Plant Circular RNA Database

Detail information of Zm00001d038097_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d038097_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009101
					
						Alias
						zma_circ_0002367
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 147750906-147773764  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d038097						
					
						Parent gene annotation
						
							Probable transmembrane GTPase FZO-like chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d038097_circ_g.1 Zm00001d038097_circ_g.2 Zm00001d038097_circ_g.3 Zm00001d038097_circ_g.5 						
					
						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
						Zm00001d038097_T002:6
Zm00001d038097_T001:3
Zm00001d038097_T004:3
Zm00001d038097_T003:6

General Information
CircRNA Name	Zm00001d038097_circ_g.4
ID in PlantcircBase	zma_circ_009101
Alias	zma_circ_0002367
Organism	Zea mays
Position	chr6: 147750906-147773764 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d038097
Parent gene annotation	Probable transmembrane GTPase FZO-like chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d038097_circ_g.1 Zm00001d038097_circ_g.2 Zm00001d038097_circ_g.3 Zm00001d038097_circ_g.5
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	Zm00001d038097_T002:6 Zm00001d038097_T001:3 Zm00001d038097_T004:3 Zm00001d038097_T003:6

			
						 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  
						
							TGGGCTTGTTAATGAAGGGGAGAAACTCACCATAAAGGCACTGGAAGGCTTCAATGCCAGTGCT
GCCGCCAAAGATTTTGAAGAGGAAATTCGAGAATTGggtgaatttaactcaggaaagtcaactt
ttataaatgctttacttggaaggcagtatcttcaggagggagttgtgcctacgacaaatgagat
cacactac

									
								

					

						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: 1260
Transcript exons: 147750906-147751103,147752142-147752273,147770847-147770
933,147771045-147771488,147772315-147772482,147773534-14
7773764
GGTGAATTTAACTCAGGAAAGTCAACTTTTATAAATGCTTTACTTGGAAGGCAGTATCTTCAGG
AGGGAGTTGTGCCTACGACAAATGAGATCACACTACTATCATATTCTGAGGTTGAATCTGAAAA
CTTTGAACGATGTGAGAGGCATCCAGATGGTCAATTCATGTGCTATTTATCTGTTCCAATTTTA
AAGGAAATGAATCTAGTTGATACACCTGGAACAAATGTTATTCTTCAGAGGCAGCAACGACTCA
CTGAAGAATACGTGCCACGAGCTGATTTGGTGCTCTTTGTCCTATCATCAGATAGACCATTAAC
TGAAAGTGAGGTTGGATTTCTTCAGTATGTCCAGCAGTGGAAGAAGAAAGTTGTATTTATTCTA
AATAAATTGGACCTCTATCGGAACAGCAATGAGCTTGAAGAAGCTACTGCATTTGTCAAGGAAA
ATGCAATGAAATTGCTTACCGCAGAGGATGTCACACTGTTTCCTGTATCTTCACGCTCTGCTCT
GGAAGCCAAACTTTCATATTCCAAAAACAGTGATGGAAAGCATTCAACCGAAGCTATGTATAAT
GATCCTAGATGGAGAAGCAGCAAATTTTTTGAACTTGAGGATTACTTACTGAGTTTCTTAGATA
GTTCAACGGAAAATGGAAAAGAAAGGGTCCGGCTGAAACTTGAAACACCAATAGGCATTGCAGA
TCGATTGTTAACTTCGTGTCAAAGGCTGGTGAAACTAGAATATGAAAAGGCTGTTGAAGACTTA
GCATCCATCAAGGATCTTGTTTATGGTGCAAACAATTATGCCATCAAACTTAAGTCTGATAGCA
GTTCCTGGCAGAACCAGATTTCGTCTCTCATTGAGAGAGCAAAAGGTCGAGCAGTTACACTCAT
GGAATCTACACTTCAGCTGTCAAATATTGACCTTATTTTTGCATACACGATCAAAGGAAAAACA
GGCAGTTCCATGAGAGCCACATCATTTGTTCAGAATGATATTCTGAGTCCAACCCTTGATGATG
CTGTGAATTTACTAGGTGACTACTCGACATGGTTGAGTTCTAGCAATACCCGCGAAGCAAATGT
ATATTTGGAGTGTTTCTGTGAAAGATGGGATGCACTGGTTGCTCCGGAAGAAAGGGCTCTGTTA
GATCCAAATGGGCTTGTTAATGAAGGGGAGAAACTCACCATAAAGGCACTGGAAGGCTTCAATG
CCAGTGCTGCCGCCAAAGATTTTGAAGAGGAAATTCGAGAATTG
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	TGGGCTTGTTAATGAAGGGGAGAAACTCACCATAAAGGCACTGGAAGGCTTCAATGCCAGTGCT GCCGCCAAAGATTTTGAAGAGGAAATTCGAGAATTGggtgaatttaactcaggaaagtcaactt ttataaatgctttacttggaaggcagtatcttcaggagggagttgtgcctacgacaaatgagat cacactac
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: 1260 Transcript exons: 147750906-147751103,147752142-147752273,147770847-147770 933,147771045-147771488,147772315-147772482,147773534-14 7773764 GGTGAATTTAACTCAGGAAAGTCAACTTTTATAAATGCTTTACTTGGAAGGCAGTATCTTCAGG AGGGAGTTGTGCCTACGACAAATGAGATCACACTACTATCATATTCTGAGGTTGAATCTGAAAA CTTTGAACGATGTGAGAGGCATCCAGATGGTCAATTCATGTGCTATTTATCTGTTCCAATTTTA AAGGAAATGAATCTAGTTGATACACCTGGAACAAATGTTATTCTTCAGAGGCAGCAACGACTCA CTGAAGAATACGTGCCACGAGCTGATTTGGTGCTCTTTGTCCTATCATCAGATAGACCATTAAC TGAAAGTGAGGTTGGATTTCTTCAGTATGTCCAGCAGTGGAAGAAGAAAGTTGTATTTATTCTA AATAAATTGGACCTCTATCGGAACAGCAATGAGCTTGAAGAAGCTACTGCATTTGTCAAGGAAA ATGCAATGAAATTGCTTACCGCAGAGGATGTCACACTGTTTCCTGTATCTTCACGCTCTGCTCT GGAAGCCAAACTTTCATATTCCAAAAACAGTGATGGAAAGCATTCAACCGAAGCTATGTATAAT GATCCTAGATGGAGAAGCAGCAAATTTTTTGAACTTGAGGATTACTTACTGAGTTTCTTAGATA GTTCAACGGAAAATGGAAAAGAAAGGGTCCGGCTGAAACTTGAAACACCAATAGGCATTGCAGA TCGATTGTTAACTTCGTGTCAAAGGCTGGTGAAACTAGAATATGAAAAGGCTGTTGAAGACTTA GCATCCATCAAGGATCTTGTTTATGGTGCAAACAATTATGCCATCAAACTTAAGTCTGATAGCA GTTCCTGGCAGAACCAGATTTCGTCTCTCATTGAGAGAGCAAAAGGTCGAGCAGTTACACTCAT GGAATCTACACTTCAGCTGTCAAATATTGACCTTATTTTTGCATACACGATCAAAGGAAAAACA GGCAGTTCCATGAGAGCCACATCATTTGTTCAGAATGATATTCTGAGTCCAACCCTTGATGATG CTGTGAATTTACTAGGTGACTACTCGACATGGTTGAGTTCTAGCAATACCCGCGAAGCAAATGT ATATTTGGAGTGTTTCTGTGAAAGATGGGATGCACTGGTTGCTCCGGAAGAAAGGGCTCTGTTA GATCCAAATGGGCTTGTTAATGAAGGGGAGAAACTCACCATAAAGGCACTGGAAGGCTTCAATG CCAGTGCTGCCGCCAAAGATTTTGAAGAGGAAATTCGAGAATTG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.128580311

Conservation Information
Conserved circRNAs	NA
PMCS	0.128580311

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							147751072-147773761(+)
147773719-147750936(+)
						
					

						Potential amino acid sequence
						
							MCYLSVPILKEMNLVDTPGTNVILQRQQRLTEEYVPRADLVLFVLSSDRPLTESEVGFLQYVQQ
WKKKVVFILNKLDLYRNSNELEEATAFVKENAMKLLTAEDVTLFPVSSRSALEAKLSYSKNSDG
KHSTEAMYNDPRWRSSKFFELEDYLLSFLDSSTENGKERVRLKLETPIGIADRLLTSCQRLVKL
EYEKAVEDLASIKDLVYGANNYAIKLKSDSSSWQNQISSLIERAKGRAVTLMESTLQLSNIDLI
FAYTIKGKTGSSMRATSFVQNDILSPTLDDAVNLLGDYSTWLSSSNTREANVYLECFCERWDAL
VAPEERALLDPNGLVNEGEKLTIKALEGFNASAAAKDFEEEIRELGEFNSGKSTFINALLGRQY
LQEGVVPTTNEITLLSYSEVESENFERCERHPDGQFMCYLSVPILKEMNLVDTPGTNVILQRQQ
RLTEEYVPRADLVLFVLSSDRPLTESEVGFLQYVQQWKKKVVFILNKLDLYRNSNELEEATAFV
KENAMKLLTAEDVTLFPVSSRSALEAKLSYSKNSDGKHSTEAMYNDPRWRSSKFFELEDYLLSF
LDSSTENGKERVRLKLETPIGIADRLLTSCQRLVKLEYEKAVEDLASIKDLVYGANNYAIKLKS
DSSSWQNQISSLIERAKGRAVTLMESTLQLSNIDLIFAYTIKGKTGSSMRATSFVQNDILSPTL
DDAVNLLGDYSTWLSSSNTREANVYLECFCERWDALVAPEERALLDPNGLVNEGEKLTIKALEG
FNASAAAKDFEEEIRELGEFNSGKSTFINALLGRQYLQEGVVPTTNEITLLSYSEVESENFERC
ERHPDGQFMCYLSVPILKEMNLVDTPGTNVILQRQQRLTEEYVPRADLVLFVLSSDRPLTESEV
GFLQYVQQWKKKVVFILNKLDLYRNSNELEEATAFVKENAMKLLTAEDVTLFPVSSRSALEAKL
SYSKNSDGKHSTEAMYNDPRWRSSKFFELEDYLLSFLDSSTENGKERVRLKLETPIGIADRLLT
SCQRLVKLEYEKAVEDLASIKDLVYGANNYAIKLKSDSSSWQNQISSLIERAKGRAVTLMESTL
QLSNIDLIFAYTIKGKTGSSMRATSFVQNDILSPTLDDAVNLLGDYSTWLSSSNTREANVYLEC
FCERWDALVAPEERALLDPNGLVNEGEKLTIKALEGFNASAAAKDFEEEIRELGEFNSGKSTFI
NALLGRQYLQEGVVPTTNEITLLSYSEVESENFERCERHPDGQFMCYLSVPILKEMNLVDTPGT
NVILQRQQRLTEEYVPRADLVLFVLSSDRPLTESEVGFLQYVQQWKKKVVFILNKLDLYRNSNE
LEEATAFVKENAMKLLTAEDVTLFPVSSRSALEAKLSYSKNSDGKHSTEAMYNDPRWRSSKFFE
LEDYLLSFLDSSTENGKERVRLKLETPIGIADRLLTSCQRLVKLEYEKAVEDLASIKDLVYGAN
NYAIKLKSDSSSWQNQISSLIERAKGRAVTLMESTLQLSNIDLIFAYTIKGKTGSSMRATSFVQ
NDILSPTLDDAVNLLGDYSTWLSSSNTREANVYLECFCERWDALVAPEERALLDPNGLVNEGEK
LTIKALEGFNASAAAKDFEEEIREL(+)
MPVLPPKILKRKFENWVNLTQESQLL*(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	147751072-147773761(+) 147773719-147750936(+)
Potential amino acid sequence	MCYLSVPILKEMNLVDTPGTNVILQRQQRLTEEYVPRADLVLFVLSSDRPLTESEVGFLQYVQQ WKKKVVFILNKLDLYRNSNELEEATAFVKENAMKLLTAEDVTLFPVSSRSALEAKLSYSKNSDG KHSTEAMYNDPRWRSSKFFELEDYLLSFLDSSTENGKERVRLKLETPIGIADRLLTSCQRLVKL EYEKAVEDLASIKDLVYGANNYAIKLKSDSSSWQNQISSLIERAKGRAVTLMESTLQLSNIDLI FAYTIKGKTGSSMRATSFVQNDILSPTLDDAVNLLGDYSTWLSSSNTREANVYLECFCERWDAL VAPEERALLDPNGLVNEGEKLTIKALEGFNASAAAKDFEEEIRELGEFNSGKSTFINALLGRQY LQEGVVPTTNEITLLSYSEVESENFERCERHPDGQFMCYLSVPILKEMNLVDTPGTNVILQRQQ RLTEEYVPRADLVLFVLSSDRPLTESEVGFLQYVQQWKKKVVFILNKLDLYRNSNELEEATAFV KENAMKLLTAEDVTLFPVSSRSALEAKLSYSKNSDGKHSTEAMYNDPRWRSSKFFELEDYLLSF LDSSTENGKERVRLKLETPIGIADRLLTSCQRLVKLEYEKAVEDLASIKDLVYGANNYAIKLKS DSSSWQNQISSLIERAKGRAVTLMESTLQLSNIDLIFAYTIKGKTGSSMRATSFVQNDILSPTL DDAVNLLGDYSTWLSSSNTREANVYLECFCERWDALVAPEERALLDPNGLVNEGEKLTIKALEG FNASAAAKDFEEEIRELGEFNSGKSTFINALLGRQYLQEGVVPTTNEITLLSYSEVESENFERC ERHPDGQFMCYLSVPILKEMNLVDTPGTNVILQRQQRLTEEYVPRADLVLFVLSSDRPLTESEV GFLQYVQQWKKKVVFILNKLDLYRNSNELEEATAFVKENAMKLLTAEDVTLFPVSSRSALEAKL SYSKNSDGKHSTEAMYNDPRWRSSKFFELEDYLLSFLDSSTENGKERVRLKLETPIGIADRLLT SCQRLVKLEYEKAVEDLASIKDLVYGANNYAIKLKSDSSSWQNQISSLIERAKGRAVTLMESTL QLSNIDLIFAYTIKGKTGSSMRATSFVQNDILSPTLDDAVNLLGDYSTWLSSSNTREANVYLEC FCERWDALVAPEERALLDPNGLVNEGEKLTIKALEGFNASAAAKDFEEEIRELGEFNSGKSTFI NALLGRQYLQEGVVPTTNEITLLSYSEVESENFERCERHPDGQFMCYLSVPILKEMNLVDTPGT NVILQRQQRLTEEYVPRADLVLFVLSSDRPLTESEVGFLQYVQQWKKKVVFILNKLDLYRNSNE LEEATAFVKENAMKLLTAEDVTLFPVSSRSALEAKLSYSKNSDGKHSTEAMYNDPRWRSSKFFE LEDYLLSFLDSSTENGKERVRLKLETPIGIADRLLTSCQRLVKLEYEKAVEDLASIKDLVYGAN NYAIKLKSDSSSWQNQISSLIERAKGRAVTLMESTLQLSNIDLIFAYTIKGKTGSSMRATSFVQ NDILSPTLDDAVNLLGDYSTWLSSSNTREANVYLECFCERWDALVAPEERALLDPNGLVNEGEK LTIKALEGFNASAAAKDFEEEIREL(+) MPVLPPKILKRKFENWVNLTQESQLL*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d038097_circ_g.4

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