Plant Circular RNA Database

Detail information of Os04g0566500_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os04g0566500_circ_g.4
					
						ID in PlantcircBase
						osa_circ_024915
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 28429974-28432004  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0566500						
					
						Parent gene annotation
						
							Similar to Isoform 2 of Protein argonaute 1B. (Os04t0566500-01);
Similar to Isoform 2 of Protein argonaute 1B. (Os04t0566500-02);
Similar to Argonaute protein. (Os04t0566500-03);Similar to Argon
aute protein. (Os04t0566500-04)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0566500_circ_g.3 Os04g0566500_circ_g.5 Os04g0566500_circ_g.6 Os04g0566500_circ_g.7 Os04g0566500_circ_g.8 Os04g0566500_circ_g.9 Os04g0566500_circ_g.10 Os04g0566500_circ_g.11 Os04g0566500_circ_g.12 Os04g0566500_circ_g.13 						
					
						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
						Os04t0566500-01:6
Os04t0566500-04:6
Os04t0566500-03:6
Os04t0566500-02:6

General Information
CircRNA Name	Os04g0566500_circ_g.4
ID in PlantcircBase	osa_circ_024915
Alias	NA
Organism	Oryza sativa
Position	chr4: 28429974-28432004 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0566500
Parent gene annotation	Similar to Isoform 2 of Protein argonaute 1B. (Os04t0566500-01); Similar to Isoform 2 of Protein argonaute 1B. (Os04t0566500-02); Similar to Argonaute protein. (Os04t0566500-03);Similar to Argon aute protein. (Os04t0566500-04)
Parent gene strand	-
Alternative splicing	Os04g0566500_circ_g.3 Os04g0566500_circ_g.5 Os04g0566500_circ_g.6 Os04g0566500_circ_g.7 Os04g0566500_circ_g.8 Os04g0566500_circ_g.9 Os04g0566500_circ_g.10 Os04g0566500_circ_g.11 Os04g0566500_circ_g.12 Os04g0566500_circ_g.13
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	Os04t0566500-01:6 Os04t0566500-04:6 Os04t0566500-03:6 Os04t0566500-02:6

			
						 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  
						
							TATGCTTTGGTAAAAACCACGCCAACTTTCCAAACCCTCACCAAGTTGCTGGCGTCTCCCTAAA
TTGGGAGAATAAAATGACCGACCAACTGGTGAGTACccttgggggaggcagaacacgagcttca
acagatgcaagacgctcatcaatttttatgccaaattcctgcgcatactgatcttcatggtatg
cattgtga

									
								

					

						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: 715
Transcript exons: 28429974-28430081,28430942-28431058,28431188-28431326,28
431432-28431538,28431634-28431743,28431871-28432004
CCTTGGGGGAGGCAGAACACGAGCTTCAACAGATGCAAGACGCTCATCAATTTTTATGCCAAAT
TCCTGCGCATACTGATCTTCATGGTATGCATTGTGAGATACAGTCCGCAAAATATCCAGTTCAC
GCTCTTGAGGTCGCTGGCAAGTCACTTTCAATAGCGCAGTAATCTGTTTCTCGTTAAGCCGCTT
CGAGTAACGCTGTCCCTCAACGATCTTACAAACCTCCATAGGCAGATAATTGGGCCTTTGCTGA
TTGCCCACTTGAAGGCAAGGCAAAGTGGTGTGCTGAATACTAAAACCATATGTCTCCAGAAAAT
ATTGCACCACAGTCTTCACAGTACCACGATCATCGACAGGGAATGATAACTCCCTTGTTGCCTG
TGAAGTGAGTCCAGATATACGATATTTTCTACGCATGTTTCCTCTATGCGTCACCTCAACCTTC
ACACCTCTTAGAGCTTTCTTTATCTTCACACGATCAGAATCAGATAATGGTCTAACTGAGATGT
CTCTGTTCAGAAGCTGAGCAACAAAGTCAATCACAGGTAGAGGCTCAATAAATGCAGTTGATGA
CATATCAATATTCAGTGAGAGACCCATCTGGGTAGGCCTTATGCTTTGGTAAAAACCACGCCAA
CTTTCCAAACCCTCACCAAGTTGCTGGCGTCTCCCTAAATTGGGAGAATAAAATGACCGACCAA
CTGGTGAGTAC
						
					

						Genomic sequence
						
							CCTTGGGGGAGGCAGAACACGAGCTTCAACAGATGCAAGACGCTCATCAATTTTTATGCCAAAT
TCCTGCGCATACTGATCTTCATGGTATGCATTGTGAGATACAGTCTGATCAAAACAAGGAAAAA
CAAAGATTTAGATCCCTGAACTCAGTATCTCAGTGAAGGGTAGATAATTAAAATAAACAAAAAC
TGCTCCATCGGAAGTTTGCCATATTCTCTTATACATTCATGACAGATTCCACTACACTCACAAA
TAGCTGGAACAAAAGAGGTGGCAAAATGCATGAGAATCAACCCCTCAATATAGCTGTTTTAATC
TTGGAGAAAATAAATACAACCAAAAGCAATACCATATTTATGTTTTTTCATAGTACATAACCAT
AACATATAACACTATTCTGGTAGATCGACAAAATATACAAAAAAGGACGACTTTGTGTTGTAAC
ATCAGAAGTCTAGCAACAGCCAAAATATTTTTTTTTAAAAAAAAAAGAAGAAAGAAAGAAAGAA
ACCAACATAATTAAGCGTCTTAGAGATCGCCTACAACCAAGGATTTTCCTCTTCAAACACACAA
AGTAAATGTGAAAGTACAGAGAGCAGAAATCAAAAGGCTAAAGATCATCCTAGAAGTTTTAACT
ACAGCAGCATGCTAATGGACATGAAACATACAACTCATGGATTCATCAGATTATCAGCCCCATC
GTTTCGCTTATGCTTATGCTTATAAACCAAAATTTGAATTTTAAAGCTTAATTTTGGAGTTGAT
TTTGTGGCTTTCTCATCGAAGTTTATTTTACAACATTTGCGTTTGAATTGCTAAGAACACATAT
ATACAAGTTTTACCCATAAATTATTTTTTAGTTAGTAGTAAGTGGTTCAGATAAGTGCATTTAT
AAGTGAAAAGATGGGGCCGATAATACAGCACTATCAAAACAAATGTCATCACAAAATATGATCA
ACAGTTACCCGCAAAATATCCAGTTCACGCTCTTGAGGTCGCTGGCAAGTCACTTTCAATAGCG
CAGTAATCTGTTTCTCGTTAAGCCGCTTCGAGTAACGCTGTCCCTCAACGATCTTACAAACCTG
AACTCAATTCCAAAGGCAAGGTAAATACTTGATAACATGCTGAAGCTGGATTTAGCATTTGGAA
AATATTTTCGTACAAAAACAGCATGATACATCACTATAATTGAGCACAGCAAACATACTGACCT
CCATAGGCAGATAATTGGGCCTTTGCTGATTGCCCACTTGAAGGCAAGGCAAAGTGGTGTGCTG
AATACTAAAACCATATGTCTCCAGAAAATATTGCACCACAGTCTTCACAGTACCACGATCATCG
ACAGGGAATCTATCACAGGAGAACGGACCAAATCATATCAGTGCACAATCCTTTCAAATACCCA
TCTGCAGGAGTGCAATAGATTCTCATATAAGCTAGGGAAGAAGTGCATACGATAACTCCCTTGT
TGCCTGTGAAGTGAGTCCAGATATACGATATTTTCTACGCATGTTTCCTCTATGCGTCACCTCA
ACCTTCACACCTCTTAGAGCTTTCTTTATCTGTGAGAAAAAGGACAATGACGGTTAAAAAAAAC
ATTTTCTTAAGCACATACGGAGGTATTGTCAACAAAGGTGGTGAGGTAATATAACCAAACCTTC
ACACGATCAGAATCAGATAATGGTCTAACTGAGATGTCTCTGTTCAGAAGCTGAGCAACAAAGT
CAATCACAGGTAGAGGCTCAATAAATGCAGTTGATGACATATCTGAAACAACAAATAAGCAATT
TCAGTACGCCAGATGACACCAATGGTGAATCTGATTATACCAAAAAAATGTTTTTTGCATCTAG
ATACACAATGACAAATCAGGAGAAGTGCAACAGTATCTAACCAATATTCAGTGAGAGACCCATC
TGGGTAGGCCTTATGCTTTGGTAAAAACCACGCCAACTTTCCAAACCCTCACCAAGTTGCTGGC
GTCTCCCTAAATTGGGAGAATAAAATGACCGACCAACTGGTGAGTAC
						
					

			
		

Sequences
Splice junction sequence	TATGCTTTGGTAAAAACCACGCCAACTTTCCAAACCCTCACCAAGTTGCTGGCGTCTCCCTAAA TTGGGAGAATAAAATGACCGACCAACTGGTGAGTACccttgggggaggcagaacacgagcttca acagatgcaagacgctcatcaatttttatgccaaattcctgcgcatactgatcttcatggtatg cattgtga
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: 715 Transcript exons: 28429974-28430081,28430942-28431058,28431188-28431326,28 431432-28431538,28431634-28431743,28431871-28432004 CCTTGGGGGAGGCAGAACACGAGCTTCAACAGATGCAAGACGCTCATCAATTTTTATGCCAAAT TCCTGCGCATACTGATCTTCATGGTATGCATTGTGAGATACAGTCCGCAAAATATCCAGTTCAC GCTCTTGAGGTCGCTGGCAAGTCACTTTCAATAGCGCAGTAATCTGTTTCTCGTTAAGCCGCTT CGAGTAACGCTGTCCCTCAACGATCTTACAAACCTCCATAGGCAGATAATTGGGCCTTTGCTGA TTGCCCACTTGAAGGCAAGGCAAAGTGGTGTGCTGAATACTAAAACCATATGTCTCCAGAAAAT ATTGCACCACAGTCTTCACAGTACCACGATCATCGACAGGGAATGATAACTCCCTTGTTGCCTG TGAAGTGAGTCCAGATATACGATATTTTCTACGCATGTTTCCTCTATGCGTCACCTCAACCTTC ACACCTCTTAGAGCTTTCTTTATCTTCACACGATCAGAATCAGATAATGGTCTAACTGAGATGT CTCTGTTCAGAAGCTGAGCAACAAAGTCAATCACAGGTAGAGGCTCAATAAATGCAGTTGATGA CATATCAATATTCAGTGAGAGACCCATCTGGGTAGGCCTTATGCTTTGGTAAAAACCACGCCAA CTTTCCAAACCCTCACCAAGTTGCTGGCGTCTCCCTAAATTGGGAGAATAAAATGACCGACCAA CTGGTGAGTAC
Genomic sequence	CCTTGGGGGAGGCAGAACACGAGCTTCAACAGATGCAAGACGCTCATCAATTTTTATGCCAAAT TCCTGCGCATACTGATCTTCATGGTATGCATTGTGAGATACAGTCTGATCAAAACAAGGAAAAA CAAAGATTTAGATCCCTGAACTCAGTATCTCAGTGAAGGGTAGATAATTAAAATAAACAAAAAC TGCTCCATCGGAAGTTTGCCATATTCTCTTATACATTCATGACAGATTCCACTACACTCACAAA TAGCTGGAACAAAAGAGGTGGCAAAATGCATGAGAATCAACCCCTCAATATAGCTGTTTTAATC TTGGAGAAAATAAATACAACCAAAAGCAATACCATATTTATGTTTTTTCATAGTACATAACCAT AACATATAACACTATTCTGGTAGATCGACAAAATATACAAAAAAGGACGACTTTGTGTTGTAAC ATCAGAAGTCTAGCAACAGCCAAAATATTTTTTTTTAAAAAAAAAAGAAGAAAGAAAGAAAGAA ACCAACATAATTAAGCGTCTTAGAGATCGCCTACAACCAAGGATTTTCCTCTTCAAACACACAA AGTAAATGTGAAAGTACAGAGAGCAGAAATCAAAAGGCTAAAGATCATCCTAGAAGTTTTAACT ACAGCAGCATGCTAATGGACATGAAACATACAACTCATGGATTCATCAGATTATCAGCCCCATC GTTTCGCTTATGCTTATGCTTATAAACCAAAATTTGAATTTTAAAGCTTAATTTTGGAGTTGAT TTTGTGGCTTTCTCATCGAAGTTTATTTTACAACATTTGCGTTTGAATTGCTAAGAACACATAT ATACAAGTTTTACCCATAAATTATTTTTTAGTTAGTAGTAAGTGGTTCAGATAAGTGCATTTAT AAGTGAAAAGATGGGGCCGATAATACAGCACTATCAAAACAAATGTCATCACAAAATATGATCA ACAGTTACCCGCAAAATATCCAGTTCACGCTCTTGAGGTCGCTGGCAAGTCACTTTCAATAGCG CAGTAATCTGTTTCTCGTTAAGCCGCTTCGAGTAACGCTGTCCCTCAACGATCTTACAAACCTG AACTCAATTCCAAAGGCAAGGTAAATACTTGATAACATGCTGAAGCTGGATTTAGCATTTGGAA AATATTTTCGTACAAAAACAGCATGATACATCACTATAATTGAGCACAGCAAACATACTGACCT CCATAGGCAGATAATTGGGCCTTTGCTGATTGCCCACTTGAAGGCAAGGCAAAGTGGTGTGCTG AATACTAAAACCATATGTCTCCAGAAAATATTGCACCACAGTCTTCACAGTACCACGATCATCG ACAGGGAATCTATCACAGGAGAACGGACCAAATCATATCAGTGCACAATCCTTTCAAATACCCA TCTGCAGGAGTGCAATAGATTCTCATATAAGCTAGGGAAGAAGTGCATACGATAACTCCCTTGT TGCCTGTGAAGTGAGTCCAGATATACGATATTTTCTACGCATGTTTCCTCTATGCGTCACCTCA ACCTTCACACCTCTTAGAGCTTTCTTTATCTGTGAGAAAAAGGACAATGACGGTTAAAAAAAAC ATTTTCTTAAGCACATACGGAGGTATTGTCAACAAAGGTGGTGAGGTAATATAACCAAACCTTC ACACGATCAGAATCAGATAATGGTCTAACTGAGATGTCTCTGTTCAGAAGCTGAGCAACAAAGT CAATCACAGGTAGAGGCTCAATAAATGCAGTTGATGACATATCTGAAACAACAAATAAGCAATT TCAGTACGCCAGATGACACCAATGGTGAATCTGATTATACCAAAAAAATGTTTTTTGCATCTAG ATACACAATGACAAATCAGGAGAAGTGCAACAGTATCTAACCAATATTCAGTGAGAGACCCATC TGGGTAGGCCTTATGCTTTGGTAAAAACCACGCCAACTTTCCAAACCCTCACCAAGTTGCTGGC GTCTCCCTAAATTGGGAGAATAAAATGACCGACCAACTGGTGAGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.249784445

Conservation Information
Conserved circRNAs	NA
PMCS	0.249784445

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28431983-28430049(+)
28431894-28431944(-)
28430022-28431944(-)
						
						Potential amino acid sequence
						
							MTDQLVSTLGGGRTRASTDARRSSIFMPNSCAY*(+)
MGLSLNIDMSSTAFIEPLPVIDFVAQLLNRDISVRPLSDSDRVKIKKALRGVKVEVTHRGNMRR
KYRISGLTSQATRELSFPVDDRGTVKTVVQYFLETYGFSIQHTTLPCLQVGNQQRPNYLPMEVC
KIVEGQRYSKRLNEKQITALLKVTCQRPQERELDILRTVSHNAYHEDQYAQEFGIKIDERLASV
EARVLPPPRVLTSWSVILFSQFRETPATW*(-)
MSVLHLLKLVFCLPQGYSPVGRSFYSPNLGRRQQLGEGLESWRGFYQSIRPTQMGLSLNIDMSS
TAFIEPLPVIDFVAQLLNRDISVRPLSDSDRVKIKKALRGVKVEVTHRGNMRRKYRISGLTSQA
TRELSFPVDDRGTVKTVVQYFLETYGFSIQHTTLPCLQVGNQQRPNYLPMEVCKIVEGQRYSKR
LNEKQITALLKVTCQRPQERELDILRTVSHNAYHEDQYAQEFGIKIDERLASVEARVLPPPRVL
TSWSVILFSQFRETPATW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28431983-28430049(+) 28431894-28431944(-) 28430022-28431944(-)
Potential amino acid sequence	MTDQLVSTLGGGRTRASTDARRSSIFMPNSCAY(+) MGLSLNIDMSSTAFIEPLPVIDFVAQLLNRDISVRPLSDSDRVKIKKALRGVKVEVTHRGNMRR KYRISGLTSQATRELSFPVDDRGTVKTVVQYFLETYGFSIQHTTLPCLQVGNQQRPNYLPMEVC KIVEGQRYSKRLNEKQITALLKVTCQRPQERELDILRTVSHNAYHEDQYAQEFGIKIDERLASV EARVLPPPRVLTSWSVILFSQFRETPATW(-) MSVLHLLKLVFCLPQGYSPVGRSFYSPNLGRRQQLGEGLESWRGFYQSIRPTQMGLSLNIDMSS TAFIEPLPVIDFVAQLLNRDISVRPLSDSDRVKIKKALRGVKVEVTHRGNMRRKYRISGLTSQA TRELSFPVDDRGTVKTVVQYFLETYGFSIQHTTLPCLQVGNQQRPNYLPMEVCKIVEGQRYSKR LNEKQITALLKVTCQRPQERELDILRTVSHNAYHEDQYAQEFGIKIDERLASVEARVLPPPRVL TSWSVILFSQFRETPATW*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0566500_circ_g.4

Address

Any questions?

Supported by