Plant Circular RNA Database

Detail information of Zm00001d015505_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d015505_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008625
					
						Alias
						Zm05circ00069, GRMZM2G059363_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 94168258-94169810  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d015505						
					
						Parent gene annotation
						
							Nucleoid-associated protein  chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d015505_circ_g.1 Zm00001d015505_circ_g.2 Zm00001d015505_circ_g.4 Zm00001d015505_circ_g.5 						
					
						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  
						
							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
						Zm00001d015505_T001:3

General Information
CircRNA Name	Zm00001d015505_circ_g.3
ID in PlantcircBase	zma_circ_008625
Alias	Zm05circ00069, GRMZM2G059363_C1
Organism	Zea mays
Position	chr5: 94168258-94169810 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d015505
Parent gene annotation	Nucleoid-associated protein chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d015505_circ_g.1 Zm00001d015505_circ_g.2 Zm00001d015505_circ_g.4 Zm00001d015505_circ_g.5
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	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	Zm00001d015505_T001:3

			
						 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  
						
							TCTCATGTTTGATGCAAAATAGCCTGACTCTGTGACTTTTTCTGTGTCTCCTATTTTTAGGACT
GAGATTGATGGTTATTGTGAAGGCGAACTAATCAAGgtaatagaatgaacatagagggcgcttt
ctgtttgccgtgttccacaaggaagagagcaagttatagacctttccgagtgtacagtttattt
ggagggaa

									
								

					

						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: 281
Transcript exons: 94168258-94168397,94169582-94169682,94169771-94169810
GTAATAGAATGAACATAGAGGGCGCTTTCTGTTTGCCGTGTTCCACAAGGAAGAGAGCAAGTTA
TAGACCTTTCCGAGTGTACAGTTTATTTGGAGGGAAGAAGGATAAAGATGAGAATGGTGATGAG
GCGCCATCGAAAGCAGGAATTTTTGGAAATATGCAAAATCTCTATGAAACTGTTAAGAAGGCCC
AAATGGTTGTCCAAGTTGAGGCTGTCCGGGTGCAAAAGGAGCTTGCAGCGACTGAGATTGATGG
TTATTGTGAAGGCGAACTAATCAAG
						
					

						Genomic sequence
						
							GTAATAGAATGAACATAGAGGGCGCTTTCTGTTTGCCGTGTTCCACAAGGAAGAGAGCAAGTTA
TAGACCTTTCCGAGTGTACAGTTTATTTGGAGGGAAGAAGGATAAAGATGAGAATGGTGATGAG
GCGCCATCGAAAGTAAGCAATTGACTGATCTGGTGTCATTGTTAAGGTTTTGTTCCTCTTCTTC
GAATTAGCTAGAAGCCTAGAACTAAAAAACTCTAATTTCATTGTTTTGGGATGATTCATTATGT
ATATATTTATGGCAGGAGTCCATTTTTGGCCATTCAACTATAGCTACGTTAGATTTTGGCAATT
GAACTCTGTTACCAGAAATCTTTGGCCATTGAACAATGAAAGCCATTAATGTTTAGTCACTGAG
CTGGTTTCAATGGTGGTTTTGTTGACATGGACGACATGTGGCAATAGGCCCACTCATCAGAGCT
CTCTCTTCTTTCTCCTCCCCACGTCATCTGTCTCACGGTCTCTCCCCATGTCATCTATCTCACC
GTCTCTCTCCTCATACGTGCCTCCCCCTCAAGTGTGCCGCTCTCCCTTCTCCATTAGGGCACCG
CTACGGCGCTACCACTTCCTTGAATGTGCAGCATGCATCCTAGCCTAGGTACGCGTCTGTGCCT
GCACCCTTGGCGCACTTTGGCCAACGTGGAATAGGAGGATCGCGGTGCGGATAGAAGGAAGAGG
AGCACCTGGAGTCCCCTAGATCTGTCTACACTGCCCCTGTGCAGCGTGTCTCACATTGGCTAGA
GCCATATTTGTGGCAGTGGCAGTAGACGCAGAGGAAGAGGTGGCTCGTGGTGGCGGCAGCAAGG
GAGTGACAAGAGAGGATATAGAGAAAGGCGAGAGAGATAGGGATGTGAAGCTGACAAGTGGGTC
CCACTGCAACGTGTAGTCCAAATGTAAACACTTTCAGTAGTTGGGTGGTCAGAGATTTCTGGTT
TTCGAGTTTCATGGTCGAAAGGGCGATAGTTTGATGGCCAAAATGGATTTATCCCTATACTTAT
GGGGCAAACAAAGAAAAGCATGCAAAGAATTCCAGTGAAACAATCTTTTATTAGTAGCTAACAC
CTACTCCATACTGCGAGTTATGCAATCCAAAATGTTAAGCTCTTTCTTTGTTTAGATCCTTGAT
TAGTGATTGTTCATGTGAAAACCAATATGTGCTCGTACATTGCTTGTGAAAACCTTTGAAGATT
GCCGAATTGGTTCCTGTCATTTATTTTTTTGATATATATCTTCTAATTTCGTAATTGACATTTT
GTTTATAACAATATTGAAGCCCTCTGATATTTTAATAACGTTAGGCAGGAATTTTTGGAAATAT
GCAAAATCTCTATGAAACTGTTAAGAAGGCCCAAATGGTTGTCCAAGTTGAGGCTGTCCGGGTG
CAAAAGGAGCTTGCAGCGTATGCATTTATTTCGTTAAGTTATATTTCTCATGTTTGATGCAAAA
TAGCCTGACTCTGTGACTTTTTCTGTGTCTCCTATTTTTAGGACTGAGATTGATGGTTATTGTG
AAGGCGAACTAATCAAG
						
					

			
		

Sequences
Splice junction sequence	TCTCATGTTTGATGCAAAATAGCCTGACTCTGTGACTTTTTCTGTGTCTCCTATTTTTAGGACT GAGATTGATGGTTATTGTGAAGGCGAACTAATCAAGgtaatagaatgaacatagagggcgcttt ctgtttgccgtgttccacaaggaagagagcaagttatagacctttccgagtgtacagtttattt ggagggaa
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: 281 Transcript exons: 94168258-94168397,94169582-94169682,94169771-94169810 GTAATAGAATGAACATAGAGGGCGCTTTCTGTTTGCCGTGTTCCACAAGGAAGAGAGCAAGTTA TAGACCTTTCCGAGTGTACAGTTTATTTGGAGGGAAGAAGGATAAAGATGAGAATGGTGATGAG GCGCCATCGAAAGCAGGAATTTTTGGAAATATGCAAAATCTCTATGAAACTGTTAAGAAGGCCC AAATGGTTGTCCAAGTTGAGGCTGTCCGGGTGCAAAAGGAGCTTGCAGCGACTGAGATTGATGG TTATTGTGAAGGCGAACTAATCAAG
Genomic sequence	GTAATAGAATGAACATAGAGGGCGCTTTCTGTTTGCCGTGTTCCACAAGGAAGAGAGCAAGTTA TAGACCTTTCCGAGTGTACAGTTTATTTGGAGGGAAGAAGGATAAAGATGAGAATGGTGATGAG GCGCCATCGAAAGTAAGCAATTGACTGATCTGGTGTCATTGTTAAGGTTTTGTTCCTCTTCTTC GAATTAGCTAGAAGCCTAGAACTAAAAAACTCTAATTTCATTGTTTTGGGATGATTCATTATGT ATATATTTATGGCAGGAGTCCATTTTTGGCCATTCAACTATAGCTACGTTAGATTTTGGCAATT GAACTCTGTTACCAGAAATCTTTGGCCATTGAACAATGAAAGCCATTAATGTTTAGTCACTGAG CTGGTTTCAATGGTGGTTTTGTTGACATGGACGACATGTGGCAATAGGCCCACTCATCAGAGCT CTCTCTTCTTTCTCCTCCCCACGTCATCTGTCTCACGGTCTCTCCCCATGTCATCTATCTCACC GTCTCTCTCCTCATACGTGCCTCCCCCTCAAGTGTGCCGCTCTCCCTTCTCCATTAGGGCACCG CTACGGCGCTACCACTTCCTTGAATGTGCAGCATGCATCCTAGCCTAGGTACGCGTCTGTGCCT GCACCCTTGGCGCACTTTGGCCAACGTGGAATAGGAGGATCGCGGTGCGGATAGAAGGAAGAGG AGCACCTGGAGTCCCCTAGATCTGTCTACACTGCCCCTGTGCAGCGTGTCTCACATTGGCTAGA GCCATATTTGTGGCAGTGGCAGTAGACGCAGAGGAAGAGGTGGCTCGTGGTGGCGGCAGCAAGG GAGTGACAAGAGAGGATATAGAGAAAGGCGAGAGAGATAGGGATGTGAAGCTGACAAGTGGGTC CCACTGCAACGTGTAGTCCAAATGTAAACACTTTCAGTAGTTGGGTGGTCAGAGATTTCTGGTT TTCGAGTTTCATGGTCGAAAGGGCGATAGTTTGATGGCCAAAATGGATTTATCCCTATACTTAT GGGGCAAACAAAGAAAAGCATGCAAAGAATTCCAGTGAAACAATCTTTTATTAGTAGCTAACAC CTACTCCATACTGCGAGTTATGCAATCCAAAATGTTAAGCTCTTTCTTTGTTTAGATCCTTGAT TAGTGATTGTTCATGTGAAAACCAATATGTGCTCGTACATTGCTTGTGAAAACCTTTGAAGATT GCCGAATTGGTTCCTGTCATTTATTTTTTTGATATATATCTTCTAATTTCGTAATTGACATTTT GTTTATAACAATATTGAAGCCCTCTGATATTTTAATAACGTTAGGCAGGAATTTTTGGAAATAT GCAAAATCTCTATGAAACTGTTAAGAAGGCCCAAATGGTTGTCCAAGTTGAGGCTGTCCGGGTG CAAAAGGAGCTTGCAGCGTATGCATTTATTTCGTTAAGTTATATTTCTCATGTTTGATGCAAAA TAGCCTGACTCTGTGACTTTTTCTGTGTCTCCTATTTTTAGGACTGAGATTGATGGTTATTGTG AAGGCGAACTAATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.102135477

Conservation Information
Conserved circRNAs	NA
PMCS	0.102135477

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							94168267-94168266(+)
94168394-94169804(-)
						
						Potential amino acid sequence
						
							MNIEGAFCLPCSTRKRASYRPFRVYSLFGGKKDKDENGDEAPSKAGIFGNMQNLYETVKKAQMV
VQVEAVRVQKELAATEIDGYCEGELIKVIE*(+)
MAPHHHSHLYPSSLQINCTLGKVYNLLSSLWNTANRKRPLCSFYYLD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	94168267-94168266(+) 94168394-94169804(-)
Potential amino acid sequence	MNIEGAFCLPCSTRKRASYRPFRVYSLFGGKKDKDENGDEAPSKAGIFGNMQNLYETVKKAQMV VQVEAVRVQKELAATEIDGYCEGELIKVIE(+) MAPHHHSHLYPSSLQINCTLGKVYNLLSSLWNTANRKRPLCSFYYLD(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d015505_circ_g.3

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