Plant Circular RNA Database

Detail information of Os07g0658400_circ_g.24

			
						 General Information
					
						CircRNA Name
						Os07g0658400_circ_g.24
					
						ID in PlantcircBase
						osa_circ_035130
					
						Alias
						Os_ciR5578
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 27730309-27731661  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os07g0658400						
					
						Parent gene annotation
						
							Ferredoxin-dependent glutamate synthase, Leaf senescence and nit
rogen remobilization (Os07t0658400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os07g0658400_circ_g.13 Os07g0658400_circ_g.14 Os07g0658400_circ_g.15 Os07g0658400_circ_g.16 Os07g0658400_circ_g.17 Os07g0658400_circ_g.18 Os07g0658400_circ_g.19 Os07g0658400_circ_g.20 Os07g0658400_circ_g.21 Os07g0658400_circ_g.22 Os07g0658400_circ_g.23 Os07g0658400_circ_g.25 Os07g0658400_circ_g.26 Os07g0658400_circ_g.27 Os07g0658400_circ_g.28 Os07g0658400_circ_g.29 Os07g0658400_circ_g.30 Os07g0658400_circ_g.31 Os07g0658400_circ_g.32 Os07g0658400_circ_g.33 Os07g0658400_circ_g.34 Os07g0658400_circ_g.35 Os07g0658400_circ_g.36 Os07g0658400_circ_g.37 Os07g0658400_circ_g.38 Os07g0658400_circ_g.39 						
					
						Support reads
						3/3
					
						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  
						
							CT-AC							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
						Os07t0658400-02:3

General Information
CircRNA Name	Os07g0658400_circ_g.24
ID in PlantcircBase	osa_circ_035130
Alias	Os_ciR5578
Organism	Oryza sativa
Position	chr7: 27730309-27731661 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os07g0658400
Parent gene annotation	Ferredoxin-dependent glutamate synthase, Leaf senescence and nit rogen remobilization (Os07t0658400-02)
Parent gene strand	-
Alternative splicing	Os07g0658400_circ_g.13 Os07g0658400_circ_g.14 Os07g0658400_circ_g.15 Os07g0658400_circ_g.16 Os07g0658400_circ_g.17 Os07g0658400_circ_g.18 Os07g0658400_circ_g.19 Os07g0658400_circ_g.20 Os07g0658400_circ_g.21 Os07g0658400_circ_g.22 Os07g0658400_circ_g.23 Os07g0658400_circ_g.25 Os07g0658400_circ_g.26 Os07g0658400_circ_g.27 Os07g0658400_circ_g.28 Os07g0658400_circ_g.29 Os07g0658400_circ_g.30 Os07g0658400_circ_g.31 Os07g0658400_circ_g.32 Os07g0658400_circ_g.33 Os07g0658400_circ_g.34 Os07g0658400_circ_g.35 Os07g0658400_circ_g.36 Os07g0658400_circ_g.37 Os07g0658400_circ_g.38 Os07g0658400_circ_g.39
Support reads	3/3
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	CT-AC 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	Os07t0658400-02:3

			
						 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  
						
							TTTCAGGGCCAACTTCCAAGATATTGCGCCGTTTACCAATATTGACTTCAAGAGACATAACCAA
ACCTTCTCTGAGGGGATCAATAGCAGGATTTGTAACctggcaccatatccgatcaagcaagcaa
actgatgggtgctaaaacactgagcagtatcagcaacaatggaagcagacatccgaagaccatt
ttgaatca

									
								

					

						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: 485
Transcript exons: 27730309-27730466,27731251-27731466,27731551-27731661
CTGGCACCATATCCGATCAAGCAAGCAAACTGATGGGTGCTAAAACACTGAGCAGTATCAGCAA
CAATGGAAGCAGACATCCGAAGACCATTTTGAATCAAATGCTGGTGGATGGCACCAACAGCTAG
AAGTATCGGGATGGCAGGGCGAGTTGGTTCGAGTGCTTCAGAACGATCAGAAAGCACAAGAAGT
TGAGAACCATTCCGCACAGCAGCATCAGCTTCATCACAAAGAACCTTAATAGCCTTATCAAGGG
AACCATCTAGACCTTTACGGATGTCGAAGTATGTCGAGAGTACTTTAGGCTTCAGTTTTGAGTC
ATTCAAAAGTGATTCTAGTTCACCTTCATTAAGCACAGGACTTGATAGGGTAACCTGATCAGCA
TTTTCAGGGCCAACTTCCAAGATATTGCGCCGTTTACCAATATTGACTTCAAGAGACATAACCA
AACCTTCTCTGAGGGGATCAATAGCAGGATTTGTAAC
						
					

						Genomic sequence
						
							CTGGCACCATATCCGATCAAGCAAGCAAACTGATGGGTGCTAAAACACTGAGCAGTATCAGCAA
CAATGGAAGCAGACATCCGAAGACCATTTTGAATCAAATGCTGGTGGATGGCACCAACAGCTAG
AAGTATCGGGATGGCAGGGCGAGTTGGTTCCTACATCATTAAGCAATTTAATATTGCAATCTAG
GAAACATGAATAAAGCAAATAGCACAATCCTATCTCAACTGTATATCTCATTGTACTAGTAAAT
AGTCCGAATTTGAATAAAAAAACCTTTGCATTTTGATCTAAACATGGAAGAGAAAAAAAAACTA
GGTAGATTAGCATTCGGTCATGAAGCTTTCATGCTACAAACTTATGTGCATCTGTGGATACATC
AGTACTGCAGTAGTCATCATTACAAAATTCTATAAATCTAAACTGTGATAGTAAGTAATGCTCC
TGACAGACATATAACTGGGCAGGTAACATATAAAATGTAACTAATCGATACTACCGAGGTACCA
ATTATGTGGCCTCGTCAGAGTATCATTGCACCATGGATGTAAGTGTTTATAATAATTATAATTA
TTATTAGAGTTCAAATAAGGATAATTGGTTAATATTATCCACTACGGAGTAATAAACATTTGAA
TAAAGAAATAAAACACACTCAATCTGTTGGTTATGTAAAGGAGTGAAATAAAAATGTAAAGATG
TCTTAGCCATCCAAGACTATGAAAATAGCACAGCTTTTACGTTAAATGCTACTACCTCCGTTTC
AGGTTATAAGACTTTCTAGCATTGCCCACATTCATAAAGATGTTAATGAATCTAGACATATATA
TTTGACTAGATTCATTAACATCTATATGAATGTGGGCAATGCTAGAAAGTCTTATAACCTGAAA
CAGAGGAAGTAGGATTTTAAAATGTCAGAACTCAGAAGCTACTCACGAGTGCTTCAGAACGATC
AGAAAGCACAAGAAGTTGAGAACCATTCCGCACAGCAGCATCAGCTTCATCACAAAGAACCTTA
ATAGCCTTATCAAGGGAACCATCTAGACCTTTACGGATGTCGAAGTATGTCGAGAGTACTTTAG
GCTTCAGTTTTGAGTCATTCAAAAGTGATTCTAGTTCACCTTCATTAAGCACAGGACTTGATAG
GGTAACCTGAAAATTCAACAAGATGGTGTCTTTATATTCCCCATGAATTCAAAAAAAAAAAAAA
AAAACTATTTCCTTCAAAAGAACTACCTGATCAGCATTTTCAGGGCCAACTTCCAAGATATTGC
GCCGTTTACCAATATTGACTTCAAGAGACATAACCAAACCTTCTCTGAGGGGATCAATAGCAGG
ATTTGTAAC
						
					

			
		

Sequences
Splice junction sequence	TTTCAGGGCCAACTTCCAAGATATTGCGCCGTTTACCAATATTGACTTCAAGAGACATAACCAA ACCTTCTCTGAGGGGATCAATAGCAGGATTTGTAACctggcaccatatccgatcaagcaagcaa actgatgggtgctaaaacactgagcagtatcagcaacaatggaagcagacatccgaagaccatt ttgaatca
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: 485 Transcript exons: 27730309-27730466,27731251-27731466,27731551-27731661 CTGGCACCATATCCGATCAAGCAAGCAAACTGATGGGTGCTAAAACACTGAGCAGTATCAGCAA CAATGGAAGCAGACATCCGAAGACCATTTTGAATCAAATGCTGGTGGATGGCACCAACAGCTAG AAGTATCGGGATGGCAGGGCGAGTTGGTTCGAGTGCTTCAGAACGATCAGAAAGCACAAGAAGT TGAGAACCATTCCGCACAGCAGCATCAGCTTCATCACAAAGAACCTTAATAGCCTTATCAAGGG AACCATCTAGACCTTTACGGATGTCGAAGTATGTCGAGAGTACTTTAGGCTTCAGTTTTGAGTC ATTCAAAAGTGATTCTAGTTCACCTTCATTAAGCACAGGACTTGATAGGGTAACCTGATCAGCA TTTTCAGGGCCAACTTCCAAGATATTGCGCCGTTTACCAATATTGACTTCAAGAGACATAACCA AACCTTCTCTGAGGGGATCAATAGCAGGATTTGTAAC
Genomic sequence	CTGGCACCATATCCGATCAAGCAAGCAAACTGATGGGTGCTAAAACACTGAGCAGTATCAGCAA CAATGGAAGCAGACATCCGAAGACCATTTTGAATCAAATGCTGGTGGATGGCACCAACAGCTAG AAGTATCGGGATGGCAGGGCGAGTTGGTTCCTACATCATTAAGCAATTTAATATTGCAATCTAG GAAACATGAATAAAGCAAATAGCACAATCCTATCTCAACTGTATATCTCATTGTACTAGTAAAT AGTCCGAATTTGAATAAAAAAACCTTTGCATTTTGATCTAAACATGGAAGAGAAAAAAAAACTA GGTAGATTAGCATTCGGTCATGAAGCTTTCATGCTACAAACTTATGTGCATCTGTGGATACATC AGTACTGCAGTAGTCATCATTACAAAATTCTATAAATCTAAACTGTGATAGTAAGTAATGCTCC TGACAGACATATAACTGGGCAGGTAACATATAAAATGTAACTAATCGATACTACCGAGGTACCA ATTATGTGGCCTCGTCAGAGTATCATTGCACCATGGATGTAAGTGTTTATAATAATTATAATTA TTATTAGAGTTCAAATAAGGATAATTGGTTAATATTATCCACTACGGAGTAATAAACATTTGAA TAAAGAAATAAAACACACTCAATCTGTTGGTTATGTAAAGGAGTGAAATAAAAATGTAAAGATG TCTTAGCCATCCAAGACTATGAAAATAGCACAGCTTTTACGTTAAATGCTACTACCTCCGTTTC AGGTTATAAGACTTTCTAGCATTGCCCACATTCATAAAGATGTTAATGAATCTAGACATATATA TTTGACTAGATTCATTAACATCTATATGAATGTGGGCAATGCTAGAAAGTCTTATAACCTGAAA CAGAGGAAGTAGGATTTTAAAATGTCAGAACTCAGAAGCTACTCACGAGTGCTTCAGAACGATC AGAAAGCACAAGAAGTTGAGAACCATTCCGCACAGCAGCATCAGCTTCATCACAAAGAACCTTA ATAGCCTTATCAAGGGAACCATCTAGACCTTTACGGATGTCGAAGTATGTCGAGAGTACTTTAG GCTTCAGTTTTGAGTCATTCAAAAGTGATTCTAGTTCACCTTCATTAAGCACAGGACTTGATAG GGTAACCTGAAAATTCAACAAGATGGTGTCTTTATATTCCCCATGAATTCAAAAAAAAAAAAAA AAAACTATTTCCTTCAAAAGAACTACCTGATCAGCATTTTCAGGGCCAACTTCCAAGATATTGC GCCGTTTACCAATATTGACTTCAAGAGACATAACCAAACCTTCTCTGAGGGGATCAATAGCAGG ATTTGTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.285412127

Conservation Information
Conserved circRNAs	NA
PMCS	0.285412127

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27731621-27731429(-)
						
						Potential amino acid sequence
						
							MSLEVNIGKRRNILEVGPENADQVTLSSPVLNEGELESLLNDSKLKPKVLSTYFDIRKGLDGSL
DKAIKVLCDEADAAVRNGSQLLVLSDRSEALEPTRPAIPILLAVGAIHQHLIQNGLRMSASIVA
DTAQCFSTHQFACLIGYGARLQILLLIPSEKVWLCLLKSILVNGAISWKLALKMLIRLPYQVLC
LMKVN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27731621-27731429(-)
Potential amino acid sequence	MSLEVNIGKRRNILEVGPENADQVTLSSPVLNEGELESLLNDSKLKPKVLSTYFDIRKGLDGSL DKAIKVLCDEADAAVRNGSQLLVLSDRSEALEPTRPAIPILLAVGAIHQHLIQNGLRMSASIVA DTAQCFSTHQFACLIGYGARLQILLLIPSEKVWLCLLKSILVNGAISWKLALKMLIRLPYQVLC LMKVN*(-)
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 Os07g0658400_circ_g.24

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