Plant Circular RNA Database

Detail information of Os03g0197400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0197400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_018372
					
						Alias
						Os_ciR2990
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 5119909-5122689  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0197400						
					
						Parent gene annotation
						
							Similar to COP9 signalosome complex subunit 4 (Signalosome subun
it 4) (Constitutive photomorphogenesis protein 8) (FUSCA protein
 4) (FUSCA4) (AtS4). (Os03t0197400-01);Similar to COP9 signaloso
me complex subunit 4 (Signalosome subunit 4) (Constitutive photo
morphogenesis protein 8) (FUSCA protein 4) (FUSCA4) (AtS4). (Os0
3t0197400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0197400_circ_g.1 Os03g0197400_circ_g.2 Os03g0197400_circ_g.4 						
					
						Support reads
						4/1
					
						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  
						
							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
						Os03t0197400-02:11
Os03t0197400-01:11

General Information
CircRNA Name	Os03g0197400_circ_g.3
ID in PlantcircBase	osa_circ_018372
Alias	Os_ciR2990
Organism	Oryza sativa
Position	chr3: 5119909-5122689 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0197400
Parent gene annotation	Similar to COP9 signalosome complex subunit 4 (Signalosome subun it 4) (Constitutive photomorphogenesis protein 8) (FUSCA protein 4) (FUSCA4) (AtS4). (Os03t0197400-01);Similar to COP9 signaloso me complex subunit 4 (Signalosome subunit 4) (Constitutive photo morphogenesis protein 8) (FUSCA protein 4) (FUSCA4) (AtS4). (Os0 3t0197400-02)
Parent gene strand	-
Alternative splicing	Os03g0197400_circ_g.1 Os03g0197400_circ_g.2 Os03g0197400_circ_g.4
Support reads	4/1
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	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	Os03t0197400-02:11 Os03t0197400-01:11

			
						 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  
						
							TCCCTGAGTCCAAGTCAATCCCACTAAGCATCTGTGCAGCTTTTGACCATTGTTGTTCAGACTC
ATACAGTTCTGCAAGCTTCTCTCTAATCACTACCACctgttggtcccactgctgcagctcttca
gtgtcatcctcaaaatgtatcacagcttcaacctgtaaaataagccaggcgagttaatctcata
acaacttg

									
								

					

						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
						
							CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATCACAGCTTCAACCTGT
AAAATAAGCCAGGCGAGTTAATCTCATAACAACTTGAATTAAACCACAAACGGTAAAACATGGT
TACAGTGTAAGTCTATTTCAGATGTCTGCTCGAAATGGTGGAATAGTATGAATATCAACATAAG
GATTAAGGAAGTCATATGAATAAAACCTGATCAATTGAACCTCGCATCCTATCTTCATAAATCA
TTCGCGATGCTATCTTTTCAGCCTGCCAGCATCAAAATCAGTTGCAGTAAGACTCCAATTTGAA
TACTTTCATATTTAAAATCAAACATAAATAAAGAATTTATAGAGAAAATGCCAGTTCTTCCTGG
TACCAGTTACAGGCCAGATGATTTGAACTATCCTATTTGATTTTAAATTGTGAAATTCGGTGGT
TCTTCCCAGTTTGACTAGTTTCCAGCAAGTACCACTCAGAACCCATATATTCCAAATTCTTTTC
TTTTTCTTAGTCATATGGACTTTGTGTGAATCTGTCTCTATAAACATGAAATGATGTATCATAT
CAACAGGAAAAATTAACCAAAATACTAACCTTCCTAGGGTCAATGCCCAATAATGCTCCAAGCT
CATCAAAGCTACAGAAATAAATCAATAGTTGATCAGAATGATAAATCACAATGACCCAGGAAAA
TTTCAATGCAAAAACTAACCTGATATTAGTGTAAAGTTTACTGGCACTAAGGAGGTTATGCTCA
ATCATTGCCCGGTCAAGCACAGTAGACTTATCTGGTAACAGAGCTTTCTGTTGAACAGAAGAAA
AATCCAGTCAATAAAATTACAAGCTACTACTACAAGTTATCTTGGAAGAGAGTATGTTCACTAA
CTTGATGCGGTCTCAGCTCCTCTGCAAATGCTTCAATTTCTGGTTTCCTCAAAATCCTTTCAAG
AAAGACCTACACATTTGAAGTAGAAGGCCTGTCAATAAAGGGAGCTTATGCTCCAAATATAAAT
GCCAGGGGAGTATATCAAGATAGGCACCTTCTGCAGTATTGGGTATATCTTCAACTTTGAGCAT
CTCTCATCCTAAAGGGAAAAGACAGTATAAAATCATGCCACGAGTCATAATTTAAGCACCGCTA
TAATGAGAAAAATCAGATGCAAAACAATTGTATTTTCATGCTACTACAATGTTGATACAAGGTG
TTGGTTCATTTGATGACCATGATTACAGATTGGTCAACATCAAACAGTATGAAACTATAAACTA
CCCACTGAAACTGGATGCTAGCATATTTATTAGTTTAGCAGAACTATAAAAAAAATCCTAAATA
ACTATTTGGAAGGATCTTGATATTAGTAATTCAATATCAAATGGGTTAAGTTTTTGTATAATGA
TGCCACATTCCAATGAGTTCGGAGACAATTCCTCTGTTTCAATATACATACTTTTTTCCCCGGA
AAACATAAATTTTGGAGTGTACCAAGAATGATGTACAGTAAATGGGAATACAAATCACTGCGTA
AGGGAGAGAAGCCACAGCATGTATATCATAGTAAGCTAAAGCCACAACCTATGGTGCTCCATAA
CAGAAACCAATCAATATCGATACAGAGCTCTGCAGAGCATCTGATAATTCAGATTTGTCCATTT
GATAAACATGGCACAGGGAAAGGGCAAAGATGATTACGATAGTATGATACATAAAAAGTTATTG
CAGACAATAAATGACATGTAGATATAACAAGCACTGCAAACCAGAATGTTATGATAAACCAACA
AAGCAAATACCTTGTACAATGTAGCAAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATAT
TGTGCATGTCACAGCAGCACTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCTCTGAGATCA
CATGCAGAGTGTTCCATCAGGAATTTTTATAAGTAGTATCAGCTGCTAATGTAACAACTGTAAA
ATTTAAGTGGAAATATCCAAGATGTTAATAGCAAGGGGGCAGGGGAATTGGAAAATATATAATG
TATTGCTAGAAGGGTGCAGAAATAGAGTAGTCACCACAGAACAAGCAAACTACAGATAATGGAG
ATAAGAAACACATGAATTGAAAAGGGAAACAAATCTGCAACTATGTAGAGAAAATCTTACTCGT
CACCAATTTGGCGTTGTTCAATCTGAGAGATGTCATAGTATCGAAGTGCAGCTTCCAAGAATCT
TCTCTTCAGATCCAAAATTCTAGCGTAGCATACCTTAAATATATATAAAAAAAGAAGAAAATAA
GTAAAAGTGTCTGTTTTAATGTAGACAAAAATATTGAACTGAGCCAGCATCAACAAACCTTGTA
CTGTAAGTTCAGAAGTTCTTGGTGACTGTTTGTTACCAAAAATGAAGCTTTGTTAATAAAAGCT
TCAGCATTAACAGAATCATCATCCTATAAATGAAGAACTAAATTAGTAAGCTGGAAATATGTAC
CATTAAAGCCAACAGCAAACAAACAATGCTAACCTCTAAATAAAGTCGTGCAATCTGGACACAT
TTGGATAATTTGTTTGTGTCATCCAGCATCCTGATAATTTAAATTTGAATCAGATGCTTCATGT
CCTGAAGAAAAAGCCATACACATGTTCAGAAAGAAAAGTAAGTCAGTTTCTACCTGATCCCTGA
GTCCAAGTCAATCCCACTAAGCATCTGTGCAGCTTTTGACCATTGTTGTTCAGACTCATACAGT
TCTGCAAGCTTCTCTCTAATCACTACCAC
						
					

			
		

Sequences
Splice junction sequence	TCCCTGAGTCCAAGTCAATCCCACTAAGCATCTGTGCAGCTTTTGACCATTGTTGTTCAGACTC ATACAGTTCTGCAAGCTTCTCTCTAATCACTACCACctgttggtcccactgctgcagctcttca gtgtcatcctcaaaatgtatcacagcttcaacctgtaaaataagccaggcgagttaatctcata acaacttg
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	CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATCACAGCTTCAACCTGT AAAATAAGCCAGGCGAGTTAATCTCATAACAACTTGAATTAAACCACAAACGGTAAAACATGGT TACAGTGTAAGTCTATTTCAGATGTCTGCTCGAAATGGTGGAATAGTATGAATATCAACATAAG GATTAAGGAAGTCATATGAATAAAACCTGATCAATTGAACCTCGCATCCTATCTTCATAAATCA TTCGCGATGCTATCTTTTCAGCCTGCCAGCATCAAAATCAGTTGCAGTAAGACTCCAATTTGAA TACTTTCATATTTAAAATCAAACATAAATAAAGAATTTATAGAGAAAATGCCAGTTCTTCCTGG TACCAGTTACAGGCCAGATGATTTGAACTATCCTATTTGATTTTAAATTGTGAAATTCGGTGGT TCTTCCCAGTTTGACTAGTTTCCAGCAAGTACCACTCAGAACCCATATATTCCAAATTCTTTTC TTTTTCTTAGTCATATGGACTTTGTGTGAATCTGTCTCTATAAACATGAAATGATGTATCATAT CAACAGGAAAAATTAACCAAAATACTAACCTTCCTAGGGTCAATGCCCAATAATGCTCCAAGCT CATCAAAGCTACAGAAATAAATCAATAGTTGATCAGAATGATAAATCACAATGACCCAGGAAAA TTTCAATGCAAAAACTAACCTGATATTAGTGTAAAGTTTACTGGCACTAAGGAGGTTATGCTCA ATCATTGCCCGGTCAAGCACAGTAGACTTATCTGGTAACAGAGCTTTCTGTTGAACAGAAGAAA AATCCAGTCAATAAAATTACAAGCTACTACTACAAGTTATCTTGGAAGAGAGTATGTTCACTAA CTTGATGCGGTCTCAGCTCCTCTGCAAATGCTTCAATTTCTGGTTTCCTCAAAATCCTTTCAAG AAAGACCTACACATTTGAAGTAGAAGGCCTGTCAATAAAGGGAGCTTATGCTCCAAATATAAAT GCCAGGGGAGTATATCAAGATAGGCACCTTCTGCAGTATTGGGTATATCTTCAACTTTGAGCAT CTCTCATCCTAAAGGGAAAAGACAGTATAAAATCATGCCACGAGTCATAATTTAAGCACCGCTA TAATGAGAAAAATCAGATGCAAAACAATTGTATTTTCATGCTACTACAATGTTGATACAAGGTG TTGGTTCATTTGATGACCATGATTACAGATTGGTCAACATCAAACAGTATGAAACTATAAACTA CCCACTGAAACTGGATGCTAGCATATTTATTAGTTTAGCAGAACTATAAAAAAAATCCTAAATA ACTATTTGGAAGGATCTTGATATTAGTAATTCAATATCAAATGGGTTAAGTTTTTGTATAATGA TGCCACATTCCAATGAGTTCGGAGACAATTCCTCTGTTTCAATATACATACTTTTTTCCCCGGA AAACATAAATTTTGGAGTGTACCAAGAATGATGTACAGTAAATGGGAATACAAATCACTGCGTA AGGGAGAGAAGCCACAGCATGTATATCATAGTAAGCTAAAGCCACAACCTATGGTGCTCCATAA CAGAAACCAATCAATATCGATACAGAGCTCTGCAGAGCATCTGATAATTCAGATTTGTCCATTT GATAAACATGGCACAGGGAAAGGGCAAAGATGATTACGATAGTATGATACATAAAAAGTTATTG CAGACAATAAATGACATGTAGATATAACAAGCACTGCAAACCAGAATGTTATGATAAACCAACA AAGCAAATACCTTGTACAATGTAGCAAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATAT TGTGCATGTCACAGCAGCACTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCTCTGAGATCA CATGCAGAGTGTTCCATCAGGAATTTTTATAAGTAGTATCAGCTGCTAATGTAACAACTGTAAA ATTTAAGTGGAAATATCCAAGATGTTAATAGCAAGGGGGCAGGGGAATTGGAAAATATATAATG TATTGCTAGAAGGGTGCAGAAATAGAGTAGTCACCACAGAACAAGCAAACTACAGATAATGGAG ATAAGAAACACATGAATTGAAAAGGGAAACAAATCTGCAACTATGTAGAGAAAATCTTACTCGT CACCAATTTGGCGTTGTTCAATCTGAGAGATGTCATAGTATCGAAGTGCAGCTTCCAAGAATCT TCTCTTCAGATCCAAAATTCTAGCGTAGCATACCTTAAATATATATAAAAAAAGAAGAAAATAA GTAAAAGTGTCTGTTTTAATGTAGACAAAAATATTGAACTGAGCCAGCATCAACAAACCTTGTA CTGTAAGTTCAGAAGTTCTTGGTGACTGTTTGTTACCAAAAATGAAGCTTTGTTAATAAAAGCT TCAGCATTAACAGAATCATCATCCTATAAATGAAGAACTAAATTAGTAAGCTGGAAATATGTAC CATTAAAGCCAACAGCAAACAAACAATGCTAACCTCTAAATAAAGTCGTGCAATCTGGACACAT TTGGATAATTTGTTTGTGTCATCCAGCATCCTGATAATTTAAATTTGAATCAGATGCTTCATGT CCTGAAGAAAAAGCCATACACATGTTCAGAAAGAAAAGTAAGTCAGTTTCTACCTGATCCCTGA GTCCAAGTCAATCCCACTAAGCATCTGTGCAGCTTTTGACCATTGTTGTTCAGACTCATACAGT TCTGCAAGCTTCTCTCTAATCACTACCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014013 						
					
						PMCS
						0.136549374

Conservation Information
Conserved circRNAs	osi_circ_014013
PMCS	0.136549374

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5122622-5119911(-)
						
						Potential amino acid sequence
						
							MLSGIDLDSGIRMLDDTNKLSKCVQIARLYLEDDDSVNAEAFINKASFLVTNSHQELLNLQYKV
CYARILDLKRRFLEAALRYYDISQIEQRQIGDEEIDENALEQALSAAVTCTILAGAGPQRSRVL
ATLYKDERCSKLKIYPILQKVFLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMIEHNLL
SASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQQWDQQ
VVVIREKLAELYESEQQWSKAAQMLSGIDLDSGIRMLDDTNKLSKCVQIARLYLEDDDSVNAEA
FINKASFLVTNSHQELLNLQYKVCYARILDLKRRFLEAALRYYDISQIEQRQIGDEEIDENALE
QALSAAVTCTILAGAGPQRSRVLATLYKDERCSKLKIYPILQKVFLERILRKPEIEAFAEELRP
HQKALLPDKSTVLDRAMIEHNLLSASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGS
IDQVEAVIHFEDDTEELQQWDQQVVVIREKLAELYESEQQWSKAAQMLSGIDLDSGIRMLDDTN
KLSKCVQIARLYLEDDDSVNAEAFINKASFLVTNSHQELLNLQYKVCYARILDLKRRFLEAALR
YYDISQIEQRQIGDEEIDENALEQALSAAVTCTILAGAGPQRSRVLATLYKDERCSKLKIYPIL
QKVFLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMIEHNLLSASKLYTNISFDELGALL
GIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQQWDQQVVVIREKLAELYESEQQW
SKAAQMLSGIDLDSGIRMLDDTNKLSKCVQIARLYLEDDDSVNAEAFINKASFLVTNSHQELLN
LQYKVCYARILDLKRRFLEAALRYYDISQIEQRQIGDEEIDENALEQALSAAVTCTILAGAGPQ
RSRVLATLYKDERCSKLKIYPILQKVFLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMI
EHNLLSASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQ
QWDQQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5122622-5119911(-)
Potential amino acid sequence	MLSGIDLDSGIRMLDDTNKLSKCVQIARLYLEDDDSVNAEAFINKASFLVTNSHQELLNLQYKV CYARILDLKRRFLEAALRYYDISQIEQRQIGDEEIDENALEQALSAAVTCTILAGAGPQRSRVL ATLYKDERCSKLKIYPILQKVFLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMIEHNLL SASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQQWDQQ VVVIREKLAELYESEQQWSKAAQMLSGIDLDSGIRMLDDTNKLSKCVQIARLYLEDDDSVNAEA FINKASFLVTNSHQELLNLQYKVCYARILDLKRRFLEAALRYYDISQIEQRQIGDEEIDENALE QALSAAVTCTILAGAGPQRSRVLATLYKDERCSKLKIYPILQKVFLERILRKPEIEAFAEELRP HQKALLPDKSTVLDRAMIEHNLLSASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGS IDQVEAVIHFEDDTEELQQWDQQVVVIREKLAELYESEQQWSKAAQMLSGIDLDSGIRMLDDTN KLSKCVQIARLYLEDDDSVNAEAFINKASFLVTNSHQELLNLQYKVCYARILDLKRRFLEAALR YYDISQIEQRQIGDEEIDENALEQALSAAVTCTILAGAGPQRSRVLATLYKDERCSKLKIYPIL QKVFLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMIEHNLLSASKLYTNISFDELGALL GIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQQWDQQVVVIREKLAELYESEQQW SKAAQMLSGIDLDSGIRMLDDTNKLSKCVQIARLYLEDDDSVNAEAFINKASFLVTNSHQELLN LQYKVCYARILDLKRRFLEAALRYYDISQIEQRQIGDEEIDENALEQALSAAVTCTILAGAGPQ RSRVLATLYKDERCSKLKIYPILQKVFLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMI EHNLLSASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQ QWDQQ(-)
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 Os03g0197400_circ_g.3

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