Plant Circular RNA Database

Detail information of Os04g0467800_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0467800_circ_g.2
					
						ID in PlantcircBase
						osa_circ_024134
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 23367855-23368896  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0467800						
					
						Parent gene annotation
						
							Similar to OSIGBa0128P10.4 protein. (Os04t0467800-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0467800_circ_g.1 Os04g0467800_circ_g.3 						
					
						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
						Os04t0467800-01:3

General Information
CircRNA Name	Os04g0467800_circ_g.2
ID in PlantcircBase	osa_circ_024134
Alias	NA
Organism	Oryza sativa
Position	chr4: 23367855-23368896 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0467800
Parent gene annotation	Similar to OSIGBa0128P10.4 protein. (Os04t0467800-01)
Parent gene strand	-
Alternative splicing	Os04g0467800_circ_g.1 Os04g0467800_circ_g.3
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	Os04t0467800-01:3

			
						 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  
						
							AAGTTAAGCTCAATTGTCCATACCAGCAATATCAGAAGCATTGGGGAGGCTTGCCATTGGCTGA
CGATGAATTTGGGTGGCAATGCGACTGTCGAATAGCcccatcgtccttgtggatgtacgcatga
attcttgccgtaggatcctcaagagtcaaccttagacaacaattgccagccaatagtgaacaaa
gatgacta

						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: 292
Transcript exons: 23367855-23368010,23368205-23368263,23368820-23368896
CCCATCGTCCTTGTGGATGTACGCATGAATTCTTGCCGTAGGATCCTCAAGAGTCAACCTTAGA
CAACAATTGCCAGCCAATAGTGAACAAAGATGACTAGCTCCACGTGGATATGCTGCAACAACTC
GAACCAAGGTTTTGAATTTGTGCGTCACCTCTCCATGGGTGAGCGACTCCATCAATGTTGTGTA
ACCTGCTCTCTCGTATTCTACATCAGCAATATCAGAAGCATTGGGGAGGCTTGCCATTGGCTGA
CGATGAATTTGGGTGGCAATGCGACTGTCGAATAGC
						
						Genomic sequence
						
							CCCATCGTCCTTGTGGATGTACGCATGAATTCTTGCCGTAGGATCCTCAAGAGTCAACCTTAGA
CAACAATTGCCAGCCAATAGTGAACAAAGATGACTAGCTCCACGTGGATATGCTGCAACAACTC
GAACCAAGGTTTTGAATTTGTGCGTCACCTGGCAAAAAAAGGAGATATAGATGCTGGTTTTTAG
ACAGAATTCAGAACACCACCACTGGTGAAAACAGTAGAATGTACTCATAAGGGAAACATTCTCA
TGACACCTACAGAGGAATCTCGTTATTGGGGTAGCATCAGGGGGGGACTAGCACCACGAATTAA
ACAATAGAACAGTTGGGAAAAGAGTATTACCTCTCCATGGGTGAGCGACTCCATCAATGTTGTG
TAACCTGCTCTCTCGTATTCTACATCTGACAGAATTGATGAGTTAACATCAAATGGCAAGTTTG
GGAACAACAGATGGTGGTAACAGAAGTGCATTAATCAGCATGAATCAGGGCAAAAATGCAAGAC
AACAAAAAGATCACCATTCGTAATGGTAGCACATGAAAAAAAAAACGAATTTTCTCTCTCTGGA
GTGGGAAATGGCAAGGCCGGACTTAGTAGGCTAGAATTTTTGTTCTTAAGCAATTAACCACTGA
ACAAGAAGTATAGTAAGATGAAACAGAAATAGCAGACAGATATCACCATCTGTGAAAAGGTAGT
GCATTAAAAAAAAAGAAAGATGAGAGAAATTGGCATGGTCTTTTGTTCTTATGCAATTCAATTA
ACCAGTGAACAGAAATTTAGTCAATGGAAGAGGAAATCATAGCATTCAAAGCACCTGCACAGAA
GATACTAGAACCTTGCAAACAATTAGAAGGATAACAACCAGCACATGCATCGGAGAACTTCACA
CCATGTAACAAAATAAGCTCAGAGCAATCATGCAAGACTGACTAAAAAGTTAAGCTCAATTGTC
CATACCAGCAATATCAGAAGCATTGGGGAGGCTTGCCATTGGCTGACGATGAATTTGGGTGGCA
ATGCGACTGTCGAATAGC

Sequences
Splice junction sequence	AAGTTAAGCTCAATTGTCCATACCAGCAATATCAGAAGCATTGGGGAGGCTTGCCATTGGCTGA CGATGAATTTGGGTGGCAATGCGACTGTCGAATAGCcccatcgtccttgtggatgtacgcatga attcttgccgtaggatcctcaagagtcaaccttagacaacaattgccagccaatagtgaacaaa gatgacta
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: 292 Transcript exons: 23367855-23368010,23368205-23368263,23368820-23368896 CCCATCGTCCTTGTGGATGTACGCATGAATTCTTGCCGTAGGATCCTCAAGAGTCAACCTTAGA CAACAATTGCCAGCCAATAGTGAACAAAGATGACTAGCTCCACGTGGATATGCTGCAACAACTC GAACCAAGGTTTTGAATTTGTGCGTCACCTCTCCATGGGTGAGCGACTCCATCAATGTTGTGTA ACCTGCTCTCTCGTATTCTACATCAGCAATATCAGAAGCATTGGGGAGGCTTGCCATTGGCTGA CGATGAATTTGGGTGGCAATGCGACTGTCGAATAGC
Genomic sequence	CCCATCGTCCTTGTGGATGTACGCATGAATTCTTGCCGTAGGATCCTCAAGAGTCAACCTTAGA CAACAATTGCCAGCCAATAGTGAACAAAGATGACTAGCTCCACGTGGATATGCTGCAACAACTC GAACCAAGGTTTTGAATTTGTGCGTCACCTGGCAAAAAAAGGAGATATAGATGCTGGTTTTTAG ACAGAATTCAGAACACCACCACTGGTGAAAACAGTAGAATGTACTCATAAGGGAAACATTCTCA TGACACCTACAGAGGAATCTCGTTATTGGGGTAGCATCAGGGGGGGACTAGCACCACGAATTAA ACAATAGAACAGTTGGGAAAAGAGTATTACCTCTCCATGGGTGAGCGACTCCATCAATGTTGTG TAACCTGCTCTCTCGTATTCTACATCTGACAGAATTGATGAGTTAACATCAAATGGCAAGTTTG GGAACAACAGATGGTGGTAACAGAAGTGCATTAATCAGCATGAATCAGGGCAAAAATGCAAGAC AACAAAAAGATCACCATTCGTAATGGTAGCACATGAAAAAAAAAACGAATTTTCTCTCTCTGGA GTGGGAAATGGCAAGGCCGGACTTAGTAGGCTAGAATTTTTGTTCTTAAGCAATTAACCACTGA ACAAGAAGTATAGTAAGATGAAACAGAAATAGCAGACAGATATCACCATCTGTGAAAAGGTAGT GCATTAAAAAAAAAGAAAGATGAGAGAAATTGGCATGGTCTTTTGTTCTTATGCAATTCAATTA ACCAGTGAACAGAAATTTAGTCAATGGAAGAGGAAATCATAGCATTCAAAGCACCTGCACAGAA GATACTAGAACCTTGCAAACAATTAGAAGGATAACAACCAGCACATGCATCGGAGAACTTCACA CCATGTAACAAAATAAGCTCAGAGCAATCATGCAAGACTGACTAAAAAGTTAAGCTCAATTGTC CATACCAGCAATATCAGAAGCATTGGGGAGGCTTGCCATTGGCTGACGATGAATTTGGGTGGCA ATGCGACTGTCGAATAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.228902439

Conservation Information
Conserved circRNAs	NA
PMCS	0.228902439

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23368880-23367914(+)
23368232-23367879(+)
23368855-23368830(-)
23367882-23368830(-)
						
						Potential amino acid sequence
						
							MRLSNSPIVLVDVRMNSCRRILKSQP*(+)
MLCNLLSRILHQQYQKHWGGLPLADDEFGWQCDCRIAPSSLWMYA*(+)
MASLPNASDIADVEYERAGYTTLMESLTHGEVTHKFKTLVRVVAAYPRGASHLCSLLAGNCCLR
LTLEDPTARIHAYIHKDDGAIRQSHCHPNSSSANGKPPQCF*(-)
MRTSTRTMGLFDSRIATQIHRQPMASLPNASDIADVEYERAGYTTLMESLTHGEVTHKFKTLVR
VVAAYPRGASHLCSLLAGNCCLRLTLEDPTARIHAYIHKDDGAIRQSHCHPNSSSANGKPPQCF
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23368880-23367914(+) 23368232-23367879(+) 23368855-23368830(-) 23367882-23368830(-)
Potential amino acid sequence	MRLSNSPIVLVDVRMNSCRRILKSQP(+) MLCNLLSRILHQQYQKHWGGLPLADDEFGWQCDCRIAPSSLWMYA(+) MASLPNASDIADVEYERAGYTTLMESLTHGEVTHKFKTLVRVVAAYPRGASHLCSLLAGNCCLR LTLEDPTARIHAYIHKDDGAIRQSHCHPNSSSANGKPPQCF(-) MRTSTRTMGLFDSRIATQIHRQPMASLPNASDIADVEYERAGYTTLMESLTHGEVTHKFKTLVR VVAAYPRGASHLCSLLAGNCCLRLTLEDPTARIHAYIHKDDGAIRQSHCHPNSSSANGKPPQCF (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0467800_circ_g.2

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