Plant Circular RNA Database

Detail information of Os12g0540900_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os12g0540900_circ_g.1
					
						ID in PlantcircBase
						osa_circ_011901
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 21626001-21629200  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0540900						
					
						Parent gene annotation
						
							Similar to Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan
--tRNA ligase) (TrpRS). (Os12t0540900-01);Similar to tryptophany
l-tRNA synthetase. (Os12t0540900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os12g0540900_circ_g.2 						
					
						Support reads
						1
					
						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
						Os12t0540900-01:9
Os12t0540900-02:8

General Information
CircRNA Name	Os12g0540900_circ_g.1
ID in PlantcircBase	osa_circ_011901
Alias	NA
Organism	Oryza sativa
Position	chr12: 21626001-21629200 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0540900
Parent gene annotation	Similar to Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan --tRNA ligase) (TrpRS). (Os12t0540900-01);Similar to tryptophany l-tRNA synthetase. (Os12t0540900-02)
Parent gene strand	-
Alternative splicing	Os12g0540900_circ_g.2
Support reads	1
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	Os12t0540900-01:9 Os12t0540900-02:8

			
						 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  
						
							GAGATGGCCGAGGTGCAGCGCCTCCGACGAGGGCCCCCTCCCCGTGTAGAGGTAGAACTTCTCC
CCCTTCTCGTACAAATCCAGTATCTCGTTCAAATCCctcctcggtcactagtgctctagctctt
tgatgtctcgcaaccagttcggatagaactgcaacaaggcgctgcttcacttcacccgtcagca
tccttcct

									
								

					

						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
						
							CTCCTCGGTCACTAGTGCTCTAGCTCTTTGATGTCTCGCAACCAGTTCGGATAGAACTGCAACA
AGGCGCTGCTTCACTTCACCCGTCAGCATCCTTCCTTCCTTGTACTCCTGATGAGTTTCAGAAA
TGTTAGCGGAAATCAGTTGAAGAAAACATGTTAAAGAAACACATCAGGCAAATTAGCTCTACGC
CTCTACATATATAGCATAATTTGTATTACCTTCTTTATGTGCTCGAGCTCATTGTCATCTTCAA
GGAAGAAGTTCAGGTACTTGATTGGAACATCCACCTGAACATCACAATCACAACTGACATTGAT
TTAAGGAGAAAAATAAAATACTTTTTTCTGAATCTAAAAATACAAATACAGAACTTGAGCATTG
CACATGCGTTAAAGTAATGAAAGTGCCTAAAAAGGTAAAATTTTTGCATGTGTTAGTGTTTGGG
GGAAAAATATTGATGGCTTCAATAAATGACAAAAGTACAAACGAAAAGGAAAGGTCCTGAATGT
ATGAACTGTGAATTAGCATTCTTCCTATATTCAAATTATTTTTCTTTAATTTACATGTTGCATT
TCAAACAAATATATGTCAACAGTGCATAACTCAGGTAATCGGGGGAAAGCATACTTTACTAAGT
ACACACGTTTCACAATTAACAATAAGTTCAATATAACAAGAAAATGACTTACATCAAGGTTAGC
TCCAAGTTTTCTATGGAGCTCAATTGAGTCCCGGCCACCTGAGAACGCATATTTGTTCACCTGG
AAAAAATGGTAAAATAAATGACAGGCCCATGAAAAGCAGAACCATAAGGCTACAGGACGCTTGA
CTTAATTGAAGACCAAAATTTGAATGGCCTCAGGTAAAATATAAAATTGCAGTAGTTTTCCACT
AAAATACAATGCTTAAAGCAAACCTTTGTCTTTATTTCTTTAGCACTATCTGTCACATATATTG
CAGAATTTGGATCACTGGCCGACATTTTTGTGTTCTCCCCCTGTAAATGGAAATAAGCAGCTCA
CATAAATCAATGTCCCAAATATTATGCTATCTAAAATAGGAAATAAGAAAAATAAATGCTGAGC
AATGGACATGAGCGATGAACTTGGCGAATGAAGATGCAATCTTATCAGACATAGATAAATGCAA
TATAAGAAAATAGCAAGTTACTAATTAACCAGGAGCTGTCAAACAGCACAGGAAAATTAAGTGG
AATTTCACTTAAAAAATCGTGATTAATTGCGATTGCCTTTTTTTTAACTTTACTAGTAATAATG
ATTCTAGTGACAAAACTTGCAAGAAAAATAGATAACCCGTCCTTTCAACTGAAATTTCGTATGT
AAACAATCGCTTTGCTATCATTGAAGGACTAACTTCAGATTGAGGTACTGAGCATGAGCTCTGT
ATTATGCCTCCATTGTTGAATTCCTTTTCTATGCTCATTTTACACTTCTATACAGTGAAGATAT
TAAGCTATAAACCCATGGTCCTAAAAAAACGTACCTGAAGAGCAGGGAAAAATCTCGATTCAAT
TAATGATGGTTTCTGGTAACCAATTCTTGGAGCAACGTCCCGGGTCATCCTGAAATAAGGATCC
TGGAAGAACAAATCCAATGAGCAACTCAAATCCAATGAGCAACTCAAACTTGCATAACAGAACA
TGAACATCTACAATAGCTACCTAAAATTAAAGAAATTACAAGAATAAATGTATCATGGTCTGAT
TGATGTGTTCCTAGACGAAATGGCATGATAGCAGCATGGAAAGGCAGCCAAACCACAAATTCAC
AGGGAGAAATGGAATCAGGGAGCCCAGATATGTTTATACCTGGTCTATTGCACATGGGATTAAG
CACCGTAGTTGGTCATTCCCAGAGAAGAGATGTGGAAATGAAGAAGGGAATGATGGAACCGCTT
GCACAGGAGGAAAGCTGACTTTTCCTATATGATCCTCTGGGGTGAATCCAAATATTCCAACAAC
CTGTCGTTCAAGAGTAAACAATATCAGCAAAAGACAATGGTTGGATGCAAACAAGCAAGTAACC
AAGCGATCCACTGCCCAAAATATTGCTAGACTAACTTAAACTGCTCACCTTATTATATGTCACA
CATCTGGCAACTTTAACCATGTTTTCATAAAAAGCACTGTAAGAAAATGACAGAGGATTACTTT
TCTATAGAATAAATAAATCTCAAGAATTACTTGCTTAGCAGAAGAACAGTCATTAAATTAGTCA
TAAATGAAAGATAAATCAAGACTACAGTTAAGAAGAACCTTACCCTCCAACATAATTAAAATCA
GAGAAAATGAAAGTCCTTTCGACATCAAATCCACAAGCAATGATATCTTTTGCATTTTCACGGG
CAAGCCTTTTAGTTTCCTCAACAGTCAAATTCTTCCATAAGAACTTCTCATCATCAGTTAGCTG
TATTACTAGGGGCACCTTGAAAGCATCCTGCAGATATCTGAAAAGGGATACTGACAGTTAATCG
ACGTTGTCCAAGCATTCTCACAATTATAAATTAGAATTAAGCCAACAATGTAAAGGTTCATCAA
ACAAGATATTGCAACAAAGTTTGGAAGCTACATTCAGACTAGAAAGCATAGGAAACATTACACA
AAGCAGCATATCTATGTTATATTGTTTCCGTGCAAGATGTAAAAGCATGTCTTGTTTTAAAAAA
ATGTTTAAATACCGAATTTTCTTTCATGCAAGGAACATGGTAAGATGAAATGTTCCGGGGTAAC
ATTCATCACACCCGACCTTTCAACTGGTCCGGTAATCTATTGCATCGCTCTGCTGATTCACCAC
ATAAACTACAATAAGCATATGAAAGGTTCTACCAACACTGAAAATAGGTAAAGTTCACTAGGTC
ATCCCAGCAAATAACACATAAAAGGTTTGTGCACATCACCAACAAACGCATTATCCAAGATTCG
GCTGCTCTAGCCAAACATACAACTACTCCCTCTCAATACTGCCGCGGCATTGCCCAGTTATTTA
TACAACAACACGAGTGAATCAAGAACATTGCAGGGGACAGCGAGTATTGCAGATTGGAACAATC
GCGCTTACTTGGTGAACATGAAGGGGATGAGATGGCCGAGGTGCAGCGCCTCCGACGAGGGCCC
CCTCCCCGTGTAGAGGTAGAACTTCTCCCCCTTCTCGTACAAATCCAGTATCTCGTTCAAATCC
						
					

			
		

Sequences
Splice junction sequence	GAGATGGCCGAGGTGCAGCGCCTCCGACGAGGGCCCCCTCCCCGTGTAGAGGTAGAACTTCTCC CCCTTCTCGTACAAATCCAGTATCTCGTTCAAATCCctcctcggtcactagtgctctagctctt tgatgtctcgcaaccagttcggatagaactgcaacaaggcgctgcttcacttcacccgtcagca tccttcct
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	CTCCTCGGTCACTAGTGCTCTAGCTCTTTGATGTCTCGCAACCAGTTCGGATAGAACTGCAACA AGGCGCTGCTTCACTTCACCCGTCAGCATCCTTCCTTCCTTGTACTCCTGATGAGTTTCAGAAA TGTTAGCGGAAATCAGTTGAAGAAAACATGTTAAAGAAACACATCAGGCAAATTAGCTCTACGC CTCTACATATATAGCATAATTTGTATTACCTTCTTTATGTGCTCGAGCTCATTGTCATCTTCAA GGAAGAAGTTCAGGTACTTGATTGGAACATCCACCTGAACATCACAATCACAACTGACATTGAT TTAAGGAGAAAAATAAAATACTTTTTTCTGAATCTAAAAATACAAATACAGAACTTGAGCATTG CACATGCGTTAAAGTAATGAAAGTGCCTAAAAAGGTAAAATTTTTGCATGTGTTAGTGTTTGGG GGAAAAATATTGATGGCTTCAATAAATGACAAAAGTACAAACGAAAAGGAAAGGTCCTGAATGT ATGAACTGTGAATTAGCATTCTTCCTATATTCAAATTATTTTTCTTTAATTTACATGTTGCATT TCAAACAAATATATGTCAACAGTGCATAACTCAGGTAATCGGGGGAAAGCATACTTTACTAAGT ACACACGTTTCACAATTAACAATAAGTTCAATATAACAAGAAAATGACTTACATCAAGGTTAGC TCCAAGTTTTCTATGGAGCTCAATTGAGTCCCGGCCACCTGAGAACGCATATTTGTTCACCTGG AAAAAATGGTAAAATAAATGACAGGCCCATGAAAAGCAGAACCATAAGGCTACAGGACGCTTGA CTTAATTGAAGACCAAAATTTGAATGGCCTCAGGTAAAATATAAAATTGCAGTAGTTTTCCACT AAAATACAATGCTTAAAGCAAACCTTTGTCTTTATTTCTTTAGCACTATCTGTCACATATATTG CAGAATTTGGATCACTGGCCGACATTTTTGTGTTCTCCCCCTGTAAATGGAAATAAGCAGCTCA CATAAATCAATGTCCCAAATATTATGCTATCTAAAATAGGAAATAAGAAAAATAAATGCTGAGC AATGGACATGAGCGATGAACTTGGCGAATGAAGATGCAATCTTATCAGACATAGATAAATGCAA TATAAGAAAATAGCAAGTTACTAATTAACCAGGAGCTGTCAAACAGCACAGGAAAATTAAGTGG AATTTCACTTAAAAAATCGTGATTAATTGCGATTGCCTTTTTTTTAACTTTACTAGTAATAATG ATTCTAGTGACAAAACTTGCAAGAAAAATAGATAACCCGTCCTTTCAACTGAAATTTCGTATGT AAACAATCGCTTTGCTATCATTGAAGGACTAACTTCAGATTGAGGTACTGAGCATGAGCTCTGT ATTATGCCTCCATTGTTGAATTCCTTTTCTATGCTCATTTTACACTTCTATACAGTGAAGATAT TAAGCTATAAACCCATGGTCCTAAAAAAACGTACCTGAAGAGCAGGGAAAAATCTCGATTCAAT TAATGATGGTTTCTGGTAACCAATTCTTGGAGCAACGTCCCGGGTCATCCTGAAATAAGGATCC TGGAAGAACAAATCCAATGAGCAACTCAAATCCAATGAGCAACTCAAACTTGCATAACAGAACA TGAACATCTACAATAGCTACCTAAAATTAAAGAAATTACAAGAATAAATGTATCATGGTCTGAT TGATGTGTTCCTAGACGAAATGGCATGATAGCAGCATGGAAAGGCAGCCAAACCACAAATTCAC AGGGAGAAATGGAATCAGGGAGCCCAGATATGTTTATACCTGGTCTATTGCACATGGGATTAAG CACCGTAGTTGGTCATTCCCAGAGAAGAGATGTGGAAATGAAGAAGGGAATGATGGAACCGCTT GCACAGGAGGAAAGCTGACTTTTCCTATATGATCCTCTGGGGTGAATCCAAATATTCCAACAAC CTGTCGTTCAAGAGTAAACAATATCAGCAAAAGACAATGGTTGGATGCAAACAAGCAAGTAACC AAGCGATCCACTGCCCAAAATATTGCTAGACTAACTTAAACTGCTCACCTTATTATATGTCACA CATCTGGCAACTTTAACCATGTTTTCATAAAAAGCACTGTAAGAAAATGACAGAGGATTACTTT TCTATAGAATAAATAAATCTCAAGAATTACTTGCTTAGCAGAAGAACAGTCATTAAATTAGTCA TAAATGAAAGATAAATCAAGACTACAGTTAAGAAGAACCTTACCCTCCAACATAATTAAAATCA GAGAAAATGAAAGTCCTTTCGACATCAAATCCACAAGCAATGATATCTTTTGCATTTTCACGGG CAAGCCTTTTAGTTTCCTCAACAGTCAAATTCTTCCATAAGAACTTCTCATCATCAGTTAGCTG TATTACTAGGGGCACCTTGAAAGCATCCTGCAGATATCTGAAAAGGGATACTGACAGTTAATCG ACGTTGTCCAAGCATTCTCACAATTATAAATTAGAATTAAGCCAACAATGTAAAGGTTCATCAA ACAAGATATTGCAACAAAGTTTGGAAGCTACATTCAGACTAGAAAGCATAGGAAACATTACACA AAGCAGCATATCTATGTTATATTGTTTCCGTGCAAGATGTAAAAGCATGTCTTGTTTTAAAAAA ATGTTTAAATACCGAATTTTCTTTCATGCAAGGAACATGGTAAGATGAAATGTTCCGGGGTAAC ATTCATCACACCCGACCTTTCAACTGGTCCGGTAATCTATTGCATCGCTCTGCTGATTCACCAC ATAAACTACAATAAGCATATGAAAGGTTCTACCAACACTGAAAATAGGTAAAGTTCACTAGGTC ATCCCAGCAAATAACACATAAAAGGTTTGTGCACATCACCAACAAACGCATTATCCAAGATTCG GCTGCTCTAGCCAAACATACAACTACTCCCTCTCAATACTGCCGCGGCATTGCCCAGTTATTTA TACAACAACACGAGTGAATCAAGAACATTGCAGGGGACAGCGAGTATTGCAGATTGGAACAATC GCGCTTACTTGGTGAACATGAAGGGGATGAGATGGCCGAGGTGCAGCGCCTCCGACGAGGGCCC CCTCCCCGTGTAGAGGTAGAACTTCTCCCCCTTCTCGTACAAATCCAGTATCTCGTTCAAATCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.123026768

Conservation Information
Conserved circRNAs	NA
PMCS	0.123026768

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21629105-21626020(+)
21629093-21628424(-)
						
						Potential amino acid sequence
						
							MAEVQRLRRGPPPRVEVELLPLLVQIQYLVQIPPRSLVL*(+)
MFTKYLQDAFKVPLVIQLTDDEKFLWKNLTVEETKRLARENAKDIIACGFDVERTFIFSDFNYV
GGAFYENMVKVARCVTYNKVVGIFGFTPEDHIGKVSFPPVQAVPSFPSSFPHLFSGNDQLRCLI
PCAIDQDPYFRMTRDVAPRIGYQKPSLIESRFFPALQGENTKMSASDPNSAIYVTDSAKEIKTK
VNKYAFSGGRDSIELHRKLGANLDVDVPIKYLNFFLEDDNELEHIKKEYKEGRMLTGEVKQRLV
AVLSELVARHQRARALVTEEGFERDTGFVREGGEVLPLHGEGALVGGAAPRPSHPLHVHQISAG
CFQGAPSNTAN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21629105-21626020(+) 21629093-21628424(-)
Potential amino acid sequence	MAEVQRLRRGPPPRVEVELLPLLVQIQYLVQIPPRSLVL(+) MFTKYLQDAFKVPLVIQLTDDEKFLWKNLTVEETKRLARENAKDIIACGFDVERTFIFSDFNYV GGAFYENMVKVARCVTYNKVVGIFGFTPEDHIGKVSFPPVQAVPSFPSSFPHLFSGNDQLRCLI PCAIDQDPYFRMTRDVAPRIGYQKPSLIESRFFPALQGENTKMSASDPNSAIYVTDSAKEIKTK VNKYAFSGGRDSIELHRKLGANLDVDVPIKYLNFFLEDDNELEHIKKEYKEGRMLTGEVKQRLV AVLSELVARHQRARALVTEEGFERDTGFVREGGEVLPLHGEGALVGGAAPRPSHPLHVHQISAG CFQGAPSNTAN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0540900_circ_g.1

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