Plant Circular RNA Database

Detail information of Zm00001d044099_circ_g.28

			
						 General Information
					
						CircRNA Name
						Zm00001d044099_circ_g.28
					
						ID in PlantcircBase
						zma_circ_007868
					
						Alias
						Zm03circ00119, GRMZM2G121878_C9
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 219080583-219080855  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d044099						
					
						Parent gene annotation
						
							 carbonic anhydrase1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d044095_circ_ag.1 Zm00001d044095_circ_ag.2 Zm00001d044095_circ_ag.3 Zm00001d044095_circ_ag.4 Zm00001d044096_circ_g.1 Zm00001d044096_circ_ag.1 Zm00001d044096_circ_ag.2 Zm00001d044096_circ_ag.3 Zm00001d044096_circ_ag.4 Zm00001d044099_circ_g.1 Zm00001d044099_circ_g.2 Zm00001d044099_circ_g.3 Zm00001d044099_circ_g.4 Zm00001d044099_circ_g.5 Zm00001d044099_circ_g.6 Zm00001d044099_circ_g.7 Zm00001d044099_circ_g.8 Zm00001d044099_circ_g.9 Zm00001d044099_circ_g.10 Zm00001d044099_circ_g.11 Zm00001d044099_circ_g.12 Zm00001d044099_circ_g.13 Zm00001d044099_circ_g.14 Zm00001d044099_circ_g.15 Zm00001d044099_circ_g.16 Zm00001d044099_circ_g.17 Zm00001d044099_circ_g.18 Zm00001d044099_circ_g.19 Zm00001d044099_circ_g.20 Zm00001d044099_circ_g.21 Zm00001d044099_circ_g.22 Zm00001d044099_circ_g.23 Zm00001d044099_circ_g.24 Zm00001d044099_circ_g.25 Zm00001d044099_circ_g.26 Zm00001d044099_circ_g.27 Zm00001d044099_circ_g.29 						
					
						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
						Zm00001d044099_T002:1
Zm00001d044099_T004:1

General Information
CircRNA Name	Zm00001d044099_circ_g.28
ID in PlantcircBase	zma_circ_007868
Alias	Zm03circ00119, GRMZM2G121878_C9
Organism	Zea mays
Position	chr3: 219080583-219080855 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d044099
Parent gene annotation	carbonic anhydrase1
Parent gene strand	-
Alternative splicing	Zm00001d044095_circ_ag.1 Zm00001d044095_circ_ag.2 Zm00001d044095_circ_ag.3 Zm00001d044095_circ_ag.4 Zm00001d044096_circ_g.1 Zm00001d044096_circ_ag.1 Zm00001d044096_circ_ag.2 Zm00001d044096_circ_ag.3 Zm00001d044096_circ_ag.4 Zm00001d044099_circ_g.1 Zm00001d044099_circ_g.2 Zm00001d044099_circ_g.3 Zm00001d044099_circ_g.4 Zm00001d044099_circ_g.5 Zm00001d044099_circ_g.6 Zm00001d044099_circ_g.7 Zm00001d044099_circ_g.8 Zm00001d044099_circ_g.9 Zm00001d044099_circ_g.10 Zm00001d044099_circ_g.11 Zm00001d044099_circ_g.12 Zm00001d044099_circ_g.13 Zm00001d044099_circ_g.14 Zm00001d044099_circ_g.15 Zm00001d044099_circ_g.16 Zm00001d044099_circ_g.17 Zm00001d044099_circ_g.18 Zm00001d044099_circ_g.19 Zm00001d044099_circ_g.20 Zm00001d044099_circ_g.21 Zm00001d044099_circ_g.22 Zm00001d044099_circ_g.23 Zm00001d044099_circ_g.24 Zm00001d044099_circ_g.25 Zm00001d044099_circ_g.26 Zm00001d044099_circ_g.27 Zm00001d044099_circ_g.29
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	Zm00001d044099_T002:1 Zm00001d044099_T004:1

			
						 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  
						
							CTCTCTCCTCCCCTCTTATCGCCGGCGGCTGGTGGATGCCCTCCCTTTCTTTCTCTCGATCTCT
CTCGTTTGACTCCTCAGCTGCCCGCCGTCCCGTTTActtggaggaagccttggagggaggaggt
ggaggttgggagggcttctggttctgaaggagtgacgaggtgggggtatctgtggacggcttct
ccttcgct

						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: 273
Transcript exons: 219080583-219080855
CTTGGAGGAAGCCTTGGAGGGAGGAGGTGGAGGTTGGGAGGGCTTCTGGTTCTGAAGGAGTGAC
GAGGTGGGGGTATCTGTGGACGGCTTCTCCTTCGCTGGCCCCTCCTTTTTTTTCGGAAGGCAGA
GGCAGCTGCTCATTTTCTTCTTCTTCTCCTCCTCTTCTCTGGCCTCTCTCTCCTCCCCTCTTAT
CGCCGGCGGCTGGTGGATGCCCTCCCTTTCTTTCTCTCGATCTCTCTCGTTTGACTCCTCAGCT
GCCCGCCGTCCCGTTTA
						
						Genomic sequence
						
							CTTGGAGGAAGCCTTGGAGGGAGGAGGTGGAGGTTGGGAGGGCTTCTGGTTCTGAAGGAGTGAC
GAGGTGGGGGTATCTGTGGACGGCTTCTCCTTCGCTGGCCCCTCCTTTTTTTTCGGAAGGCAGA
GGCAGCTGCTCATTTTCTTCTTCTTCTCCTCCTCTTCTCTGGCCTCTCTCTCCTCCCCTCTTAT
CGCCGGCGGCTGGTGGATGCCCTCCCTTTCTTTCTCTCGATCTCTCTCGTTTGACTCCTCAGCT
GCCCGCCGTCCCGTTTA

Sequences
Splice junction sequence	CTCTCTCCTCCCCTCTTATCGCCGGCGGCTGGTGGATGCCCTCCCTTTCTTTCTCTCGATCTCT CTCGTTTGACTCCTCAGCTGCCCGCCGTCCCGTTTActtggaggaagccttggagggaggaggt ggaggttgggagggcttctggttctgaaggagtgacgaggtgggggtatctgtggacggcttct ccttcgct
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: 273 Transcript exons: 219080583-219080855 CTTGGAGGAAGCCTTGGAGGGAGGAGGTGGAGGTTGGGAGGGCTTCTGGTTCTGAAGGAGTGAC GAGGTGGGGGTATCTGTGGACGGCTTCTCCTTCGCTGGCCCCTCCTTTTTTTTCGGAAGGCAGA GGCAGCTGCTCATTTTCTTCTTCTTCTCCTCCTCTTCTCTGGCCTCTCTCTCCTCCCCTCTTAT CGCCGGCGGCTGGTGGATGCCCTCCCTTTCTTTCTCTCGATCTCTCTCGTTTGACTCCTCAGCT GCCCGCCGTCCCGTTTA
Genomic sequence	CTTGGAGGAAGCCTTGGAGGGAGGAGGTGGAGGTTGGGAGGGCTTCTGGTTCTGAAGGAGTGAC GAGGTGGGGGTATCTGTGGACGGCTTCTCCTTCGCTGGCCCCTCCTTTTTTTTCGGAAGGCAGA GGCAGCTGCTCATTTTCTTCTTCTTCTCCTCCTCTTCTCTGGCCTCTCTCTCCTCCCCTCTTAT CGCCGGCGGCTGGTGGATGCCCTCCCTTTCTTTCTCTCGATCTCTCTCGTTTGACTCCTCAGCT GCCCGCCGTCCCGTTTA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.224865781

Conservation Information
Conserved circRNAs	NA
PMCS	0.224865781

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							219080792-219080634(+)
						
						Potential amino acid sequence
						
							MPSLSFSRSLSFDSSAARRPVYLEEALEGGGGGWEGFWF*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	219080792-219080634(+)
Potential amino acid sequence	MPSLSFSRSLSFDSSAARRPVYLEEALEGGGGGWEGFWF*(+)
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 Zm00001d044099_circ_g.28

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