Plant Circular RNA Database

Detail information of Os11g0562100_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os11g0562100_circ_g.4
					
						ID in PlantcircBase
						osa_circ_009617
					
						Alias
						Os_ciR1258
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 20947082-20956148  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os11g0562100						
					
						Parent gene annotation
						
							Squalene cyclase domain containing protein. (Os11t0562100-01);Si
milar to cycloartenol synthase. (Os11t0562100-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0562100_circ_g.1 Os11g0562100_circ_g.2 Os11g0562100_circ_g.3 Os11g0562100_circ_g.5 Os11g0562100_circ_g.6 Os11g0562100_circ_g.7 Os11g0562100_circ_g.8 Os11g0562100_circ_g.9 Os11g0562100_circ_g.10 Os11g0562100_circ_g.11 						
					
						Support reads
						12/2
					
						Tissues
						root/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
						Os11t0562100-02:11
Os11t0562100-01:11

General Information
CircRNA Name	Os11g0562100_circ_g.4
ID in PlantcircBase	osa_circ_009617
Alias	Os_ciR1258
Organism	Oryza sativa
Position	chr11: 20947082-20956148 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os11g0562100
Parent gene annotation	Squalene cyclase domain containing protein. (Os11t0562100-01);Si milar to cycloartenol synthase. (Os11t0562100-02)
Parent gene strand	+
Alternative splicing	Os11g0562100_circ_g.1 Os11g0562100_circ_g.2 Os11g0562100_circ_g.3 Os11g0562100_circ_g.5 Os11g0562100_circ_g.6 Os11g0562100_circ_g.7 Os11g0562100_circ_g.8 Os11g0562100_circ_g.9 Os11g0562100_circ_g.10 Os11g0562100_circ_g.11
Support reads	12/2
Tissues	root/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	Os11t0562100-02:11 Os11t0562100-01:11

			
						 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  
						
							ACCATTTGGATGTCAGATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATC
AATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgaggatttggtctgcccgcgcacgctgc
tgcagaatgtggtgtggacttcgctctacaagtgggtggagccggtgctaggcagcaggccgat
gaacaagc

									
								

					

						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: 1239
Transcript exons: 20947082-20947270,20948687-20948800,20951953-20952075,20
952164-20952286,20952764-20952862,20954371-20954427,2095
4721-20954767,20954881-20955024,20955125-20955302,209559
03-20955983,20956065-20956148
GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG
TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT
GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGCT
CTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAA
GGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAGATATATGATGGTTGCCA
GAGCTGGGAAACAGCATTTATAATTCAAGCGTTTTGTGCTACTGATCTTGTAAATGAGTATGGT
TCAACTGTTAGGAGAGCCCACGAGTTCATGAAAAATTCACAGATTATGAGGAATCATCCTGGTG
ACCAAAGTTACTGGCATCGCCATAGATCAAAGGGTTCATGGACTCTTTCGTCAGCAGACAATGG
ATGGGCTGTGTCTGACACTACAGCAGAAGCGCTGAAGGCTGTACTGTTACTGGAAAAGATCTCT
AGCAACGTGGTCGGGGATCCAATTGAAATAGAAAGGCTGCATGATGCTGTTGATTGCCTCCTAT
CTTTCGTGAACAAAGATGGTACCCTTTCTACATATGAATGTAAAAGAACTTATACTTGGATAGA
GGTTCTCAGTCCTTGTGAGAGTTTTCCAAACATAGTGGTTGATTATCCATTTCCAGAATGCACC
TCCTCTGTGCTTCAAGCTCTGGTGCTGTTCAAACAACTACACCCTAGTTACCGTATTAAAGAGA
TAGAAAAATGTGTCAGAAACGCAGCGATGTTTATTGAGAGCACACAAGGCGAAGATGGTTCATG
GCTAGGCACTTGGGGTGTGTGTTTCACCTATGGGGCCTTTCTTTCAGTAAAAGGGTTAATTGCT
GCTGGAAGAACATATGAGAATAGTTCTTCCATCAGGAAAGCATGCGACTTTATATTATCAAAGC
AGCTCGATACTGGTGGGTGGGGAGAAAGTTATGTCTCTAATATTACTAAGGTTTACGTAAACAT
TAAAGATGATCAAGCTCATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGA
CAGATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGG
AAACAGGAGAGTTCCCCCAACAA
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	ACCATTTGGATGTCAGATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATC AATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgaggatttggtctgcccgcgcacgctgc tgcagaatgtggtgtggacttcgctctacaagtgggtggagccggtgctaggcagcaggccgat gaacaagc
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: 1239 Transcript exons: 20947082-20947270,20948687-20948800,20951953-20952075,20 952164-20952286,20952764-20952862,20954371-20954427,2095 4721-20954767,20954881-20955024,20955125-20955302,209559 03-20955983,20956065-20956148 GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGCT CTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAA GGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAGATATATGATGGTTGCCA GAGCTGGGAAACAGCATTTATAATTCAAGCGTTTTGTGCTACTGATCTTGTAAATGAGTATGGT TCAACTGTTAGGAGAGCCCACGAGTTCATGAAAAATTCACAGATTATGAGGAATCATCCTGGTG ACCAAAGTTACTGGCATCGCCATAGATCAAAGGGTTCATGGACTCTTTCGTCAGCAGACAATGG ATGGGCTGTGTCTGACACTACAGCAGAAGCGCTGAAGGCTGTACTGTTACTGGAAAAGATCTCT AGCAACGTGGTCGGGGATCCAATTGAAATAGAAAGGCTGCATGATGCTGTTGATTGCCTCCTAT CTTTCGTGAACAAAGATGGTACCCTTTCTACATATGAATGTAAAAGAACTTATACTTGGATAGA GGTTCTCAGTCCTTGTGAGAGTTTTCCAAACATAGTGGTTGATTATCCATTTCCAGAATGCACC TCCTCTGTGCTTCAAGCTCTGGTGCTGTTCAAACAACTACACCCTAGTTACCGTATTAAAGAGA TAGAAAAATGTGTCAGAAACGCAGCGATGTTTATTGAGAGCACACAAGGCGAAGATGGTTCATG GCTAGGCACTTGGGGTGTGTGTTTCACCTATGGGGCCTTTCTTTCAGTAAAAGGGTTAATTGCT GCTGGAAGAACATATGAGAATAGTTCTTCCATCAGGAAAGCATGCGACTTTATATTATCAAAGC AGCTCGATACTGGTGGGTGGGGAGAAAGTTATGTCTCTAATATTACTAAGGTTTACGTAAACAT TAAAGATGATCAAGCTCATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGA CAGATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGG AAACAGGAGAGTTCCCCCAACAA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003189* 						
					
						PMCS
						0.324462456

Conservation Information
Conserved circRNAs	osi_circ_003189*
PMCS	0.324462456

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							20947173-20956145(+)
						
					

						Potential amino acid sequence
						
							MNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLS
EDGMKAQIYDGCQSWETAFIIQAFCATDLVNEYGSTVRRAHEFMKNSQIMRNHPGDQSYWHRHR
SKGSWTLSSADNGWAVSDTTAEALKAVLLLEKISSNVVGDPIEIERLHDAVDCLLSFVNKDGTL
STYECKRTYTWIEVLSPCESFPNIVVDYPFPECTSSVLQALVLFKQLHPSYRIKEIEKCVRNAA
MFIESTQGEDGSWLGTWGVCFTYGAFLSVKGLIAAGRTYENSSSIRKACDFILSKQLDTGGWGE
SYVSNITKVYVNIKDDQAHAVNTAWAMLALICAGQMERDPAPLHRAAKELINMQLETGEFPQQE
DLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLCLCPVNKAL
NMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKAQIYDGCQSWETAFIIQAFCATDLVNEYGS
TVRRAHEFMKNSQIMRNHPGDQSYWHRHRSKGSWTLSSADNGWAVSDTTAEALKAVLLLEKISS
NVVGDPIEIERLHDAVDCLLSFVNKDGTLSTYECKRTYTWIEVLSPCESFPNIVVDYPFPECTS
SVLQALVLFKQLHPSYRIKEIEKCVRNAAMFIESTQGEDGSWLGTWGVCFTYGAFLSVKGLIAA
GRTYENSSSIRKACDFILSKQLDTGGWGESYVSNITKVYVNIKDDQAHAVNTAWAMLALICAGQ
MERDPAPLHRAAKELINMQLETGEFPQQEDLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRE
RALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKA
QIYDGCQSWETAFIIQAFCATDLVNEYGSTVRRAHEFMKNSQIMRNHPGDQSYWHRHRSKGSWT
LSSADNGWAVSDTTAEALKAVLLLEKISSNVVGDPIEIERLHDAVDCLLSFVNKDGTLSTYECK
RTYTWIEVLSPCESFPNIVVDYPFPECTSSVLQALVLFKQLHPSYRIKEIEKCVRNAAMFIEST
QGEDGSWLGTWGVCFTYGAFLSVKGLIAAGRTYENSSSIRKACDFILSKQLDTGGWGESYVSNI
TKVYVNIKDDQAHAVNTAWAMLALICAGQMERDPAPLHRAAKELINMQLETGEFPQQEDLVCPR
TLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCW
VEDPNSDSFKRHLARIPDFLWLSEDGMKAQIYDGCQSWETAFIIQAFCATDLVNEYGSTVRRAH
EFMKNSQIMRNHPGDQSYWHRHRSKGSWTLSSADNGWAVSDTTAEALKAVLLLEKISSNVVGDP
IEIERLHDAVDCLLSFVNKDGTLSTYECKRTYTWIEVLSPCESFPNIVVDYPFPECTSSVLQAL
VLFKQLHPSYRIKEIEKCVRNAAMFIESTQGEDGSWLGTWGVCFTYGAFLSVKGLIAAGRTYEN
SSSIRKACDFILSKQLDTGGWGESYVSNITKVYVNIKDDQAHAVNTAWAMLALICAGQMERDPA
PLHRAAKELINMQLETGEFPQQ(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						responsive to Pi-starvation
					

			
		

Functional Information
Coding potential	Y
Potential coding position	20947173-20956145(+)
Potential amino acid sequence	MNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLS EDGMKAQIYDGCQSWETAFIIQAFCATDLVNEYGSTVRRAHEFMKNSQIMRNHPGDQSYWHRHR SKGSWTLSSADNGWAVSDTTAEALKAVLLLEKISSNVVGDPIEIERLHDAVDCLLSFVNKDGTL STYECKRTYTWIEVLSPCESFPNIVVDYPFPECTSSVLQALVLFKQLHPSYRIKEIEKCVRNAA MFIESTQGEDGSWLGTWGVCFTYGAFLSVKGLIAAGRTYENSSSIRKACDFILSKQLDTGGWGE SYVSNITKVYVNIKDDQAHAVNTAWAMLALICAGQMERDPAPLHRAAKELINMQLETGEFPQQE DLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLCLCPVNKAL NMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKAQIYDGCQSWETAFIIQAFCATDLVNEYGS TVRRAHEFMKNSQIMRNHPGDQSYWHRHRSKGSWTLSSADNGWAVSDTTAEALKAVLLLEKISS NVVGDPIEIERLHDAVDCLLSFVNKDGTLSTYECKRTYTWIEVLSPCESFPNIVVDYPFPECTS SVLQALVLFKQLHPSYRIKEIEKCVRNAAMFIESTQGEDGSWLGTWGVCFTYGAFLSVKGLIAA GRTYENSSSIRKACDFILSKQLDTGGWGESYVSNITKVYVNIKDDQAHAVNTAWAMLALICAGQ MERDPAPLHRAAKELINMQLETGEFPQQEDLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRE RALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKA QIYDGCQSWETAFIIQAFCATDLVNEYGSTVRRAHEFMKNSQIMRNHPGDQSYWHRHRSKGSWT LSSADNGWAVSDTTAEALKAVLLLEKISSNVVGDPIEIERLHDAVDCLLSFVNKDGTLSTYECK RTYTWIEVLSPCESFPNIVVDYPFPECTSSVLQALVLFKQLHPSYRIKEIEKCVRNAAMFIEST QGEDGSWLGTWGVCFTYGAFLSVKGLIAAGRTYENSSSIRKACDFILSKQLDTGGWGESYVSNI TKVYVNIKDDQAHAVNTAWAMLALICAGQMERDPAPLHRAAKELINMQLETGEFPQQEDLVCPR TLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCW VEDPNSDSFKRHLARIPDFLWLSEDGMKAQIYDGCQSWETAFIIQAFCATDLVNEYGSTVRRAH EFMKNSQIMRNHPGDQSYWHRHRSKGSWTLSSADNGWAVSDTTAEALKAVLLLEKISSNVVGDP IEIERLHDAVDCLLSFVNKDGTLSTYECKRTYTWIEVLSPCESFPNIVVDYPFPECTSSVLQAL VLFKQLHPSYRIKEIEKCVRNAAMFIESTQGEDGSWLGTWGVCFTYGAFLSVKGLIAAGRTYEN SSSIRKACDFILSKQLDTGGWGESYVSNITKVYVNIKDDQAHAVNTAWAMLALICAGQMERDPA PLHRAAKELINMQLETGEFPQQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to Pi-starvation

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os11g0562100_circ_g.4

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