Plant Circular RNA Database

Detail information of Os03g0123500_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0123500_circ_g.1
					
						ID in PlantcircBase
						osa_circ_017664
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 1340805-1343774  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0123500						
					
						Parent gene annotation
						
							Similar to HOS66 protein. (Os03t0123500-01);Similar to Homeobox 
protein knotted-1-like 3. (Os03t0123500-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0123500_circ_g.2 Os03g0123500_circ_g.3 						
					
						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
						Os03t0123500-02:2
Os03t0123500-01:2

General Information
CircRNA Name	Os03g0123500_circ_g.1
ID in PlantcircBase	osa_circ_017664
Alias	NA
Organism	Oryza sativa
Position	chr3: 1340805-1343774 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0123500
Parent gene annotation	Similar to HOS66 protein. (Os03t0123500-01);Similar to Homeobox protein knotted-1-like 3. (Os03t0123500-02)
Parent gene strand	+
Alternative splicing	Os03g0123500_circ_g.2 Os03g0123500_circ_g.3
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	Os03t0123500-02:2 Os03t0123500-01:2

			
						 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  
						
							CGGGCACGACCTCATGGGCTTCGGCCCGCTCATGCCCACCGACTCCGAGCGATCCCTCATGGAG
CGGGTCAGGCAAGAGCTCAAGATTGAGCTCAAGCAGgcgcagtacatgatgctgctgtgctcgt
tcagggagcagctgcagcagcacgtccgggtgcacgccgtggaggccgtcatggcgtgccgcga
gatcgagc

									
								

					

						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: 315
Transcript exons: 1340805-1340925,1343581-1343774
GCGCAGTACATGATGCTGCTGTGCTCGTTCAGGGAGCAGCTGCAGCAGCACGTCCGGGTGCACG
CCGTGGAGGCCGTCATGGCGTGCCGCGAGATCGAGCAATCCTTGCAGGACCTAACCGGTGCAAC
TTTGGAGGAAGGGACAGGGGCGACCATGTCGGAGGACGAGGATGAGACGGCGCCGATGCTGGAG
GGCCCGATGGATATGGGCTCGGACGGGCACGACCTCATGGGCTTCGGCCCGCTCATGCCCACCG
ACTCCGAGCGATCCCTCATGGAGCGGGTCAGGCAAGAGCTCAAGATTGAGCTCAAGCAG
						
					

						Genomic sequence
						
							GCGCAGTACATGATGCTGCTGTGCTCGTTCAGGGAGCAGCTGCAGCAGCACGTCCGGGTGCACG
CCGTGGAGGCCGTCATGGCGTGCCGCGAGATCGAGCAATCCTTGCAGGACCTAACCGGTAATTA
ACTACTACAGTATCATACATGCATTACATATTTTCCACTATATATTACATATTTCATTACTTTC
CCTCTCCTTCTCGCCGCCTTCTTTTCTGTATTTTTTTTTCGATTTCCATGGTGTCGTCTTTATG
ATTTTTGTTCACCTTTTTGCTCTTCTCGTTAGTTAGATTAGATGGTGAAATTGTTTTTTTTTAG
TTCGTTGCCGCTAGCTCTTGCAGTGATATATTAGTTGCAGCGTCTTGTTCAAACATATATATGG
TCTCTTGATTCCCTCTCAACAGATTTGCATGCCTTGACTTCTAAGGTTCCGGTTTCTACAGGTG
TATTCAGAGGAGATTAGTTAAATATGAAAACTCTAACACACGTACCTAACAGCGACTTTATTGC
TGATGTTTATACTCGAATCAATGGAATGATAAATAACACGGAATTACCAAGGCCCACATAGATG
GCAGCCCGTATACTAGGGAAAGCCCAGAAGCCCAACGGTAGATGTCACGAAAACAATTTCAGAT
ATTCCTTTTTAGCATAAAATCCTTCCAGTTCAAAAACAAGGGCACCAATTTTTTTTATAATCAT
TTTGTGTTATTAACAGAGAATAGCATAGTCAAGGTTTCTAAGGCCTATATATATATATATGTGT
ACGTAGTTAGACGTGATACCCTTGGTAAAATTAACTTAATCAGTTCATATATATACTGATATGA
GGTGACTAGCTAGCTATTTTTCTTCTTTTCTCACAAAGTCTCAATTGGAGGTTTATGATCAGTT
GAAATAAAAAAAATTCCAACAACAAAATTTGAACCAACTATTTGGCATAAATCTAATGAAACTA
TCCTTTGCTAAGAGAACCATGGGTTGGATATATACATCCTTATTAGTGTAGAGGCTGGATATTA
ATCTGTTATCTAAGAAAACAATCCATGAACTTATAAAATGCATTTAGCCATCTCCGGCGCAGAT
CAAGCGCTGCCATTCGGTCATGGCCGATTGGTTGGTTGGTTGCTAGCTAGCGAGAAATCGCTGA
GAGGATATTGAAAAGCTAGTAGGTAGTGTAACAGCTACCTAAGCCTTATTTGGAGAGCTTTGAG
ATTTTAGGAAGCATAGCTAGTTAGTAGTCAATCACTCAATTGGTGAGAATATGGAAAAAAATAG
GTTTTCTAACTTTAAACTTCTAGTTCATTTTTTAAATTCAATAACTATAATTTCTTAGAATCTA
GATGAAAATTTAAACTGTTTGAAAAAAAAGGTTATATAAAAGAAGCTACGACTATCAAAAGCTC
CCTCAAACAGAATCTAGGTTACATGAAAGTCATCTAGGTTCCATGCTAATCCTGGCTCGGAGTT
GAAAGTCCATGCCTCTCGTCTAATCGACTAGCTAATTAAATGATTCAGGTGCTTCGCTTCTGTC
GAATAATATATATCACACACGACCATGGAAAGTGGAAGGTGTGTCACATGACATGATATGACCG
GCCGATCGAGCTCTTGGCGATCGTCCTCTTATCATGAGGGGCATCGTCATAATCATGATGCATC
GATTGGGATTCAACTATAGTAGTCATTGCATATTCAAAAAGCATCAGGGTTGATGTAATGTAAC
TGAAGAAAAACACCCATGATGATTGGCGAAATAGATGTTGAAAACTTAGCATGCGCATACATAC
GTAAACTTCAATTGTAGGTAGAGAAAAATTACATTTCACCTGTAAATTAGGACACTGGGAAGTT
GTTAAATTACTAGTCCACTCTTTTGACCTGGATTCTAAGGTTCTTTATAGGTTGAATTTTTATT
TTTATTTTTTATTTTGGTGTGTGTGCGCGCGCGCGCTTCAGTTGGTTTTGGTTGCTTTAGAGCA
TAACATCAAAGCCATGCTACTTTAAAAAAACTATAATAATAATAATAATAATAATAATAATAAT
AATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATA
ATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAGAAGAA
GAAGAAGAAGAAGAAGAAGAAGAAATAAAGACGAAGATCGAATTGGAGCTATAATATGCTAACT
TATCTAGCTAGGCAGTTCAAAGTACACTGGTAGCTAGCTAGTAGTTCCTGCGAGCTGTTTCATG
CAGGCAATGCAGCTGGCGAGAGCTGCATATGCAAAACTCCAAATCAGAGACATCTTTTCGATTG
GGTAGCTTTCAAGCTGTTTCAAGTGGCCATGCGCATAGCTCGTACAACTGTCTATCTCTGCTCG
ATCTCACACGTTCCAGTTCATGCAGCTCGATCGATCGCCGACGTCGACAAAGCCCTCATGCATG
CCTCCGTACTGCATGCATGCCCTAGCTAATTAGCTCTAACTCACTGTGTAGCACAATCTAGATT
GAATATAACCGACAAACTTTGCTAGCTACTAGCTCTTCTTTTTCATGTTATTATACTTGCTTCA
AGCTAATCTTTAATTTTTCATGTTATTAGATATAGGAATAACTAATCAAATAAATTAAAGAAAT
AGGACAGTTACAAGAGATGTGATCATCAATTAATTAACTACAGTAGTTGATTTACACTTACCTG
GATGCATATGCAATTGATCATCAGGTGCAACTTTGGAGGAAGGGACAGGGGCGACCATGTCGGA
GGACGAGGATGAGACGGCGCCGATGCTGGAGGGCCCGATGGATATGGGCTCGGACGGGCACGAC
CTCATGGGCTTCGGCCCGCTCATGCCCACCGACTCCGAGCGATCCCTCATGGAGCGGGTCAGGC
AAGAGCTCAAGATTGAGCTCAAGCAG
						
					

			
		

Sequences
Splice junction sequence	CGGGCACGACCTCATGGGCTTCGGCCCGCTCATGCCCACCGACTCCGAGCGATCCCTCATGGAG CGGGTCAGGCAAGAGCTCAAGATTGAGCTCAAGCAGgcgcagtacatgatgctgctgtgctcgt tcagggagcagctgcagcagcacgtccgggtgcacgccgtggaggccgtcatggcgtgccgcga gatcgagc
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: 315 Transcript exons: 1340805-1340925,1343581-1343774 GCGCAGTACATGATGCTGCTGTGCTCGTTCAGGGAGCAGCTGCAGCAGCACGTCCGGGTGCACG CCGTGGAGGCCGTCATGGCGTGCCGCGAGATCGAGCAATCCTTGCAGGACCTAACCGGTGCAAC TTTGGAGGAAGGGACAGGGGCGACCATGTCGGAGGACGAGGATGAGACGGCGCCGATGCTGGAG GGCCCGATGGATATGGGCTCGGACGGGCACGACCTCATGGGCTTCGGCCCGCTCATGCCCACCG ACTCCGAGCGATCCCTCATGGAGCGGGTCAGGCAAGAGCTCAAGATTGAGCTCAAGCAG
Genomic sequence	GCGCAGTACATGATGCTGCTGTGCTCGTTCAGGGAGCAGCTGCAGCAGCACGTCCGGGTGCACG CCGTGGAGGCCGTCATGGCGTGCCGCGAGATCGAGCAATCCTTGCAGGACCTAACCGGTAATTA ACTACTACAGTATCATACATGCATTACATATTTTCCACTATATATTACATATTTCATTACTTTC CCTCTCCTTCTCGCCGCCTTCTTTTCTGTATTTTTTTTTCGATTTCCATGGTGTCGTCTTTATG ATTTTTGTTCACCTTTTTGCTCTTCTCGTTAGTTAGATTAGATGGTGAAATTGTTTTTTTTTAG TTCGTTGCCGCTAGCTCTTGCAGTGATATATTAGTTGCAGCGTCTTGTTCAAACATATATATGG TCTCTTGATTCCCTCTCAACAGATTTGCATGCCTTGACTTCTAAGGTTCCGGTTTCTACAGGTG TATTCAGAGGAGATTAGTTAAATATGAAAACTCTAACACACGTACCTAACAGCGACTTTATTGC TGATGTTTATACTCGAATCAATGGAATGATAAATAACACGGAATTACCAAGGCCCACATAGATG GCAGCCCGTATACTAGGGAAAGCCCAGAAGCCCAACGGTAGATGTCACGAAAACAATTTCAGAT ATTCCTTTTTAGCATAAAATCCTTCCAGTTCAAAAACAAGGGCACCAATTTTTTTTATAATCAT TTTGTGTTATTAACAGAGAATAGCATAGTCAAGGTTTCTAAGGCCTATATATATATATATGTGT ACGTAGTTAGACGTGATACCCTTGGTAAAATTAACTTAATCAGTTCATATATATACTGATATGA GGTGACTAGCTAGCTATTTTTCTTCTTTTCTCACAAAGTCTCAATTGGAGGTTTATGATCAGTT GAAATAAAAAAAATTCCAACAACAAAATTTGAACCAACTATTTGGCATAAATCTAATGAAACTA TCCTTTGCTAAGAGAACCATGGGTTGGATATATACATCCTTATTAGTGTAGAGGCTGGATATTA ATCTGTTATCTAAGAAAACAATCCATGAACTTATAAAATGCATTTAGCCATCTCCGGCGCAGAT CAAGCGCTGCCATTCGGTCATGGCCGATTGGTTGGTTGGTTGCTAGCTAGCGAGAAATCGCTGA GAGGATATTGAAAAGCTAGTAGGTAGTGTAACAGCTACCTAAGCCTTATTTGGAGAGCTTTGAG ATTTTAGGAAGCATAGCTAGTTAGTAGTCAATCACTCAATTGGTGAGAATATGGAAAAAAATAG GTTTTCTAACTTTAAACTTCTAGTTCATTTTTTAAATTCAATAACTATAATTTCTTAGAATCTA GATGAAAATTTAAACTGTTTGAAAAAAAAGGTTATATAAAAGAAGCTACGACTATCAAAAGCTC CCTCAAACAGAATCTAGGTTACATGAAAGTCATCTAGGTTCCATGCTAATCCTGGCTCGGAGTT GAAAGTCCATGCCTCTCGTCTAATCGACTAGCTAATTAAATGATTCAGGTGCTTCGCTTCTGTC GAATAATATATATCACACACGACCATGGAAAGTGGAAGGTGTGTCACATGACATGATATGACCG GCCGATCGAGCTCTTGGCGATCGTCCTCTTATCATGAGGGGCATCGTCATAATCATGATGCATC GATTGGGATTCAACTATAGTAGTCATTGCATATTCAAAAAGCATCAGGGTTGATGTAATGTAAC TGAAGAAAAACACCCATGATGATTGGCGAAATAGATGTTGAAAACTTAGCATGCGCATACATAC GTAAACTTCAATTGTAGGTAGAGAAAAATTACATTTCACCTGTAAATTAGGACACTGGGAAGTT GTTAAATTACTAGTCCACTCTTTTGACCTGGATTCTAAGGTTCTTTATAGGTTGAATTTTTATT TTTATTTTTTATTTTGGTGTGTGTGCGCGCGCGCGCTTCAGTTGGTTTTGGTTGCTTTAGAGCA TAACATCAAAGCCATGCTACTTTAAAAAAACTATAATAATAATAATAATAATAATAATAATAAT AATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATA ATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAGAAGAA GAAGAAGAAGAAGAAGAAGAAGAAATAAAGACGAAGATCGAATTGGAGCTATAATATGCTAACT TATCTAGCTAGGCAGTTCAAAGTACACTGGTAGCTAGCTAGTAGTTCCTGCGAGCTGTTTCATG CAGGCAATGCAGCTGGCGAGAGCTGCATATGCAAAACTCCAAATCAGAGACATCTTTTCGATTG GGTAGCTTTCAAGCTGTTTCAAGTGGCCATGCGCATAGCTCGTACAACTGTCTATCTCTGCTCG ATCTCACACGTTCCAGTTCATGCAGCTCGATCGATCGCCGACGTCGACAAAGCCCTCATGCATG CCTCCGTACTGCATGCATGCCCTAGCTAATTAGCTCTAACTCACTGTGTAGCACAATCTAGATT GAATATAACCGACAAACTTTGCTAGCTACTAGCTCTTCTTTTTCATGTTATTATACTTGCTTCA AGCTAATCTTTAATTTTTCATGTTATTAGATATAGGAATAACTAATCAAATAAATTAAAGAAAT AGGACAGTTACAAGAGATGTGATCATCAATTAATTAACTACAGTAGTTGATTTACACTTACCTG GATGCATATGCAATTGATCATCAGGTGCAACTTTGGAGGAAGGGACAGGGGCGACCATGTCGGA GGACGAGGATGAGACGGCGCCGATGCTGGAGGGCCCGATGGATATGGGCTCGGACGGGCACGAC CTCATGGGCTTCGGCCCGCTCATGCCCACCGACTCCGAGCGATCCCTCATGGAGCGGGTCAGGC AAGAGCTCAAGATTGAGCTCAAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.227138524

Conservation Information
Conserved circRNAs	NA
PMCS	0.227138524

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1340815-1343771(+)
1343630-1340814(+)
1343736-1340807(-)
						
						Potential amino acid sequence
						
							MMLLCSFREQLQQHVRVHAVEAVMACREIEQSLQDLTGATLEEGTGATMSEDEDETAPMLEGPM
DMGSDGHDLMGFGPLMPTDSERSLMERVRQELKIELKQAQYMMLLCSFREQLQQHVRVHAVEAV
MACREIEQSLQDLTGATLEEGTGATMSEDEDETAPMLEGPMDMGSDGHDLMGFGPLMPTDSERS
LMERVRQELKIELKQAQYMMLLCSFREQLQQHVRVHAVEAVMACREIEQSLQDLTGATLEEGTG
ATMSEDEDETAPMLEGPMDMGSDGHDLMGFGPLMPTDSERSLMERVRQELKIELKQAQYMMLLC
SFREQLQQHVRVHAVEAVMACREIEQSLQDLTGATLEEGTGATMSEDEDETAPMLEGPMDMGSD
GHDLMGFGPLMPTDSERSLMERVRQELKIELKQ(+)
MRRRRCWRARWIWARTGTTSWASARSCPPTPSDPSWSGSGKSSRLSSSRRST*(+)
MRDRSESVGMSGPKPMRSCPSEPISIGPSSIGAVSSSSSDMVAPVPSSKVAPVRSCKDCSISRH
AMTASTACTRTCCCSCSLNEHSSIMYCACLSSILSSCLTRSMRDRSESVGMSGPKPMRSCPSEP
ISIGPSSIGAVSSSSSDMVAPVPSSKVAPVRSCKDCSISRHAMTASTACTRTCCCSCSLNEHSS
IMYCACLSSILSSCLTRSMRDRSESVGMSGPKPMRSCPSEPISIGPSSIGAVSSSSSDMVAPVP
SSKVAPVRSCKDCSISRHAMTASTACTRTCCCSCSLNEHSSIMYCACLSSILSSCLTRSMRDRS
ESVGMSGPKPMRSCPSEPISIGPSSIGAVSSSSSDMVAPVPSSKVAPVRSCKDCSISRHAMTAS
TACTRTCCCSCSLNEHSSIMYC(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1340815-1343771(+) 1343630-1340814(+) 1343736-1340807(-)
Potential amino acid sequence	MMLLCSFREQLQQHVRVHAVEAVMACREIEQSLQDLTGATLEEGTGATMSEDEDETAPMLEGPM DMGSDGHDLMGFGPLMPTDSERSLMERVRQELKIELKQAQYMMLLCSFREQLQQHVRVHAVEAV MACREIEQSLQDLTGATLEEGTGATMSEDEDETAPMLEGPMDMGSDGHDLMGFGPLMPTDSERS LMERVRQELKIELKQAQYMMLLCSFREQLQQHVRVHAVEAVMACREIEQSLQDLTGATLEEGTG ATMSEDEDETAPMLEGPMDMGSDGHDLMGFGPLMPTDSERSLMERVRQELKIELKQAQYMMLLC SFREQLQQHVRVHAVEAVMACREIEQSLQDLTGATLEEGTGATMSEDEDETAPMLEGPMDMGSD GHDLMGFGPLMPTDSERSLMERVRQELKIELKQ(+) MRRRRCWRARWIWARTGTTSWASARSCPPTPSDPSWSGSGKSSRLSSSRRST*(+) MRDRSESVGMSGPKPMRSCPSEPISIGPSSIGAVSSSSSDMVAPVPSSKVAPVRSCKDCSISRH AMTASTACTRTCCCSCSLNEHSSIMYCACLSSILSSCLTRSMRDRSESVGMSGPKPMRSCPSEP ISIGPSSIGAVSSSSSDMVAPVPSSKVAPVRSCKDCSISRHAMTASTACTRTCCCSCSLNEHSS IMYCACLSSILSSCLTRSMRDRSESVGMSGPKPMRSCPSEPISIGPSSIGAVSSSSSDMVAPVP SSKVAPVRSCKDCSISRHAMTASTACTRTCCCSCSLNEHSSIMYCACLSSILSSCLTRSMRDRS ESVGMSGPKPMRSCPSEPISIGPSSIGAVSSSSSDMVAPVPSSKVAPVRSCKDCSISRHAMTAS TACTRTCCCSCSLNEHSSIMYC(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0123500_circ_g.1

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