Plant Circular RNA Database

Detail information of Zm00001d015239_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d015239_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008594
					
						Alias
						Zm05circ00065, zma_circ_0001913, GRMZM2G006937_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 80588478-80588971  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d015239						
					
						Parent gene annotation
						
							Camelliol C synthase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d015239_circ_g.1 Zm00001d015239_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d015239_T001:2
Zm00001d015239_T005:2
Zm00001d015239_T007:2
Zm00001d015239_T002:2
Zm00001d015239_T006:2
Zm00001d015239_T008:2
Zm00001d015239_T009:2
Zm00001d015239_T003:2
Zm00001d015239_T004:2

General Information
CircRNA Name	Zm00001d015239_circ_g.3
ID in PlantcircBase	zma_circ_008594
Alias	Zm05circ00065, zma_circ_0001913, GRMZM2G006937_C3
Organism	Zea mays
Position	chr5: 80588478-80588971 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d015239
Parent gene annotation	Camelliol C synthase
Parent gene strand	-
Alternative splicing	Zm00001d015239_circ_g.1 Zm00001d015239_circ_g.2
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d015239_T001:2 Zm00001d015239_T005:2 Zm00001d015239_T007:2 Zm00001d015239_T002:2 Zm00001d015239_T006:2 Zm00001d015239_T008:2 Zm00001d015239_T009:2 Zm00001d015239_T003:2 Zm00001d015239_T004:2

			
						 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  
						
							GCTTGTTGATAGGCCAACTGCTCAATACTGGTTCCACACACCTATAAAGTGAAGTCCAAATAAC
ATTCTGCAACAGTGTGCGTGGACAGATGAGGTCCTCctgtgccttcatgccatcttctgaaatc
cacaagaagtctggtatccttgcaaggtgacgcttgaatgcatctgaatttggatcttctaccc
agcagcag

						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: 303
Transcript exons: 80588478-80588591,80588783-80588971
CTGTGCCTTCATGCCATCTTCTGAAATCCACAAGAAGTCTGGTATCCTTGCAAGGTGACGCTTG
AATGCATCTGAATTTGGATCTTCTACCCAGCAGCAGACCATGTTTAGAGCCTTATTCACAGGAC
ATATGCATAGGTATTGTGTGTTCTCATCTTCATAATGGATATGCTCCATGATGTTTCCCAGAGC
TCTCTCTCTCAGCTTGTTGATAGGCCAACTGCTCAATACTGGTTCCACACACCTATAAAGTGAA
GTCCAAATAACATTCTGCAACAGTGTGCGTGGACAGATGAGGTCCTC
						
						Genomic sequence
						
							CTGTGCCTTCATGCCATCTTCTGAAATCCACAAGAAGTCTGGTATCCTTGCAAGGTGACGCTTG
AATGCATCTGAATTTGGATCTTCTACCCAGCAGCAGACCATGTTTAGAGCCTAAATGGCAAAGT
AACCAATATTAATAGGCACCAATCAGAAGTTCATCATCCACAAGACAATAATTAACAAGAAACA
GTAAACACTAAATCATGAAGTAGGAGAATTAATAATAAGACCACAACAACAGAACAGAAGCATG
GACAATTAAAGTTCCAGTAACAAGACATCAAACTTTTGGAGATATTTACCTTATTCACAGGACA
TATGCATAGGTATTGTGTGTTCTCATCTTCATAATGGATATGCTCCATGATGTTTCCCAGAGCT
CTCTCTCTCAGCTTGTTGATAGGCCAACTGCTCAATACTGGTTCCACACACCTATAAAGTGAAG
TCCAAATAACATTCTGCAACAGTGTGCGTGGACAGATGAGGTCCTC

Sequences
Splice junction sequence	GCTTGTTGATAGGCCAACTGCTCAATACTGGTTCCACACACCTATAAAGTGAAGTCCAAATAAC ATTCTGCAACAGTGTGCGTGGACAGATGAGGTCCTCctgtgccttcatgccatcttctgaaatc cacaagaagtctggtatccttgcaaggtgacgcttgaatgcatctgaatttggatcttctaccc agcagcag
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: 303 Transcript exons: 80588478-80588591,80588783-80588971 CTGTGCCTTCATGCCATCTTCTGAAATCCACAAGAAGTCTGGTATCCTTGCAAGGTGACGCTTG AATGCATCTGAATTTGGATCTTCTACCCAGCAGCAGACCATGTTTAGAGCCTTATTCACAGGAC ATATGCATAGGTATTGTGTGTTCTCATCTTCATAATGGATATGCTCCATGATGTTTCCCAGAGC TCTCTCTCTCAGCTTGTTGATAGGCCAACTGCTCAATACTGGTTCCACACACCTATAAAGTGAA GTCCAAATAACATTCTGCAACAGTGTGCGTGGACAGATGAGGTCCTC
Genomic sequence	CTGTGCCTTCATGCCATCTTCTGAAATCCACAAGAAGTCTGGTATCCTTGCAAGGTGACGCTTG AATGCATCTGAATTTGGATCTTCTACCCAGCAGCAGACCATGTTTAGAGCCTAAATGGCAAAGT AACCAATATTAATAGGCACCAATCAGAAGTTCATCATCCACAAGACAATAATTAACAAGAAACA GTAAACACTAAATCATGAAGTAGGAGAATTAATAATAAGACCACAACAACAGAACAGAAGCATG GACAATTAAAGTTCCAGTAACAAGACATCAAACTTTTGGAGATATTTACCTTATTCACAGGACA TATGCATAGGTATTGTGTGTTCTCATCTTCATAATGGATATGCTCCATGATGTTTCCCAGAGCT CTCTCTCTCAGCTTGTTGATAGGCCAACTGCTCAATACTGGTTCCACACACCTATAAAGTGAAG TCCAAATAACATTCTGCAACAGTGTGCGTGGACAGATGAGGTCCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_009615 osa_circ_009614 						
					
						PMCS
						0.190397959

Conservation Information
Conserved circRNAs	osa_circ_009615 osa_circ_009614
PMCS	0.190397959

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							80588962-80588532(+)
80588847-80588480(-)
						
						Potential amino acid sequence
						
							MRSSCAFMPSSEIHKKSGILAR*(+)
MEHIHYEDENTQYLCICPVNKALNMVCCWVEDPNSDAFKRHLARIPDFLWISEDGMKAQEDLIC
PRTLLQNVIWTSLYRCVEPVLSSWPINKLRERALGNIMEHIHYEDENTQYLCICPVNKALNMVC
CWVEDPNSDAFKRHLARIPDFLWISEDGMKAQEDLICPRTLLQNVIWTSLYRCVEPVLSSWPIN
KLRERALGNIMEHIHYEDENTQYLCICPVNKALNMVCCWVEDPNSDAFKRHLARIPDFLWISED
GMKAQEDLICPRTLLQNVIWTSLYRCVEPVLSSWPINKLRERALGNIMEHIHYEDENTQYLCIC
PVNKALNMVCCWVEDPNSDAFKRHLARIPDFLWISEDGMKAQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	80588962-80588532(+) 80588847-80588480(-)
Potential amino acid sequence	MRSSCAFMPSSEIHKKSGILAR*(+) MEHIHYEDENTQYLCICPVNKALNMVCCWVEDPNSDAFKRHLARIPDFLWISEDGMKAQEDLIC PRTLLQNVIWTSLYRCVEPVLSSWPINKLRERALGNIMEHIHYEDENTQYLCICPVNKALNMVC CWVEDPNSDAFKRHLARIPDFLWISEDGMKAQEDLICPRTLLQNVIWTSLYRCVEPVLSSWPIN KLRERALGNIMEHIHYEDENTQYLCICPVNKALNMVCCWVEDPNSDAFKRHLARIPDFLWISED GMKAQEDLICPRTLLQNVIWTSLYRCVEPVLSSWPINKLRERALGNIMEHIHYEDENTQYLCIC PVNKALNMVCCWVEDPNSDAFKRHLARIPDFLWISEDGMKAQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d015239_circ_g.3

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