Plant Circular RNA Database

Detail information of Os04g0165700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0165700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023005
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 4458147-4459627  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0165700						
					
						Parent gene annotation
						
							Cysteine synthase (EC 2.5.1.47). (Os04t0165700-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0165700_circ_g.1 Os04g0165700_circ_g.2 Os04g0165700_circ_g.4 Os04g0165700_circ_g.5 Os04g0165700_circ_g.6 Os04g0165700_circ_g.7 Os04g0165700_circ_g.8 						
					
						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  
						
							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
						Os04t0165700-01:5

General Information
CircRNA Name	Os04g0165700_circ_g.3
ID in PlantcircBase	osa_circ_023005
Alias	NA
Organism	Oryza sativa
Position	chr4: 4458147-4459627 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0165700
Parent gene annotation	Cysteine synthase (EC 2.5.1.47). (Os04t0165700-01)
Parent gene strand	-
Alternative splicing	Os04g0165700_circ_g.1 Os04g0165700_circ_g.2 Os04g0165700_circ_g.4 Os04g0165700_circ_g.5 Os04g0165700_circ_g.6 Os04g0165700_circ_g.7 Os04g0165700_circ_g.8
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	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	Os04t0165700-01:5

			
						 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  
						
							TGTATGAAGGCATTGTGAGTATGAGTTCATACCCTTTAAGAGCAGCCATGAATGCCAGGCCAAT
ACCCATGTTCCCTGATGTCGGCTCGATCAGTGTGGTcagaagaccctccttcagtgccaattct
cgagccatcttaacagcatcctcacctttcacctaccatatgccagttttacttagcaacttag
tattgcct

									
								

					

						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: 594
Transcript exons: 4458147-4458206,4458630-4458709,4458838-4458889,4458960-
4459097,4459364-4459627
CAGAAGACCCTCCTTCAGTGCCAATTCTCGAGCCATCTTAACAGCATCCTCACCTTTCACCTCA
ATAACCTTTTCCATTATATCCATATTCAAAATTTCCGGCTTAAATCCCACTCCATTTCCAGTGA
TGAGGTGAGGACCTGGTTTGCCACCATTCAAAACATTTGCTTCAGCAGGTTCAACTCCATAGAT
CTTTGCATTGGGGTTCTTCTCCTTAAGATACTTGCCAACACCAGTGACGGTGCCGCCGCTCCCG
ATTCCCATGACAAAAATATCAACCTGCCCAAGTGTATCCTCCCAGATTTCTGGACCAGTTGTCT
CATAGTGTACCTTGACATTTGCAGGATTCTCAAACTGCTGCAGCATGAACGCGCTAGGATGGTT
CTCATACAGCTCGGCGGCCTTCCTCACCGTGCCTCCCATACCTTTTGTTGGGTCGGTAAGGACG
AGTTTTGCGCCGAAGGCCCTCATGGTCACCCTCCTCTCAAGGCTGGTGTATGAAGGCATTGTGA
GTATGAGTTCATACCCTTTAAGAGCAGCCATGAATGCCAGGCCAATACCCATGTTCCCTGATGT
CGGCTCGATCAGTGTGGT
						
					

						Genomic sequence
						
							CAGAAGACCCTCCTTCAGTGCCAATTCTCGAGCCATCTTAACAGCATCCTCACCTTTCACCTAC
CATATGCCAGTTTTACTTAGCAACTTAGTATTGCCTATATAGTATAATGTAAAAAAAAAAAAAG
CTGGATACGAAAGAAAGGAATCGATGGTTTTTTTTTTTATTTTTTTTAATTTTTTTTTTAAGAT
AAGGGTATTTTTTTTACCTGGCCTCTACATCCAACCGGATATATACGGCCATTGAAATAGGGAA
CTTAGCCCCGGAAATAACTCAATCTGAAATTCGCTCCATAGGAGATTTGAACTTAGGACCTTGG
AGTATTACTCAGGTCACTGTAACCACTAGGCTACATGCCCTTTCGTAATCGATGGTATTAAGGA
GGAGGTGAGTCTCGAAAGCCAACTTGTGGTGCTAGCCAGTAAAACTCTGAATCTTTCTCATAAT
GTACTAAGAAAAGAAGTGAACCTAAATTCATTTACCTCAATAACCTTTTCCATTATATCCATAT
TCAAAATTTCCGGCTTAAATCCCACTCCATTTCCAGTGATGAGGTGAGGACCTGCAATTCGGTT
CAGTGAACAACATTATGACAAGTGAAATGATAAGTAATTAATTACCTACTACAAAAGGATAAAT
CTTCATTATCTAAAAAAAAAGGGATAAATCTTCCTGAGAGCTAGATCTTACCTGGTTTGCCACC
ATTCAAAACATTTGCTTCAGCAGGTTCAACTCCATAGATCTGCATACACACACAAATGGCATTA
ATTTCACACATATATCTGGAGTTTTTTTTTTTTTTGTTTTAGTACCTTTGCATTGGGGTTCTTC
TCCTTAAGATACTTGCCAACACCAGTGACGGTGCCGCCGCTCCCGATTCCCATGACAAAAATAT
CAACCTGCCCAAGTGTATCCTCCCAGATTTCTGGACCAGTTGTCTCATAGTGTACCTTCAATTT
TGATCAACACAAATCAGAAACAATAGCAATTGAAGTATCATACTTACTCCAGAATATGAAACTT
ATATGTCTGAATTGAGCTTTAATTCGCTCACATGGGAAGCTTTACGCATATAATCTTGGTCTAT
AAACATAATATATCATCTTACAGCAAGAATTTGCAGGATTGACCAAAACCAAGATTTCGCATTT
CATCAAAGATTACAACAAGTACTACTGCGTGCAGATTTTTTGCATTGAAGAATAGAAGACTTTA
CCTTGACATTTGCAGGATTCTCAAACTGCTGCAGCATGAACGCGCTAGGATGGTTCTCATACAG
CTCGGCGGCCTTCCTCACCGTGCCTCCCATACCTTTTGTTGGGTCGGTAAGGACGAGTTTTGCG
CCGAAGGCCCTCATGGTCACCCTCCTCTCAAGGCTGGTGTATGAAGGCATTGTGAGTATGAGTT
CATACCCTTTAAGAGCAGCCATGAATGCCAGGCCAATACCCATGTTCCCTGATGTCGGCTCGAT
CAGTGTGGT
						
					

			
		

Sequences
Splice junction sequence	TGTATGAAGGCATTGTGAGTATGAGTTCATACCCTTTAAGAGCAGCCATGAATGCCAGGCCAAT ACCCATGTTCCCTGATGTCGGCTCGATCAGTGTGGTcagaagaccctccttcagtgccaattct cgagccatcttaacagcatcctcacctttcacctaccatatgccagttttacttagcaacttag tattgcct
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: 594 Transcript exons: 4458147-4458206,4458630-4458709,4458838-4458889,4458960- 4459097,4459364-4459627 CAGAAGACCCTCCTTCAGTGCCAATTCTCGAGCCATCTTAACAGCATCCTCACCTTTCACCTCA ATAACCTTTTCCATTATATCCATATTCAAAATTTCCGGCTTAAATCCCACTCCATTTCCAGTGA TGAGGTGAGGACCTGGTTTGCCACCATTCAAAACATTTGCTTCAGCAGGTTCAACTCCATAGAT CTTTGCATTGGGGTTCTTCTCCTTAAGATACTTGCCAACACCAGTGACGGTGCCGCCGCTCCCG ATTCCCATGACAAAAATATCAACCTGCCCAAGTGTATCCTCCCAGATTTCTGGACCAGTTGTCT CATAGTGTACCTTGACATTTGCAGGATTCTCAAACTGCTGCAGCATGAACGCGCTAGGATGGTT CTCATACAGCTCGGCGGCCTTCCTCACCGTGCCTCCCATACCTTTTGTTGGGTCGGTAAGGACG AGTTTTGCGCCGAAGGCCCTCATGGTCACCCTCCTCTCAAGGCTGGTGTATGAAGGCATTGTGA GTATGAGTTCATACCCTTTAAGAGCAGCCATGAATGCCAGGCCAATACCCATGTTCCCTGATGT CGGCTCGATCAGTGTGGT
Genomic sequence	CAGAAGACCCTCCTTCAGTGCCAATTCTCGAGCCATCTTAACAGCATCCTCACCTTTCACCTAC CATATGCCAGTTTTACTTAGCAACTTAGTATTGCCTATATAGTATAATGTAAAAAAAAAAAAAG CTGGATACGAAAGAAAGGAATCGATGGTTTTTTTTTTTATTTTTTTTAATTTTTTTTTTAAGAT AAGGGTATTTTTTTTACCTGGCCTCTACATCCAACCGGATATATACGGCCATTGAAATAGGGAA CTTAGCCCCGGAAATAACTCAATCTGAAATTCGCTCCATAGGAGATTTGAACTTAGGACCTTGG AGTATTACTCAGGTCACTGTAACCACTAGGCTACATGCCCTTTCGTAATCGATGGTATTAAGGA GGAGGTGAGTCTCGAAAGCCAACTTGTGGTGCTAGCCAGTAAAACTCTGAATCTTTCTCATAAT GTACTAAGAAAAGAAGTGAACCTAAATTCATTTACCTCAATAACCTTTTCCATTATATCCATAT TCAAAATTTCCGGCTTAAATCCCACTCCATTTCCAGTGATGAGGTGAGGACCTGCAATTCGGTT CAGTGAACAACATTATGACAAGTGAAATGATAAGTAATTAATTACCTACTACAAAAGGATAAAT CTTCATTATCTAAAAAAAAAGGGATAAATCTTCCTGAGAGCTAGATCTTACCTGGTTTGCCACC ATTCAAAACATTTGCTTCAGCAGGTTCAACTCCATAGATCTGCATACACACACAAATGGCATTA ATTTCACACATATATCTGGAGTTTTTTTTTTTTTTGTTTTAGTACCTTTGCATTGGGGTTCTTC TCCTTAAGATACTTGCCAACACCAGTGACGGTGCCGCCGCTCCCGATTCCCATGACAAAAATAT CAACCTGCCCAAGTGTATCCTCCCAGATTTCTGGACCAGTTGTCTCATAGTGTACCTTCAATTT TGATCAACACAAATCAGAAACAATAGCAATTGAAGTATCATACTTACTCCAGAATATGAAACTT ATATGTCTGAATTGAGCTTTAATTCGCTCACATGGGAAGCTTTACGCATATAATCTTGGTCTAT AAACATAATATATCATCTTACAGCAAGAATTTGCAGGATTGACCAAAACCAAGATTTCGCATTT CATCAAAGATTACAACAAGTACTACTGCGTGCAGATTTTTTGCATTGAAGAATAGAAGACTTTA CCTTGACATTTGCAGGATTCTCAAACTGCTGCAGCATGAACGCGCTAGGATGGTTCTCATACAG CTCGGCGGCCTTCCTCACCGTGCCTCCCATACCTTTTGTTGGGTCGGTAAGGACGAGTTTTGCG CCGAAGGCCCTCATGGTCACCCTCCTCTCAAGGCTGGTGTATGAAGGCATTGTGAGTATGAGTT CATACCCTTTAAGAGCAGCCATGAATGCCAGGCCAATACCCATGTTCCCTGATGTCGGCTCGAT CAGTGTGGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24990135

Conservation Information
Conserved circRNAs	NA
PMCS	0.24990135

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4459399-4458702(+)
4459580-4458184(+)
4459599-4458149(-)
						
						Potential amino acid sequence
						
							MNALGWFSYSSAAFLTVPPIPFVGSVRTSFAPKALMVTLLSRLVYEGIVSMSSYPLRAAMNARP
IPMFPDVGSISVVRRPSFSANSRAILTASSPFTSITFSIISIFKISGLNPTPFPVMR*(+)
MPGQYPCSLMSARSVWSEDPPSVPILEPS*(+)
MGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTKGMGGTVRKAAELYENHPS
AFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVTGVGKYLKEKNPNAKIYGV
EPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDAVKMARELALKEGLLTTLI
EPTSGNMGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTKGMGGTVRKAAEL
YENHPSAFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVTGVGKYLKEKNPN
AKIYGVEPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDAVKMARELALKEG
LLTTLIEPTSGNMGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTKGMGGTV
RKAAELYENHPSAFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVTGVGKYL
KEKNPNAKIYGVEPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDAVKMARE
LALKEGLLTTLIEPTSGNMGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTK
GMGGTVRKAAELYENHPSAFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVT
GVGKYLKEKNPNAKIYGVEPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDA
VKMARELALKEGLL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4459399-4458702(+) 4459580-4458184(+) 4459599-4458149(-)
Potential amino acid sequence	MNALGWFSYSSAAFLTVPPIPFVGSVRTSFAPKALMVTLLSRLVYEGIVSMSSYPLRAAMNARP IPMFPDVGSISVVRRPSFSANSRAILTASSPFTSITFSIISIFKISGLNPTPFPVMR(+) MPGQYPCSLMSARSVWSEDPPSVPILEPS(+) MGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTKGMGGTVRKAAELYENHPS AFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVTGVGKYLKEKNPNAKIYGV EPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDAVKMARELALKEGLLTTLI EPTSGNMGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTKGMGGTVRKAAEL YENHPSAFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVTGVGKYLKEKNPN AKIYGVEPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDAVKMARELALKEG LLTTLIEPTSGNMGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTKGMGGTV RKAAELYENHPSAFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVTGVGKYL KEKNPNAKIYGVEPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDAVKMARE LALKEGLLTTLIEPTSGNMGIGLAFMAALKGYELILTMPSYTSLERRVTMRAFGAKLVLTDPTK GMGGTVRKAAELYENHPSAFMLQQFENPANVKVHYETTGPEIWEDTLGQVDIFVMGIGSGGTVT GVGKYLKEKNPNAKIYGVEPAEANVLNGGKPGPHLITGNGVGFKPEILNMDIMEKVIEVKGEDA VKMARELALKEGLL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0165700_circ_g.3

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