Plant Circular RNA Database

Detail information of Os12g0138900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os12g0138900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_010453
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 1891201-1892607  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0138900						
					
						Parent gene annotation
						
							Similar to Plastid isopropylmalate synthase (Fragment). (Os12t01
38900-01);Similar to Plastid isopropylmalate synthase (Fragment)
. (Os12t0138900-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0138900_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os12t0138900-01:5
Os12t0138900-02:5

General Information
CircRNA Name	Os12g0138900_circ_g.3
ID in PlantcircBase	osa_circ_010453
Alias	NA
Organism	Oryza sativa
Position	chr12: 1891201-1892607 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0138900
Parent gene annotation	Similar to Plastid isopropylmalate synthase (Fragment). (Os12t01 38900-01);Similar to Plastid isopropylmalate synthase (Fragment) . (Os12t0138900-02)
Parent gene strand	+
Alternative splicing	Os12g0138900_circ_g.2
Support reads	1
Tissues	shoot
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	Os12t0138900-01:5 Os12t0138900-02:5

			
						 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  
						
							ATGGGATGCTTAAGTACAAAGGAACTTATGAAATAATTTCTCCTGATGATATTGGTCTAACACG
TGCAAATGAGTTTGGTATTGTTCTTGGGAAGCTCAGgtcaaacagagagtttctatatcatata
ctagaggaagtcataaaagctggagcaacaacactcaatatcccagacactgttggatacactc
ttccttat

						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
						
							GTCAAACAGAGAGTTTCTATATCATATACTAGAGGAAGTCATAAAAGCTGGAGCAACAACACTC
AATATCCCAGACACTGTTGGATACACTCTTCCTTATGAATTTGGGAAACTAATTGCTGATATAA
AAGCAAACACTCCAGGAATTGAAAATGCCATTATTTCTACTCATTGCCAGAATGACCTTGGTCT
AGCAACCGCAAATACATTAGCGGTACTACCTTTTCCTTATCTCTTTGATCCATTATCATTGGTT
TAATCATGTCACTAATGTGACTTAACCTTTAGGGCGCTCATGCAGGAGCACGGCAATTAGAGGT
GACTATCAATGGTATTGGTGAAAGGGCTGGAAATGCTTCTTTGGAAGAGGTGAACTCATATACT
ATGTTTATGTTGTTTGTTGGTATTTTGCACATGTTCATCTAATGGTTTGCAGAAGAATGAATGC
AAGTAATATTGATTTCCTATATATGCAACTTTTTTTTTAAAAAAAATATATTTTTCAGGTTGTG
ATGGCAATTAAATGTCGTCGAGAACTCTTAGGAGGTCTGTATACTGGAATCAATACCCAACATA
TCACTATGTCAAGCAAAATGGTACAATTATGTTTGTTTTCTTTCTTCTTTTGTTTTTTTTTTAT
CTTTTGTCTTTTTCAGGTGACTGGAAATTTCATGCACTTTTGCAAATACTCTGCTTATTCTAGG
TACAAGAGCACAGTGGACTTCATGTACAACCACATAAAGCTATTGTCGGTGCCAATGCCTTTGC
ACATGAAAGTGGAATTCATCAGGTAACTAAATTTGCATTCTTGCCGTAATATTGCCATCAAATT
TCTTGACTGGGTTCTCTTTAGTGTTGTTTTGGTGGTACCTCAATTTCACATCTATCTATATTTC
TTGACTTTTAGTGTTGCCTGGGTTCTTGTTTCTGTTTGCCATTTATCTATATTTTATAACTCTA
AAAGTGTTTCTTGCCATCAATTTACATTTTAGGACTAAGGAATTGATTATCATTACTTTTTATT
TCCTATCTAAATTTTGGAAGTTTCAGAAATCTTTCTAGTTGTCAGTTTGCATATGTGCACTAGG
AAAAAGTTTTGCTCACATTTTTATAGTATCACATACTGAGGGAAGTCAAATTATTTTTATGGAT
GCCTTTTTTTTTCTCAGCTCCGATGAAATCATTTTCTCATATATGATAGATCAATCACGGTTTT
ATATGAACCTTGCCTTGCATATTCTCATATTAATTGTGTTGGTTCTAAGTGAAGTGATCTTGAT
ATTCACTTTTGTTATTCTGTTTTCAGGATGGGATGCTTAAGTACAAAGGAACTTATGAAATAAT
TTCTCCTGATGATATTGGTCTAACACGTGCAAATGAGTTTGGTATTGTTCTTGGGAAGCTCAG

Sequences
Splice junction sequence	ATGGGATGCTTAAGTACAAAGGAACTTATGAAATAATTTCTCCTGATGATATTGGTCTAACACG TGCAAATGAGTTTGGTATTGTTCTTGGGAAGCTCAGgtcaaacagagagtttctatatcatata ctagaggaagtcataaaagctggagcaacaacactcaatatcccagacactgttggatacactc ttccttat
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	GTCAAACAGAGAGTTTCTATATCATATACTAGAGGAAGTCATAAAAGCTGGAGCAACAACACTC AATATCCCAGACACTGTTGGATACACTCTTCCTTATGAATTTGGGAAACTAATTGCTGATATAA AAGCAAACACTCCAGGAATTGAAAATGCCATTATTTCTACTCATTGCCAGAATGACCTTGGTCT AGCAACCGCAAATACATTAGCGGTACTACCTTTTCCTTATCTCTTTGATCCATTATCATTGGTT TAATCATGTCACTAATGTGACTTAACCTTTAGGGCGCTCATGCAGGAGCACGGCAATTAGAGGT GACTATCAATGGTATTGGTGAAAGGGCTGGAAATGCTTCTTTGGAAGAGGTGAACTCATATACT ATGTTTATGTTGTTTGTTGGTATTTTGCACATGTTCATCTAATGGTTTGCAGAAGAATGAATGC AAGTAATATTGATTTCCTATATATGCAACTTTTTTTTTAAAAAAAATATATTTTTCAGGTTGTG ATGGCAATTAAATGTCGTCGAGAACTCTTAGGAGGTCTGTATACTGGAATCAATACCCAACATA TCACTATGTCAAGCAAAATGGTACAATTATGTTTGTTTTCTTTCTTCTTTTGTTTTTTTTTTAT CTTTTGTCTTTTTCAGGTGACTGGAAATTTCATGCACTTTTGCAAATACTCTGCTTATTCTAGG TACAAGAGCACAGTGGACTTCATGTACAACCACATAAAGCTATTGTCGGTGCCAATGCCTTTGC ACATGAAAGTGGAATTCATCAGGTAACTAAATTTGCATTCTTGCCGTAATATTGCCATCAAATT TCTTGACTGGGTTCTCTTTAGTGTTGTTTTGGTGGTACCTCAATTTCACATCTATCTATATTTC TTGACTTTTAGTGTTGCCTGGGTTCTTGTTTCTGTTTGCCATTTATCTATATTTTATAACTCTA AAAGTGTTTCTTGCCATCAATTTACATTTTAGGACTAAGGAATTGATTATCATTACTTTTTATT TCCTATCTAAATTTTGGAAGTTTCAGAAATCTTTCTAGTTGTCAGTTTGCATATGTGCACTAGG AAAAAGTTTTGCTCACATTTTTATAGTATCACATACTGAGGGAAGTCAAATTATTTTTATGGAT GCCTTTTTTTTTCTCAGCTCCGATGAAATCATTTTCTCATATATGATAGATCAATCACGGTTTT ATATGAACCTTGCCTTGCATATTCTCATATTAATTGTGTTGGTTCTAAGTGAAGTGATCTTGAT ATTCACTTTTGTTATTCTGTTTTCAGGATGGGATGCTTAAGTACAAAGGAACTTATGAAATAAT TTCTCCTGATGATATTGGTCTAACACGTGCAAATGAGTTTGGTATTGTTCTTGGGAAGCTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.289120043

Conservation Information
Conserved circRNAs	NA
PMCS	0.289120043

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1891714-1892604(+)
1892578-1891229(+)
						
						Potential amino acid sequence
						
							MAIKCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYK
GTYEIISPDDIGLTRANEFGIVLGKLRSNREFLYHILEEVIKAGATTLNIPDTVGYTLPYEFGK
LIADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGERAGNASLEEVVM
AIKCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYKG
TYEIISPDDIGLTRANEFGIVLGKLRSNREFLYHILEEVIKAGATTLNIPDTVGYTLPYEFGKL
IADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGERAGNASLEEVVMA
IKCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYKGT
YEIISPDDIGLTRANEFGIVLGKLRSNREFLYHILEEVIKAGATTLNIPDTVGYTLPYEFGKLI
ADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGERAGNASLEEVVMAI
KCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYKGTY
EIISPDDIGLTRANEFGIVLGKL(+)
MSLVLFLGSSGQTESFYIIY*(+)
						
						Sponge-miRNAs
						
							osa-miR2923 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1891714-1892604(+) 1892578-1891229(+)
Potential amino acid sequence	MAIKCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYK GTYEIISPDDIGLTRANEFGIVLGKLRSNREFLYHILEEVIKAGATTLNIPDTVGYTLPYEFGK LIADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGERAGNASLEEVVM AIKCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYKG TYEIISPDDIGLTRANEFGIVLGKLRSNREFLYHILEEVIKAGATTLNIPDTVGYTLPYEFGKL IADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGERAGNASLEEVVMA IKCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYKGT YEIISPDDIGLTRANEFGIVLGKLRSNREFLYHILEEVIKAGATTLNIPDTVGYTLPYEFGKLI ADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGERAGNASLEEVVMAI KCRRELLGGLYTGINTQHITMSSKMVQEHSGLHVQPHKAIVGANAFAHESGIHQDGMLKYKGTY EIISPDDIGLTRANEFGIVLGKL(+) MSLVLFLGSSGQTESFYIIY*(+)
Sponge-miRNAs	osa-miR2923
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0138900_circ_g.3

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