Plant Circular RNA Database

Detail information of Os01g0563000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0563000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_002239
					
						Alias
						Os_ciR2232
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 21424262-21433322  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os01g0563000						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os01t0563000-01);Peptidyl-prolyl c
is-trans isomerase, FKBP-type domain containing protein. (Os01t0
563000-02);Hypothetical conserved gene. (Os01t0563000-03);Hypoth
etical conserved gene. (Os01t0563000-04);Hypothetical conserved 
gene. (Os01t0563000-05);Hypothetical conserved gene. (Os01t05630
00-06)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0563000_circ_igg.1 Os01g0563000_circ_igg.2 Os01g0563000_circ_igg.3 Os01g0563000_circ_igg.4 Os01g0563000_circ_g.1 Os01g0563000_circ_g.2 Os01g0563000_circ_g.4 Os01g0563000_circ_g.5 Os01g0563000_circ_g.6 Os01g0563000_circ_g.7 Os01g0563000_circ_g.8 Os01g0563000_circ_g.9 Os01g0563000_circ_g.10 Os01g0563000_circ_g.11 Os01g0563000_circ_g.12 Os01g0563000_circ_g.13 Os01g0563000_circ_g.14 						
					
						Support reads
						5
					
						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  
						
							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
						Os01t0563000-02:8
Os01t0563000-01:7
Os01t0563000-04:8
Os01t0563000-03:2
Os01t0563000-05:3
Os01t0563000-06:1

General Information
CircRNA Name	Os01g0563000_circ_g.3
ID in PlantcircBase	osa_circ_002239
Alias	Os_ciR2232
Organism	Oryza sativa
Position	chr1: 21424262-21433322 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Os01g0563000
Parent gene annotation	Hypothetical conserved gene. (Os01t0563000-01);Peptidyl-prolyl c is-trans isomerase, FKBP-type domain containing protein. (Os01t0 563000-02);Hypothetical conserved gene. (Os01t0563000-03);Hypoth etical conserved gene. (Os01t0563000-04);Hypothetical conserved gene. (Os01t0563000-05);Hypothetical conserved gene. (Os01t05630 00-06)
Parent gene strand	+
Alternative splicing	Os01g0563000_circ_igg.1 Os01g0563000_circ_igg.2 Os01g0563000_circ_igg.3 Os01g0563000_circ_igg.4 Os01g0563000_circ_g.1 Os01g0563000_circ_g.2 Os01g0563000_circ_g.4 Os01g0563000_circ_g.5 Os01g0563000_circ_g.6 Os01g0563000_circ_g.7 Os01g0563000_circ_g.8 Os01g0563000_circ_g.9 Os01g0563000_circ_g.10 Os01g0563000_circ_g.11 Os01g0563000_circ_g.12 Os01g0563000_circ_g.13 Os01g0563000_circ_g.14
Support reads	5
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	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	Os01t0563000-02:8 Os01t0563000-01:7 Os01t0563000-04:8 Os01t0563000-03:2 Os01t0563000-05:3 Os01t0563000-06:1

			
						 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  
						
							TGCACAGCTGGAAGAAATGTGGATTTCCTGCACTTTTAAAGCGGCTAAGTGCGCAATCCAGCTA
GGGTGCTACATGCAAGCATCGTGCTATTACAGCGAGttcacttcactggagaactagttgacgg
tacgcagttcgtgtcaagccgagaaaatgacattccagagaggtttatactggggcaaggtata
aaactata

									
								

					

						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: 1298
Transcript exons: 21424262-21424348,21424515-21424790,21425450-21425524,21
425626-21425706,21426007-21426198,21431623-21431712,2143
1817-21431995,21433005-21433322
TTCACTTCACTGGAGAACTAGTTGACGGTACGCAGTTCGTGTCAAGCCGAGAAAATGACATTCC
AGAGAGGTTTATACTGGGGCAAGAGGATGTGATGCATGGTTTCAACTTAGCTGTCAGTTCGATG
CAACCAGGGGAGAAAGCTATATTCACTATCCCTTCAGCGTTAACCATGACAAAAGCTGGCTCCC
CTGCTAGCATCCCGTCAAACATACCTCCCAACCAAACACTACGGTTTGAGATTGAGCTCATCGC
CATGTTTACTATAATTGACATTTTCAAAGATGAAGGCATATTGAAAAAGATTGTCAAGAACGCA
GAACCCGACAGAAAACAATCTCACTCAAGTGATTTTGTATTTGTGAAATACGACGCATGCCTGA
TGGATGGAACTTCAGTGTCCAAATCTGAAGGTGTTGAATTCAGCCTTACCGACGGCTTCTTCTG
TCCTGCATTTGCACATGCTGTGCATACTATGAAAGAAGGAGAGGAAGCAGTACTAATTGTGAAA
CCAAAATATGCTTTCGGTGAACAAGGAAGACCTTCTCAAGGAGAGGAAGCTGCTGTGCCCCCAG
ATGCAACTCTTTATGTGCACCTCCTATTTGTGTGCTGGATACGGCGAATTGGGGAAGACCAAGC
AATTGCCAAGAAAACTCTAAGGATAGGGAACTCACAGAGGATACACACACAAAGTCAAGCTGTG
GTGAAAGTGCGGTTGCTCGGCAAACTTCAAGATGGAACTGTTTTTGATCGTAGAGGTTACGGCG
ACGATGAACCGTTCGAGTTCGTGGTAGATGAAGGTCAAGTTATTGATGGCCTGGATGAATCTGT
AATGACAATGGAGGAGGGAGAAGTTGCCGAGTTCACTATTCCACCCCAGCACGCATTTGATGCC
GTTGGGTCAGATCAGCATCAGTTTGCCTTTGTGCCGCGCAATGCAACCGTCGTCTACAAGATCG
AGCTCTTGTCCGTCGTTAATGAGAAACATCCGTTGTACATTCCGAGCCGTGATGAAATTGTTGA
ATATGCAAGTAGGAAGGAAGAGGAAGGGGACATATACTTTAACTTGGGTAAACATTTGAGAGCT
CACAGGAGATATTTCAAGGCCAGACAAATCATTGAATATTCACGCTTCGGGGTAAGGAGAGGGA
AAATTAATTTAATAAAACTGCTGTCCATCCCAACATCAGAAATTGATGCACAGCTGGAAGAAAT
GTGGATTTCCTGCACTTTTAAAGCGGCTAAGTGCGCAATCCAGCTAGGGTGCTACATGCAAGCA
TCGTGCTATTACAGCGAG
Transcript length: 1323
Transcript exons: 21424262-21424348,21424515-21424790,21425450-21425524,21
425626-21425706,21426007-21426198,21431623-21431712,2143
1817-21432020,21433005-21433322
TTCACTTCACTGGAGAACTAGTTGACGGTACGCAGTTCGTGTCAAGCCGAGAAAATGACATTCC
AGAGAGGTTTATACTGGGGCAAGAGGATGTGATGCATGGTTTCAACTTAGCTGTCAGTTCGATG
CAACCAGGGGAGAAAGCTATATTCACTATCCCTTCAGCGTTAACCATGACAAAAGCTGGCTCCC
CTGCTAGCATCCCGTCAAACATACCTCCCAACCAAACACTACGGTTTGAGATTGAGCTCATCGC
CATGTTTACTATAATTGACATTTTCAAAGATGAAGGCATATTGAAAAAGATTGTCAAGAACGCA
GAACCCGACAGAAAACAATCTCACTCAAGTGATTTTGTATTTGTGAAATACGACGCATGCCTGA
TGGATGGAACTTCAGTGTCCAAATCTGAAGGTGTTGAATTCAGCCTTACCGACGGCTTCTTCTG
TCCTGCATTTGCACATGCTGTGCATACTATGAAAGAAGGAGAGGAAGCAGTACTAATTGTGAAA
CCAAAATATGCTTTCGGTGAACAAGGAAGACCTTCTCAAGGAGAGGAAGCTGCTGTGCCCCCAG
ATGCAACTCTTTATGTGCACCTCCTATTTGTGTGCTGGATACGGCGAATTGGGGAAGACCAAGC
AATTGCCAAGAAAACTCTAAGGATAGGGAACTCACAGAGGATACACACACAAAGTCAAGCTGTG
GTGAAAGTGCGGTTGCTCGGCAAACTTCAAGATGGAACTGTTTTTGATCGTAGAGGTTACGGCG
ACGATGAACCGTTCGAGTTCGTGGTAGATGAAGGTCAAGTTATTGATGGCCTGGATGAATCTGT
AATGACAATGGAGGAGGGAGAAGTTGCCGAGTTCACTATTCCACCCCAGCACGCATTTGATGCC
GTTGGGTCAGATCAGCATCAGTTTGCCTTTGTGCCGCGCAATGCAACCGTCGTCTACAAGATCG
AGCTCTTGTCCGTCGTTAATGTACGTTATTATGTTCGTATTACTGGAGAAACATCCGTTGTACA
TTCCGAGCCGTGATGAAATTGTTGAATATGCAAGTAGGAAGGAAGAGGAAGGGGACATATACTT
TAACTTGGGTAAACATTTGAGAGCTCACAGGAGATATTTCAAGGCCAGACAAATCATTGAATAT
TCACGCTTCGGGGTAAGGAGAGGGAAAATTAATTTAATAAAACTGCTGTCCATCCCAACATCAG
AAATTGATGCACAGCTGGAAGAAATGTGGATTTCCTGCACTTTTAAAGCGGCTAAGTGCGCAAT
CCAGCTAGGGTGCTACATGCAAGCATCGTGCTATTACAGCGAG
						
					

						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	TGCACAGCTGGAAGAAATGTGGATTTCCTGCACTTTTAAAGCGGCTAAGTGCGCAATCCAGCTA GGGTGCTACATGCAAGCATCGTGCTATTACAGCGAGttcacttcactggagaactagttgacgg tacgcagttcgtgtcaagccgagaaaatgacattccagagaggtttatactggggcaaggtata aaactata
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: 1298 Transcript exons: 21424262-21424348,21424515-21424790,21425450-21425524,21 425626-21425706,21426007-21426198,21431623-21431712,2143 1817-21431995,21433005-21433322 TTCACTTCACTGGAGAACTAGTTGACGGTACGCAGTTCGTGTCAAGCCGAGAAAATGACATTCC AGAGAGGTTTATACTGGGGCAAGAGGATGTGATGCATGGTTTCAACTTAGCTGTCAGTTCGATG CAACCAGGGGAGAAAGCTATATTCACTATCCCTTCAGCGTTAACCATGACAAAAGCTGGCTCCC CTGCTAGCATCCCGTCAAACATACCTCCCAACCAAACACTACGGTTTGAGATTGAGCTCATCGC CATGTTTACTATAATTGACATTTTCAAAGATGAAGGCATATTGAAAAAGATTGTCAAGAACGCA GAACCCGACAGAAAACAATCTCACTCAAGTGATTTTGTATTTGTGAAATACGACGCATGCCTGA TGGATGGAACTTCAGTGTCCAAATCTGAAGGTGTTGAATTCAGCCTTACCGACGGCTTCTTCTG TCCTGCATTTGCACATGCTGTGCATACTATGAAAGAAGGAGAGGAAGCAGTACTAATTGTGAAA CCAAAATATGCTTTCGGTGAACAAGGAAGACCTTCTCAAGGAGAGGAAGCTGCTGTGCCCCCAG ATGCAACTCTTTATGTGCACCTCCTATTTGTGTGCTGGATACGGCGAATTGGGGAAGACCAAGC AATTGCCAAGAAAACTCTAAGGATAGGGAACTCACAGAGGATACACACACAAAGTCAAGCTGTG GTGAAAGTGCGGTTGCTCGGCAAACTTCAAGATGGAACTGTTTTTGATCGTAGAGGTTACGGCG ACGATGAACCGTTCGAGTTCGTGGTAGATGAAGGTCAAGTTATTGATGGCCTGGATGAATCTGT AATGACAATGGAGGAGGGAGAAGTTGCCGAGTTCACTATTCCACCCCAGCACGCATTTGATGCC GTTGGGTCAGATCAGCATCAGTTTGCCTTTGTGCCGCGCAATGCAACCGTCGTCTACAAGATCG AGCTCTTGTCCGTCGTTAATGAGAAACATCCGTTGTACATTCCGAGCCGTGATGAAATTGTTGA ATATGCAAGTAGGAAGGAAGAGGAAGGGGACATATACTTTAACTTGGGTAAACATTTGAGAGCT CACAGGAGATATTTCAAGGCCAGACAAATCATTGAATATTCACGCTTCGGGGTAAGGAGAGGGA AAATTAATTTAATAAAACTGCTGTCCATCCCAACATCAGAAATTGATGCACAGCTGGAAGAAAT GTGGATTTCCTGCACTTTTAAAGCGGCTAAGTGCGCAATCCAGCTAGGGTGCTACATGCAAGCA TCGTGCTATTACAGCGAG Transcript length: 1323 Transcript exons: 21424262-21424348,21424515-21424790,21425450-21425524,21 425626-21425706,21426007-21426198,21431623-21431712,2143 1817-21432020,21433005-21433322 TTCACTTCACTGGAGAACTAGTTGACGGTACGCAGTTCGTGTCAAGCCGAGAAAATGACATTCC AGAGAGGTTTATACTGGGGCAAGAGGATGTGATGCATGGTTTCAACTTAGCTGTCAGTTCGATG CAACCAGGGGAGAAAGCTATATTCACTATCCCTTCAGCGTTAACCATGACAAAAGCTGGCTCCC CTGCTAGCATCCCGTCAAACATACCTCCCAACCAAACACTACGGTTTGAGATTGAGCTCATCGC CATGTTTACTATAATTGACATTTTCAAAGATGAAGGCATATTGAAAAAGATTGTCAAGAACGCA GAACCCGACAGAAAACAATCTCACTCAAGTGATTTTGTATTTGTGAAATACGACGCATGCCTGA TGGATGGAACTTCAGTGTCCAAATCTGAAGGTGTTGAATTCAGCCTTACCGACGGCTTCTTCTG TCCTGCATTTGCACATGCTGTGCATACTATGAAAGAAGGAGAGGAAGCAGTACTAATTGTGAAA CCAAAATATGCTTTCGGTGAACAAGGAAGACCTTCTCAAGGAGAGGAAGCTGCTGTGCCCCCAG ATGCAACTCTTTATGTGCACCTCCTATTTGTGTGCTGGATACGGCGAATTGGGGAAGACCAAGC AATTGCCAAGAAAACTCTAAGGATAGGGAACTCACAGAGGATACACACACAAAGTCAAGCTGTG GTGAAAGTGCGGTTGCTCGGCAAACTTCAAGATGGAACTGTTTTTGATCGTAGAGGTTACGGCG ACGATGAACCGTTCGAGTTCGTGGTAGATGAAGGTCAAGTTATTGATGGCCTGGATGAATCTGT AATGACAATGGAGGAGGGAGAAGTTGCCGAGTTCACTATTCCACCCCAGCACGCATTTGATGCC GTTGGGTCAGATCAGCATCAGTTTGCCTTTGTGCCGCGCAATGCAACCGTCGTCTACAAGATCG AGCTCTTGTCCGTCGTTAATGTACGTTATTATGTTCGTATTACTGGAGAAACATCCGTTGTACA TTCCGAGCCGTGATGAAATTGTTGAATATGCAAGTAGGAAGGAAGAGGAAGGGGACATATACTT TAACTTGGGTAAACATTTGAGAGCTCACAGGAGATATTTCAAGGCCAGACAAATCATTGAATAT TCACGCTTCGGGGTAAGGAGAGGGAAAATTAATTTAATAAAACTGCTGTCCATCCCAACATCAG AAATTGATGCACAGCTGGAAGAAATGTGGATTTCCTGCACTTTTAAAGCGGCTAAGTGCGCAAT CCAGCTAGGGTGCTACATGCAAGCATCGTGCTATTACAGCGAG
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
						0.537900178

Conservation Information
Conserved circRNAs	NA
PMCS	0.537900178

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21431908-21424279(+)
						
						Potential amino acid sequence
						
							MPLGQISISLPLCRAMQPSSTRSSSCPSLMYVIMFVLLEKHPLYIPSRDEIVEYASRKEEEGDI
YFNLGKHLRAHRRYFKARQIIEYSRFGVRRGKINLIKLLSIPTSEIDAQLEEMWISCTFKAAKC
AIQLGCYMQASCYYSEFTSLEN*(+)
						
						Sponge-miRNAs
						
							osa-miR530-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21431908-21424279(+)
Potential amino acid sequence	MPLGQISISLPLCRAMQPSSTRSSSCPSLMYVIMFVLLEKHPLYIPSRDEIVEYASRKEEEGDI YFNLGKHLRAHRRYFKARQIIEYSRFGVRRGKINLIKLLSIPTSEIDAQLEEMWISCTFKAAKC AIQLGCYMQASCYYSEFTSLEN*(+)
Sponge-miRNAs	osa-miR530-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os01g0563000_circ_g.3

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