Plant Circular RNA Database

Detail information of Os12g0297500_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os12g0297500_circ_g.6
					
						ID in PlantcircBase
						osa_circ_011257
					
						Alias
						Os12circ05110/Os_ciR1553
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 11734617-11737572  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os12g0297500						
					
						Parent gene annotation
						
							Pyruvate phosphate dikinase, PEP/pyruvate-binding domain contain
ing protein. (Os12t0297500-01);Similar to Phosphoglucan, water d
ikinase, chloroplastic. (Os12t0297500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os12g0297500_circ_g.4 Os12g0297500_circ_g.5 Os12g0297500_circ_g.7 Os12g0297500_circ_g.8 Os12g0297500_circ_g.9 Os12g0297500_circ_g.10 						
					
						Support reads
						5/12/3
					
						Tissues
						leaf and panicle/root/shoot, root, seed
					
						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
						Os12t0297500-01:5

General Information
CircRNA Name	Os12g0297500_circ_g.6
ID in PlantcircBase	osa_circ_011257
Alias	Os12circ05110/Os_ciR1553
Organism	Oryza sativa
Position	chr12: 11734617-11737572 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os12g0297500
Parent gene annotation	Pyruvate phosphate dikinase, PEP/pyruvate-binding domain contain ing protein. (Os12t0297500-01);Similar to Phosphoglucan, water d ikinase, chloroplastic. (Os12t0297500-02)
Parent gene strand	-
Alternative splicing	Os12g0297500_circ_g.4 Os12g0297500_circ_g.5 Os12g0297500_circ_g.7 Os12g0297500_circ_g.8 Os12g0297500_circ_g.9 Os12g0297500_circ_g.10
Support reads	5/12/3
Tissues	leaf and panicle/root/shoot, root, seed
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	Os12t0297500-01:5

			
						 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  
						
							TTCAGCAAAGTTTACCCTTTTGGTTTCCACAAAGGATGAGAGAACTTCTAAGCCTGACTCGTTC
AGAGATTCCTTGATGGACTCCAGTTGCTCAAATAGGcattactttttcagggaatatagaaaga
agtgcttcagagtactcttccgttaatctccgtgctctgtccagtgtagctttaagtcttagtg
accaaata

									
								

					

						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: 631
Transcript exons: 11734617-11734735,11734843-11735048,11736835-11736887,11
736967-11737134,11737488-11737572
CATTACTTTTTCAGGGAATATAGAAAGAAGTGCTTCAGAGTACTCTTCCGTTAATCTCCGTGCT
CTGTCCAGTGTAGCTTTAAGTCTTAGTGACCAAATATATTTCCCATCTTCACAACCTTCACTTT
CAGATAGACCTTTTTGCTTCCAGGAAAGAATCTCATTCCCTATGGCAATACATTCATCTGTTTT
CCAACCTGAAAAGCTAACTTGATTGATGCCAATGACAAGGGCATCAAGAGTAGTATCCCATAGA
GTAGTATTTCTAGCTACATCCTTTGCAAGTGAAGCTGATCCACCTAAGGCTTCAAGAGTATTGA
TGAATCTGCTTAACAGAACAAATGAATAATCCTCAAGACTAATTTCACAAAGGCGCCACTTTTG
TCGCATTGCTATAGCATTATCAGGCGCATCATTTCTAAGGCCACTTTCAAGGCCCTTCATTAGA
ACCGATCTTAGAGAAGATAATGATTGCAAGGTAGTCATCAAAATTTGAATGGTATCATTTTTAT
CCAAATCTTCTGCATGATCCACTTGGTCCAAACTCCTTTTGGTTTCCACAAAGGATGAGAGAAC
TTCTAAGCCTGACTCGTTCAGAGATTCCTTGATGGACTCCAGTTGCTCAAATAGG
						
					

						Genomic sequence
						
							CATTACTTTTTCAGGGAATATAGAAAGAAGTGCTTCAGAGTACTCTTCCGTTAATCTCCGTGCT
CTGTCCAGTGTAGCTTTAAGTCTTAGTGACCAAATATATTTCCCATCTTCACAACCTTCACACA
TGACAAGAAACAGTCAGGGTATTTCTGAGTCTTGACTACAATAAAGGTATTTAGGCATGGGCAT
ATAAAATAGATAGATATTAAAGAAGAAACAGCACCTTCACTTTCAGATAGACCTTTTTGCTTCC
AGGAAAGAATCTCATTCCCTATGGCAATACATTCATCTGTTTTCCAACCTGAAAAGCTAACTTG
ATTGATGCCAATGACAAGGGCATCAAGAGTAGTATCCCATAGAGTAGTATTTCTAGCTACATCC
TTTGCAAGTGAAGCTGATCCACCTAAGGCTTCAAGAGTATTGATGAATCTGTTATAGTACCAGA
GCAAAGTACATAAGCTCACTGATACCGCCAAGAGTAATATAAGTTTGCCTAGCTACGATTTTAT
TTTGAAGCTATAAATGATAACATAGAGTCATGGAGTGAATTAACCTATAAATCATAACAAATAA
GTCAGCAAAAATTGATACCATTTTAATCAATGCAATGCATTAGCATTATTTGGAAAAACAGACT
GCAAAGTCTATCTTTTCACTAAAGCACAAAGGAAATTAGTTCACTGTTGCAAAAGTCGAACAAG
TGAAATACACTGTTCTTCTCACTTCACACACACACACACACAAGTAGGTGATGGACTGAAGGTG
TTTTCAGTTTGCTACAATAGCTACTTCTGCTAGCTTGCATTACTACCAATTATAGAGAACATGT
TTCAGTCGATTCTGCTCCAAAACCAACATATACTACAGCTGCTTGCAATCTCTGCAGGTCTCTG
ATTACTACTGATCCTAGAGCAGGAAAACTCTATCCTGACTTCTATCTTGTCAAAGGAAACTTAT
TAGCCCAGCAGCCTACAAACATTTCTAGTGTTCAGACATCAGTTGTTATGGGTTAGGGTTCATA
GGGGTAAACACCGCCGGGAGGATGGTGACGGCTGCTAGGGATGAGAGAGGGACTTAGGTTGGGA
GAGACTGATTCATCGCTTAATCCAAAATTCCAAATGACGATACAATCCATCCTTATATAGATGG
ATAAGATGGAGGGAAAGACCCAGTCTAATCCTATCCAACCAACTCTATCCAACTGAGCTACCAT
AGGATGATGGAACTGATCCCTAGGGCCTCAACCCATCGGCTCACTAGGACCTCCACCTCTCGGC
CCACTACCTATGACAACAGTTGCCTACAATCTATTGTTTGTACACATGAGTAAGCTGCTGGTTT
TATTTAACAAATTTGATGCCTAAGCATTAGATTCACCTAACAATTATGACTCTGCATGCCCTCG
AATAGATCAATATCCACTCTATATATGCACATAGATAATATGGCTTCACTAAAGATGACTACAT
CACATGAGAGTGCAACCTCTACATTCACTTTTTATCCATATTCGTCAGTATTTTCCTTTAATAT
TTGTATTCAACAAGACTCCACACCACATGATATAGATAAGCTTGAAACAGGGGTCAAAAAGAGG
TAGGGCACTCGTCCACATCTATCCAATGACTTTTTCCTATCATGATAGAGAGGCTTCAAGCAAT
TCTTGGTTTCTCATTGCAGAATTCTAGTGGTAAATTAGTTGATCTTATTGGGATAACTCAAACT
AATACAGTAACCATACAACGTTTCTATCAAACCCCTAGCAATTTGTTTACTTAATCCAATATGG
TCCTTCTGGATCAAAAAGAGAAATCTAGTATGCAATCAAATTTATGTTCTGACATAATCAAGAA
AAAATTGCAATTCATGCAGCCATCAGTTTTCACCAGAGCAGCCCCCACTTCATATATACCCAAA
GTAAATACTTTATTTAAAGATTGATTATGGCATGTTAGTGTCAATAAATTTTCGATTGCCCACT
AGTTTGGAAAGGTATGTGCTTTTTTAGAGAGCACTGATGCATTTTACAAGTGCATACAAACTAA
TCAACAAAGAACATAAAATCTCAAAAAGTGACGACTATTGACTAGTAAGACAAATGAAGGGCGA
AACTAACATTTCAGAATGGAAAGAAAAGGCAATTCAAAAGTACAATTTCATAAGGTTTGTGAGA
AAGCACCAATTAAAATCACTTAGTTGAAACTAGGACAGTTACCTGCTTAACAGAACAAATGAAT
AATCCTCAAGACTAATTTCACAAAGGCGCCACTGCAAAACGTAATCAAGTATCGCTTGTGATAT
ATGCAGCCAATTTCAACCACTTATCAATTATGTTAGACAAGATAACCTTTTGTCGCATTGCTAT
AGCATTATCAGGCGCATCATTTCTAAGGCCACTTTCAAGGCCCTTCATTAGAACCGATCTTAGA
GAAGATAATGATTGCAAGGTAGTCATCAAAATTTGAATGGTATCATTTTTATCCAAATCTTCTG
CATGATCCACTTGGTCCAAACTCTGAAAAGGAAGATAAACACGAAAGGAATATGAGTTAGGCAT
GACAATGATAAGCAATGATGCCAGACCAGTACTACTTGTTCCTCTATTGAAATACCAGAAAGTA
ACAAATGTCGGTATCAACTGTCAAAACATAGAAATAACAAGGACATAGTGCAATGCAAGGTGAC
ATAAATTCGTATTTATAAGTTTATTTGATTATGTTATGTTAGGTAACCAGAGCACAGAAGTGTC
TGATTGAGAGTGATCCCTGGTAGAGCATTATCCGCAACTCCAATGCAAAGGAAATAAGGAGATA
ATTAATTGATGATCATACATATAAAGAAAAATTAACTGGTTTCAGCAAAGTTTACCCTTTTGGT
TTCCACAAAGGATGAGAGAACTTCTAAGCCTGACTCGTTCAGAGATTCCTTGATGGACTCCAGT
TGCTCAAATAGG
						
					

			
		

Sequences
Splice junction sequence	TTCAGCAAAGTTTACCCTTTTGGTTTCCACAAAGGATGAGAGAACTTCTAAGCCTGACTCGTTC AGAGATTCCTTGATGGACTCCAGTTGCTCAAATAGGcattactttttcagggaatatagaaaga agtgcttcagagtactcttccgttaatctccgtgctctgtccagtgtagctttaagtcttagtg accaaata
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: 631 Transcript exons: 11734617-11734735,11734843-11735048,11736835-11736887,11 736967-11737134,11737488-11737572 CATTACTTTTTCAGGGAATATAGAAAGAAGTGCTTCAGAGTACTCTTCCGTTAATCTCCGTGCT CTGTCCAGTGTAGCTTTAAGTCTTAGTGACCAAATATATTTCCCATCTTCACAACCTTCACTTT CAGATAGACCTTTTTGCTTCCAGGAAAGAATCTCATTCCCTATGGCAATACATTCATCTGTTTT CCAACCTGAAAAGCTAACTTGATTGATGCCAATGACAAGGGCATCAAGAGTAGTATCCCATAGA GTAGTATTTCTAGCTACATCCTTTGCAAGTGAAGCTGATCCACCTAAGGCTTCAAGAGTATTGA TGAATCTGCTTAACAGAACAAATGAATAATCCTCAAGACTAATTTCACAAAGGCGCCACTTTTG TCGCATTGCTATAGCATTATCAGGCGCATCATTTCTAAGGCCACTTTCAAGGCCCTTCATTAGA ACCGATCTTAGAGAAGATAATGATTGCAAGGTAGTCATCAAAATTTGAATGGTATCATTTTTAT CCAAATCTTCTGCATGATCCACTTGGTCCAAACTCCTTTTGGTTTCCACAAAGGATGAGAGAAC TTCTAAGCCTGACTCGTTCAGAGATTCCTTGATGGACTCCAGTTGCTCAAATAGG
Genomic sequence	CATTACTTTTTCAGGGAATATAGAAAGAAGTGCTTCAGAGTACTCTTCCGTTAATCTCCGTGCT CTGTCCAGTGTAGCTTTAAGTCTTAGTGACCAAATATATTTCCCATCTTCACAACCTTCACACA TGACAAGAAACAGTCAGGGTATTTCTGAGTCTTGACTACAATAAAGGTATTTAGGCATGGGCAT ATAAAATAGATAGATATTAAAGAAGAAACAGCACCTTCACTTTCAGATAGACCTTTTTGCTTCC AGGAAAGAATCTCATTCCCTATGGCAATACATTCATCTGTTTTCCAACCTGAAAAGCTAACTTG ATTGATGCCAATGACAAGGGCATCAAGAGTAGTATCCCATAGAGTAGTATTTCTAGCTACATCC TTTGCAAGTGAAGCTGATCCACCTAAGGCTTCAAGAGTATTGATGAATCTGTTATAGTACCAGA GCAAAGTACATAAGCTCACTGATACCGCCAAGAGTAATATAAGTTTGCCTAGCTACGATTTTAT TTTGAAGCTATAAATGATAACATAGAGTCATGGAGTGAATTAACCTATAAATCATAACAAATAA GTCAGCAAAAATTGATACCATTTTAATCAATGCAATGCATTAGCATTATTTGGAAAAACAGACT GCAAAGTCTATCTTTTCACTAAAGCACAAAGGAAATTAGTTCACTGTTGCAAAAGTCGAACAAG TGAAATACACTGTTCTTCTCACTTCACACACACACACACACAAGTAGGTGATGGACTGAAGGTG TTTTCAGTTTGCTACAATAGCTACTTCTGCTAGCTTGCATTACTACCAATTATAGAGAACATGT TTCAGTCGATTCTGCTCCAAAACCAACATATACTACAGCTGCTTGCAATCTCTGCAGGTCTCTG ATTACTACTGATCCTAGAGCAGGAAAACTCTATCCTGACTTCTATCTTGTCAAAGGAAACTTAT TAGCCCAGCAGCCTACAAACATTTCTAGTGTTCAGACATCAGTTGTTATGGGTTAGGGTTCATA GGGGTAAACACCGCCGGGAGGATGGTGACGGCTGCTAGGGATGAGAGAGGGACTTAGGTTGGGA GAGACTGATTCATCGCTTAATCCAAAATTCCAAATGACGATACAATCCATCCTTATATAGATGG ATAAGATGGAGGGAAAGACCCAGTCTAATCCTATCCAACCAACTCTATCCAACTGAGCTACCAT AGGATGATGGAACTGATCCCTAGGGCCTCAACCCATCGGCTCACTAGGACCTCCACCTCTCGGC CCACTACCTATGACAACAGTTGCCTACAATCTATTGTTTGTACACATGAGTAAGCTGCTGGTTT TATTTAACAAATTTGATGCCTAAGCATTAGATTCACCTAACAATTATGACTCTGCATGCCCTCG AATAGATCAATATCCACTCTATATATGCACATAGATAATATGGCTTCACTAAAGATGACTACAT CACATGAGAGTGCAACCTCTACATTCACTTTTTATCCATATTCGTCAGTATTTTCCTTTAATAT TTGTATTCAACAAGACTCCACACCACATGATATAGATAAGCTTGAAACAGGGGTCAAAAAGAGG TAGGGCACTCGTCCACATCTATCCAATGACTTTTTCCTATCATGATAGAGAGGCTTCAAGCAAT TCTTGGTTTCTCATTGCAGAATTCTAGTGGTAAATTAGTTGATCTTATTGGGATAACTCAAACT AATACAGTAACCATACAACGTTTCTATCAAACCCCTAGCAATTTGTTTACTTAATCCAATATGG TCCTTCTGGATCAAAAAGAGAAATCTAGTATGCAATCAAATTTATGTTCTGACATAATCAAGAA AAAATTGCAATTCATGCAGCCATCAGTTTTCACCAGAGCAGCCCCCACTTCATATATACCCAAA GTAAATACTTTATTTAAAGATTGATTATGGCATGTTAGTGTCAATAAATTTTCGATTGCCCACT AGTTTGGAAAGGTATGTGCTTTTTTAGAGAGCACTGATGCATTTTACAAGTGCATACAAACTAA TCAACAAAGAACATAAAATCTCAAAAAGTGACGACTATTGACTAGTAAGACAAATGAAGGGCGA AACTAACATTTCAGAATGGAAAGAAAAGGCAATTCAAAAGTACAATTTCATAAGGTTTGTGAGA AAGCACCAATTAAAATCACTTAGTTGAAACTAGGACAGTTACCTGCTTAACAGAACAAATGAAT AATCCTCAAGACTAATTTCACAAAGGCGCCACTGCAAAACGTAATCAAGTATCGCTTGTGATAT ATGCAGCCAATTTCAACCACTTATCAATTATGTTAGACAAGATAACCTTTTGTCGCATTGCTAT AGCATTATCAGGCGCATCATTTCTAAGGCCACTTTCAAGGCCCTTCATTAGAACCGATCTTAGA GAAGATAATGATTGCAAGGTAGTCATCAAAATTTGAATGGTATCATTTTTATCCAAATCTTCTG CATGATCCACTTGGTCCAAACTCTGAAAAGGAAGATAAACACGAAAGGAATATGAGTTAGGCAT GACAATGATAAGCAATGATGCCAGACCAGTACTACTTGTTCCTCTATTGAAATACCAGAAAGTA ACAAATGTCGGTATCAACTGTCAAAACATAGAAATAACAAGGACATAGTGCAATGCAAGGTGAC ATAAATTCGTATTTATAAGTTTATTTGATTATGTTATGTTAGGTAACCAGAGCACAGAAGTGTC TGATTGAGAGTGATCCCTGGTAGAGCATTATCCGCAACTCCAATGCAAAGGAAATAAGGAGATA ATTAATTGATGATCATACATATAAAGAAAAATTAACTGGTTTCAGCAAAGTTTACCCTTTTGGT TTCCACAAAGGATGAGAGAACTTCTAAGCCTGACTCGTTCAGAGATTCCTTGATGGACTCCAGT TGCTCAAATAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003411* osi_circ_010444 						
					
						PMCS
						0.328441473

Conservation Information
Conserved circRNAs	osi_circ_003411* osi_circ_010444
PMCS	0.328441473

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11737550-11734667(+)
11737076-11737566(-)
						
						Potential amino acid sequence
						
							MDSSCSNRHYFFREYRKKCFRVLFR*(+)
MTTLQSLSSLRSVLMKGLESGLRNDAPDNAIAMRQKWRLCEISLEDYSFVLLSRFINTLEALGG
SASLAKDVARNTTLWDTTLDALVIGINQVSFSGWKTDECIAIGNEILSWKQKGLSESEGCEDGK
YIWSLRLKATLDRARRLTEEYSEALLSIFPEKVMPI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11737550-11734667(+) 11737076-11737566(-)
Potential amino acid sequence	MDSSCSNRHYFFREYRKKCFRVLFR(+) MTTLQSLSSLRSVLMKGLESGLRNDAPDNAIAMRQKWRLCEISLEDYSFVLLSRFINTLEALGG SASLAKDVARNTTLWDTTLDALVIGINQVSFSGWKTDECIAIGNEILSWKQKGLSESEGCEDGK YIWSLRLKATLDRARRLTEEYSEALLSIFPEKVMPI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os12g0297500_circ_g.6

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