Plant Circular RNA Database

Detail information of Zm00001d025153_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d025153_circ_g.1
					
						ID in PlantcircBase
						zma_circ_010286
					
						Alias
						Zm10circ00041, zma_circ_0003216, GRMZM2G037335_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 106782574-106783780  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d025153						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025153_circ_g.2 Zm00001d025153_circ_g.3 Zm00001d025153_circ_g.4 Zm00001d025153_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d025153_T007:4
Zm00001d025153_T009:4
Zm00001d025153_T005:4
Zm00001d025153_T001:4
Zm00001d025153_T010:4
Zm00001d025153_T008:4
Zm00001d025153_T003:4
Zm00001d025153_T013:4
Zm00001d025153_T006:4
Zm00001d025153_T011:4
Zm00001d025153_T012:4
Zm00001d025153_T002:4
Zm00001d025153_T004:4

General Information
CircRNA Name	Zm00001d025153_circ_g.1
ID in PlantcircBase	zma_circ_010286
Alias	Zm10circ00041, zma_circ_0003216, GRMZM2G037335_C1
Organism	Zea mays
Position	chr10: 106782574-106783780 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d025153
Parent gene annotation	Phospholipid-transporting ATPase 2
Parent gene strand	-
Alternative splicing	Zm00001d025153_circ_g.2 Zm00001d025153_circ_g.3 Zm00001d025153_circ_g.4 Zm00001d025153_circ_g.5
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d025153_T007:4 Zm00001d025153_T009:4 Zm00001d025153_T005:4 Zm00001d025153_T001:4 Zm00001d025153_T010:4 Zm00001d025153_T008:4 Zm00001d025153_T003:4 Zm00001d025153_T013:4 Zm00001d025153_T006:4 Zm00001d025153_T011:4 Zm00001d025153_T012:4 Zm00001d025153_T002:4 Zm00001d025153_T004:4

			
						 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  
						
							TATTCATTTTCTTTTAAATCACGCCACCCCAAACATAAGGTTCGCAATCCCAACTGAGAATACA
TTTCTACTGCTTCAAGATATCTCTGTATTTGTTGTCctttgtttcagatgtatttttcataata
aataatgccctctctaggcttcttagcacgtcctcttcagttttcccactgatagataacaatt
gactattg

									
								

					

						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: 461
Transcript exons: 106782574-106782677,106783213-106783333,106783440-106783
520,106783626-106783780
CTTTGTTTCAGATGTATTTTTCATAATAAATAATGCCCTCTCTAGGCTTCTTAGCACGTCCTCT
TCAGTTTTCCCACTGATAGATAACAATTGACTATTGGGCCCAGAAGTTATGAGGTTACAGAGAA
GTCCAATCTGAATTGCTGTATTTTGCTTATCACCGGTTAGCATCCACACATTAATTCCAGCATT
CCTCAACAATTTAATGGTTTCAGGAACACCATCCTGAAGACGATCCTCTATAGCAGTAACACCA
AGAATTTGAAGGTCTTGCTCTAAGCTATTACAAACTTCAGCAATTTTAAACTCTCTATTGTCCA
ATGAGCAGCTAGCCTTTTGAAAGTTTTTGGACCATTCCTTATATTCATTTTCTTTTAAATCACG
CCACCCCAAACATAAGGTTCGCAATCCCAACTGAGAATACATTTCTACTGCTTCAAGATATCTC
TGTATTTGTTGTC
						
					

						Genomic sequence
						
							CTTTGTTTCAGATGTATTTTTCATAATAAATAATGCCCTCTCTAGGCTTCTTAGCACGTCCTCT
TCAGTTTTCCCACTGATAGATAACAATTGACTATTGGGCCCTGAAGGAGTGAGATATTAAGTAA
ACCATGTAGCAGACCAAAACAGCTCATGCGAAGAACACAACTCCATGACTAGAAAGATATCAGA
TGCATTAGTGTTTATATATCACAAAATAGGTCTGTGTGTTGTCCCACACTAAAAAAACAAGAAA
ATAAATATGCACAGCTGTTACATGAGTTTCTTCAGAACCACCATGTGATGACATCCAGGAACAA
CCAAACAATTACTCACCCATCTATTTCATGCATAATTTCACTAAGCTAGAATGCAGAGTACAAA
TAAGATGGTAATTTTTTTAATTTATTTTACTCATACATCACCAAGTTTAACAGAAGACTCTGCA
AAGGTATCATCTATTTGTAACTTAGAGCTCGTGATTTGCTACAACAGAATAATGTCGAAGGGAT
ACTATGATAGAGCAAGAAATTGCAATAGACCAGTGGAGAAAACATTTGCAAAGGGCAACTCGTA
TTGTTAGATGCAAATGGCCACTTGCTAAATTTAAAGGATAAATGTATCGCAATAGTACAATACC
AGAAGTTATGAGGTTACAGAGAAGTCCAATCTGAATTGCTGTATTTTGCTTATCACCGGTTAGC
ATCCACACATTAATTCCAGCATTCCTCAACAATTTAATGGTTTCAGGAACACCATCCTGTCAGC
CAAAAGAATCTATAAGGCAAGGTAGCAAGTGGAAAATTGCTGTAGGTGTTTCCACTGGTTGTTA
GTCTTAGAGATAGCAATTAATGATCAAGATATACCTGAAGACGATCCTCTATAGCAGTAACACC
AAGAATTTGAAGGTCTTGCTCTAAGCTATTACAAACTTCAGCAATTTTAAACTGTATATAAGTG
CAGTACCATTAGCCAACAGTAGAATAAGAGTTGGTGAGACAAATGACAGAACTACTAAGGTTAA
GGGAAAATGGTTAAACCAGAATAAGTACCTCTCTATTGTCCAATGAGCAGCTAGCCTTTTGAAA
GTTTTTGGACCATTCCTTATATTCATTTTCTTTTAAATCACGCCACCCCAAACATAAGGTTCGC
AATCCCAACTGAGAATACATTTCTACTGCTTCAAGATATCTCTGTATTTGTTGTC
						
					

			
		

Sequences
Splice junction sequence	TATTCATTTTCTTTTAAATCACGCCACCCCAAACATAAGGTTCGCAATCCCAACTGAGAATACA TTTCTACTGCTTCAAGATATCTCTGTATTTGTTGTCctttgtttcagatgtatttttcataata aataatgccctctctaggcttcttagcacgtcctcttcagttttcccactgatagataacaatt gactattg
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: 461 Transcript exons: 106782574-106782677,106783213-106783333,106783440-106783 520,106783626-106783780 CTTTGTTTCAGATGTATTTTTCATAATAAATAATGCCCTCTCTAGGCTTCTTAGCACGTCCTCT TCAGTTTTCCCACTGATAGATAACAATTGACTATTGGGCCCAGAAGTTATGAGGTTACAGAGAA GTCCAATCTGAATTGCTGTATTTTGCTTATCACCGGTTAGCATCCACACATTAATTCCAGCATT CCTCAACAATTTAATGGTTTCAGGAACACCATCCTGAAGACGATCCTCTATAGCAGTAACACCA AGAATTTGAAGGTCTTGCTCTAAGCTATTACAAACTTCAGCAATTTTAAACTCTCTATTGTCCA ATGAGCAGCTAGCCTTTTGAAAGTTTTTGGACCATTCCTTATATTCATTTTCTTTTAAATCACG CCACCCCAAACATAAGGTTCGCAATCCCAACTGAGAATACATTTCTACTGCTTCAAGATATCTC TGTATTTGTTGTC
Genomic sequence	CTTTGTTTCAGATGTATTTTTCATAATAAATAATGCCCTCTCTAGGCTTCTTAGCACGTCCTCT TCAGTTTTCCCACTGATAGATAACAATTGACTATTGGGCCCTGAAGGAGTGAGATATTAAGTAA ACCATGTAGCAGACCAAAACAGCTCATGCGAAGAACACAACTCCATGACTAGAAAGATATCAGA TGCATTAGTGTTTATATATCACAAAATAGGTCTGTGTGTTGTCCCACACTAAAAAAACAAGAAA ATAAATATGCACAGCTGTTACATGAGTTTCTTCAGAACCACCATGTGATGACATCCAGGAACAA CCAAACAATTACTCACCCATCTATTTCATGCATAATTTCACTAAGCTAGAATGCAGAGTACAAA TAAGATGGTAATTTTTTTAATTTATTTTACTCATACATCACCAAGTTTAACAGAAGACTCTGCA AAGGTATCATCTATTTGTAACTTAGAGCTCGTGATTTGCTACAACAGAATAATGTCGAAGGGAT ACTATGATAGAGCAAGAAATTGCAATAGACCAGTGGAGAAAACATTTGCAAAGGGCAACTCGTA TTGTTAGATGCAAATGGCCACTTGCTAAATTTAAAGGATAAATGTATCGCAATAGTACAATACC AGAAGTTATGAGGTTACAGAGAAGTCCAATCTGAATTGCTGTATTTTGCTTATCACCGGTTAGC ATCCACACATTAATTCCAGCATTCCTCAACAATTTAATGGTTTCAGGAACACCATCCTGTCAGC CAAAAGAATCTATAAGGCAAGGTAGCAAGTGGAAAATTGCTGTAGGTGTTTCCACTGGTTGTTA GTCTTAGAGATAGCAATTAATGATCAAGATATACCTGAAGACGATCCTCTATAGCAGTAACACC AAGAATTTGAAGGTCTTGCTCTAAGCTATTACAAACTTCAGCAATTTTAAACTGTATATAAGTG CAGTACCATTAGCCAACAGTAGAATAAGAGTTGGTGAGACAAATGACAGAACTACTAAGGTTAA GGGAAAATGGTTAAACCAGAATAAGTACCTCTCTATTGTCCAATGAGCAGCTAGCCTTTTGAAA GTTTTTGGACCATTCCTTATATTCATTTTCTTTTAAATCACGCCACCCCAAACATAAGGTTCGC AATCCCAACTGAGAATACATTTCTACTGCTTCAAGATATCTCTGTATTTGTTGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.162262859

Conservation Information
Conserved circRNAs	NA
PMCS	0.162262859

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							106783747-106783750(-)
						
						Potential amino acid sequence
						
							MYSQLGLRTLCLGWRDLKENEYKEWSKNFQKASCSLDNREFKIAEVCNSLEQDLQILGVTAIED
RLQDGVPETIKLLRNAGINVWMLTGDKQNTAIQIGLLCNLITSGPNSQLLSISGKTEEDVLRSL
ERALFIMKNTSETKDNKYRDILKQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	106783747-106783750(-)
Potential amino acid sequence	MYSQLGLRTLCLGWRDLKENEYKEWSKNFQKASCSLDNREFKIAEVCNSLEQDLQILGVTAIED RLQDGVPETIKLLRNAGINVWMLTGDKQNTAIQIGLLCNLITSGPNSQLLSISGKTEEDVLRSL ERALFIMKNTSETKDNKYRDILKQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d025153_circ_g.1

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