Plant Circular RNA Database

Detail information of Os01g0859500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0859500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_004895
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 37183866-37187317  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0859500						
					
						Parent gene annotation
						
							Similar to Basic leucine zipper protein (Liguleless2). (Os01t085
9500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0859500_circ_g.4 Os01g0859500_circ_g.5 Os01g0859500_circ_g.6 Os01g0859500_circ_g.7 Os01g0859500_circ_g.8 Os01g0859500_circ_g.9 Os01g0859500_circ_g.10 Os01g0859500_circ_g.11 Os01g0859500_circ_g.12 Os01g0859500_circ_g.13 						
					
						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
						Os01t0859500-01:9

General Information
CircRNA Name	Os01g0859500_circ_g.3
ID in PlantcircBase	osa_circ_004895
Alias	NA
Organism	Oryza sativa
Position	chr1: 37183866-37187317 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0859500
Parent gene annotation	Similar to Basic leucine zipper protein (Liguleless2). (Os01t085 9500-01)
Parent gene strand	-
Alternative splicing	Os01g0859500_circ_g.4 Os01g0859500_circ_g.5 Os01g0859500_circ_g.6 Os01g0859500_circ_g.7 Os01g0859500_circ_g.8 Os01g0859500_circ_g.9 Os01g0859500_circ_g.10 Os01g0859500_circ_g.11 Os01g0859500_circ_g.12 Os01g0859500_circ_g.13
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	Os01t0859500-01:9

			
						 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  
						
							CATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCCTCCAGCTCGCCG
AAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCCctgctggtagaagctttcgaggctggcg
agcttgtccagggcgatggccatgaggctcatgtagttgggcacgccggggccgtcgttgagcg
tgccggcg

									
								

					

						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
						
							CTGCTGGTAGAAGCTTTCGAGGCTGGCGAGCTTGTCCAGGGCGATGGCCATGAGGCTCATGTAG
TTGGGCACGCCGGGGCCGTCGTTGAGCGTGCCGGCGGCGACGGTGTCGGCGAGCGACTGGTGCA
GCTGCTGCAGCCCCTGCGCGAGCGCCTCCTCCGCCTGCTCCGACGACTGCTGCAGGCTGTAGAT
CCCCAGCATCTGCTGCTCCGTCAGCGGGTCCAGCTGCTGTATCAGTATCTGCATATATAGTCGA
CGATGAGTATATATTCGTGACACGCCCATGCAGGCAACGCCGGCGATGCAGGCGGCGGCGGCGG
CGGAGGCGAACCTTGAGAAGGTCGGAGGGGCGGAAGCCGCCCATCCAGAGGAAGCAGCGCTCGG
CGGGGGTAGCCCACGTGCCGGTGAGGAGGTGGAAGACGTCGGAGCGCGCGAGCGCCGCCTTGAG
CTGGAACAGCTCGTCGTAGTGCTGCATGCACTCCTCCACGATGAGGCCAAGGTTGGTGTCCAGC
AGGTGCGCCTGCAGGCCGCCACGGAGGTCGGTCAGCCGCTTGCTGTCGTCGTCCAGCCAGCGCG
CGTACTCCATGTCGAACATGGCCGCGCCTGCAAACGATTTTACTGCGCCGTGGTGAGAACTCCG
AGGCACACCCTCGTCTGCAAGCTGCAGGCTTGCAGGCTGCAGCTGCTGCTGCTCAACGCATCGA
AAAAAGAAACGGACGGCTCTGATTACCAGAACTCATGTCGCCTGCTGCTCTGCACCCCCCAAGA
AACAGGCCCTGACGATCAATCAAGCAATGCGGGTACCATATTAAATTCCTGCTAATTTATTTCA
TTTCTGGATAGTAGAAAAAAAATAGTACTAGTACTAGCATCAGAAATTCAGAATGGGTGTAACC
TGTGACCGTGCTCTTTGGAGTTCTTGCTCGATCTGCTGAAGCCTGACCCTGCTGGTCTCTAGGT
TTTGCACATAAGCCTGCGAGAAAAAAAAACACACGATCGGAAAGCAGTCTTTTGAACTAGTCTT
GAAGTTTGAGTTCACGGGTTTCTTTTCGTCACCTTTTTTCTCAGCCTGCTCTTCCTCGCAGCCT
CTCTGTTTTGCGCTAATCTCCGTTCTGTCTGAGAACACCCAGCGACCGAGCAGGTTTAACCATG
TAAGAAAAGATACTGGAGCAAGCAAATACATGTCCAAGAACTAGAAACAATGATAATGATCTGG
ATAAGGAGAATGAGAGCTACAACATTATACTATGTACATATCCCACCTTGGCATCCACTGACTT
GCCATCTTTTCTTGTGGATCCATGCTTCCTCTGTGCAAAAAGTACACAACCAGAAAGGCAGAAT
TTTAGAGAGCAGCGTATAACTAGTGTTCCTCCCTATACAGCACAGTGCATGCACACCTCTCAGC
ATCACCAGAGAGAAAGCAACTACAGGGGAGCAAGATAGTGAATCGAGGCCAAAGCTCCTGTCCT
GGCATTGTTGATCCTGCCCAGTAATCATCAGCCACTAGTTGTAGCATCCCAACAAAACTTTCGG
CTGTAGCTGTCCTGATGGCTCAGTAAGCCATGTTGGCCATCACAGCTCTGTAACCATCAGGCAT
TGCCGTGTTTTCGCCAAAGGTGCAGGAGAAACAGATAAGAGGGTGTTTAGCACAGCATCATCCC
TGCTTTTATCACCCAGCCGGGGAGAGACAAAAGGCAATTTAGGGTGACCCATACCACATCATCT
GGTGTCCTTTTGCCTAGGTTCAGCATTGACCAGATGCTAGTACTACAATTAATTAGTCAAATCA
TCCCAAGGACAATCCATTTGCATCCTGACAATCATGCGTGCCCTTTTCTATGCCTATGGCTTTA
TTTCTAGGAGTATTAGTACTAGTACTACAGTACGTCCTTGAGACATCATTAGGACTCAAAGAGA
CATAACCTAATAGGGCTGGTGCATAGTAAGCTTGTTTCGACAACTGCAAACGGGTACCGGTGAC
ATGACGGAGCGATCGATGCTATTGTCACTACCGATTCATAACAGTTTCGTCAAGGACCAGGGAG
ATTTTGGCGATTCGATTTGACAGCATTATTCTCGTAGACAAGTTACTGCCTTTTACCGGATGAG
AGGAGAGCTAGTCGTCGTGGTCCTGCTCTATCTCTTCGAGCTGGGAGGAGTAGAACTGTAGGAG
TACTATAGTACTAGGAGCAGTGGAGCAGGAGGAGGTGATGGAGAAAAGATCAAGAAGGGGAGAG
TGGTAGTAGCAGCAGTACGACCAGTAGTAGCTTGGCTGTACCTTGTCATGGTCTCCTCCTCCGT
GCAGCTGCTGCTGCTGGTGGTGCTGGAGCTGATGCTGCTGCTGAAAGCTTGGGGAGGCAGCAGC
GAGGCCTGGCTTGTAGCTGTAATCATCAGTGGTCACCATCATGACCTCCTGCCCCGGCTGCTGC
TGCTGGTGCTGGTGCTCGGAGGAGGCCCTGATACTCGCTGGGGACACCAACTCCATCTGCGGCA
TTGTGTTCTGGGCTGAGCTCGAGTCAGTGGTGCTCCCGACTGACTGCGAATTCCCCTGTTCAGC
CATTAATTGAGGCAGCGAGAGACAACAGTGAGCGGTCGGTAAGCATGAGATTAATGTGCTCTGA
ATCATCTCTCAGTCTCTCTCTCTCTTTCTCTCTCTGCTCGTGGTGATGCGAACCAAGAGCCAAG
AACAACAGCGGCAACAGTGTCGTCTCGATCTCTTTTCTTGGGTTCAGCGATGAGCAGAGAGAGA
GAGAGAGAGAGAGAGAGAGAGAGAGAGGGGAAGAAGAAGACGATGAATGAATGATCATGGGAAG
CGCGTCCATTTACACTGTGTAGCTGCTGTTGCTGCCTCATTGGCCATGAAGGGAAGATCTCCAG
CGTGGGGGGCCTGGCCGCGAGATATCCTGCCGTCGCTGCCGCTGCCGCCGCTGCATGCATACAA
AGAGAATTAAAAAGCCCGCCCTCATCGATTCCTACTACTGCTACCCTGTTCATCTCTCTCTCTC
TCTCCAACAAGGCTACAGAGAAACAGGAGAGAGAAGCTGCTACTGGTAAATCGCCAATAGTGTG
TAGGTGAAGCCGAGCTGGAGGACATGCTTGATCATGTTTCCATCTTTGTGGCATCGGCATCTCG
CCATTTATGCGGCGCCAACAACAATTTCTCTCTCTCTGTGCATGTGGCCGGCCACTGTGTGCTG
GATCGCAAAAGGCGAGGCATGTCTCGCCATGTGTGGCAATCGGACAAGGTTTGGAGAGACACCG
AAACATCGATGCAGAGAAAGAGAGAGAGAGAAAACAAGAAAGAAAGAAGAAAATTTGGCTTACA
CTTGCTGTGCACGTCGGCTCTGATCATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGG
ATGAGGGCCTCCTCCAGCTCGCCGAAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCC
						
					

			
		

Sequences
Splice junction sequence	CATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCCTCCAGCTCGCCG AAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCCctgctggtagaagctttcgaggctggcg agcttgtccagggcgatggccatgaggctcatgtagttgggcacgccggggccgtcgttgagcg tgccggcg
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	CTGCTGGTAGAAGCTTTCGAGGCTGGCGAGCTTGTCCAGGGCGATGGCCATGAGGCTCATGTAG TTGGGCACGCCGGGGCCGTCGTTGAGCGTGCCGGCGGCGACGGTGTCGGCGAGCGACTGGTGCA GCTGCTGCAGCCCCTGCGCGAGCGCCTCCTCCGCCTGCTCCGACGACTGCTGCAGGCTGTAGAT CCCCAGCATCTGCTGCTCCGTCAGCGGGTCCAGCTGCTGTATCAGTATCTGCATATATAGTCGA CGATGAGTATATATTCGTGACACGCCCATGCAGGCAACGCCGGCGATGCAGGCGGCGGCGGCGG CGGAGGCGAACCTTGAGAAGGTCGGAGGGGCGGAAGCCGCCCATCCAGAGGAAGCAGCGCTCGG CGGGGGTAGCCCACGTGCCGGTGAGGAGGTGGAAGACGTCGGAGCGCGCGAGCGCCGCCTTGAG CTGGAACAGCTCGTCGTAGTGCTGCATGCACTCCTCCACGATGAGGCCAAGGTTGGTGTCCAGC AGGTGCGCCTGCAGGCCGCCACGGAGGTCGGTCAGCCGCTTGCTGTCGTCGTCCAGCCAGCGCG CGTACTCCATGTCGAACATGGCCGCGCCTGCAAACGATTTTACTGCGCCGTGGTGAGAACTCCG AGGCACACCCTCGTCTGCAAGCTGCAGGCTTGCAGGCTGCAGCTGCTGCTGCTCAACGCATCGA AAAAAGAAACGGACGGCTCTGATTACCAGAACTCATGTCGCCTGCTGCTCTGCACCCCCCAAGA AACAGGCCCTGACGATCAATCAAGCAATGCGGGTACCATATTAAATTCCTGCTAATTTATTTCA TTTCTGGATAGTAGAAAAAAAATAGTACTAGTACTAGCATCAGAAATTCAGAATGGGTGTAACC TGTGACCGTGCTCTTTGGAGTTCTTGCTCGATCTGCTGAAGCCTGACCCTGCTGGTCTCTAGGT TTTGCACATAAGCCTGCGAGAAAAAAAAACACACGATCGGAAAGCAGTCTTTTGAACTAGTCTT GAAGTTTGAGTTCACGGGTTTCTTTTCGTCACCTTTTTTCTCAGCCTGCTCTTCCTCGCAGCCT CTCTGTTTTGCGCTAATCTCCGTTCTGTCTGAGAACACCCAGCGACCGAGCAGGTTTAACCATG TAAGAAAAGATACTGGAGCAAGCAAATACATGTCCAAGAACTAGAAACAATGATAATGATCTGG ATAAGGAGAATGAGAGCTACAACATTATACTATGTACATATCCCACCTTGGCATCCACTGACTT GCCATCTTTTCTTGTGGATCCATGCTTCCTCTGTGCAAAAAGTACACAACCAGAAAGGCAGAAT TTTAGAGAGCAGCGTATAACTAGTGTTCCTCCCTATACAGCACAGTGCATGCACACCTCTCAGC ATCACCAGAGAGAAAGCAACTACAGGGGAGCAAGATAGTGAATCGAGGCCAAAGCTCCTGTCCT GGCATTGTTGATCCTGCCCAGTAATCATCAGCCACTAGTTGTAGCATCCCAACAAAACTTTCGG CTGTAGCTGTCCTGATGGCTCAGTAAGCCATGTTGGCCATCACAGCTCTGTAACCATCAGGCAT TGCCGTGTTTTCGCCAAAGGTGCAGGAGAAACAGATAAGAGGGTGTTTAGCACAGCATCATCCC TGCTTTTATCACCCAGCCGGGGAGAGACAAAAGGCAATTTAGGGTGACCCATACCACATCATCT GGTGTCCTTTTGCCTAGGTTCAGCATTGACCAGATGCTAGTACTACAATTAATTAGTCAAATCA TCCCAAGGACAATCCATTTGCATCCTGACAATCATGCGTGCCCTTTTCTATGCCTATGGCTTTA TTTCTAGGAGTATTAGTACTAGTACTACAGTACGTCCTTGAGACATCATTAGGACTCAAAGAGA CATAACCTAATAGGGCTGGTGCATAGTAAGCTTGTTTCGACAACTGCAAACGGGTACCGGTGAC ATGACGGAGCGATCGATGCTATTGTCACTACCGATTCATAACAGTTTCGTCAAGGACCAGGGAG ATTTTGGCGATTCGATTTGACAGCATTATTCTCGTAGACAAGTTACTGCCTTTTACCGGATGAG AGGAGAGCTAGTCGTCGTGGTCCTGCTCTATCTCTTCGAGCTGGGAGGAGTAGAACTGTAGGAG TACTATAGTACTAGGAGCAGTGGAGCAGGAGGAGGTGATGGAGAAAAGATCAAGAAGGGGAGAG TGGTAGTAGCAGCAGTACGACCAGTAGTAGCTTGGCTGTACCTTGTCATGGTCTCCTCCTCCGT GCAGCTGCTGCTGCTGGTGGTGCTGGAGCTGATGCTGCTGCTGAAAGCTTGGGGAGGCAGCAGC GAGGCCTGGCTTGTAGCTGTAATCATCAGTGGTCACCATCATGACCTCCTGCCCCGGCTGCTGC TGCTGGTGCTGGTGCTCGGAGGAGGCCCTGATACTCGCTGGGGACACCAACTCCATCTGCGGCA TTGTGTTCTGGGCTGAGCTCGAGTCAGTGGTGCTCCCGACTGACTGCGAATTCCCCTGTTCAGC CATTAATTGAGGCAGCGAGAGACAACAGTGAGCGGTCGGTAAGCATGAGATTAATGTGCTCTGA ATCATCTCTCAGTCTCTCTCTCTCTTTCTCTCTCTGCTCGTGGTGATGCGAACCAAGAGCCAAG AACAACAGCGGCAACAGTGTCGTCTCGATCTCTTTTCTTGGGTTCAGCGATGAGCAGAGAGAGA GAGAGAGAGAGAGAGAGAGAGAGAGAGGGGAAGAAGAAGACGATGAATGAATGATCATGGGAAG CGCGTCCATTTACACTGTGTAGCTGCTGTTGCTGCCTCATTGGCCATGAAGGGAAGATCTCCAG CGTGGGGGGCCTGGCCGCGAGATATCCTGCCGTCGCTGCCGCTGCCGCCGCTGCATGCATACAA AGAGAATTAAAAAGCCCGCCCTCATCGATTCCTACTACTGCTACCCTGTTCATCTCTCTCTCTC TCTCCAACAAGGCTACAGAGAAACAGGAGAGAGAAGCTGCTACTGGTAAATCGCCAATAGTGTG TAGGTGAAGCCGAGCTGGAGGACATGCTTGATCATGTTTCCATCTTTGTGGCATCGGCATCTCG CCATTTATGCGGCGCCAACAACAATTTCTCTCTCTCTGTGCATGTGGCCGGCCACTGTGTGCTG GATCGCAAAAGGCGAGGCATGTCTCGCCATGTGTGGCAATCGGACAAGGTTTGGAGAGACACCG AAACATCGATGCAGAGAAAGAGAGAGAGAGAAAACAAGAAAGAAAGAAGAAAATTTGGCTTACA CTTGCTGTGCACGTCGGCTCTGATCATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGG ATGAGGGCCTCCTCCAGCTCGCCGAAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.124585407

Conservation Information
Conserved circRNAs	NA
PMCS	0.124585407

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37187255-37183915(+)
37187222-37186387(-)
						
						Potential amino acid sequence
						
							MDEGLLQLAEVGSCRGSRLEVPAGRSFRGWRACPGRWP*(+)
MIRADVHSKSAAAAATAGYLAARPPTLEIFPSWPMRQQQQLHSGNSQSVGSTTDSSSAQNTMPQ
MELVSPASIRASSEHQHQQQQPGQEVMMVTTDDYSYKPGLAAASPSFQQQHQLQHHQQQQLHGG
GDHDKRKHGSTRKDGKSVDAKTERRLAQNREAARKSRLRKKAYVQNLETSRVRLQQIEQELQRA
RSQGLFLGGCRAAGDMSSGAAMFDMEYARWLDDDSKRLTDLRGGLQAHLLDTNLGLIVEECMQH
YDELFQLKAALARSDVFHLLTGTWATPAERCFLWMGGFRPSDLLKILIQQLDPLTEQQMLGIYS
LQQSSEQAEEALAQGLQQLHQSLADTVAAGTLNDGPGVPNYMSLMAIALDKLASLESFYQQGLP
ACCRGSCLLRRAGGGPHPWRQRRRRRRSRHDQSRRAQQVGGSGSDGRISRGQAPHAGDLPFMAN
EAATAATQWEFAVSREHH*(-)
						
						Sponge-miRNAs
						
							osa-miR444a-3p.1 osa-miR3979-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37187255-37183915(+) 37187222-37186387(-)
Potential amino acid sequence	MDEGLLQLAEVGSCRGSRLEVPAGRSFRGWRACPGRWP(+) MIRADVHSKSAAAAATAGYLAARPPTLEIFPSWPMRQQQQLHSGNSQSVGSTTDSSSAQNTMPQ MELVSPASIRASSEHQHQQQQPGQEVMMVTTDDYSYKPGLAAASPSFQQQHQLQHHQQQQLHGG GDHDKRKHGSTRKDGKSVDAKTERRLAQNREAARKSRLRKKAYVQNLETSRVRLQQIEQELQRA RSQGLFLGGCRAAGDMSSGAAMFDMEYARWLDDDSKRLTDLRGGLQAHLLDTNLGLIVEECMQH YDELFQLKAALARSDVFHLLTGTWATPAERCFLWMGGFRPSDLLKILIQQLDPLTEQQMLGIYS LQQSSEQAEEALAQGLQQLHQSLADTVAAGTLNDGPGVPNYMSLMAIALDKLASLESFYQQGLP ACCRGSCLLRRAGGGPHPWRQRRRRRRSRHDQSRRAQQVGGSGSDGRISRGQAPHAGDLPFMAN EAATAATQWEFAVSREHH(-)
Sponge-miRNAs	osa-miR444a-3p.1 osa-miR3979-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0859500_circ_g.3

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