Plant Circular RNA Database

Detail information of Os11g0620400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os11g0620400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_009819
					
						Alias
						Os_ciR4197
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 24186197-24187554  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os11g0620400						
					
						Parent gene annotation
						
							Sugar/inositol transporter domain containing protein. (Os11t0620
400-01);Sugar/inositol transporter domain containing protein. (O
s11t0620400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0620400_circ_g.2 						
					
						Support reads
						8/4
					
						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
						Os11t0620400-01:2
Os11t0620400-02:2

General Information
CircRNA Name	Os11g0620400_circ_g.1
ID in PlantcircBase	osa_circ_009819
Alias	Os_ciR4197
Organism	Oryza sativa
Position	chr11: 24186197-24187554 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os11g0620400
Parent gene annotation	Sugar/inositol transporter domain containing protein. (Os11t0620 400-01);Sugar/inositol transporter domain containing protein. (O s11t0620400-02)
Parent gene strand	+
Alternative splicing	Os11g0620400_circ_g.2
Support reads	8/4
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	Os11t0620400-01:2 Os11t0620400-02:2

			
						 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  
						
							GCTATAGTACTTGATGAAATGATGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTT
ATACATTACTTGGATGGGATTTTACAACCGTTTTGGttgaaccagcaagtgacagacctaatgg
acatggaaggtgtgaagttcctgtttttgttggcctgcaactgctggggctttgagcaattgga
gtgataat

									
								

					

						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: 156
Transcript exons: 24186197-24186274,24187477-24187554
TTGAACCAGCAAGTGACAGACCTAATGGACATGGAAGGTGTGAAGTTCCTGTTTTTGTTGGCCT
GCAACTGCTGGGGCTGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTTATACATTA
CTTGGATGGGATTTTACAACCGTTTTGG
Transcript length: 227
Transcript exons: 24186197-24186301,24187433-24187554
TTGAACCAGCAAGTGACAGACCTAATGGACATGGAAGGTGTGAAGTTCCTGTTTTTGTTGGCCT
GCAACTGCTGGGGCTTTGAGCAATTGGAGTGATAATGTTGGGTCCTCAAATTATTTGGAAAGGG
CTATAGTACTTGATGAAATGATGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTTA
TACATTACTTGGATGGGATTTTACAACCGTTTTGG
						
					

						Genomic sequence
						
							TTGAACCAGCAAGTGACAGACCTAATGGACATGGAAGGTGTGAAGTTCCTGTTTTTGTTGGCCT
GCAACTGCTGGGGCTTTGAGCAATTGGAGTGATAATGTTGGGTATGACTCTTTTCTTGAACCTC
TTCAATTAGTTATATGGTTATGATTTGTTCAGTACTGACTGTATTTTACTGAATAAATCTAAAA
CTAGAAAGTTTGTAAGTATTTTCTTTATATCACGCCATATTCTGATTGTAATACTTTTATTATA
TATGATCTCTTTTGTTCTGCCTGTAGTGGTGGGATCACATGCTTTAATTATTTATGGGTAGTAT
TGTTGAATTGTAAAATGAATGTTAATACTTAATGGGTAGCATTCTTGATGCTGATGTAAATTTT
ACTGGTATTTTTAAAATTTTGTGTGCCATTATTATCACAAAGAGTTTTCTTAACTTATTCGCAT
GACAATCAGAATGATCCAGGCTACCAGGGATAAATACGTGAGTGGTAACCGGCTAGTACCATAG
CTACGAGTACTGATATGCTATGTTGTTTCTTGTACAGTTACCCATTCGTATGTGTTATTTGGAG
TTAGAAGTTCAGGGAACCTCATAGAAGATTGAGAGAAGATTTTACATTTGCATTGTTGAATAGT
GATTTTGACTTTTGAGCATAGTCAAACTGGGTAGTAATTAGCGAACAAAATTATTTGATGACTA
TGTCCATACAGTAGTAAAACTTGTTACCGCTAGTAACTGGCCATGAAATGTTGACTGCCAGGGT
ACTGTATTTTTTCCTCAATTGATTTTGAATAGTTGGATTGGACCACTTTGTCATGCATGAAGGT
TACTGTTCATTCATTATTGTTACAAGTTGTGCCAGCAAACTAATGTTTGGTGGCTTGCTCCTTT
CAATTGCCCCACCAGCTTTCCATGTTTTGACAGGTGCAACATTTTTTAGATTATGAGCTGGATG
TAATTTACCTCTTAGTAAATGAAATATTAAATTGCACAAGAATATCTGAAACAGAATAGCAGAT
AATGCATTAGTCACATATGATTTCTATAGTGAACAAGAGGTTCATATGTTGCAATATATCTGTA
ATTGTAACCCATTGAATTAAGACCCCAAACATCAAACTGTGCATCTAAAATGATTGTTTCAGGA
AGCAGACCTTGTTGGTTACCCTAAAATATTTTATGTGATTTTATTTTTAAGTAAATATTTCTCA
CATGTATTCATATATTTCAGGTCCTCAAATTATTTGGAAAGGGCTATAGTACTTGATGAAATGA
TGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTTATACATTACTTGGATGGGATTT
TACAACCGTTTTGG
						
					

			
		

Sequences
Splice junction sequence	GCTATAGTACTTGATGAAATGATGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTT ATACATTACTTGGATGGGATTTTACAACCGTTTTGGttgaaccagcaagtgacagacctaatgg acatggaaggtgtgaagttcctgtttttgttggcctgcaactgctggggctttgagcaattgga gtgataat
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: 156 Transcript exons: 24186197-24186274,24187477-24187554 TTGAACCAGCAAGTGACAGACCTAATGGACATGGAAGGTGTGAAGTTCCTGTTTTTGTTGGCCT GCAACTGCTGGGGCTGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTTATACATTA CTTGGATGGGATTTTACAACCGTTTTGG Transcript length: 227 Transcript exons: 24186197-24186301,24187433-24187554 TTGAACCAGCAAGTGACAGACCTAATGGACATGGAAGGTGTGAAGTTCCTGTTTTTGTTGGCCT GCAACTGCTGGGGCTTTGAGCAATTGGAGTGATAATGTTGGGTCCTCAAATTATTTGGAAAGGG CTATAGTACTTGATGAAATGATGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTTA TACATTACTTGGATGGGATTTTACAACCGTTTTGG
Genomic sequence	TTGAACCAGCAAGTGACAGACCTAATGGACATGGAAGGTGTGAAGTTCCTGTTTTTGTTGGCCT GCAACTGCTGGGGCTTTGAGCAATTGGAGTGATAATGTTGGGTATGACTCTTTTCTTGAACCTC TTCAATTAGTTATATGGTTATGATTTGTTCAGTACTGACTGTATTTTACTGAATAAATCTAAAA CTAGAAAGTTTGTAAGTATTTTCTTTATATCACGCCATATTCTGATTGTAATACTTTTATTATA TATGATCTCTTTTGTTCTGCCTGTAGTGGTGGGATCACATGCTTTAATTATTTATGGGTAGTAT TGTTGAATTGTAAAATGAATGTTAATACTTAATGGGTAGCATTCTTGATGCTGATGTAAATTTT ACTGGTATTTTTAAAATTTTGTGTGCCATTATTATCACAAAGAGTTTTCTTAACTTATTCGCAT GACAATCAGAATGATCCAGGCTACCAGGGATAAATACGTGAGTGGTAACCGGCTAGTACCATAG CTACGAGTACTGATATGCTATGTTGTTTCTTGTACAGTTACCCATTCGTATGTGTTATTTGGAG TTAGAAGTTCAGGGAACCTCATAGAAGATTGAGAGAAGATTTTACATTTGCATTGTTGAATAGT GATTTTGACTTTTGAGCATAGTCAAACTGGGTAGTAATTAGCGAACAAAATTATTTGATGACTA TGTCCATACAGTAGTAAAACTTGTTACCGCTAGTAACTGGCCATGAAATGTTGACTGCCAGGGT ACTGTATTTTTTCCTCAATTGATTTTGAATAGTTGGATTGGACCACTTTGTCATGCATGAAGGT TACTGTTCATTCATTATTGTTACAAGTTGTGCCAGCAAACTAATGTTTGGTGGCTTGCTCCTTT CAATTGCCCCACCAGCTTTCCATGTTTTGACAGGTGCAACATTTTTTAGATTATGAGCTGGATG TAATTTACCTCTTAGTAAATGAAATATTAAATTGCACAAGAATATCTGAAACAGAATAGCAGAT AATGCATTAGTCACATATGATTTCTATAGTGAACAAGAGGTTCATATGTTGCAATATATCTGTA ATTGTAACCCATTGAATTAAGACCCCAAACATCAAACTGTGCATCTAAAATGATTGTTTCAGGA AGCAGACCTTGTTGGTTACCCTAAAATATTTTATGTGATTTTATTTTTAAGTAAATATTTCTCA CATGTATTCATATATTTCAGGTCCTCAAATTATTTGGAAAGGGCTATAGTACTTGATGAAATGA TGAAGTCAACGGTATTTTCTGCGGTTGCTGTTTCTATTGGTTATACATTACTTGGATGGGATTT TACAACCGTTTTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.217479357

Conservation Information
Conserved circRNAs	NA
PMCS	0.217479357

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24187474-24186276(+)
24186230-24187526(-)
						
						Potential amino acid sequence
						
							MMKSTVFSAVAVSIGYTLLGWDFTTVLVEPASDRPNGHGRCEVPVFVGLQLLGL*(+)
MSIRSVTCWFNQNGCKIPSK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24187474-24186276(+) 24186230-24187526(-)
Potential amino acid sequence	MMKSTVFSAVAVSIGYTLLGWDFTTVLVEPASDRPNGHGRCEVPVFVGLQLLGL(+) MSIRSVTCWFNQNGCKIPSK(-)
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 Os11g0620400_circ_g.1

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