Plant Circular RNA Database

Detail information of Os09g0134500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0134500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_038508
					
						Alias
						Os_ciR11969
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 2608345-2609775  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os09g0134500						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os09t0134500-01);Trithorax group p
rotein, Regulation of flowering time (Os09t0134500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/1
					
						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
						Os09t0134500-01:8
Os09t0134500-02:8

General Information
CircRNA Name	Os09g0134500_circ_g.2
ID in PlantcircBase	osa_circ_038508
Alias	Os_ciR11969
Organism	Oryza sativa
Position	chr9: 2608345-2609775 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os09g0134500
Parent gene annotation	Hypothetical conserved gene. (Os09t0134500-01);Trithorax group p rotein, Regulation of flowering time (Os09t0134500-02)
Parent gene strand	-
Alternative splicing	NA
Support reads	2/1
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	Os09t0134500-01:8 Os09t0134500-02:8

			
						 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  
						
							AGTCTAGATCTTTCCAATTTACATGAACAGCTCTATACCCACGAAAGGTGTCTCCAGCATTTTC
AAAATACTTTAAGCATGACCTTGCATTGGGTAACTCcagtccttgcacaaccggatggtggaac
tgcatctgtctgaactaccacagcaggcttagcaaggttactttcaagagatggacgttcagtc
gatggttg

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CAGTCCTTGCACAACCGGATGGTGGAACTGCATCTGTCTGAACTACCACAGCAGGCTTAGCAAG
GTTACTTTCAAGAGATGGACGTTCAGTCGATGGTTGTCTGTGCTTCTTGCAGTATGAAAGTAGA
CGAATACATGGGTCCTCATCCTCATCAAGTAACATGAGGTGGATTTTGTCATCATCTTCAAGCT
AAAATTAACAAAATGGTTGCACATGAATACAAATACTTAATTAGGAAACAGAATAAGTTATCAA
GTACCCCCTCCGTCCCAAAATAGCACCCCTCTAGTTCAAATTTGAACTAGAAGAGCGCACTTAT
TTTGGGAGGGAGTAGGAGTAAATAATATGCCACATCATAAAGATCAAGAGGATACCTCAACACA
AAGATCAGCAGCACGTGCACAAAGAGGGTGATATGCAACACGACAGGTAGGATGAGAACACTAT
ATTGAGGAAGGAAAAGTATCATGATCTCTTTCAAGGAAAGAAAAGGAAATGAGCAAATAATATG
TTATGATGACCCAATCACAGGTTTAAAAACGGTTGCAAAAGTACCTGTATGCAAGCTCCATAAG
CAACTCCGCAAATGCTGCATAGAAGTTTCCAGCGGTCCTGCATAGACAACATCAGTGACACTCT
GACAAAAATAGGATCACACCAAAATCAACAGCAGAAAGGAAAAATGAACCTTGTTGATTCTGCT
CAATCCATCAATCGGTTCCATTCTCTTCACATCTTTTAAGCAAGTTTCTGTACCAAAGTTAGGA
TTAATATAATTAAAAGCATGTCCTGGCAAAACATCACTAAGATATGTGGATCAATAAAAGTCAT
TATACCAGGAATCCATATAGCACATGCAAGATGAGCCCAACGACCATCTGTTGTTGGTTTCATT
GCGCCCCCTAAATAAAGGGAATCATCACATAAGTTTATAGCCTTGTTATGCAAGAAACTGCAAC
ATGATTCTATACCTGTTACTGGACAAAGACAGCATCGTGGAGAAACACGAGGCGCCTCAGGTCG
ACACAGGTTGCAAAGCCAAAGGACTCCATTCAATGGTTCGAGTTCACCATAGCATCTAGCATGT
ACCTGTATCATGTTTAACACTTATGTAAACAACTCCATATTTAACATCTTCAAGGAGCTAGTCA
ATGAAAGCATGCCTACCATCATACGGCACTTATCACATTGCAAGAACAAATTGTCTTCGTATTC
CTGCAATTCAAAAGAGTATAAATAATAATCCATTTGGTTATTCACCCTTTGAATAGCTTATGTA
TGAGAACAGAGTAAAGATCATTTACCTCATCCATATCACAAACACTACAATAGTCTAGATCTTT
CCAATTTACATGAACAGCTCTATACCCACGAAAGGTGTCTCCAGCATTTTCAAAATACTTTAAG
CATGACCTTGCATTGGGTAACTC

Sequences
Splice junction sequence	AGTCTAGATCTTTCCAATTTACATGAACAGCTCTATACCCACGAAAGGTGTCTCCAGCATTTTC AAAATACTTTAAGCATGACCTTGCATTGGGTAACTCcagtccttgcacaaccggatggtggaac tgcatctgtctgaactaccacagcaggcttagcaaggttactttcaagagatggacgttcagtc gatggttg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CAGTCCTTGCACAACCGGATGGTGGAACTGCATCTGTCTGAACTACCACAGCAGGCTTAGCAAG GTTACTTTCAAGAGATGGACGTTCAGTCGATGGTTGTCTGTGCTTCTTGCAGTATGAAAGTAGA CGAATACATGGGTCCTCATCCTCATCAAGTAACATGAGGTGGATTTTGTCATCATCTTCAAGCT AAAATTAACAAAATGGTTGCACATGAATACAAATACTTAATTAGGAAACAGAATAAGTTATCAA GTACCCCCTCCGTCCCAAAATAGCACCCCTCTAGTTCAAATTTGAACTAGAAGAGCGCACTTAT TTTGGGAGGGAGTAGGAGTAAATAATATGCCACATCATAAAGATCAAGAGGATACCTCAACACA AAGATCAGCAGCACGTGCACAAAGAGGGTGATATGCAACACGACAGGTAGGATGAGAACACTAT ATTGAGGAAGGAAAAGTATCATGATCTCTTTCAAGGAAAGAAAAGGAAATGAGCAAATAATATG TTATGATGACCCAATCACAGGTTTAAAAACGGTTGCAAAAGTACCTGTATGCAAGCTCCATAAG CAACTCCGCAAATGCTGCATAGAAGTTTCCAGCGGTCCTGCATAGACAACATCAGTGACACTCT GACAAAAATAGGATCACACCAAAATCAACAGCAGAAAGGAAAAATGAACCTTGTTGATTCTGCT CAATCCATCAATCGGTTCCATTCTCTTCACATCTTTTAAGCAAGTTTCTGTACCAAAGTTAGGA TTAATATAATTAAAAGCATGTCCTGGCAAAACATCACTAAGATATGTGGATCAATAAAAGTCAT TATACCAGGAATCCATATAGCACATGCAAGATGAGCCCAACGACCATCTGTTGTTGGTTTCATT GCGCCCCCTAAATAAAGGGAATCATCACATAAGTTTATAGCCTTGTTATGCAAGAAACTGCAAC ATGATTCTATACCTGTTACTGGACAAAGACAGCATCGTGGAGAAACACGAGGCGCCTCAGGTCG ACACAGGTTGCAAAGCCAAAGGACTCCATTCAATGGTTCGAGTTCACCATAGCATCTAGCATGT ACCTGTATCATGTTTAACACTTATGTAAACAACTCCATATTTAACATCTTCAAGGAGCTAGTCA ATGAAAGCATGCCTACCATCATACGGCACTTATCACATTGCAAGAACAAATTGTCTTCGTATTC CTGCAATTCAAAAGAGTATAAATAATAATCCATTTGGTTATTCACCCTTTGAATAGCTTATGTA TGAGAACAGAGTAAAGATCATTTACCTCATCCATATCACAAACACTACAATAGTCTAGATCTTT CCAATTTACATGAACAGCTCTATACCCACGAAAGGTGTCTCCAGCATTTTCAAAATACTTTAAG CATGACCTTGCATTGGGTAACTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.194017424

Conservation Information
Conserved circRNAs	NA
PMCS	0.194017424

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2609755-2608382(+)
2609660-2609740(-)
2608379-2609740(-)
						
						Potential amino acid sequence
						
							MTLHWVTPVLAQPDGGTASV*(+)
MDEEYEDNLFLQCDKCRMMVHARCYGELEPLNGVLWLCNLCRPEAPRVSPRCCLCPVTGGAMKP
TTDGRWAHLACAIWIPETCLKDVKRMEPIDGLSRINKDRWKLLCSICGVAYGACIQCSHPTCRV
AYHPLCARAADLCVELEDDDKIHLMLLDEDEDPCIRLLSYCKKHRQPSTERPSLESNLAKPAVV
VQTDAVPPSGCARTGVTQCKVMLKVF*(-)
MQFHHPVVQGLELPNARSCLKYFENAGDTFRGYRAVHVNWKDLDYCSVCDMDEEYEDNLFLQCD
KCRMMVHARCYGELEPLNGVLWLCNLCRPEAPRVSPRCCLCPVTGGAMKPTTDGRWAHLACAIW
IPETCLKDVKRMEPIDGLSRINKDRWKLLCSICGVAYGACIQCSHPTCRVAYHPLCARAADLCV
ELEDDDKIHLMLLDEDEDPCIRLLSYCKKHRQPSTERPSLESNLAKPAVVVQTDAVPPSGCART
GVTQCKVMLKVF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2609755-2608382(+) 2609660-2609740(-) 2608379-2609740(-)
Potential amino acid sequence	MTLHWVTPVLAQPDGGTASV(+) MDEEYEDNLFLQCDKCRMMVHARCYGELEPLNGVLWLCNLCRPEAPRVSPRCCLCPVTGGAMKP TTDGRWAHLACAIWIPETCLKDVKRMEPIDGLSRINKDRWKLLCSICGVAYGACIQCSHPTCRV AYHPLCARAADLCVELEDDDKIHLMLLDEDEDPCIRLLSYCKKHRQPSTERPSLESNLAKPAVV VQTDAVPPSGCARTGVTQCKVMLKVF(-) MQFHHPVVQGLELPNARSCLKYFENAGDTFRGYRAVHVNWKDLDYCSVCDMDEEYEDNLFLQCD KCRMMVHARCYGELEPLNGVLWLCNLCRPEAPRVSPRCCLCPVTGGAMKPTTDGRWAHLACAIW IPETCLKDVKRMEPIDGLSRINKDRWKLLCSICGVAYGACIQCSHPTCRVAYHPLCARAADLCV ELEDDDKIHLMLLDEDEDPCIRLLSYCKKHRQPSTERPSLESNLAKPAVVVQTDAVPPSGCART GVTQCKVMLKVF*(-)
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 Os09g0134500_circ_g.2

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