Plant Circular RNA Database

Detail information of Os04g0504800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0504800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_024499
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 25195759-25199098  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0504800						
					
						Parent gene annotation
						
							Similar to Poly(A)-binding protein. (Os04t0504800-01);Similar to
 polyadenylate-binding protein 2. (Os04t0504800-02);Similar to p
olyadenylate-binding protein 2. (Os04t0504800-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0504800_circ_g.2 Os04g0504800_circ_g.3 						
					
						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
						Os04t0504800-02:4
Os04t0504800-03:3
Os04t0504800-01:7

General Information
CircRNA Name	Os04g0504800_circ_g.1
ID in PlantcircBase	osa_circ_024499
Alias	NA
Organism	Oryza sativa
Position	chr4: 25195759-25199098 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0504800
Parent gene annotation	Similar to Poly(A)-binding protein. (Os04t0504800-01);Similar to polyadenylate-binding protein 2. (Os04t0504800-02);Similar to p olyadenylate-binding protein 2. (Os04t0504800-03)
Parent gene strand	-
Alternative splicing	Os04g0504800_circ_g.2 Os04g0504800_circ_g.3
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	Os04t0504800-02:4 Os04t0504800-03:3 Os04t0504800-01:7

			
						 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  
						
							GATCCACTTCTGCGACTGCTTGGGTCACGGTTTGAGTACATTACCCGAATGGGTTTGCCATTCA
GAGGAGCAAAGTTGAGCAGCTCCAGTGCTCTTGCAGcgttctttgctgttctggattagcattt
gcaagggcagaagtcagcgttccaattggagcaggtgacaaaccagcatctcgtactgggaagc
ctcccata

									
								

					

						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
						
							CGTTCTTTGCTGTTCTGGATTAGCATTTGCAAGGGCAGAAGTCAGCGTTCCAATTGGAGCAGGT
GACAAACCAGCATCTCGTACTGGGAAGCCTCCCATATCATACGATTGAATCATACCACCAGCAA
CCCCCGGCATTGGTGGAACATCAGGCATGTTATGCGCAGGTGGGTAACGGTACACACGTCCTCT
TGGAAGCATCTGTTAAAAGAACCATGGTAAGACGTGTGTCGTCACTGTTCATTCAATTGGTCCA
CATGACAAGGATAAGTGGACAACCCATCCAATGATCCAAAATTCGAGAGGAAAGGATAAATGGT
AGAATTCATACATGAAAAAGTGGATATGGGGGTTTTCTAAGTACTACAAAACGAATAGCTCGCT
GTTTGAATAAATATATCCACCGACAAACTTCCCCTCCCCTACCACTGCTTGGGAGCTCAGCACG
GTTTCATGTTCTATTTCACTACCCACTGGGGGTTCTTTTTACCTTTCCCTCATGGCACTACTTC
GCTATCAGTCACCGTAAATCATAAAAAACTTGGCACAACAGTAGAAGGTACAATGTTATAAGGA
TGTATATTAGCAAACCTGTTGCTGAAATGGCTGAGCAGATTGCTGTCCCTGGGCAGAACCAGCA
CCAGAACGCCGGATACCTGGACGTGGACCCTGTTGACCTTGTTGGACAACTGGAACAAAGTAAT
TTGGCATATGGGCACCCCCAGGCCTCATGCCTGGAACAAGCTGTTGCTGGAAACCAAATCCAGG
CTACATGGAAGAAAATTGGTAAGAAATTGATCTACTAAATTGTCCAGAAAATACAACACATTAG
ATGGAAAATTTGAATCATTTCTATGAGATAATGATCAGACAGTAGAATTTCAAAGTAGATGCCA
AATGAACAAGATATATGCAAAATGAGTGCTTGCAGCAGAGACATAACGCCTAGTACAATGGTGT
TGATGAATGACTAACCTATTGTGTCCCAAAAACTTGCATGGCATTGATTACCATACTCAAACTC
CTGATATATGCCCAGCATCAACAAAACCAATATTGAAAACTAAATGCATAAAAGTATTGTAGGA
ATTGATCAATGATATCACTTCACTCATGAAGTTGATGTACCAATTGCAATGACCAACCAACCAT
TAGATATATAATAATGCAGAATTTCAACAACTTGACTGCAGAGGGCAGTGCTAGTCTGTTTTAT
AAACAAACAAAAACACATTGATTCTCTCTTACAGTTAAAGCTAGACGGGGAAAATGAATGCATT
GATATCGAGCAGTACCTGTGGGGGCATGATAGCAGGTGGAGCTTGTCCGTAGAAGAGTTGCTGC
CCAAGAGGAGCCATAGGAGGGTACATGGGAAGACGTGGAGCCATGGAAGGTGTCATCGGTACAG
GGCGCACCTGAGAAAATTGTGCCTAAATAACATGGAACATGCTACCGTCAGCATTTCTTTTTCA
TTATGAAATGATCAGAAACAACTCAACAAGAAGAATGAGTTATTATAAAGCATTTATTAAGAAA
CTTTGTCAAAACACAGCAGTAAGAACTATGGTACAGCCGTACAACTTAAATATATGTTGTGGAC
TGCAGGCAATTGAAGATACATTTCTGAGGATTCAACTACAGATCTATGGAGCATGCATTGTGAG
TCATCCCTGCATATCAGTATTTCCCTCAACTATTATACAGAATAATGAGTTCTGAACTGATGCT
TAAAAGTTCTTCGCCAAACCCAATGACCTACTTCCTCCGTTTCACAATGTAAGTCATTCTAATA
TTTCCCACATTCATATTGATGTTAATGAATGTAGACATATATATCTATCTAGATTCATTAACAT
CAATATGAATGTGGGAAATGCTAGAATGACTTACATTGTGAAACGGAGGGAGTAAATATCAATA
ATCATAACTTAATTGCCTAGATTATCAATAACCATAAACAAATTACTGTTGCTCTTGTAAACAT
TGAGTTCATGATGGTGCAAAACAGAACAGTAATTCATGTGGCATATCTTATTTTCATATCCATA
AATAGTACTAGGAATAGCAGTTTGGGCATGCATGTTGTCATGAATTGAATTATTCAATTACAAA
CACTCAGCTGCTTAAAGGACTACACTATACCTGCAACATCGCCTTCCTGTCTTCTTTACGTTGT
GCAAATGCGACATACAATGGCTTTCCAGATATCATTTTGCCATTCATTTCAGTTAACTGTATAA
AAGGAACTATGTAAGCCACAGTGATATACAATAGCTAATCCAATATTCAGGAAGTAAACTTACA
GCTTGAGATGCTTCCTCACGAGTTGAAAATGCAACAAATCCAGACCCTTTGCTAACACCATTTG
CATCACGCATTATCTGTCAAACAAATCCAGTTAGTTATAATCATATATCAGTAAGAAACAAAAG
TGAAGGAAAAAAGGTGGATGACATGAATCACCTTGCATGAAGTAATTTTGCCATAGTTAGAGAA
CAATTCACAAAGCTGGTCATCCCCAATGCTATCATCCAAATTCTTCATGTATAAGTTCAGTCCT
TGATATTTGTCAGCAGCATCTTTCATGCTTTGCTCAAATCTTCTCTTCAATTCAATCTCTCTTT
CTGACTTCTTCTGAGCTCTTCCAACATACCATTCTTTGTCATTAATTTTCTTTCCATTAAGTTC
CTCAACAGCACGAGCAGCATCATCTGGGCTCTTAAAATTGATGAAACCAAAGCACCTTGATTTA
CCATCCATGCCAACCATGATAACAGCACTTGTGATGTTCCCATAGGCACCAAAAATTTTGACTA
GATCCTCCTTTGTGGTGGACTCAGACAAATTTTTCACAAAAACATTGTTAAACTTTGTCTTGTC
AACAGAATTCTCTCTCTCTTGCTTGCGGAGAAAAGGTCCAACATAAACAGGCTTATCATTGATC
AGCATCCCATTTAGACTTTTTATTGCAGATTGGGCAGCCTCTCCCTTGTCATACTGAACAAAAC
CAAAGCCTTTGGATTGGCCCATTTCATCTGTGGCAACCTTACAGGAGAGAATGTTACCAAATGC
AGAAAAGGTATCATGGAGAGTTTTGTGGTCTATTGCTTTGTCAAGGTTCTGAAAAAGGCAGTTG
AATTGTTTGCATTAGAGATAACCAATAAAAGATGATTGTTTTAGCGTGACAATACACACTAACA
AATGAGTAAATGACCTAGTACCTTGATGAAAATGTTAGCAGATCCACTTCTGCGACTGCTTGGG
TCACGGTTTGAGTACATTACCCGAATGGGTTTGCCATTCAGAGGAGCAAAGTTGAGCAGCTCCA
GTGCTCTTGCAG
						
					

			
		

Sequences
Splice junction sequence	GATCCACTTCTGCGACTGCTTGGGTCACGGTTTGAGTACATTACCCGAATGGGTTTGCCATTCA GAGGAGCAAAGTTGAGCAGCTCCAGTGCTCTTGCAGcgttctttgctgttctggattagcattt gcaagggcagaagtcagcgttccaattggagcaggtgacaaaccagcatctcgtactgggaagc ctcccata
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	CGTTCTTTGCTGTTCTGGATTAGCATTTGCAAGGGCAGAAGTCAGCGTTCCAATTGGAGCAGGT GACAAACCAGCATCTCGTACTGGGAAGCCTCCCATATCATACGATTGAATCATACCACCAGCAA CCCCCGGCATTGGTGGAACATCAGGCATGTTATGCGCAGGTGGGTAACGGTACACACGTCCTCT TGGAAGCATCTGTTAAAAGAACCATGGTAAGACGTGTGTCGTCACTGTTCATTCAATTGGTCCA CATGACAAGGATAAGTGGACAACCCATCCAATGATCCAAAATTCGAGAGGAAAGGATAAATGGT AGAATTCATACATGAAAAAGTGGATATGGGGGTTTTCTAAGTACTACAAAACGAATAGCTCGCT GTTTGAATAAATATATCCACCGACAAACTTCCCCTCCCCTACCACTGCTTGGGAGCTCAGCACG GTTTCATGTTCTATTTCACTACCCACTGGGGGTTCTTTTTACCTTTCCCTCATGGCACTACTTC GCTATCAGTCACCGTAAATCATAAAAAACTTGGCACAACAGTAGAAGGTACAATGTTATAAGGA TGTATATTAGCAAACCTGTTGCTGAAATGGCTGAGCAGATTGCTGTCCCTGGGCAGAACCAGCA CCAGAACGCCGGATACCTGGACGTGGACCCTGTTGACCTTGTTGGACAACTGGAACAAAGTAAT TTGGCATATGGGCACCCCCAGGCCTCATGCCTGGAACAAGCTGTTGCTGGAAACCAAATCCAGG CTACATGGAAGAAAATTGGTAAGAAATTGATCTACTAAATTGTCCAGAAAATACAACACATTAG ATGGAAAATTTGAATCATTTCTATGAGATAATGATCAGACAGTAGAATTTCAAAGTAGATGCCA AATGAACAAGATATATGCAAAATGAGTGCTTGCAGCAGAGACATAACGCCTAGTACAATGGTGT TGATGAATGACTAACCTATTGTGTCCCAAAAACTTGCATGGCATTGATTACCATACTCAAACTC CTGATATATGCCCAGCATCAACAAAACCAATATTGAAAACTAAATGCATAAAAGTATTGTAGGA ATTGATCAATGATATCACTTCACTCATGAAGTTGATGTACCAATTGCAATGACCAACCAACCAT TAGATATATAATAATGCAGAATTTCAACAACTTGACTGCAGAGGGCAGTGCTAGTCTGTTTTAT AAACAAACAAAAACACATTGATTCTCTCTTACAGTTAAAGCTAGACGGGGAAAATGAATGCATT GATATCGAGCAGTACCTGTGGGGGCATGATAGCAGGTGGAGCTTGTCCGTAGAAGAGTTGCTGC CCAAGAGGAGCCATAGGAGGGTACATGGGAAGACGTGGAGCCATGGAAGGTGTCATCGGTACAG GGCGCACCTGAGAAAATTGTGCCTAAATAACATGGAACATGCTACCGTCAGCATTTCTTTTTCA TTATGAAATGATCAGAAACAACTCAACAAGAAGAATGAGTTATTATAAAGCATTTATTAAGAAA CTTTGTCAAAACACAGCAGTAAGAACTATGGTACAGCCGTACAACTTAAATATATGTTGTGGAC TGCAGGCAATTGAAGATACATTTCTGAGGATTCAACTACAGATCTATGGAGCATGCATTGTGAG TCATCCCTGCATATCAGTATTTCCCTCAACTATTATACAGAATAATGAGTTCTGAACTGATGCT TAAAAGTTCTTCGCCAAACCCAATGACCTACTTCCTCCGTTTCACAATGTAAGTCATTCTAATA TTTCCCACATTCATATTGATGTTAATGAATGTAGACATATATATCTATCTAGATTCATTAACAT CAATATGAATGTGGGAAATGCTAGAATGACTTACATTGTGAAACGGAGGGAGTAAATATCAATA ATCATAACTTAATTGCCTAGATTATCAATAACCATAAACAAATTACTGTTGCTCTTGTAAACAT TGAGTTCATGATGGTGCAAAACAGAACAGTAATTCATGTGGCATATCTTATTTTCATATCCATA AATAGTACTAGGAATAGCAGTTTGGGCATGCATGTTGTCATGAATTGAATTATTCAATTACAAA CACTCAGCTGCTTAAAGGACTACACTATACCTGCAACATCGCCTTCCTGTCTTCTTTACGTTGT GCAAATGCGACATACAATGGCTTTCCAGATATCATTTTGCCATTCATTTCAGTTAACTGTATAA AAGGAACTATGTAAGCCACAGTGATATACAATAGCTAATCCAATATTCAGGAAGTAAACTTACA GCTTGAGATGCTTCCTCACGAGTTGAAAATGCAACAAATCCAGACCCTTTGCTAACACCATTTG CATCACGCATTATCTGTCAAACAAATCCAGTTAGTTATAATCATATATCAGTAAGAAACAAAAG TGAAGGAAAAAAGGTGGATGACATGAATCACCTTGCATGAAGTAATTTTGCCATAGTTAGAGAA CAATTCACAAAGCTGGTCATCCCCAATGCTATCATCCAAATTCTTCATGTATAAGTTCAGTCCT TGATATTTGTCAGCAGCATCTTTCATGCTTTGCTCAAATCTTCTCTTCAATTCAATCTCTCTTT CTGACTTCTTCTGAGCTCTTCCAACATACCATTCTTTGTCATTAATTTTCTTTCCATTAAGTTC CTCAACAGCACGAGCAGCATCATCTGGGCTCTTAAAATTGATGAAACCAAAGCACCTTGATTTA CCATCCATGCCAACCATGATAACAGCACTTGTGATGTTCCCATAGGCACCAAAAATTTTGACTA GATCCTCCTTTGTGGTGGACTCAGACAAATTTTTCACAAAAACATTGTTAAACTTTGTCTTGTC AACAGAATTCTCTCTCTCTTGCTTGCGGAGAAAAGGTCCAACATAAACAGGCTTATCATTGATC AGCATCCCATTTAGACTTTTTATTGCAGATTGGGCAGCCTCTCCCTTGTCATACTGAACAAAAC CAAAGCCTTTGGATTGGCCCATTTCATCTGTGGCAACCTTACAGGAGAGAATGTTACCAAATGC AGAAAAGGTATCATGGAGAGTTTTGTGGTCTATTGCTTTGTCAAGGTTCTGAAAAAGGCAGTTG AATTGTTTGCATTAGAGATAACCAATAAAAGATGATTGTTTTAGCGTGACAATACACACTAACA AATGAGTAAATGACCTAGTACCTTGATGAAAATGTTAGCAGATCCACTTCTGCGACTGCTTGGG TCACGGTTTGAGTACATTACCCGAATGGGTTTGCCATTCAGAGGAGCAAAGTTGAGCAGCTCCA GTGCTCTTGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.269802186

Conservation Information
Conserved circRNAs	NA
PMCS	0.269802186

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25198818-25195778(+)
25195786-25199025(-)
25199041-25199062(-)
						
						Potential amino acid sequence
						
							MLPNAEKVSWRVLWSIALSRFLMKMLADPLLRLLGSRFEYITRMGLPFRGAKLSSSSALAAFFA
VLD*(+)
MLIQNSKERCKSTGAAQLCSSEWQTHSGNVLKP*(-)
MYSNRDPSSRRSGSANIFIKNLDKAIDHKTLHDTFSAFGNILSCKVATDEMGQSKGFGFVQYDK
GEAAQSAIKSLNGMLINDKPVYVGPFLRKQERENSVDKTKFNNVFVKNLSESTTKEDLVKIFGA
YGNITSAVIMVGMDGKSRCFGFINFKSPDDAARAVEELNGKKINDKEWYVGRAQKKSEREIELK
RRFEQSMKDAADKYQGLNLYMKNLDDSIGDDQLCELFSNYGKITSCKIMRDANGVSKGSGFVAF
STREEASQALTEMNGKMISGKPLYVAFAQRKEDRKAMLQAQFSQVRPVPMTPSMAPRLPMYPPM
APLGQQLFYGQAPPAIMPPQPGFGFQQQLVPGMRPGGAHMPNYFVPVVQQGQQGPRPGIRRSGA
GSAQGQQSAQPFQQQMLPRGRVYRYPPAHNMPDVPPMPGVAGGMIQSYDMGGFPVRDAGLSPAP
IGTLTSALANANPEQQRTLQEHWSCSTLLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25198818-25195778(+) 25195786-25199025(-) 25199041-25199062(-)
Potential amino acid sequence	MLPNAEKVSWRVLWSIALSRFLMKMLADPLLRLLGSRFEYITRMGLPFRGAKLSSSSALAAFFA VLD(+) MLIQNSKERCKSTGAAQLCSSEWQTHSGNVLKP(-) MYSNRDPSSRRSGSANIFIKNLDKAIDHKTLHDTFSAFGNILSCKVATDEMGQSKGFGFVQYDK GEAAQSAIKSLNGMLINDKPVYVGPFLRKQERENSVDKTKFNNVFVKNLSESTTKEDLVKIFGA YGNITSAVIMVGMDGKSRCFGFINFKSPDDAARAVEELNGKKINDKEWYVGRAQKKSEREIELK RRFEQSMKDAADKYQGLNLYMKNLDDSIGDDQLCELFSNYGKITSCKIMRDANGVSKGSGFVAF STREEASQALTEMNGKMISGKPLYVAFAQRKEDRKAMLQAQFSQVRPVPMTPSMAPRLPMYPPM APLGQQLFYGQAPPAIMPPQPGFGFQQQLVPGMRPGGAHMPNYFVPVVQQGQQGPRPGIRRSGA GSAQGQQSAQPFQQQMLPRGRVYRYPPAHNMPDVPPMPGVAGGMIQSYDMGGFPVRDAGLSPAP IGTLTSALANANPEQQRTLQEHWSCSTLLL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0504800_circ_g.1

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