Plant Circular RNA Database

Detail information of Zm00001d034516_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d034516_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006961
					
						Alias
						Zm01circ00186, GRMZM2G029396_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 295475871-295476769  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d034516						
					
						Parent gene annotation
						
							Squalene synthase 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d034516_circ_g.1 Zm00001d034516_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  
						
							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
						Zm00001d034516_T003:2
Zm00001d034516_T001:2
Zm00001d034516_T002:2
Zm00001d034516_T006:2
Zm00001d034516_T007:2
Zm00001d034516_T004:2
Zm00001d034516_T005:2

General Information
CircRNA Name	Zm00001d034516_circ_g.2
ID in PlantcircBase	zma_circ_006961
Alias	Zm01circ00186, GRMZM2G029396_C1
Organism	Zea mays
Position	chr1: 295475871-295476769 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d034516
Parent gene annotation	Squalene synthase 1
Parent gene strand	+
Alternative splicing	Zm00001d034516_circ_g.1 Zm00001d034516_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	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	Zm00001d034516_T003:2 Zm00001d034516_T001:2 Zm00001d034516_T002:2 Zm00001d034516_T006:2 Zm00001d034516_T007:2 Zm00001d034516_T004:2 Zm00001d034516_T005:2

			
						 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  
						
							TAAATTGCTATTTCCTCTTTCTAGATAATGGCAATTGGAACATGTGCTCTTTGCTACAATAACG
TGCATGTCTTTAGAGGAGTTGTAAAGATGAGACGTGgatttcaaatatgaggaaaataccgaaa
aggcagtacaatgcttgaacgatatagtgacgaatgcactgattcatgctgaagagtgccttca
gtacatgt

						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: 223
Transcript exons: 295475871-295476017,295476694-295476769
GATTTCAAATATGAGGAAAATACCGAAAAGGCAGTACAATGCTTGAACGATATAGTGACGAATG
CACTGATTCATGCTGAAGAGTGCCTTCAGTACATGTCAGCCTTGAAGAACCATGCCATCTTCCA
TTTTTGCGCAATTCCCCAGATAATGGCAATTGGAACATGTGCTCTTTGCTACAATAACGTGCAT
GTCTTTAGAGGAGTTGTAAAGATGAGACGTG
						
						Genomic sequence
						
							GATTTCAAATATGAGGAAAATACCGAAAAGGCAGTACAATGCTTGAACGATATAGTGACGAATG
CACTGATTCATGCTGAAGAGTGCCTTCAGTACATGTCAGCCTTGAAGAACCATGCCATCTTCCA
TTTTTGCGCAATTCCCCAGGTAAATAACCTGTTTAACTTTTTTGTCTATTGAGGACCTAGTTTT
TCAATGCTGTTCTGATGCTGCATTCGTAATCTTTCCAGATTGAACACTGTTATTTAGAATTTTA
ACTCAAATCTGCACATAAACCCCAAATAGTACAATTAGATGTGTTTGTAGCTCTTCAAAACGAC
GTTAAGTATGTTAGTAACTATCTGAGTAAAAAAAGGTTTAACTTAAGGCTTCTTAACCTATCTG
CTTTTGTCAGACAAAGTATACCAAGATTAGTCTCGTCCTTGAAGCATGTACTTGTGGTAATTGG
ACTAGGTTCTCAAAACTGTTATACTATCTTTTCCCTGGAAATTCTCAAAACCTTTGTATTTGTT
GCTGCTTGGAATAATAGTTCATTGGTTATGGGAGGTTTTTTTAATCATGTTTCATAGCTGAGGA
AACTGTTAGATTTTTAGGCTACAATATTTTGCCAAGTTGCTCTATGAGCTTTGTTCTAAAACAT
CTCATTTGTGGGAAAATGTAGATAACATTCCTGGTTTCTTGACTGATCAAGAATCCAAGACTGA
TTCTCCATCTATTTTGGTCAATTATTTTATTTTGTTTTTATGTTATATACTTCGTTTATCAATA
TGCTCTTGAAACAATTTCTTCCATAGGATACTAAATTGCTATTTCCTCTTTCTAGATAATGGCA
ATTGGAACATGTGCTCTTTGCTACAATAACGTGCATGTCTTTAGAGGAGTTGTAAAGATGAGAC
GTG

Sequences
Splice junction sequence	TAAATTGCTATTTCCTCTTTCTAGATAATGGCAATTGGAACATGTGCTCTTTGCTACAATAACG TGCATGTCTTTAGAGGAGTTGTAAAGATGAGACGTGgatttcaaatatgaggaaaataccgaaa aggcagtacaatgcttgaacgatatagtgacgaatgcactgattcatgctgaagagtgccttca gtacatgt
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: 223 Transcript exons: 295475871-295476017,295476694-295476769 GATTTCAAATATGAGGAAAATACCGAAAAGGCAGTACAATGCTTGAACGATATAGTGACGAATG CACTGATTCATGCTGAAGAGTGCCTTCAGTACATGTCAGCCTTGAAGAACCATGCCATCTTCCA TTTTTGCGCAATTCCCCAGATAATGGCAATTGGAACATGTGCTCTTTGCTACAATAACGTGCAT GTCTTTAGAGGAGTTGTAAAGATGAGACGTG
Genomic sequence	GATTTCAAATATGAGGAAAATACCGAAAAGGCAGTACAATGCTTGAACGATATAGTGACGAATG CACTGATTCATGCTGAAGAGTGCCTTCAGTACATGTCAGCCTTGAAGAACCATGCCATCTTCCA TTTTTGCGCAATTCCCCAGGTAAATAACCTGTTTAACTTTTTTGTCTATTGAGGACCTAGTTTT TCAATGCTGTTCTGATGCTGCATTCGTAATCTTTCCAGATTGAACACTGTTATTTAGAATTTTA ACTCAAATCTGCACATAAACCCCAAATAGTACAATTAGATGTGTTTGTAGCTCTTCAAAACGAC GTTAAGTATGTTAGTAACTATCTGAGTAAAAAAAGGTTTAACTTAAGGCTTCTTAACCTATCTG CTTTTGTCAGACAAAGTATACCAAGATTAGTCTCGTCCTTGAAGCATGTACTTGTGGTAATTGG ACTAGGTTCTCAAAACTGTTATACTATCTTTTCCCTGGAAATTCTCAAAACCTTTGTATTTGTT GCTGCTTGGAATAATAGTTCATTGGTTATGGGAGGTTTTTTTAATCATGTTTCATAGCTGAGGA AACTGTTAGATTTTTAGGCTACAATATTTTGCCAAGTTGCTCTATGAGCTTTGTTCTAAAACAT CTCATTTGTGGGAAAATGTAGATAACATTCCTGGTTTCTTGACTGATCAAGAATCCAAGACTGA TTCTCCATCTATTTTGGTCAATTATTTTATTTTGTTTTTATGTTATATACTTCGTTTATCAATA TGCTCTTGAAACAATTTCTTCCATAGGATACTAAATTGCTATTTCCTCTTTCTAGATAATGGCA ATTGGAACATGTGCTCTTTGCTACAATAACGTGCATGTCTTTAGAGGAGTTGTAAAGATGAGAC GTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.064443454

Conservation Information
Conserved circRNAs	NA
PMCS	0.064443454

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							295475968-295475881(+)
295475947-295476745(-)
						
						Potential amino acid sequence
						
							MSALKNHAIFHFCAIPQIMAIGTCALCYNNVHVFRGVVKMRRGFQI*(+)
MNQCIRHYIVQALYCLFGIFLIFEIHVSSLQLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	295475968-295475881(+) 295475947-295476745(-)
Potential amino acid sequence	MSALKNHAIFHFCAIPQIMAIGTCALCYNNVHVFRGVVKMRRGFQI(+) MNQCIRHYIVQALYCLFGIFLIFEIHVSSLQLL(-)
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 Zm00001d034516_circ_g.2

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