Plant Circular RNA Database

Detail information of Os05g0350700_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os05g0350700_circ_g.4
					
						ID in PlantcircBase
						osa_circ_027509
					
						Alias
						Os_ciR3964
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 16569564-16570300  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os05g0350700						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os05t0350700-01);Hypothetical c
onserved gene. (Os05t0350700-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0350700_circ_g.1 Os05g0350700_circ_g.2 Os05g0350700_circ_g.3 Os05g0350700_circ_g.5 Os05g0350700_circ_g.6 Os05g0350700_circ_g.7 Os05g0350700_circ_g.8 Os05g0350700_circ_g.9 Os05g0350700_circ_g.10 Os05g0350700_circ_g.11 						
					
						Support reads
						2/4
					
						Tissues
						root/seed
					
						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
						Os05t0350700-02:2
Os05t0350700-01:2

General Information
CircRNA Name	Os05g0350700_circ_g.4
ID in PlantcircBase	osa_circ_027509
Alias	Os_ciR3964
Organism	Oryza sativa
Position	chr5: 16569564-16570300 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os05g0350700
Parent gene annotation	Conserved hypothetical protein. (Os05t0350700-01);Hypothetical c onserved gene. (Os05t0350700-02)
Parent gene strand	+
Alternative splicing	Os05g0350700_circ_g.1 Os05g0350700_circ_g.2 Os05g0350700_circ_g.3 Os05g0350700_circ_g.5 Os05g0350700_circ_g.6 Os05g0350700_circ_g.7 Os05g0350700_circ_g.8 Os05g0350700_circ_g.9 Os05g0350700_circ_g.10 Os05g0350700_circ_g.11
Support reads	2/4
Tissues	root/seed
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	Os05t0350700-02:2 Os05t0350700-01:2

			
						 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  
						
							TAAGTAGGAGTGATCAAGACAGTGGATTCCATCCTACTAACAAAAGGGATCGTCAAGCTGTTTT
AGATAAGGAAATATCAGCTCCAAAATCTCATAACAAatggatgcaaggaccactgttctgtcaa
ggggactgggctctactgatagaagtgcagatcctggcaaagtcaccggtggtggtccagcagt
tccagaag

						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: 476
Transcript exons: 16569564-16569862,16570124-16570300
ATGGATGCAAGGACCACTGTTCTGTCAAGGGGACTGGGCTCTACTGATAGAAGTGCAGATCCTG
GCAAAGTCACCGGTGGTGGTCCAGCAGTTCCAGAAGAAAAAATTAGGGGGCTAGCAACTGGTAT
TGATGGTTGGGAAAAGCCAAAGATGAAGAAAAAACGTTCTGCTATTAAGGCAGATGTTTCAATG
ACTGGTCCTTCAAGAAATGTTGATGTAGACCGGGAGCAGAAACCAGGGATGCAACACAAATTTA
ATAATGAAGCTAGGGCAAGAATGACAAACTCCCCTAGTTTTAGGTCTGGAACTGTCTCATCAGT
CTCGAGCATTAGTAAATCAGATTTACTTTCTGGACAAAATGGGGTTGGGCGATCCTTAAGTAGG
AGTGATCAAGACAGTGGATTCCATCCTACTAACAAAAGGGATCGTCAAGCTGTTTTAGATAAGG
AAATATCAGCTCCAAAATCTCATAACAA
						
						Genomic sequence
						
							ATGGATGCAAGGACCACTGTTCTGTCAAGGGGACTGGGCTCTACTGATAGAAGTGCAGATCCTG
GCAAAGTCACCGGTGGTGGTCCAGCAGTTCCAGAAGAAAAAATTAGGGGGCTAGCAACTGGTAT
TGATGGTTGGGAAAAGCCAAAGATGAAGAAAAAACGTTCTGCTATTAAGGCAGATGTTTCAATG
ACTGGTCCTTCAAGAAATGTTGATGTAGACCGGGAGCAGAAACCAGGGATGCAACACAAATTTA
ATAATGAAGCTAGGGCAAGAATGACAAACTCCCCTAGTTTTAGGTCAGAGATTCTATCATCCTT
TTCTGCATGTTTTATTGTTTTGATTCTCTTTTGATGCAGTCCTTTATTCTGTTTGATCTTACAT
CATGGACAATCTGACCTTGCATATTGCATAGACATGATGATTGAAAAACATATTATCAAGTTAT
TTTTTCTCCGAACATTCAAACTAAGCAATTCAGCTAATAAGAAAATGATTTGTATATAAAGTTT
TACAATCTGACCAGGCGTTTCCTTTCTGGGTAACTTTTATATGGGCAGGTCTGGAACTGTCTCA
TCAGTCTCGAGCATTAGTAAATCAGATTTACTTTCTGGACAAAATGGGGTTGGGCGATCCTTAA
GTAGGAGTGATCAAGACAGTGGATTCCATCCTACTAACAAAAGGGATCGTCAAGCTGTTTTAGA
TAAGGAAATATCAGCTCCAAAATCTCATAACAA

Sequences
Splice junction sequence	TAAGTAGGAGTGATCAAGACAGTGGATTCCATCCTACTAACAAAAGGGATCGTCAAGCTGTTTT AGATAAGGAAATATCAGCTCCAAAATCTCATAACAAatggatgcaaggaccactgttctgtcaa ggggactgggctctactgatagaagtgcagatcctggcaaagtcaccggtggtggtccagcagt tccagaag
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: 476 Transcript exons: 16569564-16569862,16570124-16570300 ATGGATGCAAGGACCACTGTTCTGTCAAGGGGACTGGGCTCTACTGATAGAAGTGCAGATCCTG GCAAAGTCACCGGTGGTGGTCCAGCAGTTCCAGAAGAAAAAATTAGGGGGCTAGCAACTGGTAT TGATGGTTGGGAAAAGCCAAAGATGAAGAAAAAACGTTCTGCTATTAAGGCAGATGTTTCAATG ACTGGTCCTTCAAGAAATGTTGATGTAGACCGGGAGCAGAAACCAGGGATGCAACACAAATTTA ATAATGAAGCTAGGGCAAGAATGACAAACTCCCCTAGTTTTAGGTCTGGAACTGTCTCATCAGT CTCGAGCATTAGTAAATCAGATTTACTTTCTGGACAAAATGGGGTTGGGCGATCCTTAAGTAGG AGTGATCAAGACAGTGGATTCCATCCTACTAACAAAAGGGATCGTCAAGCTGTTTTAGATAAGG AAATATCAGCTCCAAAATCTCATAACAA
Genomic sequence	ATGGATGCAAGGACCACTGTTCTGTCAAGGGGACTGGGCTCTACTGATAGAAGTGCAGATCCTG GCAAAGTCACCGGTGGTGGTCCAGCAGTTCCAGAAGAAAAAATTAGGGGGCTAGCAACTGGTAT TGATGGTTGGGAAAAGCCAAAGATGAAGAAAAAACGTTCTGCTATTAAGGCAGATGTTTCAATG ACTGGTCCTTCAAGAAATGTTGATGTAGACCGGGAGCAGAAACCAGGGATGCAACACAAATTTA ATAATGAAGCTAGGGCAAGAATGACAAACTCCCCTAGTTTTAGGTCAGAGATTCTATCATCCTT TTCTGCATGTTTTATTGTTTTGATTCTCTTTTGATGCAGTCCTTTATTCTGTTTGATCTTACAT CATGGACAATCTGACCTTGCATATTGCATAGACATGATGATTGAAAAACATATTATCAAGTTAT TTTTTCTCCGAACATTCAAACTAAGCAATTCAGCTAATAAGAAAATGATTTGTATATAAAGTTT TACAATCTGACCAGGCGTTTCCTTTCTGGGTAACTTTTATATGGGCAGGTCTGGAACTGTCTCA TCAGTCTCGAGCATTAGTAAATCAGATTTACTTTCTGGACAAAATGGGGTTGGGCGATCCTTAA GTAGGAGTGATCAAGACAGTGGATTCCATCCTACTAACAAAAGGGATCGTCAAGCTGTTTTAGA TAAGGAAATATCAGCTCCAAAATCTCATAACAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.404634818

Conservation Information
Conserved circRNAs	NA
PMCS	0.404634818

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16569565-16569678(+)
16570155-16570239(-)
						
						Potential amino acid sequence
						
							MDARTTVLSRGLGSTDRSADPGKVTGGGPAVPEEKIRGLATGIDGWEKPKMKKKRSAIKADVSM
TGPSRNVDVDREQKPGMQHKFNNEARARMTNSPSFRSGTVSSVSSISKSDLLSGQNGVGRSLSR
SDQDSGFHPTNKRDRQAVLDKEISAPKSHNKWMQGPLFCQGDWALLIEVQILAKSPVVVQQFQK
KKLGG*(+)
MLETDETVPDLKLGEFVILALASLLNLCCIPGFCSRSTSTFLEGPVIETSALIAERFFFIFGFS
QPSIPVASPLIFSSGTAGPPPVTLPGSALLSVEPSPLDRTVVLASICYEILELIFPYLKQLDDP
FC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16569565-16569678(+) 16570155-16570239(-)
Potential amino acid sequence	MDARTTVLSRGLGSTDRSADPGKVTGGGPAVPEEKIRGLATGIDGWEKPKMKKKRSAIKADVSM TGPSRNVDVDREQKPGMQHKFNNEARARMTNSPSFRSGTVSSVSSISKSDLLSGQNGVGRSLSR SDQDSGFHPTNKRDRQAVLDKEISAPKSHNKWMQGPLFCQGDWALLIEVQILAKSPVVVQQFQK KKLGG(+) MLETDETVPDLKLGEFVILALASLLNLCCIPGFCSRSTSTFLEGPVIETSALIAERFFFIFGFS QPSIPVASPLIFSSGTAGPPPVTLPGSALLSVEPSPLDRTVVLASICYEILELIFPYLKQLDDP FC(-)
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 Os05g0350700_circ_g.4

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