Plant Circular RNA Database

Detail information of Zm00001d048546_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d048546_circ_g.5
					
						ID in PlantcircBase
						zma_circ_010127
					
						Alias
						zma_circ_0003152
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 158460557-158460896  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d048546						
					
						Parent gene annotation
						
							transcription regulators
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d048546_circ_g.3 Zm00001d048546_circ_igg.1 Zm00001d048546_circ_g.2 Zm00001d048546_circ_g.3 Zm00001d048546_circ_g.4 						
					
						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  
						
							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
						Zm00001d048546_T081:1
Zm00001d048546_T121:1
Zm00001d048546_T030:1
Zm00001d048546_T076:1
Zm00001d048546_T006:1
Zm00001d048546_T084:2
Zm00001d048546_T120:1
Zm00001d048546_T122:1
Zm00001d048546_T079:1
Zm00001d048546_T005:1
Zm00001d048546_T008:1
Zm00001d048546_T046:1
Zm00001d048546_T083:1
Zm00001d048546_T007:1
Zm00001d048546_T038:1
Zm00001d048546_T024:1
Zm00001d048546_T114:1
Zm00001d048546_T117:1
Zm00001d048546_T113:1
Zm00001d048546_T115:1
Zm00001d048546_T077:1
Zm00001d048546_T004:1
Zm00001d048546_T063:1
Zm00001d048546_T055:1
Zm00001d048546_T039:1
Zm00001d048546_T078:1
Zm00001d048546_T111:1
Zm00001d048546_T060:1

General Information
CircRNA Name	Zm00001d048546_circ_g.5
ID in PlantcircBase	zma_circ_010127
Alias	zma_circ_0003152
Organism	Zea mays
Position	chr9: 158460557-158460896 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d048546
Parent gene annotation	transcription regulators
Parent gene strand	-
Alternative splicing	Zm00001d048546_circ_g.3 Zm00001d048546_circ_igg.1 Zm00001d048546_circ_g.2 Zm00001d048546_circ_g.3 Zm00001d048546_circ_g.4
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	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	Zm00001d048546_T081:1 Zm00001d048546_T121:1 Zm00001d048546_T030:1 Zm00001d048546_T076:1 Zm00001d048546_T006:1 Zm00001d048546_T084:2 Zm00001d048546_T120:1 Zm00001d048546_T122:1 Zm00001d048546_T079:1 Zm00001d048546_T005:1 Zm00001d048546_T008:1 Zm00001d048546_T046:1 Zm00001d048546_T083:1 Zm00001d048546_T007:1 Zm00001d048546_T038:1 Zm00001d048546_T024:1 Zm00001d048546_T114:1 Zm00001d048546_T117:1 Zm00001d048546_T113:1 Zm00001d048546_T115:1 Zm00001d048546_T077:1 Zm00001d048546_T004:1 Zm00001d048546_T063:1 Zm00001d048546_T055:1 Zm00001d048546_T039:1 Zm00001d048546_T078:1 Zm00001d048546_T111:1 Zm00001d048546_T060:1

			
						 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  
						
							TAACTCGGCTACAATGTCAGCCATGCTTATCTCTTTCCCAATTTCAGACAGAAGTGACTCAAAA
TCATCATTTGTGCTACCAAAGTACATCTCCAAATGTaagttcattgattgagtccacaaggaca
tctgtgttccatttagtcggctgaggtgagtcattcgtgtggctattacgaatagcagatacaa
atgttgca

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							AAGTTCATTGATTGAGTCCACAAGGACATCTGTGTTCCATTTAGTCGGCTGAGGTGAGTCATTC
GTGTGGCTATTACGAATAGCAGATACAAATGTTGCATATGTGTTATGGGCCTCTCCAAGACCAA
TATGAGTGCCGACAACAGCCCCAAGCAACTTAGATATGGCGATATCATCAAGAGGCTCCACAAT
GGAAAGTATTTCCTTACAGTGAGTGCTGTCAACAGTAAATCCGTAACCTAACTCGGCTACAATG
TCAGCCATGCTTATCTCTTTCCCAATTTCAGACAGAAGTGACTCAAAATCATCATTTGTGCTAC
CAAAGTACATCTCCAAATGT

Sequences
Splice junction sequence	TAACTCGGCTACAATGTCAGCCATGCTTATCTCTTTCCCAATTTCAGACAGAAGTGACTCAAAA TCATCATTTGTGCTACCAAAGTACATCTCCAAATGTaagttcattgattgagtccacaaggaca tctgtgttccatttagtcggctgaggtgagtcattcgtgtggctattacgaatagcagatacaa atgttgca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AAGTTCATTGATTGAGTCCACAAGGACATCTGTGTTCCATTTAGTCGGCTGAGGTGAGTCATTC GTGTGGCTATTACGAATAGCAGATACAAATGTTGCATATGTGTTATGGGCCTCTCCAAGACCAA TATGAGTGCCGACAACAGCCCCAAGCAACTTAGATATGGCGATATCATCAAGAGGCTCCACAAT GGAAAGTATTTCCTTACAGTGAGTGCTGTCAACAGTAAATCCGTAACCTAACTCGGCTACAATG TCAGCCATGCTTATCTCTTTCCCAATTTCAGACAGAAGTGACTCAAAATCATCATTTGTGCTAC CAAAGTACATCTCCAAATGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.213597843

Conservation Information
Conserved circRNAs	NA
PMCS	0.213597843

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							158460811-158460568(+)
158460888-158460875(-)
158460734-158460875(-)
						
						Potential amino acid sequence
						
							MSAMLISFPISDRSDSKSSFVLPKYISKCKFID*(+)
MYFGSTNDDFESLLSEIGKEISMADIVAELGYGFTVDSTHCKEILSIVEPLDDIAISKLLGAVV
GTHIGLGEAHNTYATFVSAIRNSHTNDSPQPTKWNTDVLVDSINELTFGDVLW*(-)
MISPYLSCLGLLSALILVLERPITHMQHLYLLFVIATRMTHLSRLNGTQMSLWTQSMNLHLEMY
FGSTNDDFESLLSEIGKEISMADIVAELGYGFTVDSTHCKEILSIVEPLDDIAISKLLGAVVGT
HIGLGEAHNTYATFVSAIRNSHTNDSPQPTKWNTDVLVDSINELTFGDVLW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	158460811-158460568(+) 158460888-158460875(-) 158460734-158460875(-)
Potential amino acid sequence	MSAMLISFPISDRSDSKSSFVLPKYISKCKFID(+) MYFGSTNDDFESLLSEIGKEISMADIVAELGYGFTVDSTHCKEILSIVEPLDDIAISKLLGAVV GTHIGLGEAHNTYATFVSAIRNSHTNDSPQPTKWNTDVLVDSINELTFGDVLW(-) MISPYLSCLGLLSALILVLERPITHMQHLYLLFVIATRMTHLSRLNGTQMSLWTQSMNLHLEMY FGSTNDDFESLLSEIGKEISMADIVAELGYGFTVDSTHCKEILSIVEPLDDIAISKLLGAVVGT HIGLGEAHNTYATFVSAIRNSHTNDSPQPTKWNTDVLVDSINELTFGDVLW*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d048546_circ_g.5

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