Plant Circular RNA Database

Detail information of Os04g0252200_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os04g0252200_circ_g.4
					
						ID in PlantcircBase
						osa_circ_023189
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 9898548-9904344  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						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.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 Os04g0252200_circ_g.18 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os04t0252200-01:1
Os04t0252200-02:9

General Information
CircRNA Name	Os04g0252200_circ_g.4
ID in PlantcircBase	osa_circ_023189
Alias	NA
Organism	Oryza sativa
Position	chr4: 9898548-9904344 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
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.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 Os04g0252200_circ_g.18
Support reads	1
Tissues	shoot
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	Os04t0252200-01:1 Os04t0252200-02:9

			
						 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  
						
							TATACCTCCCAAACAAGTTGCCAGCAGCAATGGTGCTTGCTTGAACAAAGTAATCAACAGTTTC
TGTAACCTCTCCTAAGTCATCACCTGTCTCAAGTACaatgttcaggctcacaacatgcaaaggg
gcatcatagaatgcaacagcagtcaattcagcaccagtccacttgtttaatgtgatcttaggac
cagaagct

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 1817
Transcript exons: 9898548-9898721,9898814-9898942,9899309-9899535,9900182-
9900259,9901317-9901382,9901462-9901542,9901675-9902447,
9902988-9903181,9904250-9904344
AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA
GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA
CAGCTGATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCAGATTTTGAGAATTTTC
ACTTTTCGTGAAAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAA
GCAGTCCCAATGGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATTATGTAATGTAACAATGC
GCACGGTTAGAGCATTTTCAAACAATTGCATTGGAATTGTGGACTTCGTCTCCCAATGTCCACC
AGGTTTCTCCAGCTCCAAAATGCGGACCTCAAATTCATCAACAGTATATGTCTTATGAAGGGCA
TCAGTGCTTGTAACATCGTTATCCATGTGATGAACTGATTCTTGATCAGCCATAGAAGAAAGAA
CTTGATTTAGGGGACGAAAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATAATAC
GTGACCTGATGTGGGGTGCCATGCAAAGGGACCTTTTGAACAGGCCAGTAGCTGTCATAGTTAT
ATGCTGAGGGCAATTGGCATATCTTCAGAAAACCCTGTGATGTAACATATATAAAGCCATGAGA
ACAATTTACATTATGCAGAACAGTAAAGGCTTCAATGGGACCGTCACATAACTGTGGGTGCACC
CGCAATCGTTGTCGACAAACCATAACCCAAGCTGGCCTCGTGCCACTAAGAAATAATCCCTCAT
AGCCACCAACATTGTTAAAGGTTGTTATTCTTGGTCGTCCAAGAGTTGGTATGTCTTCTCGTGA
TGTTATATCTATAGAAACCCGGTGAAATCTGAGATTTCTGAGCCTGGAATCACTGGCATTGTGA
TGATCAGCAGAACCTTGAGGTGACAATGGAACCCTTTTCACATTGCTCTCCGAGGCTTCATAAG
AGAAGGCATGGTAACACAACAATGTGCCATCATTCAATAGTCCAAAAAGGAAGGGTCTACTGAA
TTGACCAGACCATCTATGCATTGCAAGCTCAACTATCCGAATGCTATCTCCTGCTTCTTTCTTT
AGGGAAGCTTTAGTGCAATCATATCTTTCTTTCGTGCTATCCTCATATATGAGCTGAGAAAATT
TATCAACCAAAAGAGCCTCGCCAGAAATAAAATTTTCCACAGAGAAAACACATCGGAAACTAGG
CACTTCAAAAATTTCCAGTTTACCGCTTTCATAGCAAATGATACAATATATATCAGATTGATCA
TGAGATGAAGTACCATTGCCATCAATTGCCTCCGCAATACCAGTAGATAACCATGCATCACTAC
GTGTCTTTGTCAGCCATGGTTCAGGACCTCTGTCACGATAAAGTGTACAGGCAGCGATTCGCTC
ACTTGAGCTAATAAATATACTGGGAGCATTCACAGAAAGAGTACAAGTACAATAATCTCCTATA
AGAAGTTGAACAGATCCATCAACCATCTTCAAAAGAACATATGGATCTGCAATGGAAGCGCATG
CCACACCGAGAGCCTCTGAACTAGATGATTCTGAAGCATGCGTAGTAAAGTTTAGCTCCTGTGT
CATGAAAGAACCATCAAGCACACGAGCACCCTTACCATATACCTGTATGACACGCCGCCTCCCA
AACAAGTTGCCAGCAGCAATGGTGCTTGCTTGAACAAAGTAATCAACAGTTTCTGTAACCTCTC
CTAAGTCATCACCTGTCTCAAGTAC
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	TATACCTCCCAAACAAGTTGCCAGCAGCAATGGTGCTTGCTTGAACAAAGTAATCAACAGTTTC TGTAACCTCTCCTAAGTCATCACCTGTCTCAAGTACaatgttcaggctcacaacatgcaaaggg gcatcatagaatgcaacagcagtcaattcagcaccagtccacttgtttaatgtgatcttaggac cagaagct
Assembled circRNA sequence	Yes 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	Transcript length: 1817 Transcript exons: 9898548-9898721,9898814-9898942,9899309-9899535,9900182- 9900259,9901317-9901382,9901462-9901542,9901675-9902447, 9902988-9903181,9904250-9904344 AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA CAGCTGATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCAGATTTTGAGAATTTTC ACTTTTCGTGAAAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAA GCAGTCCCAATGGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATTATGTAATGTAACAATGC GCACGGTTAGAGCATTTTCAAACAATTGCATTGGAATTGTGGACTTCGTCTCCCAATGTCCACC AGGTTTCTCCAGCTCCAAAATGCGGACCTCAAATTCATCAACAGTATATGTCTTATGAAGGGCA TCAGTGCTTGTAACATCGTTATCCATGTGATGAACTGATTCTTGATCAGCCATAGAAGAAAGAA CTTGATTTAGGGGACGAAAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATAATAC GTGACCTGATGTGGGGTGCCATGCAAAGGGACCTTTTGAACAGGCCAGTAGCTGTCATAGTTAT ATGCTGAGGGCAATTGGCATATCTTCAGAAAACCCTGTGATGTAACATATATAAAGCCATGAGA ACAATTTACATTATGCAGAACAGTAAAGGCTTCAATGGGACCGTCACATAACTGTGGGTGCACC CGCAATCGTTGTCGACAAACCATAACCCAAGCTGGCCTCGTGCCACTAAGAAATAATCCCTCAT AGCCACCAACATTGTTAAAGGTTGTTATTCTTGGTCGTCCAAGAGTTGGTATGTCTTCTCGTGA TGTTATATCTATAGAAACCCGGTGAAATCTGAGATTTCTGAGCCTGGAATCACTGGCATTGTGA TGATCAGCAGAACCTTGAGGTGACAATGGAACCCTTTTCACATTGCTCTCCGAGGCTTCATAAG AGAAGGCATGGTAACACAACAATGTGCCATCATTCAATAGTCCAAAAAGGAAGGGTCTACTGAA TTGACCAGACCATCTATGCATTGCAAGCTCAACTATCCGAATGCTATCTCCTGCTTCTTTCTTT AGGGAAGCTTTAGTGCAATCATATCTTTCTTTCGTGCTATCCTCATATATGAGCTGAGAAAATT TATCAACCAAAAGAGCCTCGCCAGAAATAAAATTTTCCACAGAGAAAACACATCGGAAACTAGG CACTTCAAAAATTTCCAGTTTACCGCTTTCATAGCAAATGATACAATATATATCAGATTGATCA TGAGATGAAGTACCATTGCCATCAATTGCCTCCGCAATACCAGTAGATAACCATGCATCACTAC GTGTCTTTGTCAGCCATGGTTCAGGACCTCTGTCACGATAAAGTGTACAGGCAGCGATTCGCTC ACTTGAGCTAATAAATATACTGGGAGCATTCACAGAAAGAGTACAAGTACAATAATCTCCTATA AGAAGTTGAACAGATCCATCAACCATCTTCAAAAGAACATATGGATCTGCAATGGAAGCGCATG CCACACCGAGAGCCTCTGAACTAGATGATTCTGAAGCATGCGTAGTAAAGTTTAGCTCCTGTGT CATGAAAGAACCATCAAGCACACGAGCACCCTTACCATATACCTGTATGACACGCCGCCTCCCA AACAAGTTGCCAGCAGCAATGGTGCTTGCTTGAACAAAGTAATCAACAGTTTCTGTAACCTCTC CTAAGTCATCACCTGTCTCAAGTAC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.323903184

Conservation Information
Conserved circRNAs	NA
PMCS	0.323903184

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9899508-9899526(-)
						
						Potential amino acid sequence
						
							MADQESVHHMDNDVTSTDALHKTYTVDEFEVRILELEKPGGHWETKSTIPMQLFENALTVRIVT
LHNTTTKENETLLAIGTAYVLGEDVAARGRVLLFSFTKSENSQNLVTEVYSKESKGAVSAVASL
QGHLLIASGPKITLNKWTGAELTAVAFYDAPLHVVSLNIVLETGDDLGEVTETVDYFVQASTIA
AGNLFGRRRVIQVYGKGARVLDGSFMTQELNFTTHASESSSSEALGVACASIADPYVLLKMVDG
SVQLLIGDYCTCTLSVNAPSIFISSSERIAACTLYRDRGPEPWLTKTRSDAWLSTGIAEAIDGN
GTSSHDQSDIYCIICYESGKLEIFEVPSFRCVFSVENFISGEALLVDKFSQLIYEDSTKERYDC
TKASLKKEAGDSIRIVELAMHRWSGQFSRPFLFGLLNDGTLLCYHAFSYEASESNVKRVPLSPQ
GSADHHNASDSRLRNLRFHRVSIDITSREDIPTLGRPRITTFNNVGGYEGLFLSGTRPAWVMVC
RQRLRVHPQLCDGPIEAFTVLHNVNCSHGFIYVTSQGFLKICQLPSAYNYDSYWPVQKVPLHGT
PHQVTYYAEQSLYPLIVSVPFVP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9899508-9899526(-)
Potential amino acid sequence	MADQESVHHMDNDVTSTDALHKTYTVDEFEVRILELEKPGGHWETKSTIPMQLFENALTVRIVT LHNTTTKENETLLAIGTAYVLGEDVAARGRVLLFSFTKSENSQNLVTEVYSKESKGAVSAVASL QGHLLIASGPKITLNKWTGAELTAVAFYDAPLHVVSLNIVLETGDDLGEVTETVDYFVQASTIA AGNLFGRRRVIQVYGKGARVLDGSFMTQELNFTTHASESSSSEALGVACASIADPYVLLKMVDG SVQLLIGDYCTCTLSVNAPSIFISSSERIAACTLYRDRGPEPWLTKTRSDAWLSTGIAEAIDGN GTSSHDQSDIYCIICYESGKLEIFEVPSFRCVFSVENFISGEALLVDKFSQLIYEDSTKERYDC TKASLKKEAGDSIRIVELAMHRWSGQFSRPFLFGLLNDGTLLCYHAFSYEASESNVKRVPLSPQ GSADHHNASDSRLRNLRFHRVSIDITSREDIPTLGRPRITTFNNVGGYEGLFLSGTRPAWVMVC RQRLRVHPQLCDGPIEAFTVLHNVNCSHGFIYVTSQGFLKICQLPSAYNYDSYWPVQKVPLHGT PHQVTYYAEQSLYPLIVSVPFVP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0252200_circ_g.4

Address

Any questions?

Supported by