Plant Circular RNA Database

Detail information of Os04g0684500_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os04g0684500_circ_g.5
					
						ID in PlantcircBase
						osa_circ_026033
					
						Alias
						Os04circ18467
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 34964387-34965270  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os04g0684500						
					
						Parent gene annotation
						
							Pentatricopeptide repeat domain containing protein. (Os04t068450
0-01);Hypothetical conserved gene. (Os04t0684500-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0684500_circ_g.2 Os04g0684500_circ_g.3 Os04g0684500_circ_g.4 Os04g0684500_circ_g.6 Os04g0684500_circ_g.7 Os04g0684500_circ_g.8 						
					
						Support reads
						2/1
					
						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
						Os04t0684500-01:2
Os04t0684500-02:2

General Information
CircRNA Name	Os04g0684500_circ_g.5
ID in PlantcircBase	osa_circ_026033
Alias	Os04circ18467
Organism	Oryza sativa
Position	chr4: 34964387-34965270 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os04g0684500
Parent gene annotation	Pentatricopeptide repeat domain containing protein. (Os04t068450 0-01);Hypothetical conserved gene. (Os04t0684500-02)
Parent gene strand	+
Alternative splicing	Os04g0684500_circ_g.2 Os04g0684500_circ_g.3 Os04g0684500_circ_g.4 Os04g0684500_circ_g.6 Os04g0684500_circ_g.7 Os04g0684500_circ_g.8
Support reads	2/1
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	Os04t0684500-01:2 Os04t0684500-02:2

			
						 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  
						
							AGAGGACTTGATGAAGCAGATGAAAGAAGATGGTGTCCCTCCTAACATCCATACTTATACCTCC
TATATAAATGCATGCTGCAAGGCAGGAGACATGCAGgttcaaagagctgtctctgtgcttgata
agatgtccatcgctggcattacaccaaatgagcatacatacacaatcattatgagaggttatgc
tgccagtg

						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: 426
Transcript exons: 34964387-34964682,34965141-34965270
GTTCAAAGAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATA
CATACACAATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTT
CACCAAAATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCC
TGTTGCAAATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGA
TACCAAGGAATACATTTATATATAATATTTTGATTGATGGATGGGCTCGGAGAGGTGATGTTTG
GGAAGCAGAGGACTTGATGAAGCAGATGAAAGAAGATGGTGTCCCTCCTAACATCCATACTTAT
ACCTCCTATATAAATGCATGCTGCAAGGCAGGAGACATGCAG
						
						Genomic sequence
						
							GTTCAAAGAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATA
CATACACAATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTT
CACCAAAATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCC
TGTTGCAAATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGA
TACCAAGGAATACATTTATATATAATATTTTGATTGATGGGTAGGTGTTCTAGATAAGCTCTTT
AGCCAATGTTTTTACTGACTAGTAACGATCTTTTTACCGACTCAGTACTCAGGGACGCTTGTGA
CCATTTATTTATGTGTTGACTGCATCGAACTACTTAGTCAACTGCTGTACTGACTCAGGGATAC
AAGAAAGTATTATGGAAAAAAATAATATAGGGGGTAGAGAACAACCCCTCAATATTTTTAGTAG
AAGGTTGTGGTTGAACCTGTGGAGGGCTAGCACAGCGAACTGTGCTGTTAGCCAGTAGGTCCTA
ATAGTCTCCTCACATGAAACTATTATGATATTTCATTGGATTAGTCATACATTAGTTTTGAAAA
TTTGTATTATATACTGAGTTCATGTTTTATTTGAGTCTTGCTGTAATTTATGAAGTTTTATAAA
AGCGGTATATTTTCCTTTTTGCCTGTTTCGTCACAAATCCTTTTGTGTAGATGGGCTCGGAGAG
GTGATGTTTGGGAAGCAGAGGACTTGATGAAGCAGATGAAAGAAGATGGTGTCCCTCCTAACAT
CCATACTTATACCTCCTATATAAATGCATGCTGCAAGGCAGGAGACATGCAG

Sequences
Splice junction sequence	AGAGGACTTGATGAAGCAGATGAAAGAAGATGGTGTCCCTCCTAACATCCATACTTATACCTCC TATATAAATGCATGCTGCAAGGCAGGAGACATGCAGgttcaaagagctgtctctgtgcttgata agatgtccatcgctggcattacaccaaatgagcatacatacacaatcattatgagaggttatgc tgccagtg
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: 426 Transcript exons: 34964387-34964682,34965141-34965270 GTTCAAAGAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATA CATACACAATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTT CACCAAAATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCC TGTTGCAAATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGA TACCAAGGAATACATTTATATATAATATTTTGATTGATGGATGGGCTCGGAGAGGTGATGTTTG GGAAGCAGAGGACTTGATGAAGCAGATGAAAGAAGATGGTGTCCCTCCTAACATCCATACTTAT ACCTCCTATATAAATGCATGCTGCAAGGCAGGAGACATGCAG
Genomic sequence	GTTCAAAGAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATA CATACACAATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTT CACCAAAATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCC TGTTGCAAATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGA TACCAAGGAATACATTTATATATAATATTTTGATTGATGGGTAGGTGTTCTAGATAAGCTCTTT AGCCAATGTTTTTACTGACTAGTAACGATCTTTTTACCGACTCAGTACTCAGGGACGCTTGTGA CCATTTATTTATGTGTTGACTGCATCGAACTACTTAGTCAACTGCTGTACTGACTCAGGGATAC AAGAAAGTATTATGGAAAAAAATAATATAGGGGGTAGAGAACAACCCCTCAATATTTTTAGTAG AAGGTTGTGGTTGAACCTGTGGAGGGCTAGCACAGCGAACTGTGCTGTTAGCCAGTAGGTCCTA ATAGTCTCCTCACATGAAACTATTATGATATTTCATTGGATTAGTCATACATTAGTTTTGAAAA TTTGTATTATATACTGAGTTCATGTTTTATTTGAGTCTTGCTGTAATTTATGAAGTTTTATAAA AGCGGTATATTTTCCTTTTTGCCTGTTTCGTCACAAATCCTTTTGTGTAGATGGGCTCGGAGAG GTGATGTTTGGGAAGCAGAGGACTTGATGAAGCAGATGAAAGAAGATGGTGTCCCTCCTAACAT CCATACTTATACCTCCTATATAAATGCATGCTGCAAGGCAGGAGACATGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015026 						
					
						PMCS
						0.286719363

Conservation Information
Conserved circRNAs	osi_circ_015026
PMCS	0.286719363

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34964418-34965267(+)
34965243-34964465(+)
34964451-34964611(-)
						
						Potential amino acid sequence
						
							MSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKIKESGLKLDVYIYETLLRACCKSGRMQSA
LAVTREMSFQKIPRNTFIYNILIDGWARRGDVWEAEDLMKQMKEDGVPPNIHTYTSYINACCKA
GDMQVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKIKESGLKLDVYIYET
LLRACCKSGRMQSALAVTREMSFQKIPRNTFIYNILIDGWARRGDVWEAEDLMKQMKEDGVPPN
IHTYTSYINACCKAGDMQVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKI
KESGLKLDVYIYETLLRACCKSGRMQSALAVTREMSFQKIPRNTFIYNILIDGWARRGDVWEAE
DLMKQMKEDGVPPNIHTYTSYINACCKAGDMQVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAA
SGDIGKAFEYFTKIKESGLKLDVYIYETLLRACCKSGRMQSALAVTREMSFQKIPRNTFIYNIL
IDGWARRGDVWEAEDLMKQMKEDGVPPNIHTYTSYINACCKAGDMQ(+)
MHAARQETCRFKELSLCLIRCPSLALHQMSIHTQSL*(+)
MLIWCNASDGHLIKHRDSSLNLHVSCLAACIYIGGISMDVRRDTIFFHLLHQVLCFPNITSPSP
SINQNIIYKCIPWYLLEAHLTSDC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	34964418-34965267(+) 34965243-34964465(+) 34964451-34964611(-)
Potential amino acid sequence	MSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKIKESGLKLDVYIYETLLRACCKSGRMQSA LAVTREMSFQKIPRNTFIYNILIDGWARRGDVWEAEDLMKQMKEDGVPPNIHTYTSYINACCKA GDMQVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKIKESGLKLDVYIYET LLRACCKSGRMQSALAVTREMSFQKIPRNTFIYNILIDGWARRGDVWEAEDLMKQMKEDGVPPN IHTYTSYINACCKAGDMQVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKI KESGLKLDVYIYETLLRACCKSGRMQSALAVTREMSFQKIPRNTFIYNILIDGWARRGDVWEAE DLMKQMKEDGVPPNIHTYTSYINACCKAGDMQVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAA SGDIGKAFEYFTKIKESGLKLDVYIYETLLRACCKSGRMQSALAVTREMSFQKIPRNTFIYNIL IDGWARRGDVWEAEDLMKQMKEDGVPPNIHTYTSYINACCKAGDMQ(+) MHAARQETCRFKELSLCLIRCPSLALHQMSIHTQSL(+) MLIWCNASDGHLIKHRDSSLNLHVSCLAACIYIGGISMDVRRDTIFFHLLHQVLCFPNITSPSP SINQNIIYKCIPWYLLEAHLTSDC(-)
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 Os04g0684500_circ_g.5

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