Plant Circular RNA Database

Detail information of Os01g0972900_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0972900_circ_g.2
					
						ID in PlantcircBase
						osa_circ_006023
					
						Alias
						Os_ciR3573
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 42950843-42952236  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0972900						
					
						Parent gene annotation
						
							Similar to Clone ZZD405 mRNA sequence. (Fragment). (Os01t0972900
-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0972900_circ_g.1 Os01g0972900_circ_g.3 						
					
						Support reads
						2/1
					
						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  
						
							GT-AG							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
						Os01t0972900-01:5

General Information
CircRNA Name	Os01g0972900_circ_g.2
ID in PlantcircBase	osa_circ_006023
Alias	Os_ciR3573
Organism	Oryza sativa
Position	chr1: 42950843-42952236 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0972900
Parent gene annotation	Similar to Clone ZZD405 mRNA sequence. (Fragment). (Os01t0972900 -01)
Parent gene strand	+
Alternative splicing	Os01g0972900_circ_g.1 Os01g0972900_circ_g.3
Support reads	2/1
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	GT-AG 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	Os01t0972900-01:5

			
						 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  
						
							GTCCTAAATGATGCATATTACTCATTTGCAGACAATAGTAACAGGAGCCGGGGATGAAACCCTC
AGATTTTGGAATATTTTTCCTTCAATGAAGACACAGatttgggatagctctcgctgtaaacgga
ttaggaacatgggaggacaccaaacacggactggtgtattagcatggagctcccgaatcttgtc
ctccggta

									
								

					

						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: 672
Transcript exons: 42950843-42951022,42951157-42951411,42951493-42951597,42
952019-42952081,42952168-42952236
ATTTGGGATAGCTCTCGCTGTAAACGGATTAGGAACATGGGAGGACACCAAACACGGACTGGTG
TATTAGCATGGAGCTCCCGAATCTTGTCCTCCGGTAGCAGGGACAAGAACATATTGCAGCATGA
CATCCGTGTCCCAAGTGACTATATCAGCAAGTTCTCAGGGCACAGATCAGAGGTCTGTGGACTG
AAATGGTCGCACGACGACCGTGAGCTTGCATCCGGTGGAAATGATAATCAGCTGCTAGTATGGA
ACCAACGTTCGCAGCAGCCGATATTGAGGCTGACAGAACACACAGCTGCAGTTAAAGCAATAGC
ATGGTCACCACATCAGCAAGGCCTCCTGGCATCAGGTGGTGGAACCGCTGATAGGTGTATCAGG
TTCTGGAACACGGTTAATGGAAACATGCTGAATTCAGTGGACACAGGCAGCCAGGTTTGTAATC
TTGCCTGGTGTAAAAATGTAAATGAGCTTGTGAGCACTCATGGGTATTCCCAAAACCAAATCAT
GGTGTGGAAGTACCCATCTATGTCAAAGGTTGCTACTCTAACTGGACACACGCTGCGAGTGCTT
TACCTTGCAATGTCACCTGATGGACAGACAATAGTAACAGGAGCCGGGGATGAAACCCTCAGAT
TTTGGAATATTTTTCCTTCAATGAAGACACAG
						
					

						Genomic sequence
						
							ATTTGGGATAGCTCTCGCTGTAAACGGATTAGGAACATGGGAGGACACCAAACACGGACTGGTG
TATTAGCATGGAGCTCCCGAATCTTGTCCTCCGGTAGCAGGGACAAGAACATATTGCAGCATGA
CATCCGTGTCCCAAGTGACTATATCAGCAAGTTCTCAGGGCACAGATCAGAGGTGAGACTTCTA
ACTACTTCCAAGCCATAGGTTTTTGGAAAATAGCTCACTAACTATGCAAGTTAAAATCATCCCA
TCTCACAGTAAGATTTCAGAACCATGTATGTGCATCAAGTGACAGTTTTTTTGGTCAGGTCTGT
GGACTGAAATGGTCGCACGACGACCGTGAGCTTGCATCCGGTGGAAATGATAATCAGCTGCTAG
TATGGAACCAACGTTCGCAGCAGCCGATATTGAGGCTGACAGAACACACAGCTGCAGTTAAAGC
AATAGCATGGTCACCACATCAGCAAGGCCTCCTGGCATCAGGTGGTGGAACCGCTGATAGGTGT
ATCAGGTTCTGGAACACGGTTAATGGAAACATGCTGAATTCAGTGGACACAGGCAGCCAGGCGA
GTAGTTCTGAACAAGCCTCTAAAAAGTAGTTCAGTGAATTTTTACTGTCATCCTCACCAGCTGC
TTTCTGTTTTCAGGTTTGTAATCTTGCCTGGTGTAAAAATGTAAATGAGCTTGTGAGCACTCAT
GGGTATTCCCAAAACCAAATCATGGTGTGGAAGTACCCATCTATGTCAAAGGTAAGCTTAAATT
CCCGTGGGCTGTCAAGCCTACTAATTCACCAGTTAGACAATTGTGCATCAAGTAATCACTCATT
CGGATAAAAACGTGAAAAAAAGCAGAGGAAGTTATGTGTCTGATTTCTCCTAGGGTTGTTTCCA
AAGAACTCATTCCTTTCTGTGGGCCGAGACATTGACTCATGGATTGCTTAAACGCTTAAAAGGA
ATTTAGTATCAACATAGTTGACGAGCATGTAATGCTTAAAAAGAACAATATCAGTATGGCTGCA
AATCCAAGTGAAGTATTTCACAGGGGGCTATTTTCATTTGTATTTGCAGATAAGGATAAGAGTA
GAATAATTCCTTTGAATTTTTAATATCTGTTCAAGAAAGATTTCCACTAGTGCAGTACCACTAA
GTATTTTATGTTTTCGATAAACAGGTTGCTACTCTAACTGGACACACGCTGCGAGTGCTTTACC
TTGCAATGTCACCTGATGGACAGGTAAATCTTTTTCCAAACTGCAAATCATGTATCCGGAAAAA
TATTCCTGGGAATCGTCCTAAATGATGCATATTACTCATTTGCAGACAATAGTAACAGGAGCCG
GGGATGAAACCCTCAGATTTTGGAATATTTTTCCTTCAATGAAGACACAG
						
					

			
		

Sequences
Splice junction sequence	GTCCTAAATGATGCATATTACTCATTTGCAGACAATAGTAACAGGAGCCGGGGATGAAACCCTC AGATTTTGGAATATTTTTCCTTCAATGAAGACACAGatttgggatagctctcgctgtaaacgga ttaggaacatgggaggacaccaaacacggactggtgtattagcatggagctcccgaatcttgtc ctccggta
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: 672 Transcript exons: 42950843-42951022,42951157-42951411,42951493-42951597,42 952019-42952081,42952168-42952236 ATTTGGGATAGCTCTCGCTGTAAACGGATTAGGAACATGGGAGGACACCAAACACGGACTGGTG TATTAGCATGGAGCTCCCGAATCTTGTCCTCCGGTAGCAGGGACAAGAACATATTGCAGCATGA CATCCGTGTCCCAAGTGACTATATCAGCAAGTTCTCAGGGCACAGATCAGAGGTCTGTGGACTG AAATGGTCGCACGACGACCGTGAGCTTGCATCCGGTGGAAATGATAATCAGCTGCTAGTATGGA ACCAACGTTCGCAGCAGCCGATATTGAGGCTGACAGAACACACAGCTGCAGTTAAAGCAATAGC ATGGTCACCACATCAGCAAGGCCTCCTGGCATCAGGTGGTGGAACCGCTGATAGGTGTATCAGG TTCTGGAACACGGTTAATGGAAACATGCTGAATTCAGTGGACACAGGCAGCCAGGTTTGTAATC TTGCCTGGTGTAAAAATGTAAATGAGCTTGTGAGCACTCATGGGTATTCCCAAAACCAAATCAT GGTGTGGAAGTACCCATCTATGTCAAAGGTTGCTACTCTAACTGGACACACGCTGCGAGTGCTT TACCTTGCAATGTCACCTGATGGACAGACAATAGTAACAGGAGCCGGGGATGAAACCCTCAGAT TTTGGAATATTTTTCCTTCAATGAAGACACAG
Genomic sequence	ATTTGGGATAGCTCTCGCTGTAAACGGATTAGGAACATGGGAGGACACCAAACACGGACTGGTG TATTAGCATGGAGCTCCCGAATCTTGTCCTCCGGTAGCAGGGACAAGAACATATTGCAGCATGA CATCCGTGTCCCAAGTGACTATATCAGCAAGTTCTCAGGGCACAGATCAGAGGTGAGACTTCTA ACTACTTCCAAGCCATAGGTTTTTGGAAAATAGCTCACTAACTATGCAAGTTAAAATCATCCCA TCTCACAGTAAGATTTCAGAACCATGTATGTGCATCAAGTGACAGTTTTTTTGGTCAGGTCTGT GGACTGAAATGGTCGCACGACGACCGTGAGCTTGCATCCGGTGGAAATGATAATCAGCTGCTAG TATGGAACCAACGTTCGCAGCAGCCGATATTGAGGCTGACAGAACACACAGCTGCAGTTAAAGC AATAGCATGGTCACCACATCAGCAAGGCCTCCTGGCATCAGGTGGTGGAACCGCTGATAGGTGT ATCAGGTTCTGGAACACGGTTAATGGAAACATGCTGAATTCAGTGGACACAGGCAGCCAGGCGA GTAGTTCTGAACAAGCCTCTAAAAAGTAGTTCAGTGAATTTTTACTGTCATCCTCACCAGCTGC TTTCTGTTTTCAGGTTTGTAATCTTGCCTGGTGTAAAAATGTAAATGAGCTTGTGAGCACTCAT GGGTATTCCCAAAACCAAATCATGGTGTGGAAGTACCCATCTATGTCAAAGGTAAGCTTAAATT CCCGTGGGCTGTCAAGCCTACTAATTCACCAGTTAGACAATTGTGCATCAAGTAATCACTCATT CGGATAAAAACGTGAAAAAAAGCAGAGGAAGTTATGTGTCTGATTTCTCCTAGGGTTGTTTCCA AAGAACTCATTCCTTTCTGTGGGCCGAGACATTGACTCATGGATTGCTTAAACGCTTAAAAGGA ATTTAGTATCAACATAGTTGACGAGCATGTAATGCTTAAAAAGAACAATATCAGTATGGCTGCA AATCCAAGTGAAGTATTTCACAGGGGGCTATTTTCATTTGTATTTGCAGATAAGGATAAGAGTA GAATAATTCCTTTGAATTTTTAATATCTGTTCAAGAAAGATTTCCACTAGTGCAGTACCACTAA GTATTTTATGTTTTCGATAAACAGGTTGCTACTCTAACTGGACACACGCTGCGAGTGCTTTACC TTGCAATGTCACCTGATGGACAGGTAAATCTTTTTCCAAACTGCAAATCATGTATCCGGAAAAA TATTCCTGGGAATCGTCCTAAATGATGCATATTACTCATTTGCAGACAATAGTAACAGGAGCCG GGGATGAAACCCTCAGATTTTGGAATATTTTTCCTTCAATGAAGACACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.376022525

Conservation Information
Conserved circRNAs	NA
PMCS	0.376022525

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							42950880-42952233(+)
42950975-42952056(-)
						
						Potential amino acid sequence
						
							MGGHQTRTGVLAWSSRILSSGSRDKNILQHDIRVPSDYISKFSGHRSEVCGLKWSHDDRELASG
GNDNQLLVWNQRSQQPILRLTEHTAAVKAIAWSPHQQGLLASGGGTADRCIRFWNTVNGNMLNS
VDTGSQVCNLAWCKNVNELVSTHGYSQNQIMVWKYPSMSKVATLTGHTLRVLYLAMSPDGQTIV
TGAGDETLRFWNIFPSMKTQIWDSSRCKRIRNMGGHQTRTGVLAWSSRILSSGSRDKNILQHDI
RVPSDYISKFSGHRSEVCGLKWSHDDRELASGGNDNQLLVWNQRSQQPILRLTEHTAAVKAIAW
SPHQQGLLASGGGTADRCIRFWNTVNGNMLNSVDTGSQVCNLAWCKNVNELVSTHGYSQNQIMV
WKYPSMSKVATLTGHTLRVLYLAMSPDGQTIVTGAGDETLRFWNIFPSMKTQIWDSSRCKRIRN
MGGHQTRTGVLAWSSRILSSGSRDKNILQHDIRVPSDYISKFSGHRSEVCGLKWSHDDRELASG
GNDNQLLVWNQRSQQPILRLTEHTAAVKAIAWSPHQQGLLASGGGTADRCIRFWNTVNGNMLNS
VDTGSQVCNLAWCKNVNELVSTHGYSQNQIMVWKYPSMSKVATLTGHTLRVLYLAMSPDGQTIV
TGAGDETLRFWNIFPSMKTQIWDSSRCKRIRNMGGHQTRTGVLAWSSRILSSGSRDKNILQHDI
RVPSDYISKFSGHRSEVCGLKWSHDDRELASGGNDNQLLVWNQRSQQPILRLTEHTAAVKAIAW
SPHQQGLLASGGGTADRCIRFWNTVNGNMLNSVDTGSQVCNLAWCKNVNELVSTHGYSQNQIMV
WKYPSMSKVATLTGHTLRVLYLAMSPDGQTIVTGAGDETLRFWNIFPSMKTQ(+)
MSCCNMFLSLLPEDKIRELHANTPVRVWCPPMFLIRLQRELSQICVFIEGKIFQNLRVSSPAPV
TIVCPSGDIAR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	42950880-42952233(+) 42950975-42952056(-)
Potential amino acid sequence	MGGHQTRTGVLAWSSRILSSGSRDKNILQHDIRVPSDYISKFSGHRSEVCGLKWSHDDRELASG GNDNQLLVWNQRSQQPILRLTEHTAAVKAIAWSPHQQGLLASGGGTADRCIRFWNTVNGNMLNS VDTGSQVCNLAWCKNVNELVSTHGYSQNQIMVWKYPSMSKVATLTGHTLRVLYLAMSPDGQTIV TGAGDETLRFWNIFPSMKTQIWDSSRCKRIRNMGGHQTRTGVLAWSSRILSSGSRDKNILQHDI RVPSDYISKFSGHRSEVCGLKWSHDDRELASGGNDNQLLVWNQRSQQPILRLTEHTAAVKAIAW SPHQQGLLASGGGTADRCIRFWNTVNGNMLNSVDTGSQVCNLAWCKNVNELVSTHGYSQNQIMV WKYPSMSKVATLTGHTLRVLYLAMSPDGQTIVTGAGDETLRFWNIFPSMKTQIWDSSRCKRIRN MGGHQTRTGVLAWSSRILSSGSRDKNILQHDIRVPSDYISKFSGHRSEVCGLKWSHDDRELASG GNDNQLLVWNQRSQQPILRLTEHTAAVKAIAWSPHQQGLLASGGGTADRCIRFWNTVNGNMLNS VDTGSQVCNLAWCKNVNELVSTHGYSQNQIMVWKYPSMSKVATLTGHTLRVLYLAMSPDGQTIV TGAGDETLRFWNIFPSMKTQIWDSSRCKRIRNMGGHQTRTGVLAWSSRILSSGSRDKNILQHDI RVPSDYISKFSGHRSEVCGLKWSHDDRELASGGNDNQLLVWNQRSQQPILRLTEHTAAVKAIAW SPHQQGLLASGGGTADRCIRFWNTVNGNMLNSVDTGSQVCNLAWCKNVNELVSTHGYSQNQIMV WKYPSMSKVATLTGHTLRVLYLAMSPDGQTIVTGAGDETLRFWNIFPSMKTQ(+) MSCCNMFLSLLPEDKIRELHANTPVRVWCPPMFLIRLQRELSQICVFIEGKIFQNLRVSSPAPV TIVCPSGDIAR*(-)
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 Os01g0972900_circ_g.2

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