Plant Circular RNA Database

Detail information of Os04g0511600_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0511600_circ_g.1
					
						ID in PlantcircBase
						osa_circ_024553
					
						Alias
						Os_ciR9460
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 25575913-25578289  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os04g0511600						
					
						Parent gene annotation
						
							Similar to RING-H2 finger protein ATL3G. (Os04t0511600-01);Simil
ar to OSIGBa0157K09-H0214G12.17 protein. (Os04t0511600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0511600_circ_g.2 Os04g0511600_circ_g.3 						
					
						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
						Os04t0511600-01:3
Os04t0511600-02:3

General Information
CircRNA Name	Os04g0511600_circ_g.1
ID in PlantcircBase	osa_circ_024553
Alias	Os_ciR9460
Organism	Oryza sativa
Position	chr4: 25575913-25578289 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Os04g0511600
Parent gene annotation	Similar to RING-H2 finger protein ATL3G. (Os04t0511600-01);Simil ar to OSIGBa0157K09-H0214G12.17 protein. (Os04t0511600-02)
Parent gene strand	-
Alternative splicing	Os04g0511600_circ_g.2 Os04g0511600_circ_g.3
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	Os04t0511600-01:3 Os04t0511600-02:3

			
						 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  
						
							TTATGTCAACCATGGTATCCCACCGAAACTATTTCAGTTACAGATAGCTTGCCTCCTCTCCTTT
ACATGTCAATTTATGATTAAAATTCTCCAACACTTCtgtagtgctttggaaccgcctcgcagtt
ctagatgtcggctgcgcattatcttcatgttgaagtgacattgctatgatcgcatcaatctgct
ttattaaa

									
								

					

						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
						
							TGTAGTGCTTTGGAACCGCCTCGCAGTTCTAGATGTCGGCTGCGCATTATCTTCATGTTGAAGT
GACATTGCTATGATCGCATCAATCTGCTTTATTAAAATAAAATATCATTGTACAGCTCGCAAAA
GTATTTTGAGAGAGAGAGAGAGAGAGTCAGGAATTACACCTCTTCTGTGGGAACAACATGAGGA
GTTTCATTGTAAAGCTGCTCCTGAAGTTGGCGAGCCAATAACTCATCAGACTCCAACTGTTCTC
TTATGTTGGGATCCACTGAGGTCCGATTGCTGCTACCAATCCCACTCAAACTAGGCCTTACTTC
AGGAGAGCATATGTCATCAATATCTACTACAGGAATATGATGACGGTGAGTGGTATGATTTCTA
GCAGCTGTTGAGTCTGATGATGCAACTCTAGGTTGATCAACATCAACAGAGCTAGAGCTTTCAC
CAGGATGGTAAGAACTTGCGATGCGCTTCCTCTTTCTGCTACTGATCCTTATTGTTCTATTAAC
AAAACTAGCAGTCTGCAATGTTTTTGCTCCACCAATTGAGTTATTGTTGTCTCCTCCCTCAATT
GAGTTATTGCTGTCTCCTGCTGCAGATGCTCGATCCAGATTAGACTGTTCAGAAGATCCAGATT
CTCTTCCACAACTATTGGTCATCTTACCTGATAGTGGCATGGGTATATTACTAGTATTATTGTG
CGTTGTTCTCCAACCTTGCTCAGAACCTATACCGGTGTGATCATTGTTTGCAACGGAAGAAGAA
TCTCCCATGGATCTTGGACAAACCCTAACAATAGTGAAAGTGCAGGTAAAGGTTCTAGACATGC
AATAATCTAAACATAGCAACAAATTAATCATGCATTTTTGTAAGTCCAACAATGGAGCAAAACT
AGTTTAGTCATACTGTATGATTTTAAAGGAAGGTTATTTTGCTGAAAAAAAAAGATTTGTAAAA
AGAATTAGCATCTCCTGCTTACAATTTTCAAAAGTTCACAAATTGTAACCACATGCACAAGAAT
TTTGTAAACTTAAATTCAACCAATAAAATTACTACCCTAAAAGCCAGAATTTACCTTATCGCAA
ATTCACAGTTCTTTTAAACAAAAACATTTCCTCCATATCTTGTACTCATATTGATACATCCTAG
ATATAAATGAAATGAACTGACAATGCCCATAGGAAAAAAGAGACAGGACATACCTCCTCATATA
AGCCTCTCCAGACTGCTTAGCACCCACGACATCATGGGAAATTTCTTTTCCTTTATTCTTGTTA
CCTTCAGAAAAAATACTGTTCACTTGATTTGCAGCCAGTGGAATTACCGTCTCCCCAGCTCTGC
CTATTGCCGACTTTCTCCCTGACCTTTTTTCCATGTCAGTTGCAGTGTTTCCCTGCCTTCTTAT
TATAGGTGAACTATCAGTAAGATCTATCACATTTCCCTTCCCAGAAGCATCAACCTGAGTATCT
GGATAGTGTAAGAGTCCACTTGTAGAGCATATTTCTCGCTTTTCATCAACCTTCAGACTTCTTT
TGGCTATGTTGGAGGGAGAAATACAACCATTCCGCACCAGCTTTCTTTGGCCCACATGCCTTTG
AGGAACAATGCTTGGTGTAGAGCTTGAAATTCCTGTTGTGCCCTTGTCAGTGATCTCTTCCCCT
TTGCCCTCTCTAGGACTCGATACTGAACAGACATTAGCACCTACTACTTCCTTCGGCTTCTTAA
AGGTGATAGTCCCCATTCTGTTTCGTGGTTTTCCCACCGTAGTAGTAGGAAGACCTGATCCTAA
ACAGAGAAAGTCAGCATTGCAGCTATTGGCATCCCGTGCACTAATATCCCCTTTTCTGATTTGG
CAACTACGGTCCCTTTCTCCAGAGCCCCTGCAATTTATATTGTTTGAAATATTCATGCTCTGAT
CCAAACCAGATTTTTTTGGCACCTTTTCATTCTCAACAGATGTCTCTATCGTCCGACCTGATTT
TAGCAAGGATGATCTTGCTTCAGGATCTTCTGCCACTGGCAGCAATCGTGCCAACTCGGCTTGT
TTAAAAATATCGCCAGCATCTAAAGGTGCAGGCGACACACTACTTGCATTGCCTCTACTTGATT
GACCCTGGATGGAGTTATTTGTGATCTTAAATTTAATTCTTCGCGATGGTAATGGAGTTCCAGC
TGCTTTTGCAATACCTCTCCTAGCAGCTGGGCTAGATACAGGGCATGTTGACTGCTGTATTCGG
TCAGGGGTGTCCGGAACCTCAAAGATGTGATCAGGGTTTATGTCAACCATGGTATCCCACCGAA
ACTATTTCAGTTACAGATAGCTTGCCTCCTCTCCTTTACATGTCAATTTATGATTAAAATTCTC
CAACACTTC
						
					

			
		

Sequences
Splice junction sequence	TTATGTCAACCATGGTATCCCACCGAAACTATTTCAGTTACAGATAGCTTGCCTCCTCTCCTTT ACATGTCAATTTATGATTAAAATTCTCCAACACTTCtgtagtgctttggaaccgcctcgcagtt ctagatgtcggctgcgcattatcttcatgttgaagtgacattgctatgatcgcatcaatctgct ttattaaa
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	TGTAGTGCTTTGGAACCGCCTCGCAGTTCTAGATGTCGGCTGCGCATTATCTTCATGTTGAAGT GACATTGCTATGATCGCATCAATCTGCTTTATTAAAATAAAATATCATTGTACAGCTCGCAAAA GTATTTTGAGAGAGAGAGAGAGAGAGTCAGGAATTACACCTCTTCTGTGGGAACAACATGAGGA GTTTCATTGTAAAGCTGCTCCTGAAGTTGGCGAGCCAATAACTCATCAGACTCCAACTGTTCTC TTATGTTGGGATCCACTGAGGTCCGATTGCTGCTACCAATCCCACTCAAACTAGGCCTTACTTC AGGAGAGCATATGTCATCAATATCTACTACAGGAATATGATGACGGTGAGTGGTATGATTTCTA GCAGCTGTTGAGTCTGATGATGCAACTCTAGGTTGATCAACATCAACAGAGCTAGAGCTTTCAC CAGGATGGTAAGAACTTGCGATGCGCTTCCTCTTTCTGCTACTGATCCTTATTGTTCTATTAAC AAAACTAGCAGTCTGCAATGTTTTTGCTCCACCAATTGAGTTATTGTTGTCTCCTCCCTCAATT GAGTTATTGCTGTCTCCTGCTGCAGATGCTCGATCCAGATTAGACTGTTCAGAAGATCCAGATT CTCTTCCACAACTATTGGTCATCTTACCTGATAGTGGCATGGGTATATTACTAGTATTATTGTG CGTTGTTCTCCAACCTTGCTCAGAACCTATACCGGTGTGATCATTGTTTGCAACGGAAGAAGAA TCTCCCATGGATCTTGGACAAACCCTAACAATAGTGAAAGTGCAGGTAAAGGTTCTAGACATGC AATAATCTAAACATAGCAACAAATTAATCATGCATTTTTGTAAGTCCAACAATGGAGCAAAACT AGTTTAGTCATACTGTATGATTTTAAAGGAAGGTTATTTTGCTGAAAAAAAAAGATTTGTAAAA AGAATTAGCATCTCCTGCTTACAATTTTCAAAAGTTCACAAATTGTAACCACATGCACAAGAAT TTTGTAAACTTAAATTCAACCAATAAAATTACTACCCTAAAAGCCAGAATTTACCTTATCGCAA ATTCACAGTTCTTTTAAACAAAAACATTTCCTCCATATCTTGTACTCATATTGATACATCCTAG ATATAAATGAAATGAACTGACAATGCCCATAGGAAAAAAGAGACAGGACATACCTCCTCATATA AGCCTCTCCAGACTGCTTAGCACCCACGACATCATGGGAAATTTCTTTTCCTTTATTCTTGTTA CCTTCAGAAAAAATACTGTTCACTTGATTTGCAGCCAGTGGAATTACCGTCTCCCCAGCTCTGC CTATTGCCGACTTTCTCCCTGACCTTTTTTCCATGTCAGTTGCAGTGTTTCCCTGCCTTCTTAT TATAGGTGAACTATCAGTAAGATCTATCACATTTCCCTTCCCAGAAGCATCAACCTGAGTATCT GGATAGTGTAAGAGTCCACTTGTAGAGCATATTTCTCGCTTTTCATCAACCTTCAGACTTCTTT TGGCTATGTTGGAGGGAGAAATACAACCATTCCGCACCAGCTTTCTTTGGCCCACATGCCTTTG AGGAACAATGCTTGGTGTAGAGCTTGAAATTCCTGTTGTGCCCTTGTCAGTGATCTCTTCCCCT TTGCCCTCTCTAGGACTCGATACTGAACAGACATTAGCACCTACTACTTCCTTCGGCTTCTTAA AGGTGATAGTCCCCATTCTGTTTCGTGGTTTTCCCACCGTAGTAGTAGGAAGACCTGATCCTAA ACAGAGAAAGTCAGCATTGCAGCTATTGGCATCCCGTGCACTAATATCCCCTTTTCTGATTTGG CAACTACGGTCCCTTTCTCCAGAGCCCCTGCAATTTATATTGTTTGAAATATTCATGCTCTGAT CCAAACCAGATTTTTTTGGCACCTTTTCATTCTCAACAGATGTCTCTATCGTCCGACCTGATTT TAGCAAGGATGATCTTGCTTCAGGATCTTCTGCCACTGGCAGCAATCGTGCCAACTCGGCTTGT TTAAAAATATCGCCAGCATCTAAAGGTGCAGGCGACACACTACTTGCATTGCCTCTACTTGATT GACCCTGGATGGAGTTATTTGTGATCTTAAATTTAATTCTTCGCGATGGTAATGGAGTTCCAGC TGCTTTTGCAATACCTCTCCTAGCAGCTGGGCTAGATACAGGGCATGTTGACTGCTGTATTCGG TCAGGGGTGTCCGGAACCTCAAAGATGTGATCAGGGTTTATGTCAACCATGGTATCCCACCGAA ACTATTTCAGTTACAGATAGCTTGCCTCCTCTCCTTTACATGTCAATTTATGATTAAAATTCTC CAACACTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.126480238

Conservation Information
Conserved circRNAs	NA
PMCS	0.126480238

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25578267-25575975(+)
25578204-25578229(-)
25575970-25578261(-)
						
						Potential amino acid sequence
						
							MIKILQHFCSALEPPRSSRCRLRIIFMLK*(+)
MVDINPDHIFEVPDTPDRIQQSTCPVSSPAARRGIAKAAGTPLPSRRIKFKITNNSIQGQSSRG
NASSVSPAPLDAGDIFKQAELARLLPVAEDPEARSSLLKSGRTIETSVENEKVPKKSGLDQSMN
ISNNINCRGSGERDRSCQIRKGDISARDANSCNADFLCLGSGLPTTTVGKPRNRMGTITFKKPK
EVVGANVCSVSSPREGKGEEITDKGTTGISSSTPSIVPQRHVGQRKLVRNGCISPSNIAKRSLK
VDEKREICSTSGLLHYPDTQVDASGKGNVIDLTDSSPIIRRQGNTATDMEKRSGRKSAIGRAGE
TVIPLAANQVNSIFSEGNKNKGKEISHDVVGAKQSGEAYMRRVCPRSMGDSSSVANNDHTGIGS
EQGWRTTHNNTSNIPMPLSGKMTNSCGRESGSSEQSNLDRASAAGDSNNSIEGGDNNNSIGGAK
TLQTASFVNRTIRISSRKRKRIASSYHPGESSSSVDVDQPRVASSDSTAARNHTTHRHHIPVVD
IDDICSPEVRPSLSGIGSSNRTSVDPNIREQLESDELLARQLQEQLYNETPHVVPTEEIDAIIA
MSLQHEDNAQPTSRTARRFQSTTEVLENFNHKLTCKGEEASYL*(-)
MKIMRSRHLELRGGSKALQKCWRILIIN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25578267-25575975(+) 25578204-25578229(-) 25575970-25578261(-)
Potential amino acid sequence	MIKILQHFCSALEPPRSSRCRLRIIFMLK(+) MVDINPDHIFEVPDTPDRIQQSTCPVSSPAARRGIAKAAGTPLPSRRIKFKITNNSIQGQSSRG NASSVSPAPLDAGDIFKQAELARLLPVAEDPEARSSLLKSGRTIETSVENEKVPKKSGLDQSMN ISNNINCRGSGERDRSCQIRKGDISARDANSCNADFLCLGSGLPTTTVGKPRNRMGTITFKKPK EVVGANVCSVSSPREGKGEEITDKGTTGISSSTPSIVPQRHVGQRKLVRNGCISPSNIAKRSLK VDEKREICSTSGLLHYPDTQVDASGKGNVIDLTDSSPIIRRQGNTATDMEKRSGRKSAIGRAGE TVIPLAANQVNSIFSEGNKNKGKEISHDVVGAKQSGEAYMRRVCPRSMGDSSSVANNDHTGIGS EQGWRTTHNNTSNIPMPLSGKMTNSCGRESGSSEQSNLDRASAAGDSNNSIEGGDNNNSIGGAK TLQTASFVNRTIRISSRKRKRIASSYHPGESSSSVDVDQPRVASSDSTAARNHTTHRHHIPVVD IDDICSPEVRPSLSGIGSSNRTSVDPNIREQLESDELLARQLQEQLYNETPHVVPTEEIDAIIA MSLQHEDNAQPTSRTARRFQSTTEVLENFNHKLTCKGEEASYL(-) MKIMRSRHLELRGGSKALQKCWRILIIN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os04g0511600_circ_g.1

Address

Any questions?

Supported by