTGGAGCATTTCTTCCTTGTTAATCATCCTGATCATTATCTAAGACACCA
GGTGGTTTACAATGCAAATAAACTTGCTGATCTGGTTGAGAAGAAGAAGAAACTGCAAAATTGG
CTTGATTACTACCAGCTCAAGTATGAAAGAAATCCATCAAAAAGGCCCACCACTAAGACTGGCT
TTCTTGGCTGTTTTGGTTCCGAGGTGGATGCCATTGAATACTACAAAGCAGAGATTGAGAAGAT
TGGGAAAGAA
						
					

						Genomic sequence
						
							GATCAAGATATTCGTTCCAATATCAATTTTAGCTTCGCTTGTTCTGTTCCCTGTGAACTGGACA
AATGACACCCTAGACAGCATGAAGGTAGTCCACAGTAAAATTGACAAACTTTCAATATCAAACA
TACCTTATGGGTCAAACAGGTAAGCCTCCATAAATCATTTGATATCTGGATGCGGTGTATTTTG
ATGAGTTGTGTAGAGATAAATGTTTCTTTTTTTGGTCTGGTTCAATATAAATTGTACGTAAAAC
ATCAATAAGATTGCCCATTGGTCCACCAATTACACAAACAAAATCTGTATAGTGATTCATTTTA
CATGCAGATTCAACCTTTTTAAGTTTTGGGCGGCACCTGAAATCCAACCACTTTTACTTATCTT
CATGCTGATTATGCACATGTACTTGGTACAATTTTTAGGAGCATTATCATCTTATGGTTTTGGG
TGATTTGATAAATATGCCACTTGCCTGTGTGACTGTCTAATTTAGTAAGGTACAAGCACTCTAT
TTTGGCCTGTGTGCTTGGGACTTAGCAGCTGCCCTGCCAAGTTCAATATTGGGTGGCAGTTGCT
CTGGTTGAAAATAAATTCATCCACACTGAACTTCTAGGTTTCATTTATTAATTTCTGTTGATGC
TAGCACATGTCTTTGCTGTTCATGATGAACATTCCATCTGTTTTACAGGTTTGTTACTCACTTG
GTTATGGCTTATGCTGTCACGTTTTGGACCTGCTATGTACTGTTCCGAGAGTATGAGATAATTA
CAACGATGAGATTGCGGTTTCTTGCTTCAGAGAAACGGCGACCAGACCAGTTTACAGTATGATC
TTGTCAACTTTGCAAATCCCCTCTCTATTTAGTACCAACATGTTTACATTGGATCCACAAGAAG
GGTAAAAAATTGTAATATTAATGGACTGAAACTATTCACCACTGGAAATAGTCTAAGAGATTGT
GGCTAAGCATTTTGTCTCTGAGCACCCTGATACTCACTTTGCACTGACTTGGTTTATATTATCT
AAAGCAATGTTGTAGACGGGAATGGTTTCATATCTCAATTGAATAAACACGATGAGTTAATTTC
CTTCTGGTTGGTTTGTTGAATGCACCTCAAATGATTTATTTTAGGTTCTTGTGCGGAATATACC
TCCAGATCCTGATGAATCAATTAGTGAGCTCGTGGAGCATTTCTTCCTTGTTAATCATCCTGAT
CATTATCTAAGACACCAGGTAATCTTTGGTAAAAATTTGTGGATAACTAAGTCAGATGTAGTTC
TGTTGCTTTTCTCTTCTGGGGGTTTCAACAGGTCATCATCTGCTTAGGTAGGAGCTGTGTTTCT
AGTTATGCTGATTGGCCTAATGCAAATAGATTTTTTTTCTACTCAACAGAACCCCCTTCATATA
TTATCCTTTTCCCACAAATTATTGATGGTTTCAAATGAACCTAATATTAATGTTTGCTAGTTTC
ATGTTGAGATTTTTTCCCCCAGATTCTGAGAATAGTCCACATAATAGCCTACCCACAGATTATT
TGGATATTAATACATAAATATTTTGGTTTTGCCAAGTAACAGGAAAGTTATGATCTCTTGGTTA
TCTAGATTTTCATTTAAATAATCATATTCATATGTTAAAGGGTCTAAAAACTGTCTCTCTGTGC
TAACACTTCACAGTGCTAATTGCTGAATGAGATTTAGAAGGGTCATATCCAAATTTGTGTATCA
TATGCACTTGGGTTTTCTACCCTGACTTCATTGATTTTTTTATTCTTCCTTATACTAATTACTG
TATTTATTCCGTCCTTTTTCTGGCCGATTGTCTATATCTATAGGTGGTTTACAATGCAAATAAA
CTTGCTGATCTGGTTGAGAAGAAGAAGAAACTGCAAAATTGGCTTGATTACTACCAGCTCAAGT
ATGAAAGAAATCCATCAAAAAGGCCCACCACTAAGGTTAGTCTGCCATATGGACCTTGATCAAT
TTATTTTTCATTTCAATTATAATATTACATTAGGATCTTTTTTCTTTTTAATTCTCTGTCCCCC
TGTTGGATTTTTGTTCCAGACTGGCTTTCTTGGCTGTTTTGGTTCCGAGGTGGATGCCATTGAA
TACTACAAAGCAGAGATTGAGAAGATTGGGAAAGAA
						
					

			
		

Sequences
Splice junction sequence	TGTTGGATTTTTGTTCCAGACTGGCTTTCTTGGCTGTTTTGGTTCCGAGGTGGATGCCATTGAA TACTACAAAGCAGAGATTGAGAAGATTGGGAAAGAAgatcaagatattcgttccaatatcaatt ttagcttcgcttgttctgttccctgtgaactggacaaatgacaccctagacagcatgaaggtag tccacagt
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: 586 Transcript exons: 29610291-29610437,29610979-29611114,29611423-29611524,29 612126-29612245,29612358-29612438 GATCAAGATATTCGTTCCAATATCAATTTTAGCTTCGCTTGTTCTGTTCCCTGTGAACTGGACA AATGACACCCTAGACAGCATGAAGGTAGTCCACAGTAAAATTGACAAACTTTCAATATCAAACA TACCTTATGGGTCAAACAGGTTTGTTACTCACTTGGTTATGGCTTATGCTGTCACGTTTTGGAC CTGCTATGTACTGTTCCGAGAGTATGAGATAATTACAACGATGAGATTGCGGTTTCTTGCTTCA GAGAAACGGCGACCAGACCAGTTTACAGTTCTTGTGCGGAATATACCTCCAGATCCTGATGAAT CAATTAGTGAGCTCGTGGAGCATTTCTTCCTTGTTAATCATCCTGATCATTATCTAAGACACCA GGTGGTTTACAATGCAAATAAACTTGCTGATCTGGTTGAGAAGAAGAAGAAACTGCAAAATTGG CTTGATTACTACCAGCTCAAGTATGAAAGAAATCCATCAAAAAGGCCCACCACTAAGACTGGCT TTCTTGGCTGTTTTGGTTCCGAGGTGGATGCCATTGAATACTACAAAGCAGAGATTGAGAAGAT TGGGAAAGAA
Genomic sequence	GATCAAGATATTCGTTCCAATATCAATTTTAGCTTCGCTTGTTCTGTTCCCTGTGAACTGGACA AATGACACCCTAGACAGCATGAAGGTAGTCCACAGTAAAATTGACAAACTTTCAATATCAAACA TACCTTATGGGTCAAACAGGTAAGCCTCCATAAATCATTTGATATCTGGATGCGGTGTATTTTG ATGAGTTGTGTAGAGATAAATGTTTCTTTTTTTGGTCTGGTTCAATATAAATTGTACGTAAAAC ATCAATAAGATTGCCCATTGGTCCACCAATTACACAAACAAAATCTGTATAGTGATTCATTTTA CATGCAGATTCAACCTTTTTAAGTTTTGGGCGGCACCTGAAATCCAACCACTTTTACTTATCTT CATGCTGATTATGCACATGTACTTGGTACAATTTTTAGGAGCATTATCATCTTATGGTTTTGGG TGATTTGATAAATATGCCACTTGCCTGTGTGACTGTCTAATTTAGTAAGGTACAAGCACTCTAT TTTGGCCTGTGTGCTTGGGACTTAGCAGCTGCCCTGCCAAGTTCAATATTGGGTGGCAGTTGCT CTGGTTGAAAATAAATTCATCCACACTGAACTTCTAGGTTTCATTTATTAATTTCTGTTGATGC TAGCACATGTCTTTGCTGTTCATGATGAACATTCCATCTGTTTTACAGGTTTGTTACTCACTTG GTTATGGCTTATGCTGTCACGTTTTGGACCTGCTATGTACTGTTCCGAGAGTATGAGATAATTA CAACGATGAGATTGCGGTTTCTTGCTTCAGAGAAACGGCGACCAGACCAGTTTACAGTATGATC TTGTCAACTTTGCAAATCCCCTCTCTATTTAGTACCAACATGTTTACATTGGATCCACAAGAAG GGTAAAAAATTGTAATATTAATGGACTGAAACTATTCACCACTGGAAATAGTCTAAGAGATTGT GGCTAAGCATTTTGTCTCTGAGCACCCTGATACTCACTTTGCACTGACTTGGTTTATATTATCT AAAGCAATGTTGTAGACGGGAATGGTTTCATATCTCAATTGAATAAACACGATGAGTTAATTTC CTTCTGGTTGGTTTGTTGAATGCACCTCAAATGATTTATTTTAGGTTCTTGTGCGGAATATACC TCCAGATCCTGATGAATCAATTAGTGAGCTCGTGGAGCATTTCTTCCTTGTTAATCATCCTGAT CATTATCTAAGACACCAGGTAATCTTTGGTAAAAATTTGTGGATAACTAAGTCAGATGTAGTTC TGTTGCTTTTCTCTTCTGGGGGTTTCAACAGGTCATCATCTGCTTAGGTAGGAGCTGTGTTTCT AGTTATGCTGATTGGCCTAATGCAAATAGATTTTTTTTCTACTCAACAGAACCCCCTTCATATA TTATCCTTTTCCCACAAATTATTGATGGTTTCAAATGAACCTAATATTAATGTTTGCTAGTTTC ATGTTGAGATTTTTTCCCCCAGATTCTGAGAATAGTCCACATAATAGCCTACCCACAGATTATT TGGATATTAATACATAAATATTTTGGTTTTGCCAAGTAACAGGAAAGTTATGATCTCTTGGTTA TCTAGATTTTCATTTAAATAATCATATTCATATGTTAAAGGGTCTAAAAACTGTCTCTCTGTGC TAACACTTCACAGTGCTAATTGCTGAATGAGATTTAGAAGGGTCATATCCAAATTTGTGTATCA TATGCACTTGGGTTTTCTACCCTGACTTCATTGATTTTTTTATTCTTCCTTATACTAATTACTG TATTTATTCCGTCCTTTTTCTGGCCGATTGTCTATATCTATAGGTGGTTTACAATGCAAATAAA CTTGCTGATCTGGTTGAGAAGAAGAAGAAACTGCAAAATTGGCTTGATTACTACCAGCTCAAGT ATGAAAGAAATCCATCAAAAAGGCCCACCACTAAGGTTAGTCTGCCATATGGACCTTGATCAAT TTATTTTTCATTTCAATTATAATATTACATTAGGATCTTTTTTCTTTTTAATTCTCTGTCCCCC TGTTGGATTTTTGTTCCAGACTGGCTTTCTTGGCTGTTTTGGTTCCGAGGTGGATGCCATTGAA TACTACAAAGCAGAGATTGAGAAGATTGGGAAAGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015869 						
					
						PMCS
						0.215939843

Conservation Information
Conserved circRNAs	osi_circ_015869
PMCS	0.215939843

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29610374-29610356(+)
29612137-29610356(+)
29610421-29612227(-)
						
						Potential amino acid sequence
						
							MKVVHSKIDKLSISNIPYGSNRFVTHLVMAYAVTFWTCYVLFREYEIITTMRLRFLASEKRRPD
QFTVLVRNIPPDPDESISELVEHFFLVNHPDHYLRHQVVYNANKLADLVEKKKKLQNWLDYYQL
KYERNPSKRPTTKTGFLGCFGSEVDAIEYYKAEIEKIGKEDQDIRSNINFSFACSVPCELDK*(
+)
MQINLLIWLRRRRNCKIGLITTSSSMKEIHQKGPPLRLAFLAVLVPRWMPLNTTKQRLRRLGKK
IKIFVPISILASLVLFPVNWTNDTLDSMKVVHSKIDKLSISNIPYGSNRFVTHLVMAYAVTFWT
CYVLFREYEIITTMRLRFLASEKRRPDQFTVLVRNIPPDPDESISELVEHFFLVNHPDHYLRHQ
VVYNANKLADLVEKKKKLQNWLDYYQLKYERNPSKRPTTKTGFLGCFGSEVDAIEYYKAEIEKI
GKEDQDIRSNINFSFACSVPCELDK*(+)
MFDIESLSILLWTTFMLSRVSFVQFTGNRTSEAKIDIGTNILIFFPNLLNLCFVVFNGIHLGTK
TAKKASLSGGPF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29610374-29610356(+) 29612137-29610356(+) 29610421-29612227(-)
Potential amino acid sequence	MKVVHSKIDKLSISNIPYGSNRFVTHLVMAYAVTFWTCYVLFREYEIITTMRLRFLASEKRRPD QFTVLVRNIPPDPDESISELVEHFFLVNHPDHYLRHQVVYNANKLADLVEKKKKLQNWLDYYQL KYERNPSKRPTTKTGFLGCFGSEVDAIEYYKAEIEKIGKEDQDIRSNINFSFACSVPCELDK( +) MQINLLIWLRRRRNCKIGLITTSSSMKEIHQKGPPLRLAFLAVLVPRWMPLNTTKQRLRRLGKK IKIFVPISILASLVLFPVNWTNDTLDSMKVVHSKIDKLSISNIPYGSNRFVTHLVMAYAVTFWT CYVLFREYEIITTMRLRFLASEKRRPDQFTVLVRNIPPDPDESISELVEHFFLVNHPDHYLRHQ VVYNANKLADLVEKKKKLQNWLDYYQLKYERNPSKRPTTKTGFLGCFGSEVDAIEYYKAEIEKI GKEDQDIRSNINFSFACSVPCELDK(+) MFDIESLSILLWTTFMLSRVSFVQFTGNRTSEAKIDIGTNILIFFPNLLNLCFVVFNGIHLGTK TAKKASLSGGPF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0594700_circ_g.3

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