Plant Circular RNA Database

Detail information of Os04g0623400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0623400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025375
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31680343-31682406  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os04g0623400						
					
						Parent gene annotation
						
							Exonuclease domain containing protein. (Os04t0623400-01);Similar
 to H0215F08.4 protein. (Os04t0623400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0623400_circ_g.2 						
					
						Support reads
						11
					
						Tissues
						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
						Os04t0623400-02:2
Os04t0623400-01:3

General Information
CircRNA Name	Os04g0623400_circ_g.1
ID in PlantcircBase	osa_circ_025375
Alias	NA
Organism	Oryza sativa
Position	chr4: 31680343-31682406 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os04g0623400
Parent gene annotation	Exonuclease domain containing protein. (Os04t0623400-01);Similar to H0215F08.4 protein. (Os04t0623400-02)
Parent gene strand	-
Alternative splicing	Os04g0623400_circ_g.2
Support reads	11
Tissues	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	Os04t0623400-02:2 Os04t0623400-01:3

			
						 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  
						
							ATCAAATTGTTTTGCGTTATGAGCAACCCACAGAACTGGCTTGCCAGGAGCTTGGCGACTTCGA
ACGAATGCCAATAGTAGTGGGATTACATCACTAAACctccgagacatctaaatttcttctctct
ctggttcagactgctgttcgaaactggtccatagaaaaagcaagcagacagaatcacagaacac
atggaacg

									
								

					

						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: 480
Transcript exons: 31680343-31680446,31681377-31681546,31682201-31682406
CTCCGAGACATCTAAATTTCTTCTCTCTCTGGTTCAGACTGCTGTTCGAAACTGGTCCATAGAA
AAAGCAAGCAGACAGAATCACAGAACACATGGAACGGGAGCTTCATGGCCTCGTTTATTAGTTC
TTCATTTGTCAGTTTTAGATCAAAAGTCATTTTCTGGAAAACCTGAGACAATATCATAACATCT
CGCATTGCTCTATGCGCATCGTCATGCGAGACGATGCCATAGTGTTCTCTCAGTGCCTCCAAGC
TTGTACGACGTTTTTTCCCCTCTGCTTTCACCATCTTTTTTGCCAAGAGAAGGGTGTCAAAAAA
CAGCCAATCTGCAGGAAGTGGTGCTGAACAACGATCAAACTCCTGAGCAAGGAAACGAGCATCA
AATTGTTTTGCGTTATGAGCAACCCACAGAACTGGCTTGCCAGGAGCTTGGCGACTTCGAACGA
ATGCCAATAGTAGTGGGATTACATCACTAAAC
						
					

						Genomic sequence
						
							CTCCGAGACATCTAAATTTCTTCTCTCTCTGGTTCAGACTGCTGTTCGAAACTGGTCCATAGAA
AAAGCAAGCAGACAGAATCACAGAACACATGGAACGGGAGCTGGCAACAAGAAAAAGGCCAAGC
ATTACAGTCCCTAGTATATTTCAACTGAGCAGTATTCAACAAGTATCGTAGGGAAGCAAAAAAT
GACAAACATATGGTCACAAAGGGGATGAATAATATGCGATTGAAACAAGTAATTTCTGCAGCGC
TCTCTAATCAAGTGGAACAAAAATAAGTCATGGTGCACAGGGCTACAACAAGATTGTAAAACAC
TGACGCTTGTAACATTCAGAACATGCAATTCCAACATGGCATCAGCACCATACCAGAAACAAGA
GCTCAGACGAGAAAGTTGGTTGCATCCAAAGTCATACAAGATACCAAAATTAGCAAACAGAGTT
GACAGTGACAAAATAAACACTAAAGCGCTTCTTCATTCTACTACAAATCAATCATACTACTAAA
TTAGAGAAACCAATGACTAATGCAGGAAATGCAGCCGCTGTATCCTATTGAACTGAAGTTAGAT
TGAATAACAGGTCCCAACTAACTTCCACCAGGATGTATTGATCTCACAAGTTCAAATAATTTAA
ATGGCATATGCTACCCAAGAATAAAAAGCACTAATAATACTTTTCAATAGCTGACAGCTCATAG
ATAAAGCAAGACAAATCAAAGAAATATCATTCCACACTGAATCCAGCACCGAAGCATATCAAAT
AGATGTGATGGTCATCCAATGCAAATGGTTCAGCCATGGTTTTATCATCCTGGTAGCAATGAAG
ATATCAACTTGTTCGGTCCAAATTGCAGGTTTTTATTGAAAAATACAGGTACTATTTCAATAGT
AAAAAAGGCATAGTTCTTTAATGCCGAGATGACACCAGCTAGAAAAATATCCAGCATGTGCACA
GAAGGTTAAATAAGTTTAAGCACTAAAAAAAGCTGGAGTTTTAAAAATTAAGAAATCTTGCTGA
ATTCACTTGCCTTCATGGCCTCGTTTATTAGTTCTTCATTTGTCAGTTTTAGATCAAAAGTCAT
TTTCTGGAAAACCTGAGACAATATCATAACATCTCGCATTGCTCTATGCGCATCGTCATGCGAG
ACGATGCCATAGTGTTCTCTCAGTGCCTCCAAGCTTGTACGACGTTTTTTCCCTGCAACAGAAT
AGTAACAATATGTAACTTCGGCTAGTTATTATTAAATGAATAGACCAAATAGCACAGATAGGGA
ACCTAATTGAGAAATGAAAACAGTAAGGCAGAACAAAATAAAATGAGATGTGTCCCTAACTGGG
CCCCAACATATGTACAGCTCCAAGCTACTGCTCCTAACTAGGACAATATATCAGCATTTCACTT
TTCTGTTAATCCTCATTATGACATACACTCAAAGCAGTACATACGGGAACTTCCAGAAAAGAAT
AATATGTTCGCTTTTCGACAAACAATACAATGTCATATAAAAACCTCAAGAACGGTCAGCAAAT
TCCAAGAACTACGGATTTGCTAATAGCAGAAACATGGAAACTGAGTTGTACTACTAAACCATAC
ACAACATCCTAACAGAAGCACTCTTTTTGCATGGTTAAAAGATGAAGTGTGGGTTTCATCTTAC
TCAATATGCTCCTGGCAAGCAGATAGTGAGTCGTAATTAAATGAAGAATCTAGCTTAAAAGGAT
GAAGATAGTGAGAATGACACACTCCAAAATGCTGCGAGAAGTGTGTCCTTTTTTTCGCATGCTC
AAATCAAATTGACCCCAAAATATACAGTATCTTCACATGCAAAAGACTTAGAGTGAGAGTACTT
ACCCTCTGCTTTCACCATCTTTTTTGCCAAGAGAAGGGTGTCAAAAAACAGCCAATCTGCAGGA
AGTGGTGCTGAACAACGATCAAACTCCTGAGCAAGGAAACGAGCATCAAATTGTTTTGCGTTAT
GAGCAACCCACAGAACTGGCTTGCCAGGAGCTTGGCGACTTCGAACGAATGCCAATAGTAGTGG
GATTACATCACTAAAC
						
					

			
		

Sequences
Splice junction sequence	ATCAAATTGTTTTGCGTTATGAGCAACCCACAGAACTGGCTTGCCAGGAGCTTGGCGACTTCGA ACGAATGCCAATAGTAGTGGGATTACATCACTAAACctccgagacatctaaatttcttctctct ctggttcagactgctgttcgaaactggtccatagaaaaagcaagcagacagaatcacagaacac atggaacg
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: 480 Transcript exons: 31680343-31680446,31681377-31681546,31682201-31682406 CTCCGAGACATCTAAATTTCTTCTCTCTCTGGTTCAGACTGCTGTTCGAAACTGGTCCATAGAA AAAGCAAGCAGACAGAATCACAGAACACATGGAACGGGAGCTTCATGGCCTCGTTTATTAGTTC TTCATTTGTCAGTTTTAGATCAAAAGTCATTTTCTGGAAAACCTGAGACAATATCATAACATCT CGCATTGCTCTATGCGCATCGTCATGCGAGACGATGCCATAGTGTTCTCTCAGTGCCTCCAAGC TTGTACGACGTTTTTTCCCCTCTGCTTTCACCATCTTTTTTGCCAAGAGAAGGGTGTCAAAAAA CAGCCAATCTGCAGGAAGTGGTGCTGAACAACGATCAAACTCCTGAGCAAGGAAACGAGCATCA AATTGTTTTGCGTTATGAGCAACCCACAGAACTGGCTTGCCAGGAGCTTGGCGACTTCGAACGA ATGCCAATAGTAGTGGGATTACATCACTAAAC
Genomic sequence	CTCCGAGACATCTAAATTTCTTCTCTCTCTGGTTCAGACTGCTGTTCGAAACTGGTCCATAGAA AAAGCAAGCAGACAGAATCACAGAACACATGGAACGGGAGCTGGCAACAAGAAAAAGGCCAAGC ATTACAGTCCCTAGTATATTTCAACTGAGCAGTATTCAACAAGTATCGTAGGGAAGCAAAAAAT GACAAACATATGGTCACAAAGGGGATGAATAATATGCGATTGAAACAAGTAATTTCTGCAGCGC TCTCTAATCAAGTGGAACAAAAATAAGTCATGGTGCACAGGGCTACAACAAGATTGTAAAACAC TGACGCTTGTAACATTCAGAACATGCAATTCCAACATGGCATCAGCACCATACCAGAAACAAGA GCTCAGACGAGAAAGTTGGTTGCATCCAAAGTCATACAAGATACCAAAATTAGCAAACAGAGTT GACAGTGACAAAATAAACACTAAAGCGCTTCTTCATTCTACTACAAATCAATCATACTACTAAA TTAGAGAAACCAATGACTAATGCAGGAAATGCAGCCGCTGTATCCTATTGAACTGAAGTTAGAT TGAATAACAGGTCCCAACTAACTTCCACCAGGATGTATTGATCTCACAAGTTCAAATAATTTAA ATGGCATATGCTACCCAAGAATAAAAAGCACTAATAATACTTTTCAATAGCTGACAGCTCATAG ATAAAGCAAGACAAATCAAAGAAATATCATTCCACACTGAATCCAGCACCGAAGCATATCAAAT AGATGTGATGGTCATCCAATGCAAATGGTTCAGCCATGGTTTTATCATCCTGGTAGCAATGAAG ATATCAACTTGTTCGGTCCAAATTGCAGGTTTTTATTGAAAAATACAGGTACTATTTCAATAGT AAAAAAGGCATAGTTCTTTAATGCCGAGATGACACCAGCTAGAAAAATATCCAGCATGTGCACA GAAGGTTAAATAAGTTTAAGCACTAAAAAAAGCTGGAGTTTTAAAAATTAAGAAATCTTGCTGA ATTCACTTGCCTTCATGGCCTCGTTTATTAGTTCTTCATTTGTCAGTTTTAGATCAAAAGTCAT TTTCTGGAAAACCTGAGACAATATCATAACATCTCGCATTGCTCTATGCGCATCGTCATGCGAG ACGATGCCATAGTGTTCTCTCAGTGCCTCCAAGCTTGTACGACGTTTTTTCCCTGCAACAGAAT AGTAACAATATGTAACTTCGGCTAGTTATTATTAAATGAATAGACCAAATAGCACAGATAGGGA ACCTAATTGAGAAATGAAAACAGTAAGGCAGAACAAAATAAAATGAGATGTGTCCCTAACTGGG CCCCAACATATGTACAGCTCCAAGCTACTGCTCCTAACTAGGACAATATATCAGCATTTCACTT TTCTGTTAATCCTCATTATGACATACACTCAAAGCAGTACATACGGGAACTTCCAGAAAAGAAT AATATGTTCGCTTTTCGACAAACAATACAATGTCATATAAAAACCTCAAGAACGGTCAGCAAAT TCCAAGAACTACGGATTTGCTAATAGCAGAAACATGGAAACTGAGTTGTACTACTAAACCATAC ACAACATCCTAACAGAAGCACTCTTTTTGCATGGTTAAAAGATGAAGTGTGGGTTTCATCTTAC TCAATATGCTCCTGGCAAGCAGATAGTGAGTCGTAATTAAATGAAGAATCTAGCTTAAAAGGAT GAAGATAGTGAGAATGACACACTCCAAAATGCTGCGAGAAGTGTGTCCTTTTTTTCGCATGCTC AAATCAAATTGACCCCAAAATATACAGTATCTTCACATGCAAAAGACTTAGAGTGAGAGTACTT ACCCTCTGCTTTCACCATCTTTTTTGCCAAGAGAAGGGTGTCAAAAAACAGCCAATCTGCAGGA AGTGGTGCTGAACAACGATCAAACTCCTGAGCAAGGAAACGAGCATCAAATTGTTTTGCGTTAT GAGCAACCCACAGAACTGGCTTGCCAGGAGCTTGGCGACTTCGAACGAATGCCAATAGTAGTGG GATTACATCACTAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005758* osi_circ_014891 						
					
						PMCS
						0.20099954

Conservation Information
Conserved circRNAs	osi_circ_005758* osi_circ_014891
PMCS	0.20099954

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31680355-31680356(-)
31680438-31682395(-)
						
						Potential amino acid sequence
						
							MSRRFSDVIPLLLAFVRSRQAPGKPVLWVAHNAKQFDARFLAQEFDRCSAPLPADWLFFDTLLL
AKKMVKAEGKKRRTSLEALREHYGIVSHDDAHRAMRDVMILSQVFQKMTFDLKLTNEELINEAM
KLPFHVFCDSVCLLFLWTSFEQQSEPEREEI*(-)
MCSVILSACFFYGPVSNSSLNQREKKFRCLGGLVM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31680355-31680356(-) 31680438-31682395(-)
Potential amino acid sequence	MSRRFSDVIPLLLAFVRSRQAPGKPVLWVAHNAKQFDARFLAQEFDRCSAPLPADWLFFDTLLL AKKMVKAEGKKRRTSLEALREHYGIVSHDDAHRAMRDVMILSQVFQKMTFDLKLTNEELINEAM KLPFHVFCDSVCLLFLWTSFEQQSEPEREEI(-) MCSVILSACFFYGPVSNSSLNQREKKFRCLGGLVM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0623400_circ_g.1

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