Plant Circular RNA Database

Detail information of Os01g0960400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0960400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_005920
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 42337887-42340020  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0960400						
					
						Parent gene annotation
						
							Protein kinase, core domain containing protein. (Os01t0960400-01
);Similar to predicted protein. (Os01t0960400-02);Similar to Leu
cine-rich repeat transmembrane protein kinase. (Os01t0960400-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0960400_circ_g.2 Os01g0960400_circ_g.3 Os01g0960400_circ_g.4 Os01g0960400_circ_g.5 Os01g0960400_circ_g.6 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						Os01t0960400-03:5
Os01t0960400-01:5
Os01t0960400-02:5

General Information
CircRNA Name	Os01g0960400_circ_g.1
ID in PlantcircBase	osa_circ_005920
Alias	NA
Organism	Oryza sativa
Position	chr1: 42337887-42340020 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0960400
Parent gene annotation	Protein kinase, core domain containing protein. (Os01t0960400-01 );Similar to predicted protein. (Os01t0960400-02);Similar to Leu cine-rich repeat transmembrane protein kinase. (Os01t0960400-03)
Parent gene strand	-
Alternative splicing	Os01g0960400_circ_g.2 Os01g0960400_circ_g.3 Os01g0960400_circ_g.4 Os01g0960400_circ_g.5 Os01g0960400_circ_g.6
Support reads	1
Tissues	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	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	Os01t0960400-03:5 Os01t0960400-01:5 Os01t0960400-02:5

			
						 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  
						
							GTAATGAGGGATGAAAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATGGCAC
CTGTACTTAGGCTGGACTTTGCACGATCTGGAAATActctctaactatatttcttccatgagaa
ataggttgcatccctgtcagcagttccagaaaaacaacaccaaggctgtacacgtcacttttgt
ctgtcagc

									
								

					

						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: 872
Transcript exons: 42337887-42338021,42338425-42338675,42338932-42338983,42
339464-42339747,42339871-42340020
CTCTCTAACTATATTTCTTCCATGAGAAATAGGTTGCATCCCTGTCAGCAGTTCCAGAAAAACA
ACACCAAGGCTGTACACGTCACTTTTGTCTGTCAGCTTATGAGTAAGGAAATACTCCGGATCAA
GATAACCCGGGGTACCCTTTATAACAGTTGACACATGACCAGGAGCAATCCCCTCTGATTCTGG
CTCTGGGGCAAGCCGAGAGAGACCAAAATCAGCAACTTTTGCGACAAACTTTGAGTCCAGTAAA
ATATTGCTTGCTTTGATGTCACGGTGAAATATTGGAGGGTCTGCTTCTGTGTGTAAATAGAGGA
TGCCTCGCGACGACCCCAGCGCAATTCGTAACCTCGTGGGAAAATTTAGGGGCTCTTTTGATCG
AGCTGAAAGATGATCACGTAGAGTACCATTAGGCATAAACTCATATACCAGCATCTGCTCATCT
TCTTCATCACAATAACCAAGCAATGAAACAAGGTTCCGGTGATGCAGCCTGGACAGCAATTCTA
TCTCTGTGAAGAACTCCTTCGAACCCTGAAGAGATCCCTGCTGCGCACGTTTTATTGCTACTAT
TGTTCCATCAGAGAGAATACCTCTGTACACTTTCCCATACCCTCCTTGACCAATTAGTGCTGAG
TCACTAAAGTCGTTTGTACCATGTGACAGTTCTTGAAAACTGAAGTCTTTTACACCATCAATCT
TCATTGGAATTCTTTTTGCAGAGCGTCTTTTTGAAGAATATCTTGAACGTCTTCTCAGTATAAT
GAGAGTAATGAGGGATGAAAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATG
GCACCTGTACTTAGGCTGGACTTTGCACGATCTGGAAATA
						
					

						Genomic sequence
						
							CTCTCTAACTATATTTCTTCCATGAGAAATAGGTTGCATCCCTGTCAGCAGTTCCAGAAAAACA
ACACCAAGGCTGTACACGTCACTTTTGTCTGTCAGCTTATGAGTAAGGAAATACTCCGGATCAA
GATAACCCTGCGATTGTAAAGAAAGGAATATATACCATCAACACCATTGCAGAACACTGTGCTT
TAAACAATTTATTATTAGCTGGAAACTTAAAACAAGGCAAAATAGTTGCTTTTGCTTGTGCTAA
TCCTTATCAATTGGTAATAGTAAGAAATTTCGCTCAAGAATCCCTTAATTAATCAAGCTTTGCA
ATGACATTTAACTTATAGTTCTCTTTCCATTAATCAAATTAACCTAAGTTGAACAAGTTTCTGG
TCACATTCACCATATGCGGTTGCACACAACACCGGGATCAGACATCAGAATATGAACTGAAGTA
AAAACTGATAAAAGTGCTGGCAAATGTGGCAGACTTCTGCTCAACTAGTTGCTCACAGAGCATG
TACAAACAGATGGCATAGCTACTCACCGGGGTACCCTTTATAACAGTTGACACATGACCAGGAG
CAATCCCCTCTGATTCTGGCTCTGGGGCAAGCCGAGAGAGACCAAAATCAGCAACTTTTGCGAC
AAACTTTGAGTCCAGTAAAATATTGCTTGCTTTGATGTCACGGTGAAATATTGGAGGGTCTGCT
TCTGTGTGTAAATAGAGGATGCCTCGCGACGACCCCAGCGCAATTCGTAACCTCGTGGGAAAAT
TTAGGGGCTCTTTTGATCGAGCTGCTACATGAGACAATTGTTAGGGCAACTAGGTACACAGAAA
TAACAGCAACATAACTTCAGAAGTAACGATATATAGCACTGCCATGGAGCTTAGCACAAGATGC
TAATATTCTTCTACTAGTAATTAAGAACGTGCTAGCTAACAAAGAAACTGCGGGTTTATGATAT
TTTTATCTGTTGACTTCTGTTTAATGAATATTTAAAATTTTATGAAGAGCAGCTTTGTCAGTAG
GTACAGAAATAAAGTTCTAACCTGAAAGATGATCACGTAGAGTACCATTAGGCATAAACTCATA
TACCAGCATCTGCAATACATGCTTAACAGTATGAGTTTATATCATAATTAATGTTGAACCAAAT
GTGAGGTACTATCTATTCACAACCAACTCCGCAACAGAAGTTGATAGGCAGCTGTTCAGTTTCT
ACCGTTAAAATTGGTCAAATATGAACTTTCAAAAATAATATACTAGCCAACAAAAATAATGCAC
TGAACTGCTCTACCATTTTCCAGCACACCTATCTGAAATAGGCTGAACTATGTTCTGTTTGGCT
TTCTCCCAAAGCCAGGTAACGAAAAGTTACCTGTTCTCCAAAATAAAATCTGATAGCGGCTGAG
AACATGTGCATGCATATTTATGTACTTCAACGCAGCGAATGTATTTCAATGAATTTTGATATCA
GCCTTTTATAATCCATTTGAAAACAAGAAAGAACTTGAATATTTCAACGCTCGACAAAACTAAT
GCCCTGGACTTCTATTGAAAAAAAAAAGTACCAGGAACAACCTGCTCATCTTCTTCATCACAAT
AACCAAGCAATGAAACAAGGTTCCGGTGATGCAGCCTGGACAGCAATTCTATCTCTGTGAAGAA
CTCCTTCGAACCCTGAAGAGATCCCTGCTGCGCACGTTTTATTGCTACTATTGTTCCATCAGAG
AGAATACCTCTGTACACTTTCCCATACCCTCCTTGACCAATTAGTGCTGAGTCACTAAAGTCGT
TTGTACCATGTGACAGTTCTTGAAAACTGAAGTCTTTTACACCATCAATCTTCATTGGAATTCT
TTTTGCTGCAAATGCGATAAAAAAATGACATATTGAAGATTGAACAGAAGATAACTGATAAAAT
ATGGAAAACATAACAATAAAAAAAGAAACTGTTTCATTGAAGATAGCGGAAATGGAGGGTTTAC
CAGAGCGTCTTTTTGAAGAATATCTTGAACGTCTTCTCAGTATAATGAGAGTAATGAGGGATGA
AAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATGGCACCTGTACTTAGGCTG
GACTTTGCACGATCTGGAAATA
						
					

			
		

Sequences
Splice junction sequence	GTAATGAGGGATGAAAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATGGCAC CTGTACTTAGGCTGGACTTTGCACGATCTGGAAATActctctaactatatttcttccatgagaa ataggttgcatccctgtcagcagttccagaaaaacaacaccaaggctgtacacgtcacttttgt ctgtcagc
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: 872 Transcript exons: 42337887-42338021,42338425-42338675,42338932-42338983,42 339464-42339747,42339871-42340020 CTCTCTAACTATATTTCTTCCATGAGAAATAGGTTGCATCCCTGTCAGCAGTTCCAGAAAAACA ACACCAAGGCTGTACACGTCACTTTTGTCTGTCAGCTTATGAGTAAGGAAATACTCCGGATCAA GATAACCCGGGGTACCCTTTATAACAGTTGACACATGACCAGGAGCAATCCCCTCTGATTCTGG CTCTGGGGCAAGCCGAGAGAGACCAAAATCAGCAACTTTTGCGACAAACTTTGAGTCCAGTAAA ATATTGCTTGCTTTGATGTCACGGTGAAATATTGGAGGGTCTGCTTCTGTGTGTAAATAGAGGA TGCCTCGCGACGACCCCAGCGCAATTCGTAACCTCGTGGGAAAATTTAGGGGCTCTTTTGATCG AGCTGAAAGATGATCACGTAGAGTACCATTAGGCATAAACTCATATACCAGCATCTGCTCATCT TCTTCATCACAATAACCAAGCAATGAAACAAGGTTCCGGTGATGCAGCCTGGACAGCAATTCTA TCTCTGTGAAGAACTCCTTCGAACCCTGAAGAGATCCCTGCTGCGCACGTTTTATTGCTACTAT TGTTCCATCAGAGAGAATACCTCTGTACACTTTCCCATACCCTCCTTGACCAATTAGTGCTGAG TCACTAAAGTCGTTTGTACCATGTGACAGTTCTTGAAAACTGAAGTCTTTTACACCATCAATCT TCATTGGAATTCTTTTTGCAGAGCGTCTTTTTGAAGAATATCTTGAACGTCTTCTCAGTATAAT GAGAGTAATGAGGGATGAAAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATG GCACCTGTACTTAGGCTGGACTTTGCACGATCTGGAAATA
Genomic sequence	CTCTCTAACTATATTTCTTCCATGAGAAATAGGTTGCATCCCTGTCAGCAGTTCCAGAAAAACA ACACCAAGGCTGTACACGTCACTTTTGTCTGTCAGCTTATGAGTAAGGAAATACTCCGGATCAA GATAACCCTGCGATTGTAAAGAAAGGAATATATACCATCAACACCATTGCAGAACACTGTGCTT TAAACAATTTATTATTAGCTGGAAACTTAAAACAAGGCAAAATAGTTGCTTTTGCTTGTGCTAA TCCTTATCAATTGGTAATAGTAAGAAATTTCGCTCAAGAATCCCTTAATTAATCAAGCTTTGCA ATGACATTTAACTTATAGTTCTCTTTCCATTAATCAAATTAACCTAAGTTGAACAAGTTTCTGG TCACATTCACCATATGCGGTTGCACACAACACCGGGATCAGACATCAGAATATGAACTGAAGTA AAAACTGATAAAAGTGCTGGCAAATGTGGCAGACTTCTGCTCAACTAGTTGCTCACAGAGCATG TACAAACAGATGGCATAGCTACTCACCGGGGTACCCTTTATAACAGTTGACACATGACCAGGAG CAATCCCCTCTGATTCTGGCTCTGGGGCAAGCCGAGAGAGACCAAAATCAGCAACTTTTGCGAC AAACTTTGAGTCCAGTAAAATATTGCTTGCTTTGATGTCACGGTGAAATATTGGAGGGTCTGCT TCTGTGTGTAAATAGAGGATGCCTCGCGACGACCCCAGCGCAATTCGTAACCTCGTGGGAAAAT TTAGGGGCTCTTTTGATCGAGCTGCTACATGAGACAATTGTTAGGGCAACTAGGTACACAGAAA TAACAGCAACATAACTTCAGAAGTAACGATATATAGCACTGCCATGGAGCTTAGCACAAGATGC TAATATTCTTCTACTAGTAATTAAGAACGTGCTAGCTAACAAAGAAACTGCGGGTTTATGATAT TTTTATCTGTTGACTTCTGTTTAATGAATATTTAAAATTTTATGAAGAGCAGCTTTGTCAGTAG GTACAGAAATAAAGTTCTAACCTGAAAGATGATCACGTAGAGTACCATTAGGCATAAACTCATA TACCAGCATCTGCAATACATGCTTAACAGTATGAGTTTATATCATAATTAATGTTGAACCAAAT GTGAGGTACTATCTATTCACAACCAACTCCGCAACAGAAGTTGATAGGCAGCTGTTCAGTTTCT ACCGTTAAAATTGGTCAAATATGAACTTTCAAAAATAATATACTAGCCAACAAAAATAATGCAC TGAACTGCTCTACCATTTTCCAGCACACCTATCTGAAATAGGCTGAACTATGTTCTGTTTGGCT TTCTCCCAAAGCCAGGTAACGAAAAGTTACCTGTTCTCCAAAATAAAATCTGATAGCGGCTGAG AACATGTGCATGCATATTTATGTACTTCAACGCAGCGAATGTATTTCAATGAATTTTGATATCA GCCTTTTATAATCCATTTGAAAACAAGAAAGAACTTGAATATTTCAACGCTCGACAAAACTAAT GCCCTGGACTTCTATTGAAAAAAAAAAGTACCAGGAACAACCTGCTCATCTTCTTCATCACAAT AACCAAGCAATGAAACAAGGTTCCGGTGATGCAGCCTGGACAGCAATTCTATCTCTGTGAAGAA CTCCTTCGAACCCTGAAGAGATCCCTGCTGCGCACGTTTTATTGCTACTATTGTTCCATCAGAG AGAATACCTCTGTACACTTTCCCATACCCTCCTTGACCAATTAGTGCTGAGTCACTAAAGTCGT TTGTACCATGTGACAGTTCTTGAAAACTGAAGTCTTTTACACCATCAATCTTCATTGGAATTCT TTTTGCTGCAAATGCGATAAAAAAATGACATATTGAAGATTGAACAGAAGATAACTGATAAAAT ATGGAAAACATAACAATAAAAAAAGAAACTGTTTCATTGAAGATAGCGGAAATGGAGGGTTTAC CAGAGCGTCTTTTTGAAGAATATCTTGAACGTCTTCTCAGTATAATGAGAGTAATGAGGGATGA AAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATGGCACCTGTACTTAGGCTG GACTTTGCACGATCTGGAAATA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.230151706

Conservation Information
Conserved circRNAs	NA
PMCS	0.230151706

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							42339916-42337891(+)
42339932-42338445(+)
42339735-42339993(-)
						
						Potential amino acid sequence
						
							MRVMRDERNAAAANAATTIPTMAPVLRLDFARSGNTL*(+)
MKEMLLQQTLPRQYQQWHLYLGWTLHDLEILSNYISSMRNRLHPCQQFQKNNTKAVHVTFVCQL
MSKEILRIKITRGTLYNS*(+)
MKIDGVKDFSFQELSHGTNDFSDSALIGQGGYGKVYRGILSDGTIVAIKRAQQGSLQGSKEFFT
EIELLSRLHHRNLVSLLGYCDEEDEQMLVYEFMPNGTLRDHLSARSKEPLNFPTRLRIALGSSR
GILYLHTEADPPIFHRDIKASNILLDSKFVAKVADFGLSRLAPEPESEGIAPGHVSTVIKGTPG
YLDPEYFLTHKLTDKSDVYSLGVVFLELLTGMQPISHGRNIVREYFQIVQSPA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	42339916-42337891(+) 42339932-42338445(+) 42339735-42339993(-)
Potential amino acid sequence	MRVMRDERNAAAANAATTIPTMAPVLRLDFARSGNTL(+) MKEMLLQQTLPRQYQQWHLYLGWTLHDLEILSNYISSMRNRLHPCQQFQKNNTKAVHVTFVCQL MSKEILRIKITRGTLYNS(+) MKIDGVKDFSFQELSHGTNDFSDSALIGQGGYGKVYRGILSDGTIVAIKRAQQGSLQGSKEFFT EIELLSRLHHRNLVSLLGYCDEEDEQMLVYEFMPNGTLRDHLSARSKEPLNFPTRLRIALGSSR GILYLHTEADPPIFHRDIKASNILLDSKFVAKVADFGLSRLAPEPESEGIAPGHVSTVIKGTPG YLDPEYFLTHKLTDKSDVYSLGVVFLELLTGMQPISHGRNIVREYFQIVQSPA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0960400_circ_g.1

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