Plant Circular RNA Database

Detail information of Zm00001d028471_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d028471_circ_g.4
					
						ID in PlantcircBase
						zma_circ_006464
					
						Alias
						zma_circ_0000615
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 35960700-35961884  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d028471						
					
						Parent gene annotation
						
							 phosphoenolpyruvate carboxykinase1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d028471_circ_g.1 Zm00001d028471_circ_g.2 Zm00001d028471_circ_g.3 Zm00001d028471_circ_g.5 Zm00001d028471_circ_g.6 Zm00001d028471_circ_g.7 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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  
						
							GT-AG							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
						Zm00001d028471_T006:1
Zm00001d028471_T001:2
Zm00001d028471_T002:2
Zm00001d028471_T003:3
Zm00001d028471_T005:3
Zm00001d028471_T004:3

General Information
CircRNA Name	Zm00001d028471_circ_g.4
ID in PlantcircBase	zma_circ_006464
Alias	zma_circ_0000615
Organism	Zea mays
Position	chr1: 35960700-35961884 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d028471
Parent gene annotation	phosphoenolpyruvate carboxykinase1
Parent gene strand	+
Alternative splicing	Zm00001d028471_circ_g.1 Zm00001d028471_circ_g.2 Zm00001d028471_circ_g.3 Zm00001d028471_circ_g.5 Zm00001d028471_circ_g.6 Zm00001d028471_circ_g.7
Support reads	NA
Tissues	leaf, 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	GT-AG 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	Zm00001d028471_T006:1 Zm00001d028471_T001:2 Zm00001d028471_T002:2 Zm00001d028471_T003:3 Zm00001d028471_T005:3 Zm00001d028471_T004:3

			
						 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  
						
							AGGGCGCACCAGCAGCACCGCCACCCCGCCGCCCCCGCCATCGCCGTCAGCGACAGCTCCCTCA
AGTTCACTCATGTGCTCAACAACCTCTCGCCTGCTGgagcaggacctcgatcggccgagatggc
gacgccgaacgggcttgcgcggatcgagacgaccgggaagaagaagcaggacaacggcgtgtgg
tacgacga

									
								

					

						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: 486
Transcript exons: 35960700-35960982,35961682-35961884
GAGCAGGACCTCGATCGGCCGAGATGGCGACGCCGAACGGGCTTGCGCGGATCGAGACGACCGG
GAAGAAGAAGCAGGACAACGGCGTGTGGTACGACGACAGCTCGGCGCCGGTGCGCGCGCAGACC
ATCGACGAGCTGCACTCGCTGCAGCGGAAGCGGTCGGCGCCCAGCACGCCCAAGCGGTCGGCGC
CCACCACGCCCATCAAGGGCGGTGCCCACTCGCCCTTCGCCGTCGCGATCTCCGAGGAGGAGCG
CCACACGCAGCAGATGCAGTCCATCAGTGCGTCGTTGGCGTCTCTGACGCGTGAAACCGGGCCG
AAAGTGGTCAAGGGCGACCCGGCCGCGAAGGGCGAGGCCGCCGCGCAGGGCGCGCCATCGACGC
CGAGGGCGCACCAGCAGCACCGCCACCCCGCCGCCCCCGCCATCGCCGTCAGCGACAGCTCCCT
CAAGTTCACTCATGTGCTCAACAACCTCTCGCCTGCTG
						
					

						Genomic sequence
						
							GAGCAGGACCTCGATCGGCCGAGATGGCGACGCCGAACGGGCTTGCGCGGATCGAGACGACCGG
GAAGAAGAAGCAGGACAACGGCGTGTGGTACGACGACAGCTCGGCGCCGGTGCGCGCGCAGACC
ATCGACGAGCTGCACTCGCTGCAGCGGAAGCGGTCGGCGCCCAGCACGCCCAAGCGGTCGGCGC
CCACCACGCCCATCAAGGGCGGTGCCCACTCGCCCTTCGCCGTCGCGATCTCCGAGGAGGAGCG
CCACACGCAGCAGATGCAGTCCATCAGGTGACGTTCGTCCTTTCTCGGCTAGCAGCCGCCTTAT
TGATTCTGCCGCCACTAGGCACTATAGCTAAGTAGCTAGCCTGCCGCTATAAACGAATTGGTGA
AAACGATTTCTCGATTTGGTTGGGTTTGGTTCATTACTGAATAATAATAGCTTAACGACAATGG
CCACCAACCCAGGAACATGAAAGGTAAGCGGAGATGAGTTCCTTTACCATTTTGGGAAAGGAAA
AAAAAAGACAAAATAATTTGGCGTCTGCAGGACTTCCTCTGGGAGAAGAAGGAACGGAACAAAA
CCAGAGAGCTCTGCCACCGACGTCAGAGCCCGGCCCGTTTACGTTGACAATACACTGCCTCGTG
GGCCCTCTTGAGATAGCACTTGGTGTGAGTTGTGGACTTCATTAGAAAAAAAAAGTAAAAGGAT
GGAGAAGATAGAAATAGGTAAAAACAAAAGGGTGACGCACGAAACGAACAAGCATGCACGCAGC
TTGACGCGACACCACGGTCGCCGTCGGCCACGCAACGTGCTGCTTTATCTCTGCAGGGAACCTA
GTAATCCTTCCCGAAAATCTGTACGTCCTTCGGGGGTCGGCTGTGTCCTCCCGGTCTCGCGCAT
CACTAACCATTTTTGGTGCTGATAATCGGGAGCGTAGCGTAATTACCACTAAACTTTTTTTTCC
CGATCTCTCGTGATGGATGCAGTGCGTCGTTGGCGTCTCTGACGCGTGAAACCGGGCCGAAAGT
GGTCAAGGGCGACCCGGCCGCGAAGGGCGAGGCCGCCGCGCAGGGCGCGCCATCGACGCCGAGG
GCGCACCAGCAGCACCGCCACCCCGCCGCCCCCGCCATCGCCGTCAGCGACAGCTCCCTCAAGT
TCACTCATGTGCTCAACAACCTCTCGCCTGCTG
						
					

			
		

Sequences
Splice junction sequence	AGGGCGCACCAGCAGCACCGCCACCCCGCCGCCCCCGCCATCGCCGTCAGCGACAGCTCCCTCA AGTTCACTCATGTGCTCAACAACCTCTCGCCTGCTGgagcaggacctcgatcggccgagatggc gacgccgaacgggcttgcgcggatcgagacgaccgggaagaagaagcaggacaacggcgtgtgg tacgacga
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: 486 Transcript exons: 35960700-35960982,35961682-35961884 GAGCAGGACCTCGATCGGCCGAGATGGCGACGCCGAACGGGCTTGCGCGGATCGAGACGACCGG GAAGAAGAAGCAGGACAACGGCGTGTGGTACGACGACAGCTCGGCGCCGGTGCGCGCGCAGACC ATCGACGAGCTGCACTCGCTGCAGCGGAAGCGGTCGGCGCCCAGCACGCCCAAGCGGTCGGCGC CCACCACGCCCATCAAGGGCGGTGCCCACTCGCCCTTCGCCGTCGCGATCTCCGAGGAGGAGCG CCACACGCAGCAGATGCAGTCCATCAGTGCGTCGTTGGCGTCTCTGACGCGTGAAACCGGGCCG AAAGTGGTCAAGGGCGACCCGGCCGCGAAGGGCGAGGCCGCCGCGCAGGGCGCGCCATCGACGC CGAGGGCGCACCAGCAGCACCGCCACCCCGCCGCCCCCGCCATCGCCGTCAGCGACAGCTCCCT CAAGTTCACTCATGTGCTCAACAACCTCTCGCCTGCTG
Genomic sequence	GAGCAGGACCTCGATCGGCCGAGATGGCGACGCCGAACGGGCTTGCGCGGATCGAGACGACCGG GAAGAAGAAGCAGGACAACGGCGTGTGGTACGACGACAGCTCGGCGCCGGTGCGCGCGCAGACC ATCGACGAGCTGCACTCGCTGCAGCGGAAGCGGTCGGCGCCCAGCACGCCCAAGCGGTCGGCGC CCACCACGCCCATCAAGGGCGGTGCCCACTCGCCCTTCGCCGTCGCGATCTCCGAGGAGGAGCG CCACACGCAGCAGATGCAGTCCATCAGGTGACGTTCGTCCTTTCTCGGCTAGCAGCCGCCTTAT TGATTCTGCCGCCACTAGGCACTATAGCTAAGTAGCTAGCCTGCCGCTATAAACGAATTGGTGA AAACGATTTCTCGATTTGGTTGGGTTTGGTTCATTACTGAATAATAATAGCTTAACGACAATGG CCACCAACCCAGGAACATGAAAGGTAAGCGGAGATGAGTTCCTTTACCATTTTGGGAAAGGAAA AAAAAAGACAAAATAATTTGGCGTCTGCAGGACTTCCTCTGGGAGAAGAAGGAACGGAACAAAA CCAGAGAGCTCTGCCACCGACGTCAGAGCCCGGCCCGTTTACGTTGACAATACACTGCCTCGTG GGCCCTCTTGAGATAGCACTTGGTGTGAGTTGTGGACTTCATTAGAAAAAAAAAGTAAAAGGAT GGAGAAGATAGAAATAGGTAAAAACAAAAGGGTGACGCACGAAACGAACAAGCATGCACGCAGC TTGACGCGACACCACGGTCGCCGTCGGCCACGCAACGTGCTGCTTTATCTCTGCAGGGAACCTA GTAATCCTTCCCGAAAATCTGTACGTCCTTCGGGGGTCGGCTGTGTCCTCCCGGTCTCGCGCAT CACTAACCATTTTTGGTGCTGATAATCGGGAGCGTAGCGTAATTACCACTAAACTTTTTTTTCC CGATCTCTCGTGATGGATGCAGTGCGTCGTTGGCGTCTCTGACGCGTGAAACCGGGCCGAAAGT GGTCAAGGGCGACCCGGCCGCGAAGGGCGAGGCCGCCGCGCAGGGCGCGCCATCGACGCCGAGG GCGCACCAGCAGCACCGCCACCCCGCCGCCCCCGCCATCGCCGTCAGCGACAGCTCCCTCAAGT TCACTCATGTGCTCAACAACCTCTCGCCTGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.099732989

Conservation Information
Conserved circRNAs	NA
PMCS	0.099732989

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							35961859-35961698(+)
35960724-35961881(+)
35961861-35960702(-)
35961827-35961858(-)
						
					

						Potential amino acid sequence
						
							MCSTTSRLLEQDLDRPRWRRRTGLRGSRRPGRRSRTTACGTTTARRRCARRPSTSCTRCSGSGR
RPARPSGRRPPRPSRAVPTRPSPSRSPRRSATRSRCSPSVRRWRL*(+)
MATPNGLARIETTGKKKQDNGVWYDDSSAPVRAQTIDELHSLQRKRSAPSTPKRSAPTTPIKGG
AHSPFAVAISEEERHTQQMQSISASLASLTRETGPKVVKGDPAAKGEAAAQGAPSTPRAHQQHR
HPAAPAIAVSDSSLKFTHVLNNLSPAGAGPRSAEMATPNGLARIETTGKKKQDNGVWYDDSSAP
VRAQTIDELHSLQRKRSAPSTPKRSAPTTPIKGGAHSPFAVAISEEERHTQQMQSISASLASLT
RETGPKVVKGDPAAKGEAAAQGAPSTPRAHQQHRHPAAPAIAVSDSSLKFTHVLNNLSPAGAGP
RSAEMATPNGLARIETTGKKKQDNGVWYDDSSAPVRAQTIDELHSLQRKRSAPSTPKRSAPTTP
IKGGAHSPFAVAISEEERHTQQMQSISASLASLTRETGPKVVKGDPAAKGEAAAQGAPSTPRAH
QQHRHPAAPAIAVSDSSLKFTHVLNNLSPAGAGPRSAEMATPNGLARIETTGKKKQDNGVWYDD
SSAPVRAQTIDELHSLQRKRSAPSTPKRSAPTTPIKGGAHSPFAVAISEEERHTQQMQSISASL
ASLTRETGPKVVKGDPAAKGEAAAQGAPSTPRAHQQHRHPAAPAIAVSDSSLKFTHVLNNLSPA
(+)
MSELEGAVADGDGGGGGVAVLLVRPRRRWRALRGGLALRGRVALDHFRPGFTRQRRQRRTDGLH
LLRVALLLGDRDGEGRVGTALDGRGGRRPLGRAGRRPLPLQRVQLVDGLRAHRRRAVVVPHAVV
LLLLPGRLDPRKPVRRRHLGRSRSCSSRREVVEHMSELEGAVADGDGGGGGVAVLLVRPRRRWR
ALRGGLALRGRVALDHFRPGFTRQRRQRRTDGLHLLRVALLLGDRDGEGRVGTALDGRGGRRPL
GRAGRRPLPLQRVQLVDGLRAHRRRAVVVPHAVVLLLLPGRLDPRKPVRRRHLGRSRSCSSRRE
VVEHMSELEGAVADGDGGGGGVAVLLVRPRRRWRALRGGLALRGRVALDHFRPGFTRQRRQRRT
DGLHLLRVALLLGDRDGEGRVGTALDGRGGRRPLGRAGRRPLPLQRVQLVDGLRAHRRRAVVVP
HAVVLLLLPGRLDPRKPVRRRHLGRSRSCSSRREVVEHMSELEGAVADGDGGGGGVAVLLVRPR
RRWRALRGGLALRGRVALDHFRPGFTRQRRQRRTDGLHLLRVALLLGDRDGEGRVGTALDGRGG
RRPLGRAGRRPLPLQRVQLVDGLRAHRRRAVVVPHAVVLLLLPGRLDPRKPVRRRHLGRSRSC(
-)
MAGAAGWRCCWCALGVDGAPCAAASPFAAGSPLTTFGPVSRVRDANDALMDCICCVWRSSSEIA
TAKGEWAPPLMGVVGADRLGVLGADRFRCSECSSSMVCARTGAELSSYHTPLSCFFFPVVSIRA
SPFGVAISADRGPAPAGERLLST*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	35961859-35961698(+) 35960724-35961881(+) 35961861-35960702(-) 35961827-35961858(-)
Potential amino acid sequence	MCSTTSRLLEQDLDRPRWRRRTGLRGSRRPGRRSRTTACGTTTARRRCARRPSTSCTRCSGSGR RPARPSGRRPPRPSRAVPTRPSPSRSPRRSATRSRCSPSVRRWRL(+) MATPNGLARIETTGKKKQDNGVWYDDSSAPVRAQTIDELHSLQRKRSAPSTPKRSAPTTPIKGG AHSPFAVAISEEERHTQQMQSISASLASLTRETGPKVVKGDPAAKGEAAAQGAPSTPRAHQQHR HPAAPAIAVSDSSLKFTHVLNNLSPAGAGPRSAEMATPNGLARIETTGKKKQDNGVWYDDSSAP VRAQTIDELHSLQRKRSAPSTPKRSAPTTPIKGGAHSPFAVAISEEERHTQQMQSISASLASLT RETGPKVVKGDPAAKGEAAAQGAPSTPRAHQQHRHPAAPAIAVSDSSLKFTHVLNNLSPAGAGP RSAEMATPNGLARIETTGKKKQDNGVWYDDSSAPVRAQTIDELHSLQRKRSAPSTPKRSAPTTP IKGGAHSPFAVAISEEERHTQQMQSISASLASLTRETGPKVVKGDPAAKGEAAAQGAPSTPRAH QQHRHPAAPAIAVSDSSLKFTHVLNNLSPAGAGPRSAEMATPNGLARIETTGKKKQDNGVWYDD SSAPVRAQTIDELHSLQRKRSAPSTPKRSAPTTPIKGGAHSPFAVAISEEERHTQQMQSISASL ASLTRETGPKVVKGDPAAKGEAAAQGAPSTPRAHQQHRHPAAPAIAVSDSSLKFTHVLNNLSPA (+) MSELEGAVADGDGGGGGVAVLLVRPRRRWRALRGGLALRGRVALDHFRPGFTRQRRQRRTDGLH LLRVALLLGDRDGEGRVGTALDGRGGRRPLGRAGRRPLPLQRVQLVDGLRAHRRRAVVVPHAVV LLLLPGRLDPRKPVRRRHLGRSRSCSSRREVVEHMSELEGAVADGDGGGGGVAVLLVRPRRRWR ALRGGLALRGRVALDHFRPGFTRQRRQRRTDGLHLLRVALLLGDRDGEGRVGTALDGRGGRRPL GRAGRRPLPLQRVQLVDGLRAHRRRAVVVPHAVVLLLLPGRLDPRKPVRRRHLGRSRSCSSRRE VVEHMSELEGAVADGDGGGGGVAVLLVRPRRRWRALRGGLALRGRVALDHFRPGFTRQRRQRRT DGLHLLRVALLLGDRDGEGRVGTALDGRGGRRPLGRAGRRPLPLQRVQLVDGLRAHRRRAVVVP HAVVLLLLPGRLDPRKPVRRRHLGRSRSCSSRREVVEHMSELEGAVADGDGGGGGVAVLLVRPR RRWRALRGGLALRGRVALDHFRPGFTRQRRQRRTDGLHLLRVALLLGDRDGEGRVGTALDGRGG RRPLGRAGRRPLPLQRVQLVDGLRAHRRRAVVVPHAVVLLLLPGRLDPRKPVRRRHLGRSRSC( -) MAGAAGWRCCWCALGVDGAPCAAASPFAAGSPLTTFGPVSRVRDANDALMDCICCVWRSSSEIA TAKGEWAPPLMGVVGADRLGVLGADRFRCSECSSSMVCARTGAELSSYHTPLSCFFFPVVSIRA SPFGVAISADRGPAPAGERLLST(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d028471_circ_g.4

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