Plant Circular RNA Database

Detail information of Os04g0616700_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0616700_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025287
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31320195-31321190  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0616700						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os04t0616700-01);Hypothetical cons
erved gene. (Os04t0616700-02);Similar to H0525G02.12 protein. (O
s04t0616700-03);Similar to H0525G02.12 protein. (Os04t0616700-04
)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0616300_circ_g.1 Os04g0616300_circ_ag.1 Os04g0616300_circ_ag.2 Os04g0616300_circ_ag.3 Os04g0616300_circ_ag.4 Os04g0616300_circ_ag.5 Os04g0616300_circ_ag.6 Os04g0616300_circ_ag.7 Os04g0616300_circ_ag.8 Os04g0616300_circ_ag.9 Os04g0616300_circ_ag.10 Os04g0616300_circ_igg.1 Os04g0616300_circ_igg.2 Os04g0616300_circ_igg.3 Os04g0616300_circ_ag.4 Os04g0616300_circ_ag.5 Os04g0616300_circ_ag.6 Os04g0616300_circ_ag.7 Os04g0616300_circ_igg.8 Os04g0616300_circ_ag.9 Os04g0616300_circ_ag.10 Os04g0616300_circ_igg.11 Os04g0616300_circ_ag.12 Os04g0616300_circ_igg.13 Os04g0616400_circ_g.1 Os04g0616400_circ_ag.1 Os04g0616400_circ_igg.1 Os04g0616400_circ_ag.2 Os04g0616400_circ_ag.3 Os04g0616400_circ_ag.4 Os04g0616500_circ_ag.1 Os04g0616500_circ_ag.2 Os04g0616500_circ_ag.3 Os04g0616500_circ_igg.1 Os04g0616700_circ_igg.1 Os04g0616700_circ_g.2 						
					
						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
						Os04t0616700-02:3
Os04t0616700-04:3
Os04t0616700-01:3
Os04t0616700-03:3

General Information
CircRNA Name	Os04g0616700_circ_g.1
ID in PlantcircBase	osa_circ_025287
Alias	NA
Organism	Oryza sativa
Position	chr4: 31320195-31321190 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0616700
Parent gene annotation	Hypothetical conserved gene. (Os04t0616700-01);Hypothetical cons erved gene. (Os04t0616700-02);Similar to H0525G02.12 protein. (O s04t0616700-03);Similar to H0525G02.12 protein. (Os04t0616700-04 )
Parent gene strand	-
Alternative splicing	Os04g0616300_circ_g.1 Os04g0616300_circ_ag.1 Os04g0616300_circ_ag.2 Os04g0616300_circ_ag.3 Os04g0616300_circ_ag.4 Os04g0616300_circ_ag.5 Os04g0616300_circ_ag.6 Os04g0616300_circ_ag.7 Os04g0616300_circ_ag.8 Os04g0616300_circ_ag.9 Os04g0616300_circ_ag.10 Os04g0616300_circ_igg.1 Os04g0616300_circ_igg.2 Os04g0616300_circ_igg.3 Os04g0616300_circ_ag.4 Os04g0616300_circ_ag.5 Os04g0616300_circ_ag.6 Os04g0616300_circ_ag.7 Os04g0616300_circ_igg.8 Os04g0616300_circ_ag.9 Os04g0616300_circ_ag.10 Os04g0616300_circ_igg.11 Os04g0616300_circ_ag.12 Os04g0616300_circ_igg.13 Os04g0616400_circ_g.1 Os04g0616400_circ_ag.1 Os04g0616400_circ_igg.1 Os04g0616400_circ_ag.2 Os04g0616400_circ_ag.3 Os04g0616400_circ_ag.4 Os04g0616500_circ_ag.1 Os04g0616500_circ_ag.2 Os04g0616500_circ_ag.3 Os04g0616500_circ_igg.1 Os04g0616700_circ_igg.1 Os04g0616700_circ_g.2
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	Os04t0616700-02:3 Os04t0616700-04:3 Os04t0616700-01:3 Os04t0616700-03:3

			
						 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  
						
							GGGATATAGTTTCTATTTCAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTG
CTTCACTGCCACTATCCTTCCATCCATTAGCTTACCccattcgaaaatataaattttgtcttct
tcaagcacatcatcatagtttggccggccagctaaagtctccaataagaccacgccaaatgcaa
acacatca

									
								

					

						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: 31320195-31320345,31320659-31320890,31320980-31321190
CCATTCGAAAATATAAATTTTGTCTTCTTCAAGCACATCATCATAGTTTGGCCGGCCAGCTAAA
GTCTCCAATAAGACCACGCCAAATGCAAACACATCAACTTTCTCAGTCATATGTCCTCTCATGG
CGTACTCAGGTGCAAGATAACCAAATGTACCAGCAACTTTTGTGCTAACATGAGTCATCTTGTC
ATCATAAAGTTTGGCTAGCCCGAAATCCGAGATCTTAGGATTGAGATTGGCGTCAAGTAAGACA
TTGCTGGCCTTGATGTCCCTGTGCACAACACGGATGCTTGACTCTTCATGAAGATAAGCCAGAC
CTCTTGCAATGCCCAAGCATATTTCAAAGCGTGCTGGCCACCCTATATGTAATTTCTCAGTTCC
GAACAGTGCTTTATCAAGGCTCCCATTCTCCATATACTCATAAACCAGCAGTGGATTATTGCCT
TCAAGGCAACAACCATACAACTTCACGAGATTACGGTGTTGCACTCGGGATATAGTTTCTATTT
CAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTGCTTCACTGCCACTATCCT
TCCATCCATTAGCTTACC
						
					

						Genomic sequence
						
							CCATTCGAAAATATAAATTTTGTCTTCTTCAAGCACATCATCATAGTTTGGCCGGCCAGCTAAA
GTCTCCAATAAGACCACGCCAAATGCAAACACATCAACTTTCTCAGTCATATGTCCTCTCATGG
CGTACTCAGGTGCAAGATAACCACTGGAAAGAGCCAAAAAAACATCATTACCTTCACATGTATT
AAAAAAAAATAATATGTAAACTGCTTATGTAATTTGACATTATGTAAGGGGTTTGTATGCAAGT
TTGCTTATTAAAATCAGATTGTGTGCTGAGTAGGGCACAACCGCACAGCAAATCCCCAAATGAG
CAAATGATGCAGTATAAACACAAAGGTGGCAAAGGCAGGAAGGTCTTTTTTTTGCCCCTTAAGA
GGATGTCCTCTTATTTCTTGCATGCCATTAAAATAGTTATTTTTTTTAAAAGAAAAAATGCAAA
GATGGAATATACTTACAATGTACCAGCAACTTTTGTGCTAACATGAGTCATCTTGTCATCATAA
AGTTTGGCTAGCCCGAAATCCGAGATCTTAGGATTGAGATTGGCGTCAAGTAAGACATTGCTGG
CCTTGATGTCCCTGTGCACAACACGGATGCTTGACTCTTCATGAAGATAAGCCAGACCTCTTGC
AATGCCCAAGCATATTTCAAAGCGTGCTGGCCACCCTATATGTAATTTCTCAGTTCCTAGAAAT
ACAGGATTGAACTTTTATGTTTCTATCTACTAACAATAAATTATCAGAATCCCAGTTGCATCAA
AATGAAATAAATTGTACCGAACAGTGCTTTATCAAGGCTCCCATTCTCCATATACTCATAAACC
AGCAGTGGATTATTGCCTTCAAGGCAACAACCATACAACTTCACGAGATTACGGTGTTGCACTC
GGGATATAGTTTCTATTTCAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTG
CTTCACTGCCACTATCCTTCCATCCATTAGCTTACC
						
					

			
		

Sequences
Splice junction sequence	GGGATATAGTTTCTATTTCAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTG CTTCACTGCCACTATCCTTCCATCCATTAGCTTACCccattcgaaaatataaattttgtcttct tcaagcacatcatcatagtttggccggccagctaaagtctccaataagaccacgccaaatgcaa acacatca
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: 31320195-31320345,31320659-31320890,31320980-31321190 CCATTCGAAAATATAAATTTTGTCTTCTTCAAGCACATCATCATAGTTTGGCCGGCCAGCTAAA GTCTCCAATAAGACCACGCCAAATGCAAACACATCAACTTTCTCAGTCATATGTCCTCTCATGG CGTACTCAGGTGCAAGATAACCAAATGTACCAGCAACTTTTGTGCTAACATGAGTCATCTTGTC ATCATAAAGTTTGGCTAGCCCGAAATCCGAGATCTTAGGATTGAGATTGGCGTCAAGTAAGACA TTGCTGGCCTTGATGTCCCTGTGCACAACACGGATGCTTGACTCTTCATGAAGATAAGCCAGAC CTCTTGCAATGCCCAAGCATATTTCAAAGCGTGCTGGCCACCCTATATGTAATTTCTCAGTTCC GAACAGTGCTTTATCAAGGCTCCCATTCTCCATATACTCATAAACCAGCAGTGGATTATTGCCT TCAAGGCAACAACCATACAACTTCACGAGATTACGGTGTTGCACTCGGGATATAGTTTCTATTT CAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTGCTTCACTGCCACTATCCT TCCATCCATTAGCTTACC
Genomic sequence	CCATTCGAAAATATAAATTTTGTCTTCTTCAAGCACATCATCATAGTTTGGCCGGCCAGCTAAA GTCTCCAATAAGACCACGCCAAATGCAAACACATCAACTTTCTCAGTCATATGTCCTCTCATGG CGTACTCAGGTGCAAGATAACCACTGGAAAGAGCCAAAAAAACATCATTACCTTCACATGTATT AAAAAAAAATAATATGTAAACTGCTTATGTAATTTGACATTATGTAAGGGGTTTGTATGCAAGT TTGCTTATTAAAATCAGATTGTGTGCTGAGTAGGGCACAACCGCACAGCAAATCCCCAAATGAG CAAATGATGCAGTATAAACACAAAGGTGGCAAAGGCAGGAAGGTCTTTTTTTTGCCCCTTAAGA GGATGTCCTCTTATTTCTTGCATGCCATTAAAATAGTTATTTTTTTTAAAAGAAAAAATGCAAA GATGGAATATACTTACAATGTACCAGCAACTTTTGTGCTAACATGAGTCATCTTGTCATCATAA AGTTTGGCTAGCCCGAAATCCGAGATCTTAGGATTGAGATTGGCGTCAAGTAAGACATTGCTGG CCTTGATGTCCCTGTGCACAACACGGATGCTTGACTCTTCATGAAGATAAGCCAGACCTCTTGC AATGCCCAAGCATATTTCAAAGCGTGCTGGCCACCCTATATGTAATTTCTCAGTTCCTAGAAAT ACAGGATTGAACTTTTATGTTTCTATCTACTAACAATAAATTATCAGAATCCCAGTTGCATCAA AATGAAATAAATTGTACCGAACAGTGCTTTATCAAGGCTCCCATTCTCCATATACTCATAAACC AGCAGTGGATTATTGCCTTCAAGGCAACAACCATACAACTTCACGAGATTACGGTGTTGCACTC GGGATATAGTTTCTATTTCAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTG CTTCACTGCCACTATCCTTCCATCCATTAGCTTACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.435093083

Conservation Information
Conserved circRNAs	NA
PMCS	0.435093083

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31321140-31320680(+)
31321183-31320197(-)
						
						Potential amino acid sequence
						
							MFEIAASLPLSFHPLAYPIRKYKFCLLQAHHHSLAGQLKSPIRPRQMQTHQLSQSYVLSWRTQV
QDNQMYQQLLC*(+)
MDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLEGNNPLLVYEYMENGSLDK
ALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASNVLLDANLNPKISDFGLAK
LYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLETLAGRPNYDDVLEEDKIYI
FEWGKLMDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLEGNNPLLVYEYME
NGSLDKALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASNVLLDANLNPKIS
DFGLAKLYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLETLAGRPNYDDVLE
EDKIYIFEWGKLMDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLEGNNPLL
VYEYMENGSLDKALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASNVLLDAN
LNPKISDFGLAKLYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLETLAGRPN
YDDVLEEDKIYIFEWGKLMDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLE
GNNPLLVYEYMENGSLDKALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASN
VLLDANLNPKISDFGLAKLYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLET
LAGRPNYDDVLEEDKIYIFEW(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31321140-31320680(+) 31321183-31320197(-)
Potential amino acid sequence	MFEIAASLPLSFHPLAYPIRKYKFCLLQAHHHSLAGQLKSPIRPRQMQTHQLSQSYVLSWRTQV QDNQMYQQLLC*(+) MDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLEGNNPLLVYEYMENGSLDK ALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASNVLLDANLNPKISDFGLAK LYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLETLAGRPNYDDVLEEDKIYI FEWGKLMDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLEGNNPLLVYEYME NGSLDKALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASNVLLDANLNPKIS DFGLAKLYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLETLAGRPNYDDVLE EDKIYIFEWGKLMDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLEGNNPLL VYEYMENGSLDKALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASNVLLDAN LNPKISDFGLAKLYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLETLAGRPN YDDVLEEDKIYIFEWGKLMDGRIVAVKQLSQTSHQGKKQFATEIETISRVQHRNLVKLYGCCLE GNNPLLVYEYMENGSLDKALFGTEKLHIGWPARFEICLGIARGLAYLHEESSIRVVHRDIKASN VLLDANLNPKISDFGLAKLYDDKMTHVSTKVAGTFGYLAPEYAMRGHMTEKVDVFAFGVVLLET LAGRPNYDDVLEEDKIYIFEW(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0616700_circ_g.1

Address

Any questions?

Supported by