Plant Circular RNA Database

Detail information of Os07g0170300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os07g0170300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_032929
					
						Alias
						Os_ciR11235
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 3729187-3730113  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os07g0170300						
					
						Parent gene annotation
						
							YT521-B-like protein family protein. (Os07t0170300-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os07g0170300_circ_g.1 Os07g0170300_circ_g.2 						
					
						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
						Os07t0170300-01:3

General Information
CircRNA Name	Os07g0170300_circ_g.3
ID in PlantcircBase	osa_circ_032929
Alias	Os_ciR11235
Organism	Oryza sativa
Position	chr7: 3729187-3730113 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Os07g0170300
Parent gene annotation	YT521-B-like protein family protein. (Os07t0170300-01)
Parent gene strand	-
Alternative splicing	Os07g0170300_circ_g.1 Os07g0170300_circ_g.2
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	Os07t0170300-01:3

			
						 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  
						
							ACATGGCAGCGTCCTTGTAATCCTCCACCCGCGGAGTCTCTGTCGCTGTCTTTGGGTTCCCATC
AGCCACTGCCACGCTATTTGCCGGAGCCTCCATCAAcatgagatgaggatatgtgttctgattc
cttgactgtcccttgcttttagaattggaagttgtcagagaacgattgccagtgggaagttttt
gctgcttg

									
								

					

						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: 666
Transcript exons: 3729187-3729654,3729807-3729871,3729981-3730113
CATGAGATGAGGATATGTGTTCTGATTCCTTGACTGTCCCTTGCTTTTAGAATTGGAAGTTGTC
AGAGAACGATTGCCAGTGGGAAGTTTTTGCTGCTTGCCATTGAAGATTTGACTACTGTAGCATG
GATAAGTTGTTCGGTTAGTTTGGTTCTGGTAGTTACCAAAACGCCCACTAGGTCGGCCATAGGA
ACCGTTGGAACCTGGTGTATTCTGGCTTGCCTTCGGGAGCAGATTCGTCTTTTTCTGACCTTTC
AGACTATCAACACCATTAGCAGAGACATCCCCTTGGGGCAGTGCAGCCGGATTTTCAGTTTTTC
CATTGTTGGAAGGCTTGCCAGTGGTATTCTGTTGTTTGTTGTATGTCGGTTGGTACTGGTAATG
CTGAGATCCATACATCTGACTATCATGTCCTGAAGTTGAATAACCATATGGAGAATAGCCATAG
TACATATCCCCATAAGCACCAGCAGTTGGTGTCTCTGCACCATCATGGCTCAGGTATGTGGAGT
ACTCCCCCCAGCCACCATAGGCTCCATAGAGATAAGCCGGGTACGTTCCATAGTACATGGCAGC
GTCCTTGTAATCCTCCACCCGCGGAGTCTCTGTCGCTGTCTTTGGGTTCCCATCAGCCACTGCC
ACGCTATTTGCCGGAGCCTCCATCAA
						
					

						Genomic sequence
						
							CATGAGATGAGGATATGTGTTCTGATTCCTTGACTGTCCCTTGCTTTTAGAATTGGAAGTTGTC
AGAGAACGATTGCCAGTGGGAAGTTTTTGCTGCTTGCCATTGAAGATTTGACTACTGTAGCATG
GATAAGTTGTTCGGTTAGTTTGGTTCTGGTAGTTACCAAAACGCCCACTAGGTCGGCCATAGGA
ACCGTTGGAACCTGGTGTATTCTGGCTTGCCTTCGGGAGCAGATTCGTCTTTTTCTGACCTTTC
AGACTATCAACACCATTAGCAGAGACATCCCCTTGGGGCAGTGCAGCCGGATTTTCAGTTTTTC
CATTGTTGGAAGGCTTGCCAGTGGTATTCTGTTGTTTGTTGTATGTCGGTTGGTACTGGTAATG
CTGAGATCCATACATCTGACTATCATGTCCTGAAGTTGAATAACCATATGGAGAATAGCCATAG
TACATATCCCCATAAGCACCCTGAAATAAGCAATAGAACATTATCATTCACAAAATGGATCAAC
TCCAACGCGTATGGAAACCATCAGTATTTATATCACATCCTGAACAATGTATCAGAATAGGATA
AAAGTATTTACTGATGGAGGTGAAGCACAGTAAGGAAAACTCACAGCAGTTGGTGTCTCTGCAC
CATCATGGCTCAGGTATGTGGAGTACTCCCCCCAGCCACCATAGGCTACATTTACACAAACACA
GATCATTCAAAACTTTGACCTAGCAGTTTTGCAAAACATATAACTACAACGGTATGAACAGAAC
AATGAAAAAACTCAGCAATGCATCACCTCCATAGAGATAAGCCGGGTACGTTCCATAGTACATG
GCAGCGTCCTTGTAATCCTCCACCCGCGGAGTCTCTGTCGCTGTCTTTGGGTTCCCATCAGCCA
CTGCCACGCTATTTGCCGGAGCCTCCATCAA
						
					

			
		

Sequences
Splice junction sequence	ACATGGCAGCGTCCTTGTAATCCTCCACCCGCGGAGTCTCTGTCGCTGTCTTTGGGTTCCCATC AGCCACTGCCACGCTATTTGCCGGAGCCTCCATCAAcatgagatgaggatatgtgttctgattc cttgactgtcccttgcttttagaattggaagttgtcagagaacgattgccagtgggaagttttt gctgcttg
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: 666 Transcript exons: 3729187-3729654,3729807-3729871,3729981-3730113 CATGAGATGAGGATATGTGTTCTGATTCCTTGACTGTCCCTTGCTTTTAGAATTGGAAGTTGTC AGAGAACGATTGCCAGTGGGAAGTTTTTGCTGCTTGCCATTGAAGATTTGACTACTGTAGCATG GATAAGTTGTTCGGTTAGTTTGGTTCTGGTAGTTACCAAAACGCCCACTAGGTCGGCCATAGGA ACCGTTGGAACCTGGTGTATTCTGGCTTGCCTTCGGGAGCAGATTCGTCTTTTTCTGACCTTTC AGACTATCAACACCATTAGCAGAGACATCCCCTTGGGGCAGTGCAGCCGGATTTTCAGTTTTTC CATTGTTGGAAGGCTTGCCAGTGGTATTCTGTTGTTTGTTGTATGTCGGTTGGTACTGGTAATG CTGAGATCCATACATCTGACTATCATGTCCTGAAGTTGAATAACCATATGGAGAATAGCCATAG TACATATCCCCATAAGCACCAGCAGTTGGTGTCTCTGCACCATCATGGCTCAGGTATGTGGAGT ACTCCCCCCAGCCACCATAGGCTCCATAGAGATAAGCCGGGTACGTTCCATAGTACATGGCAGC GTCCTTGTAATCCTCCACCCGCGGAGTCTCTGTCGCTGTCTTTGGGTTCCCATCAGCCACTGCC ACGCTATTTGCCGGAGCCTCCATCAA
Genomic sequence	CATGAGATGAGGATATGTGTTCTGATTCCTTGACTGTCCCTTGCTTTTAGAATTGGAAGTTGTC AGAGAACGATTGCCAGTGGGAAGTTTTTGCTGCTTGCCATTGAAGATTTGACTACTGTAGCATG GATAAGTTGTTCGGTTAGTTTGGTTCTGGTAGTTACCAAAACGCCCACTAGGTCGGCCATAGGA ACCGTTGGAACCTGGTGTATTCTGGCTTGCCTTCGGGAGCAGATTCGTCTTTTTCTGACCTTTC AGACTATCAACACCATTAGCAGAGACATCCCCTTGGGGCAGTGCAGCCGGATTTTCAGTTTTTC CATTGTTGGAAGGCTTGCCAGTGGTATTCTGTTGTTTGTTGTATGTCGGTTGGTACTGGTAATG CTGAGATCCATACATCTGACTATCATGTCCTGAAGTTGAATAACCATATGGAGAATAGCCATAG TACATATCCCCATAAGCACCCTGAAATAAGCAATAGAACATTATCATTCACAAAATGGATCAAC TCCAACGCGTATGGAAACCATCAGTATTTATATCACATCCTGAACAATGTATCAGAATAGGATA AAAGTATTTACTGATGGAGGTGAAGCACAGTAAGGAAAACTCACAGCAGTTGGTGTCTCTGCAC CATCATGGCTCAGGTATGTGGAGTACTCCCCCCAGCCACCATAGGCTACATTTACACAAACACA GATCATTCAAAACTTTGACCTAGCAGTTTTGCAAAACATATAACTACAACGGTATGAACAGAAC AATGAAAAAACTCAGCAATGCATCACCTCCATAGAGATAAGCCGGGTACGTTCCATAGTACATG GCAGCGTCCTTGTAATCCTCCACCCGCGGAGTCTCTGTCGCTGTCTTTGGGTTCCCATCAGCCA CTGCCACGCTATTTGCCGGAGCCTCCATCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007049* osi_circ_017573 						
					
						PMCS
						0.213259331

Conservation Information
Conserved circRNAs	osi_circ_007049* osi_circ_017573
PMCS	0.213259331

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3729832-3729216(+)
3729550-3729188(+)
3730112-3729189(-)
						
						Potential amino acid sequence
						
							MAQVCGVLPPATIGSIEISRVRSIVHGSVLVILHPRSLCRCLWVPISHCHAICRSLHQHEMRIC
VLIP*(+)
MSVGTGNAEIHTSDYHVLKLNNHMENSHSTYPHKHQQLVSLHHHGSGMWSTPPSHHRLHRDKPG
TFHSTWQRPCNPPPAESLSLSLGSHQPLPRYLPEPPST*(+)
MEAPANSVAVADGNPKTATETPRVEDYKDAAMYYGTYPAYLYGAYGGWGEYSTYLSHDGAETPT
AGAYGDMYYGYSPYGYSTSGHDSQMYGSQHYQYQPTYNKQQNTTGKPSNNGKTENPAALPQGDV
SANGVDSLKGQKKTNLLPKASQNTPGSNGSYGRPSGRFGNYQNQTNRTTYPCYSSQIFNGKQQK
LPTGNRSLTTSNSKSKGQSRNQNTYPHLMLMEAPANSVAVADGNPKTATETPRVEDYKDAAMYY
GTYPAYLYGAYGGWGEYSTYLSHDGAETPTAGAYGDMYYGYSPYGYSTSGHDSQMYGSQHYQYQ
PTYNKQQNTTGKPSNNGKTENPAALPQGDVSANGVDSLKGQKKTNLLPKASQNTPGSNGSYGRP
SGRFGNYQNQTNRTTYPCYSSQIFNGKQQKLPTGNRSLTTSNSKSKGQSRNQNTYPHLMLMEAP
ANSVAVADGNPKTATETPRVEDYKDAAMYYGTYPAYLYGAYGGWGEYSTYLSHDGAETPTAGAY
GDMYYGYSPYGYSTSGHDSQMYGSQHYQYQPTYNKQQNTTGKPSNNGKTENPAALPQGDVSANG
VDSLKGQKKTNLLPKASQNTPGSNGSYGRPSGRFGNYQNQTNRTTYPCYSSQIFNGKQQKLPTG
NRSLTTSNSKSKGQSRNQNTYPHLMLMEAPANSVAVADGNPKTATETPRVEDYKDAAMYYGTYP
AYLYGAYGGWGEYSTYLSHDGAETPTAGAYGDMYYGYSPYGYSTSGHDSQMYGSQHYQYQPTYN
KQQNTTGKPSNNGKTENPAALPQGDVSANGVDSLKGQKKTNLLPKASQNTPGSNGSYGRPSGRF
GNYQNQTNRTTYPCYSSQIFNGKQQKLPTGNRSLTTSNSKSKGQSRNQNTYPHLM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3729832-3729216(+) 3729550-3729188(+) 3730112-3729189(-)
Potential amino acid sequence	MAQVCGVLPPATIGSIEISRVRSIVHGSVLVILHPRSLCRCLWVPISHCHAICRSLHQHEMRIC VLIP(+) MSVGTGNAEIHTSDYHVLKLNNHMENSHSTYPHKHQQLVSLHHHGSGMWSTPPSHHRLHRDKPG TFHSTWQRPCNPPPAESLSLSLGSHQPLPRYLPEPPST(+) MEAPANSVAVADGNPKTATETPRVEDYKDAAMYYGTYPAYLYGAYGGWGEYSTYLSHDGAETPT AGAYGDMYYGYSPYGYSTSGHDSQMYGSQHYQYQPTYNKQQNTTGKPSNNGKTENPAALPQGDV SANGVDSLKGQKKTNLLPKASQNTPGSNGSYGRPSGRFGNYQNQTNRTTYPCYSSQIFNGKQQK LPTGNRSLTTSNSKSKGQSRNQNTYPHLMLMEAPANSVAVADGNPKTATETPRVEDYKDAAMYY GTYPAYLYGAYGGWGEYSTYLSHDGAETPTAGAYGDMYYGYSPYGYSTSGHDSQMYGSQHYQYQ PTYNKQQNTTGKPSNNGKTENPAALPQGDVSANGVDSLKGQKKTNLLPKASQNTPGSNGSYGRP SGRFGNYQNQTNRTTYPCYSSQIFNGKQQKLPTGNRSLTTSNSKSKGQSRNQNTYPHLMLMEAP ANSVAVADGNPKTATETPRVEDYKDAAMYYGTYPAYLYGAYGGWGEYSTYLSHDGAETPTAGAY GDMYYGYSPYGYSTSGHDSQMYGSQHYQYQPTYNKQQNTTGKPSNNGKTENPAALPQGDVSANG VDSLKGQKKTNLLPKASQNTPGSNGSYGRPSGRFGNYQNQTNRTTYPCYSSQIFNGKQQKLPTG NRSLTTSNSKSKGQSRNQNTYPHLMLMEAPANSVAVADGNPKTATETPRVEDYKDAAMYYGTYP AYLYGAYGGWGEYSTYLSHDGAETPTAGAYGDMYYGYSPYGYSTSGHDSQMYGSQHYQYQPTYN KQQNTTGKPSNNGKTENPAALPQGDVSANGVDSLKGQKKTNLLPKASQNTPGSNGSYGRPSGRF GNYQNQTNRTTYPCYSSQIFNGKQQKLPTGNRSLTTSNSKSKGQSRNQNTYPHLM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os07g0170300_circ_g.3

Address

Any questions?

Supported by