Plant Circular RNA Database

Detail information of Os04g0659500_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0659500_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025783
					
						Alias
						Os_ciR2072
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 33651056-33652514  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0659500						
					
						Parent gene annotation
						
							Protein phosphatase 2C domain containing protein. (Os04t0659500-
01);Similar to OSIGBa0132E09-OSIGBa0108L24.16 protein. (Os04t065
9500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0659500_circ_g.2 Os04g0659500_circ_g.3 						
					
						Support reads
						9/4
					
						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  
						
							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
						Os04t0659500-02:5
Os04t0659500-01:5

General Information
CircRNA Name	Os04g0659500_circ_g.1
ID in PlantcircBase	osa_circ_025783
Alias	Os_ciR2072
Organism	Oryza sativa
Position	chr4: 33651056-33652514 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0659500
Parent gene annotation	Protein phosphatase 2C domain containing protein. (Os04t0659500- 01);Similar to OSIGBa0132E09-OSIGBa0108L24.16 protein. (Os04t065 9500-02)
Parent gene strand	-
Alternative splicing	Os04g0659500_circ_g.2 Os04g0659500_circ_g.3
Support reads	9/4
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	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	Os04t0659500-02:5 Os04t0659500-01:5

			
						 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  
						
							CTGCCCATCAACAGAGTCAATTCTTGTCTCGTAAAAGTCTTCCATGGAAGCCCTTTTACCAGGG
GAGCTCGCATACCCATAGCTAAACTTACCATTCTGGccgaatctcaggatccacaactacatac
tgctttaagagtttgtcaccaaaagcgcgagaaacagcaagcacaccaccaacacgccatgttc
ctaaggaa

						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
						
							CCGAATCTCAGGATCCACAACTACATACTGCTTTAAGAGTTTGTCACCAAAAGCGCGAGAAACA
GCAAGCACACCACCAACACGCCATGTTCCTAAGGAACAAAATACCATCATTAGGAACACGATCA
TAGTCCATTCATATACAAAATAAGATAATGTAGTGCTTAGCACCTGCCCACATTACAAAACCTC
CAGCATCTTCGATACGTTGTCGCTCATCTGTCTGATCAGGCTTGTGATCTTTTGAAACAGCTAT
AGCTGCAAAAAACCAGCAGAGCTTCTATGTGAAGAACTGATAAATTATCACAGATAACCTACAG
ATTATTTCTCATGGCACTCATTTCATCACCAACAAATCTTGATTCTCATGCCTGGTACAATGCA
GATGCTCAGTGGTAAATACAACATTCTAACAAAACAAGCAAAAATATTCGTACCTTAAGAGAGG
TCTCTATTAATAATAGAATATGCCAAACATAATCGGCTCTCTTGAATTTTTAAGCATACCATAA
AAAAGAAAAAAAATAATGTGTCATGCTATATAAAGTCAGAAAGTATCAAGTAAATGCAACCAGG
AAGCTGAAGAGATGGTACAGTGAACTGTCAATTACCATTTCCCCCCCTGCATATGATAGCCCTA
GAGTCTCCAACGTTTGCAACAAAGAGACGGTCACCAACAAGGACAGCGGTTGATGCAGTTGATC
CACACTGGTTTTGACTGCTGTCAGATTCTAAGAATTCACTGTCGGTACTTTTATAAGCATCATC
TACAGCAAACAATATCACGTGGTAGTTCTGTCAATTCTATACACAAAACTCAACATCTAGTGAA
TTATGGAAAGAGAACAAACCAATACCTATTGCCACTTTGGTGTCACTGATGAACTTTGGATGCC
TTAGAAGATGACTGAAGAGATTCTGTTTAACATACTCAGCTACTTTAGCACCACCATGACCTAT
AAAATGAACTGTATGTTTAGCATTTATTTTTCCTAAAATAAGCTCAAGAGCTTGGTATATCCAC
ACTTCTAGTTCAATTTAAAGCATTGTGCCCTAGTATGAGTAATCTTTAAAACTTTCTCCATGGA
CTTCTCACCGTCATACTAGCTCTAACTGCGGAAATAAGAAATGTTACAAGGCAAATGAATTATT
TTGAGCTTTTTTATACTATACAAGATTAGCAAAGGAAACATAAATGGTATGTTCTTTTGGTACA
AAAGAGAAAGGTCTAAAACTTGGAAGAGTGTAATCTTAGAAATGTTCCTTTCTAAAATGATAAA
GAATTATCAATGGGTAGAGATTATGCACGAATGTGACAAATTCATACATACCATCAAAAACTCC
AAAAAGACCAATAATCTGCCCATCAACAGAGTCAATTCTTGTCTCGTAAAAGTCTTCCATGGAA
GCCCTTTTACCAGGGGAGCTCGCATACCCATAGCTAAACTTACCATTCTGG

Sequences
Splice junction sequence	CTGCCCATCAACAGAGTCAATTCTTGTCTCGTAAAAGTCTTCCATGGAAGCCCTTTTACCAGGG GAGCTCGCATACCCATAGCTAAACTTACCATTCTGGccgaatctcaggatccacaactacatac tgctttaagagtttgtcaccaaaagcgcgagaaacagcaagcacaccaccaacacgccatgttc ctaaggaa
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	CCGAATCTCAGGATCCACAACTACATACTGCTTTAAGAGTTTGTCACCAAAAGCGCGAGAAACA GCAAGCACACCACCAACACGCCATGTTCCTAAGGAACAAAATACCATCATTAGGAACACGATCA TAGTCCATTCATATACAAAATAAGATAATGTAGTGCTTAGCACCTGCCCACATTACAAAACCTC CAGCATCTTCGATACGTTGTCGCTCATCTGTCTGATCAGGCTTGTGATCTTTTGAAACAGCTAT AGCTGCAAAAAACCAGCAGAGCTTCTATGTGAAGAACTGATAAATTATCACAGATAACCTACAG ATTATTTCTCATGGCACTCATTTCATCACCAACAAATCTTGATTCTCATGCCTGGTACAATGCA GATGCTCAGTGGTAAATACAACATTCTAACAAAACAAGCAAAAATATTCGTACCTTAAGAGAGG TCTCTATTAATAATAGAATATGCCAAACATAATCGGCTCTCTTGAATTTTTAAGCATACCATAA AAAAGAAAAAAAATAATGTGTCATGCTATATAAAGTCAGAAAGTATCAAGTAAATGCAACCAGG AAGCTGAAGAGATGGTACAGTGAACTGTCAATTACCATTTCCCCCCCTGCATATGATAGCCCTA GAGTCTCCAACGTTTGCAACAAAGAGACGGTCACCAACAAGGACAGCGGTTGATGCAGTTGATC CACACTGGTTTTGACTGCTGTCAGATTCTAAGAATTCACTGTCGGTACTTTTATAAGCATCATC TACAGCAAACAATATCACGTGGTAGTTCTGTCAATTCTATACACAAAACTCAACATCTAGTGAA TTATGGAAAGAGAACAAACCAATACCTATTGCCACTTTGGTGTCACTGATGAACTTTGGATGCC TTAGAAGATGACTGAAGAGATTCTGTTTAACATACTCAGCTACTTTAGCACCACCATGACCTAT AAAATGAACTGTATGTTTAGCATTTATTTTTCCTAAAATAAGCTCAAGAGCTTGGTATATCCAC ACTTCTAGTTCAATTTAAAGCATTGTGCCCTAGTATGAGTAATCTTTAAAACTTTCTCCATGGA CTTCTCACCGTCATACTAGCTCTAACTGCGGAAATAAGAAATGTTACAAGGCAAATGAATTATT TTGAGCTTTTTTATACTATACAAGATTAGCAAAGGAAACATAAATGGTATGTTCTTTTGGTACA AAAGAGAAAGGTCTAAAACTTGGAAGAGTGTAATCTTAGAAATGTTCCTTTCTAAAATGATAAA GAATTATCAATGGGTAGAGATTATGCACGAATGTGACAAATTCATACATACCATCAAAAACTCC AAAAAGACCAATAATCTGCCCATCAACAGAGTCAATTCTTGTCTCGTAAAAGTCTTCCATGGAA GCCCTTTTACCAGGGGAGCTCGCATACCCATAGCTAAACTTACCATTCTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.17686188

Conservation Information
Conserved circRNAs	NA
PMCS	0.17686188

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							33651960-33651310(+)
33651238-33651998(-)
						
						Potential amino acid sequence
						
							MTEEILFNILSYFSTTMTILAESQDPQLHTALRVCHQKREKQQAHHQHAMFLPTLQNLQHLRYV
VAHLSDQACDLLKQL*(+)
MWAGTWRVGGVLAVSRAFGDKLLKQYVVVDPEIRPEWSWWC*(-)
						
						Sponge-miRNAs
						
							osa-miR1435 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	33651960-33651310(+) 33651238-33651998(-)
Potential amino acid sequence	MTEEILFNILSYFSTTMTILAESQDPQLHTALRVCHQKREKQQAHHQHAMFLPTLQNLQHLRYV VAHLSDQACDLLKQL(+) MWAGTWRVGGVLAVSRAFGDKLLKQYVVVDPEIRPEWSWWC(-)
Sponge-miRNAs	osa-miR1435
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0659500_circ_g.1

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