Plant Circular RNA Database

Detail information of Zm00001d040960_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d040960_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007590
					
						Alias
						Zm03circ00028, GRMZM2G081380_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 83478575-83479631  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d040960						
					
						Parent gene annotation
						
							Fimbrin-2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d040960_circ_g.3 						
					
						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
						Zm00001d040960_T007:3
Zm00001d040960_T004:3
Zm00001d040960_T003:3
Zm00001d040960_T008:3
Zm00001d040960_T001:3
Zm00001d040960_T006:3
Zm00001d040960_T005:3
Zm00001d040960_T002:3

General Information
CircRNA Name	Zm00001d040960_circ_g.2
ID in PlantcircBase	zma_circ_007590
Alias	Zm03circ00028, GRMZM2G081380_C1
Organism	Zea mays
Position	chr3: 83478575-83479631 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d040960
Parent gene annotation	Fimbrin-2
Parent gene strand	-
Alternative splicing	Zm00001d040960_circ_g.3
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	Zm00001d040960_T007:3 Zm00001d040960_T004:3 Zm00001d040960_T003:3 Zm00001d040960_T008:3 Zm00001d040960_T001:3 Zm00001d040960_T006:3 Zm00001d040960_T005:3 Zm00001d040960_T002:3

			
						 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  
						
							AATCCACAGCCGGAATGACCTTTCTTCCCTGGAAACTTGAGCATCATCAGAGAGTCCATCCACA
AAGGAAACTTGTTTCATTTGTTTGGACAACCCATTTcttgaaactttgcatataagagtggtgc
tttccagaatcttttactttcttattggcccatgccaatatgtcattatctgtgatctcttttc
catttgag

									
								

					

						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: 547
Transcript exons: 83478575-83478765,83479200-83479399,83479476-83479631
CTTGAAACTTTGCATATAAGAGTGGTGCTTTCCAGAATCTTTTACTTTCTTATTGGCCCATGCC
AATATGTCATTATCTGTGATCTCTTTTCCATTTGAGTGAAATCTAAGATTCTTCAGCAGTTGTA
GAATGTTGTACCGCATCAATTGCCATAGAAAAGCTAGGATAAATGCAATTTCATTATATGGTCC
TAATATCAGTTTTTTGTTCCCTTGAACAATATCATTTCCAGCAATATTCACCAAAGAAAATTTT
AGTTCTTTTCCAATCTTCAAAACTTGATTGCAGTTTTCAACTTTCCTGAATGGTAATTTGATTG
GTGGGCGATTTGCCATCTTCCAATTAACTGAGCCTGGAGCAATCTTGTCAATCACCTCAAGGAG
AACCCATCCATTTCTAAGGTCTTCAAACACATTGTTGATGTAAGTTGAAATTCCAAGGCTGTTA
ATCCACAGCCGGAATGACCTTTCTTCCCTGGAAACTTGAGCATCATCAGAGAGTCCATCCACAA
AGGAAACTTGTTTCATTTGTTTGGACAACCCATTT
						
					

						Genomic sequence
						
							CTTGAAACTTTGCATATAAGAGTGGTGCTTTCCAGAATCTTTTACTTTCTTATTGGCCCATGCC
AATATGTCATTATCTGTGATCTCTTTTCCATTTGAGTGAAATCTAAGATTCTTCAGCAGTTGTA
GAATGTTGTACCGCATCAATTGCCATAGAAAAGCTAGGATAAATGCAATTTCATTATATGGTCC
TACCAGAAGTTGCAAAAGAGGAGCAAACCAACTAACCATCCATGGCATATAATAAAAAGAACGT
TTGAACAAATGATTGATCTTATACGATGTTTTCGATGATAGGAATAGTGTAAGGACAAATATGA
ATTTCATAGTTAACCAGTTCCTTAGTTTGACATGCTCTAGAAAATGACACCTCAGCATAGGAAA
TCTTTTACGCGACATACTTGCACAAAAGCTCCAAGAATATCTATGGAAAAGCTGCATGTAAATG
AGTGCATCTGTAAACTGACATTAAATTTAAACTTGTATAAGCATGGGTGTAATTTGTTATCTTC
AAGTTTTTGAACAAATAACCTCAAAATTAATGAGAAAACTAGGAAGCACATATAATTGTTTACA
CGAAACTATGTTAGATATTCTCTATGTAACTGGTTAAAGTATCACTTACCTAATATCAGTTTTT
TGTTCCCTTGAACAATATCATTTCCAGCAATATTCACCAAAGAAAATTTTAGTTCTTTTCCAAT
CTTCAAAACTTGATTGCAGTTTTCAACTTTCCTGAATGGTAATTTGATTGGTGGGCGATTTGCC
ATCTTCCAATTAACTGAGCCTGGAGCAATCTTGTCAATCACCTCAAGGAGAACCCATCTACAAC
TCAAGGATGAAGTATTAAGACAAAGAATGTGCTTGTTCACATATTAAGATGGATACAAGTATGT
CCTACCCATTTCTAAGGTCTTCAAACACATTGTTGATGTAAGTTGAAATTCCAAGGCTGTTAAT
CCACAGCCGGAATGACCTTTCTTCCCTGGAAACTTGAGCATCATCAGAGAGTCCATCCACAAAG
GAAACTTGTTTCATTTGTTTGGACAACCCATTT
						
					

			
		

Sequences
Splice junction sequence	AATCCACAGCCGGAATGACCTTTCTTCCCTGGAAACTTGAGCATCATCAGAGAGTCCATCCACA AAGGAAACTTGTTTCATTTGTTTGGACAACCCATTTcttgaaactttgcatataagagtggtgc tttccagaatcttttactttcttattggcccatgccaatatgtcattatctgtgatctcttttc catttgag
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: 547 Transcript exons: 83478575-83478765,83479200-83479399,83479476-83479631 CTTGAAACTTTGCATATAAGAGTGGTGCTTTCCAGAATCTTTTACTTTCTTATTGGCCCATGCC AATATGTCATTATCTGTGATCTCTTTTCCATTTGAGTGAAATCTAAGATTCTTCAGCAGTTGTA GAATGTTGTACCGCATCAATTGCCATAGAAAAGCTAGGATAAATGCAATTTCATTATATGGTCC TAATATCAGTTTTTTGTTCCCTTGAACAATATCATTTCCAGCAATATTCACCAAAGAAAATTTT AGTTCTTTTCCAATCTTCAAAACTTGATTGCAGTTTTCAACTTTCCTGAATGGTAATTTGATTG GTGGGCGATTTGCCATCTTCCAATTAACTGAGCCTGGAGCAATCTTGTCAATCACCTCAAGGAG AACCCATCCATTTCTAAGGTCTTCAAACACATTGTTGATGTAAGTTGAAATTCCAAGGCTGTTA ATCCACAGCCGGAATGACCTTTCTTCCCTGGAAACTTGAGCATCATCAGAGAGTCCATCCACAA AGGAAACTTGTTTCATTTGTTTGGACAACCCATTT
Genomic sequence	CTTGAAACTTTGCATATAAGAGTGGTGCTTTCCAGAATCTTTTACTTTCTTATTGGCCCATGCC AATATGTCATTATCTGTGATCTCTTTTCCATTTGAGTGAAATCTAAGATTCTTCAGCAGTTGTA GAATGTTGTACCGCATCAATTGCCATAGAAAAGCTAGGATAAATGCAATTTCATTATATGGTCC TACCAGAAGTTGCAAAAGAGGAGCAAACCAACTAACCATCCATGGCATATAATAAAAAGAACGT TTGAACAAATGATTGATCTTATACGATGTTTTCGATGATAGGAATAGTGTAAGGACAAATATGA ATTTCATAGTTAACCAGTTCCTTAGTTTGACATGCTCTAGAAAATGACACCTCAGCATAGGAAA TCTTTTACGCGACATACTTGCACAAAAGCTCCAAGAATATCTATGGAAAAGCTGCATGTAAATG AGTGCATCTGTAAACTGACATTAAATTTAAACTTGTATAAGCATGGGTGTAATTTGTTATCTTC AAGTTTTTGAACAAATAACCTCAAAATTAATGAGAAAACTAGGAAGCACATATAATTGTTTACA CGAAACTATGTTAGATATTCTCTATGTAACTGGTTAAAGTATCACTTACCTAATATCAGTTTTT TGTTCCCTTGAACAATATCATTTCCAGCAATATTCACCAAAGAAAATTTTAGTTCTTTTCCAAT CTTCAAAACTTGATTGCAGTTTTCAACTTTCCTGAATGGTAATTTGATTGGTGGGCGATTTGCC ATCTTCCAATTAACTGAGCCTGGAGCAATCTTGTCAATCACCTCAAGGAGAACCCATCTACAAC TCAAGGATGAAGTATTAAGACAAAGAATGTGCTTGTTCACATATTAAGATGGATACAAGTATGT CCTACCCATTTCTAAGGTCTTCAAACACATTGTTGATGTAAGTTGAAATTCCAAGGCTGTTAAT CCACAGCCGGAATGACCTTTCTTCCCTGGAAACTTGAGCATCATCAGAGAGTCCATCCACAAAG GAAACTTGTTTCATTTGTTTGGACAACCCATTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.123995612

Conservation Information
Conserved circRNAs	NA
PMCS	0.123995612

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							83479547-83478590(+)
83479614-83479580(-)
						
						Potential amino acid sequence
						
							MTFLPWKLEHHQRVHPQRKLVSFVWTTHFLKLCI*(+)
MKQVSFVDGLSDDAQVSREERSFRLWINSLGISTYINNVFEDLRNGWVLLEVIDKIAPGSVNWK
MANRPPIKLPFRKVENCNQVLKIGKELKFSLVNIAGNDIVQGNKKLILDNDILAWANKKVKDSG
KHHSYMQSFKKWVVQTNETSFLCGWTL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	83479547-83478590(+) 83479614-83479580(-)
Potential amino acid sequence	MTFLPWKLEHHQRVHPQRKLVSFVWTTHFLKLCI(+) MKQVSFVDGLSDDAQVSREERSFRLWINSLGISTYINNVFEDLRNGWVLLEVIDKIAPGSVNWK MANRPPIKLPFRKVENCNQVLKIGKELKFSLVNIAGNDIVQGNKKLILDNDILAWANKKVKDSG KHHSYMQSFKKWVVQTNETSFLCGWTL(-)
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 Zm00001d040960_circ_g.2

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