Plant Circular RNA Database

Detail information of Os12g0612400_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0612400_circ_g.4
					
						ID in PlantcircBase
						osa_circ_012276
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 25903688-25905301  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0612400						
					
						Parent gene annotation
						
							Similar to S-locus protein 5 (Fragment). (Os12t0612400-01);Simil
ar to YUP8H12R.35 protein. (Os12t0612400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os12g0612400_circ_g.3 Os12g0612400_circ_g.5 Os12g0612400_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						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
						Os12t0612400-02:6
Os12t0612400-01:6

General Information
CircRNA Name	Os12g0612400_circ_g.4
ID in PlantcircBase	osa_circ_012276
Alias	NA
Organism	Oryza sativa
Position	chr12: 25903688-25905301 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0612400
Parent gene annotation	Similar to S-locus protein 5 (Fragment). (Os12t0612400-01);Simil ar to YUP8H12R.35 protein. (Os12t0612400-02)
Parent gene strand	-
Alternative splicing	Os12g0612400_circ_g.3 Os12g0612400_circ_g.5 Os12g0612400_circ_g.6
Support reads	2
Tissues	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	Os12t0612400-02:6 Os12t0612400-01:6

			
						 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  
						
							AGAAATAGCCATACATCCACATAATCAATATTCCAAATAATCCTACAATGAAAAGACCAGGCGT
ATAGCCCATGTAATGAATGACTGCCCCAGCAGCTCCcttgaaggatgacgaaaatttattttcc
acccatccatctccatccttagctggatgaaaatcagagcaatcctacagtacatggttcccac
aaaattag

									
								

					

						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
						
							CTTGAAGGATGACGAAAATTTATTTTCCACCCATCCATCTCCATCCTTAGCTGGATGAAAATCA
GAGCAATCCTACAGTACATGGTTCCCACAAAATTAGCTGTAAGAACACTCTCGATTAAAAGTAC
CTGAAAAAAAAATTCTGGCCTCCAAACCTGACACCATCTTGCTTTTGCTTTGCTTTTCTTGGTA
CATATCCACAGATGAAAATTACCACATTTTGTGCACTGTATACGCCTGGACTCTTCGGAGAGAA
ACTCTACCCCAGTCTGCAAGATGAGTTTATCAAATTACAAATGGGCCCCATAAAGGAAAACAGC
AAGTAGGTCAGTAGGTCAAGGACATGAGAGCATGAATAAACTGCATTCGTATGCTTGGATAATT
GATAAGATATGTTAAAGAAATAATCCAACCATGTGGATTCTAAATTTGTGAAAACTAGAACCCA
CCTGTTGAGAGACAACACGTGATCTCTGAGTCATTTTACGTGATTCTTCTTTCCTCAGTTGGTC
GTCGTAAGTGTTTTTCTTTGTGAAATCTGAGAGTACCTGCAGCATAACTACAATGATTACCCTT
TATCCAGGTATAGAAGCCATGGTTGGTATCAAGAGCAGATATTCAACCAGATTTAACTGTAATA
TAATCAAGGAAGAGAAAAGACATAAACTTCCATTGTAGTTTACCTCATAAGCTGACTGAAGCTT
TTTGAATGATTCACAGGCCAGTGGATTTCCCATATTTTTATCAGGATGTACAAGCAGGACCTAG
ACAAATAAAGCATACGTACCATGAAAATGAAGTAATTGTAACATGAATTTCTCATTTTCCCTTG
TATAGAAGGCCGTGGTTTATTACCATTCTGTGGTACTCCTTTTTCAGAATCTTTTGATCAATAC
TTCTATTCCGAGGAATACCCAAAACTTCATAATGGGTCAAACCATCCATGATCCTCTTCATCTC
ATCCAATGAAACAGAATCCGATTTCACTACTTTGCTAGGAGATGCCTCTTTCTGTACATGCAAC
ACATCCTGGACGGGTGTTGAGCAAAAGGGCTTTGCAGAAGAAACAGTCTCAGGTTCACTATCAG
GAGCAGAGGGAAATTCACAACTGCGATAGAACTCATCCATGACAGGATCAGAATGTTTTGGCTC
TTCAAACTGTCTTTCTTCTGTGCTTCCCTCGTATCCTTGCAGCAACTTATTCAGAAGATCATTT
GTCAGGAAAGAAAGATTCAATGTCAAGAAGACACCAAGCGATCCAACACGAACAGCCACACAAT
AAACAGCATACATAGCCAACACAGGTATCACAAATCGTGCATGTTTCAAAGAGCACATACAGCC
TGCATTACCAGAGAGGATCCTCCTTTAGGTCAAAAGAATCAAACGGATGCAACTAGGGAGGAAG
AAAAATTTATGGATTTGACAAACAAAAACACAAAATTATCATTATGAACAGACTTAAATATTAA
GATAAAACAAACCTCCAGCAATCAGAAGCATTCCTGTAATCCAGAAATAGCCATACATCCACAT
AATCAATATTCCAAATAATCCTACAATGAAAAGACCAGGCGTATAGCCCATGTAATGAATGACT
GCCCCAGCAGCTCC
						
					

			
		

Sequences
Splice junction sequence	AGAAATAGCCATACATCCACATAATCAATATTCCAAATAATCCTACAATGAAAAGACCAGGCGT ATAGCCCATGTAATGAATGACTGCCCCAGCAGCTCCcttgaaggatgacgaaaatttattttcc acccatccatctccatccttagctggatgaaaatcagagcaatcctacagtacatggttcccac aaaattag
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	CTTGAAGGATGACGAAAATTTATTTTCCACCCATCCATCTCCATCCTTAGCTGGATGAAAATCA GAGCAATCCTACAGTACATGGTTCCCACAAAATTAGCTGTAAGAACACTCTCGATTAAAAGTAC CTGAAAAAAAAATTCTGGCCTCCAAACCTGACACCATCTTGCTTTTGCTTTGCTTTTCTTGGTA CATATCCACAGATGAAAATTACCACATTTTGTGCACTGTATACGCCTGGACTCTTCGGAGAGAA ACTCTACCCCAGTCTGCAAGATGAGTTTATCAAATTACAAATGGGCCCCATAAAGGAAAACAGC AAGTAGGTCAGTAGGTCAAGGACATGAGAGCATGAATAAACTGCATTCGTATGCTTGGATAATT GATAAGATATGTTAAAGAAATAATCCAACCATGTGGATTCTAAATTTGTGAAAACTAGAACCCA CCTGTTGAGAGACAACACGTGATCTCTGAGTCATTTTACGTGATTCTTCTTTCCTCAGTTGGTC GTCGTAAGTGTTTTTCTTTGTGAAATCTGAGAGTACCTGCAGCATAACTACAATGATTACCCTT TATCCAGGTATAGAAGCCATGGTTGGTATCAAGAGCAGATATTCAACCAGATTTAACTGTAATA TAATCAAGGAAGAGAAAAGACATAAACTTCCATTGTAGTTTACCTCATAAGCTGACTGAAGCTT TTTGAATGATTCACAGGCCAGTGGATTTCCCATATTTTTATCAGGATGTACAAGCAGGACCTAG ACAAATAAAGCATACGTACCATGAAAATGAAGTAATTGTAACATGAATTTCTCATTTTCCCTTG TATAGAAGGCCGTGGTTTATTACCATTCTGTGGTACTCCTTTTTCAGAATCTTTTGATCAATAC TTCTATTCCGAGGAATACCCAAAACTTCATAATGGGTCAAACCATCCATGATCCTCTTCATCTC ATCCAATGAAACAGAATCCGATTTCACTACTTTGCTAGGAGATGCCTCTTTCTGTACATGCAAC ACATCCTGGACGGGTGTTGAGCAAAAGGGCTTTGCAGAAGAAACAGTCTCAGGTTCACTATCAG GAGCAGAGGGAAATTCACAACTGCGATAGAACTCATCCATGACAGGATCAGAATGTTTTGGCTC TTCAAACTGTCTTTCTTCTGTGCTTCCCTCGTATCCTTGCAGCAACTTATTCAGAAGATCATTT GTCAGGAAAGAAAGATTCAATGTCAAGAAGACACCAAGCGATCCAACACGAACAGCCACACAAT AAACAGCATACATAGCCAACACAGGTATCACAAATCGTGCATGTTTCAAAGAGCACATACAGCC TGCATTACCAGAGAGGATCCTCCTTTAGGTCAAAAGAATCAAACGGATGCAACTAGGGAGGAAG AAAAATTTATGGATTTGACAAACAAAAACACAAAATTATCATTATGAACAGACTTAAATATTAA GATAAAACAAACCTCCAGCAATCAGAAGCATTCCTGTAATCCAGAAATAGCCATACATCCACAT AATCAATATTCCAAATAATCCTACAATGAAAAGACCAGGCGTATAGCCCATGTAATGAATGACT GCCCCAGCAGCTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.191999943

Conservation Information
Conserved circRNAs	NA
PMCS	0.191999943

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							25905283-25903742(+)
25905276-25903690(-)
25903733-25905246(-)
						
					

						Potential amino acid sequence
						
							MTAPAAPLKDDENLFSTHPSPSLAG*(+)
MGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSLKHARFVIPVLAMYAVYCVAVRVGS
LGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSDPVMDEFYRSCEFPSAPDSEPETVS
SAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIMDGLTHYEVLGIPRNRSIDQKILKK
EYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKKNTYDDQLRKEESRKMTQRSRVVSQ
QTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQDCSDFHPAKDGDGWVENKFSSSFKG
AAGAVIHYMGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSLKHARFVIPVLAMYAVY
CVAVRVGSLGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSDPVMDEFYRSCEFPSAP
DSEPETVSSAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIMDGLTHYEVLGIPRNRS
IDQKILKKEYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKKNTYDDQLRKEESRKMT
QRSRVVSQQTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQDCSDFHPAKDGDGWVEN
KFSSSFKGAAGAVIHYMGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSLKHARFVIP
VLAMYAVYCVAVRVGSLGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSDPVMDEFYR
SCEFPSAPDSEPETVSSAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIMDGLTHYEV
LGIPRNRSIDQKILKKEYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKKNTYDDQLR
KEESRKMTQRSRVVSQQTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQDCSDFHPAK
DGDGWVENKFSSSFKGAAGAVIHYMGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSL
KHARFVIPVLAMYAVYCVAVRVGSLGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSD
PVMDEFYRSCEFPSAPDSEPETVSSAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIM
DGLTHYEVLGIPRNRSIDQKILKKEYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKK
NTYDDQLRKEESRKMTQRSRVVSQQTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQD
CSDFHPAKDGDGWVENKFSSSFK(-)
MEMDGWKINFRHPSRELLGQSFITWAIRLVFSL*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	25905283-25903742(+) 25905276-25903690(-) 25903733-25905246(-)
Potential amino acid sequence	MTAPAAPLKDDENLFSTHPSPSLAG(+) MGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSLKHARFVIPVLAMYAVYCVAVRVGS LGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSDPVMDEFYRSCEFPSAPDSEPETVS SAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIMDGLTHYEVLGIPRNRSIDQKILKK EYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKKNTYDDQLRKEESRKMTQRSRVVSQ QTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQDCSDFHPAKDGDGWVENKFSSSFKG AAGAVIHYMGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSLKHARFVIPVLAMYAVY CVAVRVGSLGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSDPVMDEFYRSCEFPSAP DSEPETVSSAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIMDGLTHYEVLGIPRNRS IDQKILKKEYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKKNTYDDQLRKEESRKMT QRSRVVSQQTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQDCSDFHPAKDGDGWVEN KFSSSFKGAAGAVIHYMGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSLKHARFVIP VLAMYAVYCVAVRVGSLGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSDPVMDEFYR SCEFPSAPDSEPETVSSAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIMDGLTHYEV LGIPRNRSIDQKILKKEYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKKNTYDDQLR KEESRKMTQRSRVVSQQTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQDCSDFHPAK DGDGWVENKFSSSFKGAAGAVIHYMGYTPGLFIVGLFGILIMWMYGYFWITGMLLIAGGCMCSL KHARFVIPVLAMYAVYCVAVRVGSLGVFLTLNLSFLTNDLLNKLLQGYEGSTEERQFEEPKHSD PVMDEFYRSCEFPSAPDSEPETVSSAKPFCSTPVQDVLHVQKEASPSKVVKSDSVSLDEMKRIM DGLTHYEVLGIPRNRSIDQKILKKEYHRMVLLVHPDKNMGNPLACESFKKLQSAYEVLSDFTKK NTYDDQLRKEESRKMTQRSRVVSQQTGVEFLSEESRRIQCTKCGNFHLWICTKKSKAKARWCQD CSDFHPAKDGDGWVENKFSSSFK(-) MEMDGWKINFRHPSRELLGQSFITWAIRLVFSL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0612400_circ_g.4

Address

Any questions?

Supported by