Plant Circular RNA Database

Detail information of Os04g0252200_circ_g.18

			
						 General Information
					
						CircRNA Name
						Os04g0252200_circ_g.18
					
						ID in PlantcircBase
						osa_circ_023203
					
						Alias
						Os_ciR3048
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 9911286-9913088  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0252200						
					
						Parent gene annotation
						
							Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi
lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0252200_circ_g.1 Os04g0252200_circ_g.2 Os04g0252200_circ_g.3 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.16 Os04g0252200_circ_g.17 						
					
						Support reads
						4/1
					
						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
						Os04t0252200-01:4
Os04t0252200-02:4

General Information
CircRNA Name	Os04g0252200_circ_g.18
ID in PlantcircBase	osa_circ_023203
Alias	Os_ciR3048
Organism	Oryza sativa
Position	chr4: 9911286-9913088 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0252200
Parent gene annotation	Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
Parent gene strand	-
Alternative splicing	Os04g0252200_circ_g.1 Os04g0252200_circ_g.2 Os04g0252200_circ_g.3 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.16 Os04g0252200_circ_g.17
Support reads	4/1
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	Os04t0252200-01:4 Os04t0252200-02:4

			
						 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  
						
							CTAAATGCAGATATCATGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTT
GCTCATGAAGTATGACCAACACAGGCTCAATATAACcgcccatcataaaccactgtaagtaaca
gcatctctccagcctttgtcgagaacattacaatgtcattggacaaccaagttgctttagctgc
atcaagct

									
								

					

						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
						
							CGCCCATCATAAACCACTGTAAGTAACAGCATCTCTCCAGCCTTTGTCGAGAACATTACAATGT
CATTGGACAACCAAGTTGCTTTAGCTGCATCAAGCTCAACTTGGAAATTTGACTTAGAAATTTC
TGGGCTGCAAAGCCAGCAAAAGAACAGAAGGTTACCAGCATACAAATCTACTGAAAAAGAAAGA
AGCTAAGCAATATCAATACGGTATAGACTACAGAACTTAAGAATAATCAACTATTCAATATTGA
TAGGTATAACACTGCTGCCGGAGTAGTATATGTGCCATATTTCGCAGGTTTTCTATATCTTTTT
GGATCAACCCACTATTTTCATGTAAGATTTGCTCTCAGCAAGAAAAGCATGCCAGTACAGTAGA
TTTGACTACCTTTTTACAACCAAATAAGTACAATGAGGTGTGTTATGCACACCCAATCACCCAT
AATCAACAGCAAGCACCTTCTAGTAATTTCACCTTACGAATTACTCAGTTCACATGTTTACCAG
TACATCAAGATGGGCTCAAATGCTGTGCTAATGTCTCAGTTAACACCTTTAGTAATAATGGATT
TAAAAGTATGTAGCTTCAAACATAATCTTCCAAAAAAATTAAATAATTAGGTTGCTAGGACCTA
GGGGAAGTTCAAGATGGTTATTTTAATCTTATTTTCTATGGACAACCATATAAGAAGAGACCAC
ACTACACGTCTTGAGCTTATCACTTTTAAATCAGGTATCCACATTGGTGATCTTGGTATGTGAT
TGTGATGGTACTGCACCACTGATATGTGTGTAGCCGTGTAGTAGTTAAGCAGAAACAGGGCCCA
TTTGTATGTGATCCGAGAAAAAGAACAAACTATCGTAATCCAATTAGTACTTTGCATTTAACAT
ATACAAACAGTACCTGCCATCAGGGTGTGATGAGAAATTGTTCAGGTCAAGAGAACACGATGTG
GACTACAATAACAAAGAGAACTTCAAATCAATGATCCACGTTCAGCAAATCAAAATAAAGTATG
TGCCTTCACCACGAGTATTTAAAGGGATCAAACCTGACTATGGTAATGGATGGAATTTGCACAG
ATCACAAGAACACCACTAATAGGGGGAGGCACTGCAAGAAGTTGGTATGCATCGTGGGGCAGAT
TCTGAAAGGAACAAACACTTTGTAATGGTAAGTATATTATTTTGTAATGGCAAGAAGTTATATA
TAGAGTCAAATAAATCCAGTGCTTAAACGCAATGGAATCCCTAAAATATGTAATACAATTGAGC
AATCAACAAGAAAAAAAAAAAGGATTCGCGATCATAGTATGTCAACTTTGATCTATGGACAGAA
ATGATAGCACCACTAAAATCAATACCATTCACCTCAATGCGGTATTGCTGACCTAAAATGAGGG
ACTTGAATACTAGGATTAGTCCTGAAATAGAGCAAAATTTGATAACTTATCTAAATTCGGAACA
TTTACCAATCACAGATAAACCTACCGTGTTCTATGCAAAAGAAATAAGTAATTATTTAGTGAAT
ACCACAAGCCACCTTAGTACATTCTAGTACTCTGAACGCCAAAATTTATTGCCGAAAGAACATA
GGAATAAGCTACCAAAGACAGAAAAGACAATGCTTAGGAGCAATCTTGTACACTTACAGCTGCA
GACCATATCACTGGATGTTGCTTTAGAGTCATGCTGATGCTAAATGCAGATATCATGCATGTAT
GGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTTGCTCATGAAGTATGACCAACACAGG
CTCAATATAAC
						
					

			
		

Sequences
Splice junction sequence	CTAAATGCAGATATCATGCATGTATGGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTT GCTCATGAAGTATGACCAACACAGGCTCAATATAACcgcccatcataaaccactgtaagtaaca gcatctctccagcctttgtcgagaacattacaatgtcattggacaaccaagttgctttagctgc atcaagct
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	CGCCCATCATAAACCACTGTAAGTAACAGCATCTCTCCAGCCTTTGTCGAGAACATTACAATGT CATTGGACAACCAAGTTGCTTTAGCTGCATCAAGCTCAACTTGGAAATTTGACTTAGAAATTTC TGGGCTGCAAAGCCAGCAAAAGAACAGAAGGTTACCAGCATACAAATCTACTGAAAAAGAAAGA AGCTAAGCAATATCAATACGGTATAGACTACAGAACTTAAGAATAATCAACTATTCAATATTGA TAGGTATAACACTGCTGCCGGAGTAGTATATGTGCCATATTTCGCAGGTTTTCTATATCTTTTT GGATCAACCCACTATTTTCATGTAAGATTTGCTCTCAGCAAGAAAAGCATGCCAGTACAGTAGA TTTGACTACCTTTTTACAACCAAATAAGTACAATGAGGTGTGTTATGCACACCCAATCACCCAT AATCAACAGCAAGCACCTTCTAGTAATTTCACCTTACGAATTACTCAGTTCACATGTTTACCAG TACATCAAGATGGGCTCAAATGCTGTGCTAATGTCTCAGTTAACACCTTTAGTAATAATGGATT TAAAAGTATGTAGCTTCAAACATAATCTTCCAAAAAAATTAAATAATTAGGTTGCTAGGACCTA GGGGAAGTTCAAGATGGTTATTTTAATCTTATTTTCTATGGACAACCATATAAGAAGAGACCAC ACTACACGTCTTGAGCTTATCACTTTTAAATCAGGTATCCACATTGGTGATCTTGGTATGTGAT TGTGATGGTACTGCACCACTGATATGTGTGTAGCCGTGTAGTAGTTAAGCAGAAACAGGGCCCA TTTGTATGTGATCCGAGAAAAAGAACAAACTATCGTAATCCAATTAGTACTTTGCATTTAACAT ATACAAACAGTACCTGCCATCAGGGTGTGATGAGAAATTGTTCAGGTCAAGAGAACACGATGTG GACTACAATAACAAAGAGAACTTCAAATCAATGATCCACGTTCAGCAAATCAAAATAAAGTATG TGCCTTCACCACGAGTATTTAAAGGGATCAAACCTGACTATGGTAATGGATGGAATTTGCACAG ATCACAAGAACACCACTAATAGGGGGAGGCACTGCAAGAAGTTGGTATGCATCGTGGGGCAGAT TCTGAAAGGAACAAACACTTTGTAATGGTAAGTATATTATTTTGTAATGGCAAGAAGTTATATA TAGAGTCAAATAAATCCAGTGCTTAAACGCAATGGAATCCCTAAAATATGTAATACAATTGAGC AATCAACAAGAAAAAAAAAAAGGATTCGCGATCATAGTATGTCAACTTTGATCTATGGACAGAA ATGATAGCACCACTAAAATCAATACCATTCACCTCAATGCGGTATTGCTGACCTAAAATGAGGG ACTTGAATACTAGGATTAGTCCTGAAATAGAGCAAAATTTGATAACTTATCTAAATTCGGAACA TTTACCAATCACAGATAAACCTACCGTGTTCTATGCAAAAGAAATAAGTAATTATTTAGTGAAT ACCACAAGCCACCTTAGTACATTCTAGTACTCTGAACGCCAAAATTTATTGCCGAAAGAACATA GGAATAAGCTACCAAAGACAGAAAAGACAATGCTTAGGAGCAATCTTGTACACTTACAGCTGCA GACCATATCACTGGATGTTGCTTTAGAGTCATGCTGATGCTAAATGCAGATATCATGCATGTAT GGTGCTTTGATAAGATACGCCCAGCCCATGTAGGCTCTTGCTCATGAAGTATGACCAACACAGG CTCAATATAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.115811019

Conservation Information
Conserved circRNAs	NA
PMCS	0.115811019

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9911297-9913081(-)
9913007-9913081(-)
						
						Potential amino acid sequence
						
							MMGGYIEPVLVILHEQEPTWAGRILSKHHTCMISAFSISMTLKQHPVIWSAANLPHDAYQLLAV
PPPISGVLVICANSIHYHSQSTSCSLDLNNFSSHPDGSPEISKSNFQVELDAAKATWLSNDIVM
FSTKAGEMLLLTVVYDGRLY*(-)
MISAFSISMTLKQHPVIWSAANLPHDAYQLLAVPPPISGVLVICANSIHYHSQSTSCSLDLNNF
SSHPDGSPEISKSNFQVELDAAKATWLSNDIVMFSTKAGEMLLLTVVYDGRLY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9911297-9913081(-) 9913007-9913081(-)
Potential amino acid sequence	MMGGYIEPVLVILHEQEPTWAGRILSKHHTCMISAFSISMTLKQHPVIWSAANLPHDAYQLLAV PPPISGVLVICANSIHYHSQSTSCSLDLNNFSSHPDGSPEISKSNFQVELDAAKATWLSNDIVM FSTKAGEMLLLTVVYDGRLY(-) MISAFSISMTLKQHPVIWSAANLPHDAYQLLAVPPPISGVLVICANSIHYHSQSTSCSLDLNNF SSHPDGSPEISKSNFQVELDAAKATWLSNDIVMFSTKAGEMLLLTVVYDGRLY(-)
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 Os04g0252200_circ_g.18

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