Plant Circular RNA Database

Detail information of Zm00001d001809_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d001809_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006992
					
						Alias
						Zm02circ00001
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 1306576-1308914  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d001809						
					
						Parent gene annotation
						
							RNA polymerase II transcription factor B subunit 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d001809_T013:8
Zm00001d001809_T017:8
Zm00001d001809_T020:8
Zm00001d001809_T021:8
Zm00001d001809_T010:8
Zm00001d001809_T007:8
Zm00001d001809_T012:8
Zm00001d001809_T019:8
Zm00001d001809_T008:8
Zm00001d001809_T016:8
Zm00001d001809_T018:8
Zm00001d001809_T004:8
Zm00001d001809_T015:8
Zm00001d001809_T014:8
Zm00001d001809_T009:8
Zm00001d001809_T005:8
Zm00001d001809_T011:8
Zm00001d001809_T003:8
Zm00001d001809_T002:8
Zm00001d001809_T022:8
Zm00001d001809_T001:8
Zm00001d001809_T006:8

General Information
CircRNA Name	Zm00001d001809_circ_g.1
ID in PlantcircBase	zma_circ_006992
Alias	Zm02circ00001
Organism	Zea mays
Position	chr2: 1306576-1308914 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d001809
Parent gene annotation	RNA polymerase II transcription factor B subunit 2
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d001809_T013:8 Zm00001d001809_T017:8 Zm00001d001809_T020:8 Zm00001d001809_T021:8 Zm00001d001809_T010:8 Zm00001d001809_T007:8 Zm00001d001809_T012:8 Zm00001d001809_T019:8 Zm00001d001809_T008:8 Zm00001d001809_T016:8 Zm00001d001809_T018:8 Zm00001d001809_T004:8 Zm00001d001809_T015:8 Zm00001d001809_T014:8 Zm00001d001809_T009:8 Zm00001d001809_T005:8 Zm00001d001809_T011:8 Zm00001d001809_T003:8 Zm00001d001809_T002:8 Zm00001d001809_T022:8 Zm00001d001809_T001:8 Zm00001d001809_T006:8

			
						 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  
						
							CCTAACCTCCCATTGATCAAGAGCATAGGCTTCCAGATCTGCTGGTGTGGGCAATCGACCAGTG
ACACTTAATGGTAAAGGTTCCCTTGGTAAACTTCCActtgcaaaaaggcgtagaatttcacagt
gcaacttggaagtagagtatgcatacattcgaaagtttgtctccacaaccacaaatccctgcga
caacaata

									
								

					

						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: 624
Transcript exons: 1306576-1306661,1306807-1306890,1306961-1307044,1307435-
1307503,1307596-1307655,1307732-1307777,1308529-1308629,
1308821-1308914
CTTGCAAAAAGGCGTAGAATTTCACAGTGCAACTTGGAAGTAGAGTATGCATACATTCGAAAGT
TTGTCTCCACAACCACAAATCCCTCTTTGTTAGATGACGAATCTGACAAGCTTGCTGAAAGATT
AGTAGCCAATTGGGTAGGAATGAACCAGCTATCCTTTCGACCCTGCTGCTGTTTGACTAGTCCT
AATTCTGCAAGATCCCTGATGGCAATCCTCTGGACATCAGTCAGAGTGTTCAAGCTATAAGCCG
CTCCCAATTTATGAAAGCTAAGTTCCAAGAGAAATGATATCAGCTCCGTAGGGTCCACTCCACG
TTCCTCAGCAGATGAAATGTATTCTCTCATTATGTACCAAAGTTGTGCATTTGTTTCCATCAGA
AGAAATTGGAAGCCATTTTCAGTCAACTTTGAAGCTTCACCATCCCTTGAACTCAGAAGACCAC
GCTGAAACGTCTTCATCATGGAGGAGCTAAAACTTGACCCTTTTTCGACTTGAGATGAATTGAT
CAATTGCAACAAGAAGCACTCCCATTGATCAAGAGCATAGGCTTCCAGATCTGCTGGTGTGGGC
AATCGACCAGTGACACTTAATGGTAAAGGTTCCCTTGGTAAACTTCCA
						
					

						Genomic sequence
						
							CTTGCAAAAAGGCGTAGAATTTCACAGTGCAACTTGGAAGTAGAGTATGCATACATTCGAAAGT
TTGTCTCCACAACCACAAATCCCTGCGACAACAATACCAGTATCAACTCTGAGATTAAATAATC
ATGATCACTGCTTATAGGCGACAAGTAGATGGAGGTTACAAAGAAGAATTGAAAAAAAAAAACT
AAATAATTGCAGAAGGAAGTGATGTAAATGTTATTCAACCTCTTTGTTAGATGACGAATCTGAC
AAGCTTGCTGAAAGATTAGTAGCCAATTGGGTAGGAATGAACCAGCTATCCTTTCGACCCTGAA
ATTCAAAACTTCTATTATCATCAGAAAGATTGTCGGAGCAAAAGAACAAAAGATAAAATGTCTA
CCTGCTGCTGTTTGACTAGTCCTAATTCTGCAAGATCCCTGATGGCAATCCTCTGGACATCAGT
CAGAGTGTTCAAGCTATAAGCCTAAAACATTAACAAAGCAGACAGAATGCATGGCCTTGAATCT
CTCAAGCAACATACCAGGCACAAACTTGGATGTAATATGCAGGATAATTTCATCTATTAGATTC
AGACTGCAGCGCCTTAAATTTTTTTCATGTATTCTTAATCAGGCATGCAAGCTTGATGAGTTGA
TGTTCCTACCATGTAAAATACTGTGGAATAGTTACAGTTTCTTAGATATGCTCTTCTGATATCA
CTTATGAGAACTTCATTTTTCCTATTCATGTATTGTATTGCCGAAGGACAAGTTGCTATAGAAG
TTTTCACCGACATCAGACATCACCATATTGGTAAGAGAATTATGTATAGCTACTTGCTTAACAT
GATGTTCTGAAAGTACTATCACTTTACCGCTCCCAATTTATGAAAGCTAAGTTCCAAGAGAAAT
GATATCAGCTCCGTAGGGTCCACTCCACGTTCCTATTTAATAACGCAAATAATCAGCAACCAAG
TTTAACACAAAGTCACCAACGTGAATCAACAGAAATATTACAAGGATATGCCACAAATACCTCA
GCAGATGAAATGTATTCTCTCATTATGTACCAAAGTTGTGCATTTGTTTCCATCAGCTGATAGC
ATAGAAAATATTAAGAGCAAAGACGGAAATCTGCCGGTTATCGTATTAGCTGGGAACAGAGAAC
TAACAAGAAATTGGAAGCCATTTTCAGTCAACTTTGAAGCTTCACCATCCCTGCAAGCACACCA
GATCAGGAAATCATATCATCGAAAATATTGCTTATATCAAAATAAAGGGCAGGCCCAGTGCGGT
TGGCTCCCACATGAATGGAGTCTAGGGAAGGGATAAACAGAGGCAAGCATCCCCGCAAATGTGG
GGAGGCTGCTTCAAATCCGCAATCTGATGACTTGGTAAGACAGCTCTCACCACTTTACCAGGCC
TACCCTTCATTGCTTATATCAGTCAATGAAAAATATATAGAGATATCAAACATGTTTTACAAAT
ATCTTGATTATTTTAACAAAAAAACATTAAGCTGAACTGAATCATTTCTAGGATAATCAGTTAA
TCAACTCTTACAACCAGGGCATAGTACAGTAAACTAACAGTAATTTGTTGTCAGCCCCCATCAA
CTTGAATATACTACTCCCTCATTTACAAATTTTAAGATGTTGTCTTTTTAGATACATTGCTTTT
ACAGAGTACCTAGACATAATGTATATCTAAGTGCATAACAAAAACTATGTATCTAAAAAAGCCA
AAACGTCTTGTAATGAGGAATGGAGGGGGTAGTTACTACTTACTGTTTAGTGTATGTATTATTA
TGTAGAATTCTAGAAAATGCCACAGGATATATTATCCAACTGTACTAGAAGAAATAAAGAGTTG
CAGTAACTTGGCAATTCATTATTGTTCAAATAACATTTGACTACCACTAATATATGTGAAACTA
ACCTAGCTGTCAAGACAGGGAATTAGATGGAACCTTGAACTCAGAAGACCACGCTGAAACGTCT
TCATCATGGAGGAGCTAAAACTTGACCCTTTTTCGACTTGAGATGAATTGATCAATTGCAACAA
GAAGCACTATAATCCCAATACGAAATAGGAAAATTATATGTATTATATATATATATATATATAT
ATATATATATATATATATAAGCCAACACAGAATTCAAAGAAGGAAAAAAGAAGACGGTGAAGAT
ACTATAAAGAACAGTAAAAAACAGGCAGGCATGATAAACACATTCTGAGTTAAGCATTGGCATC
CTAACCTCCCATTGATCAAGAGCATAGGCTTCCAGATCTGCTGGTGTGGGCAATCGACCAGTGA
CACTTAATGGTAAAGGTTCCCTTGGTAAACTTCCA
						
					

			
		

Sequences
Splice junction sequence	CCTAACCTCCCATTGATCAAGAGCATAGGCTTCCAGATCTGCTGGTGTGGGCAATCGACCAGTG ACACTTAATGGTAAAGGTTCCCTTGGTAAACTTCCActtgcaaaaaggcgtagaatttcacagt gcaacttggaagtagagtatgcatacattcgaaagtttgtctccacaaccacaaatccctgcga caacaata
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: 624 Transcript exons: 1306576-1306661,1306807-1306890,1306961-1307044,1307435- 1307503,1307596-1307655,1307732-1307777,1308529-1308629, 1308821-1308914 CTTGCAAAAAGGCGTAGAATTTCACAGTGCAACTTGGAAGTAGAGTATGCATACATTCGAAAGT TTGTCTCCACAACCACAAATCCCTCTTTGTTAGATGACGAATCTGACAAGCTTGCTGAAAGATT AGTAGCCAATTGGGTAGGAATGAACCAGCTATCCTTTCGACCCTGCTGCTGTTTGACTAGTCCT AATTCTGCAAGATCCCTGATGGCAATCCTCTGGACATCAGTCAGAGTGTTCAAGCTATAAGCCG CTCCCAATTTATGAAAGCTAAGTTCCAAGAGAAATGATATCAGCTCCGTAGGGTCCACTCCACG TTCCTCAGCAGATGAAATGTATTCTCTCATTATGTACCAAAGTTGTGCATTTGTTTCCATCAGA AGAAATTGGAAGCCATTTTCAGTCAACTTTGAAGCTTCACCATCCCTTGAACTCAGAAGACCAC GCTGAAACGTCTTCATCATGGAGGAGCTAAAACTTGACCCTTTTTCGACTTGAGATGAATTGAT CAATTGCAACAAGAAGCACTCCCATTGATCAAGAGCATAGGCTTCCAGATCTGCTGGTGTGGGC AATCGACCAGTGACACTTAATGGTAAAGGTTCCCTTGGTAAACTTCCA
Genomic sequence	CTTGCAAAAAGGCGTAGAATTTCACAGTGCAACTTGGAAGTAGAGTATGCATACATTCGAAAGT TTGTCTCCACAACCACAAATCCCTGCGACAACAATACCAGTATCAACTCTGAGATTAAATAATC ATGATCACTGCTTATAGGCGACAAGTAGATGGAGGTTACAAAGAAGAATTGAAAAAAAAAAACT AAATAATTGCAGAAGGAAGTGATGTAAATGTTATTCAACCTCTTTGTTAGATGACGAATCTGAC AAGCTTGCTGAAAGATTAGTAGCCAATTGGGTAGGAATGAACCAGCTATCCTTTCGACCCTGAA ATTCAAAACTTCTATTATCATCAGAAAGATTGTCGGAGCAAAAGAACAAAAGATAAAATGTCTA CCTGCTGCTGTTTGACTAGTCCTAATTCTGCAAGATCCCTGATGGCAATCCTCTGGACATCAGT CAGAGTGTTCAAGCTATAAGCCTAAAACATTAACAAAGCAGACAGAATGCATGGCCTTGAATCT CTCAAGCAACATACCAGGCACAAACTTGGATGTAATATGCAGGATAATTTCATCTATTAGATTC AGACTGCAGCGCCTTAAATTTTTTTCATGTATTCTTAATCAGGCATGCAAGCTTGATGAGTTGA TGTTCCTACCATGTAAAATACTGTGGAATAGTTACAGTTTCTTAGATATGCTCTTCTGATATCA CTTATGAGAACTTCATTTTTCCTATTCATGTATTGTATTGCCGAAGGACAAGTTGCTATAGAAG TTTTCACCGACATCAGACATCACCATATTGGTAAGAGAATTATGTATAGCTACTTGCTTAACAT GATGTTCTGAAAGTACTATCACTTTACCGCTCCCAATTTATGAAAGCTAAGTTCCAAGAGAAAT GATATCAGCTCCGTAGGGTCCACTCCACGTTCCTATTTAATAACGCAAATAATCAGCAACCAAG TTTAACACAAAGTCACCAACGTGAATCAACAGAAATATTACAAGGATATGCCACAAATACCTCA GCAGATGAAATGTATTCTCTCATTATGTACCAAAGTTGTGCATTTGTTTCCATCAGCTGATAGC ATAGAAAATATTAAGAGCAAAGACGGAAATCTGCCGGTTATCGTATTAGCTGGGAACAGAGAAC TAACAAGAAATTGGAAGCCATTTTCAGTCAACTTTGAAGCTTCACCATCCCTGCAAGCACACCA GATCAGGAAATCATATCATCGAAAATATTGCTTATATCAAAATAAAGGGCAGGCCCAGTGCGGT TGGCTCCCACATGAATGGAGTCTAGGGAAGGGATAAACAGAGGCAAGCATCCCCGCAAATGTGG GGAGGCTGCTTCAAATCCGCAATCTGATGACTTGGTAAGACAGCTCTCACCACTTTACCAGGCC TACCCTTCATTGCTTATATCAGTCAATGAAAAATATATAGAGATATCAAACATGTTTTACAAAT ATCTTGATTATTTTAACAAAAAAACATTAAGCTGAACTGAATCATTTCTAGGATAATCAGTTAA TCAACTCTTACAACCAGGGCATAGTACAGTAAACTAACAGTAATTTGTTGTCAGCCCCCATCAA CTTGAATATACTACTCCCTCATTTACAAATTTTAAGATGTTGTCTTTTTAGATACATTGCTTTT ACAGAGTACCTAGACATAATGTATATCTAAGTGCATAACAAAAACTATGTATCTAAAAAAGCCA AAACGTCTTGTAATGAGGAATGGAGGGGGTAGTTACTACTTACTGTTTAGTGTATGTATTATTA TGTAGAATTCTAGAAAATGCCACAGGATATATTATCCAACTGTACTAGAAGAAATAAAGAGTTG CAGTAACTTGGCAATTCATTATTGTTCAAATAACATTTGACTACCACTAATATATGTGAAACTA ACCTAGCTGTCAAGACAGGGAATTAGATGGAACCTTGAACTCAGAAGACCACGCTGAAACGTCT TCATCATGGAGGAGCTAAAACTTGACCCTTTTTCGACTTGAGATGAATTGATCAATTGCAACAA GAAGCACTATAATCCCAATACGAAATAGGAAAATTATATGTATTATATATATATATATATATAT ATATATATATATATATATAAGCCAACACAGAATTCAAAGAAGGAAAAAAGAAGACGGTGAAGAT ACTATAAAGAACAGTAAAAAACAGGCAGGCATGATAAACACATTCTGAGTTAAGCATTGGCATC CTAACCTCCCATTGATCAAGAGCATAGGCTTCCAGATCTGCTGGTGTGGGCAATCGACCAGTGA CACTTAATGGTAAAGGTTCCCTTGGTAAACTTCCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.068790332

Conservation Information
Conserved circRNAs	NA
PMCS	0.068790332

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1308887-1306615(+)
1308568-1306578(-)
1306629-1308885(-)
						
						Potential amino acid sequence
						
							MVKVPLVNFHLQKGVEFHSATWK*(+)
MMKTFQRGLLSSRDGEASKLTENGFQFLLMETNAQLWYIMREYISSAEERGVDPTELISFLLEL
SFHKLGAAYSLNTLTDVQRIAIRDLAELGLVKQQQGRKDSWFIPTQLATNLSASLSDSSSNKEG
FVVVETNFRMYAYSTSKLHCEILRLFASGSLPREPLPLSVTGRLPTPADLEAYALDQWECFLLQ
LINSSQVEKGSSFSSSMMKTFQRGLLSSRDGEASKLTENGFQFLLMETNAQLWYIMREYISSAE
ERGVDPTELISFLLELSFHKLGAAYSLNTLTDVQRIAIRDLAELGLVKQQQGRKDSWFIPTQLA
TNLSASLSDSSSNKEGFVVVETNFRMYAYSTSKLHCEILRLFASGSLPREPLPLSVTGRLPTPA
DLEAYALDQWECFLLQLINSSQVEKGSSFSSSMMKTFQRGLLSSRDGEASKLTENGFQFLLMET
NAQLWYIMREYISSAEERGVDPTELISFLLELSFHKLGAAYSLNTLTDVQRIAIRDLAELGLVK
QQQGRKDSWFIPTQLATNLSASLSDSSSNKEGFVVVETNFRMYAYSTSKLHCEILRLFASGSLP
REPLPLSVTGRLPTPADLEAYALDQWECFLLQLINSSQVEKGSSFSSSMMKTFQRGLLSSRDGE
ASKLTENGFQFLLMETNAQLWYIMREYISSAEERGVDPTELISFLLELSFHKLGAAYSLNTLTD
VQRIAIRDLAELGLVKQQQGRKDSWFIPTQLATNLSASLSDSSSNKEGFVVVETNFRMYAYSTS
KLHCEILRLFA(-)
MHTLLPSCTVKFYAFLQVEVYQGNLYH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1308887-1306615(+) 1308568-1306578(-) 1306629-1308885(-)
Potential amino acid sequence	MVKVPLVNFHLQKGVEFHSATWK(+) MMKTFQRGLLSSRDGEASKLTENGFQFLLMETNAQLWYIMREYISSAEERGVDPTELISFLLEL SFHKLGAAYSLNTLTDVQRIAIRDLAELGLVKQQQGRKDSWFIPTQLATNLSASLSDSSSNKEG FVVVETNFRMYAYSTSKLHCEILRLFASGSLPREPLPLSVTGRLPTPADLEAYALDQWECFLLQ LINSSQVEKGSSFSSSMMKTFQRGLLSSRDGEASKLTENGFQFLLMETNAQLWYIMREYISSAE ERGVDPTELISFLLELSFHKLGAAYSLNTLTDVQRIAIRDLAELGLVKQQQGRKDSWFIPTQLA TNLSASLSDSSSNKEGFVVVETNFRMYAYSTSKLHCEILRLFASGSLPREPLPLSVTGRLPTPA DLEAYALDQWECFLLQLINSSQVEKGSSFSSSMMKTFQRGLLSSRDGEASKLTENGFQFLLMET NAQLWYIMREYISSAEERGVDPTELISFLLELSFHKLGAAYSLNTLTDVQRIAIRDLAELGLVK QQQGRKDSWFIPTQLATNLSASLSDSSSNKEGFVVVETNFRMYAYSTSKLHCEILRLFASGSLP REPLPLSVTGRLPTPADLEAYALDQWECFLLQLINSSQVEKGSSFSSSMMKTFQRGLLSSRDGE ASKLTENGFQFLLMETNAQLWYIMREYISSAEERGVDPTELISFLLELSFHKLGAAYSLNTLTD VQRIAIRDLAELGLVKQQQGRKDSWFIPTQLATNLSASLSDSSSNKEGFVVVETNFRMYAYSTS KLHCEILRLFA(-) MHTLLPSCTVKFYAFLQVEVYQGNLYH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d001809_circ_g.1

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