Plant Circular RNA Database

Detail information of Zm00001d008941_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d008941_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009574
					
						Alias
						Zm08circ00014, zma_circ_0002670, GRMZM2G372928_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 26173426-26174545  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d008941						
					
						Parent gene annotation
						
							Histone-lysine N-methyltransferase ATX3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d008941_circ_g.1 						
					
						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
						Zm00001d008941_T004:5
Zm00001d008941_T015:5
Zm00001d008941_T007:5
Zm00001d008941_T013:5
Zm00001d008941_T008:5
Zm00001d008941_T012:5
Zm00001d008941_T010:5
Zm00001d008941_T005:5
Zm00001d008941_T001:5
Zm00001d008941_T002:5

General Information
CircRNA Name	Zm00001d008941_circ_g.2
ID in PlantcircBase	zma_circ_009574
Alias	Zm08circ00014, zma_circ_0002670, GRMZM2G372928_C1
Organism	Zea mays
Position	chr8: 26173426-26174545 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d008941
Parent gene annotation	Histone-lysine N-methyltransferase ATX3
Parent gene strand	-
Alternative splicing	Zm00001d008941_circ_g.1
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	Zm00001d008941_T004:5 Zm00001d008941_T015:5 Zm00001d008941_T007:5 Zm00001d008941_T013:5 Zm00001d008941_T008:5 Zm00001d008941_T012:5 Zm00001d008941_T010:5 Zm00001d008941_T005:5 Zm00001d008941_T001:5 Zm00001d008941_T002:5

			
						 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  
						
							CACAAAATCAAGCACAAAATGTACCTTGCAATTGTAGCAGCTCTCCTTTCTTAATGCCTGGCTT
AGAAGACTTCGATGTCCCACAAGGAATATCATCCAGctccatgcgatatccagctcttgatgca
cacattgcatgataatacgtagagcacttgtagcattgtgtgcaggcaccatgcatttgcttgc
atatgacg

									
								

					

						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: 555
Transcript exons: 26173426-26173530,26173641-26173786,26174033-26174157,26
174284-26174386,26174470-26174545
CTCCATGCGATATCCAGCTCTTGATGCACACATTGCATGATAATACGTAGAGCACTTGTAGCAT
TGTGTGCAGGCACCATGCATTTGCTTGCATATGACGCAAGTCTTCTTAAAGTACTCTGCAGGGA
TGCTCATTATTCCCATAGCTGGCTCCATGGTCTCCTCAACCGGAAAAGAGACTTTAGGCTGAAA
CCAGGCACATGTAACATGAACCCACAGTCCATCAACATCTGTTGGCTTGAGAGCACCCCCTTTG
ACAGGACATAGGCAGCATTCTCTTTTCTGTTGGGAGAATTCACATGCTCGACAAAGCCATATTG
TAAGATCTTGTACAGCTCGTGCTCCATAGCACTCTTGGTGAACAGCTATTTGGCACCTGTTGCA
AATTATAATTTTGTTGTAGTCCCAATCCTCAACCCATCGACAAACAGCACAGCGTTCCGTTGTC
CATTTAGCACAGACAGGACTGTAAGCATTAGCTTGCAATTGTAGCAGCTCTCCTTTCTTAATGC
CTGGCTTAGAAGACTTCGATGTCCCACAAGGAATATCATCCAG
						
					

						Genomic sequence
						
							CTCCATGCGATATCCAGCTCTTGATGCACACATTGCATGATAATACGTAGAGCACTTGTAGCAT
TGTGTGCAGGCACCATGCATTTGCTTGCATATGACGCAAGTCTGCAGTTAAGATGAAAAAAATG
CAAATATTAGGTTAAATTTGAATGGAAAGCACAGAAATTAAGATTTTGGATGCAGATTGTGTAA
AAATATCAATTAAAAATCTCAACCTTCTTAAAGTACTCTGCAGGGATGCTCATTATTCCCATAG
CTGGCTCCATGGTCTCCTCAACCGGAAAAGAGACTTTAGGCTGAAACCAGGCACATGTAACATG
AACCCACAGTCCATCAACATCTGTTGGCTTGAGAGCACCCCCTATGTTAATGGAGGTAGTACAA
GTTAATAGCTTCAAACAACAATAACAGACAGGACATCTCATACAAACTTAAGACGGCAATAGAA
TATATAGTAAGCACGGAACAAAGTTTTATCATGCTACAAGCGTCACTGACAAGCATCACTACAA
TGAGGATTATTTGAAGAAGAAAAATCTTTAATGGCTGGTAAACATAGTAAAACGGAAGAGCATA
TTAGGCTACAAAATCCAATTATAAGCAATACCTTTGACAGGACATAGGCAGCATTCTCTTTTCT
GTTGGGAGAATTCACATGCTCGACAAAGCCATATTGTAAGATCTTGTACAGCTCGTGCTCCATA
GCACTCTTGGTGAACAGCTATTTGGCACCTGAGTAAATAAATATCAGAGTGGTAATGCAATCAA
TGCAAGTCAAACATCTACATAAAGGTCACCTTAACATACAGTGAAATATCAAATTAAGGGTGCT
AAACAAAACCAGTCCAGCAAGAATACCTGTTGCAAATTATAATTTTGTTGTAGTCCCAATCCTC
AACCCATCGACAAACAGCACAGCGTTCCGTTGTCCATTTAGCACAGACAGGACTGTAAGCATTA
GCTGCAGACATCAAAGTAATCAATTACATAAGGTCATGTTGCAACTGCCAGCTACACAAACACA
AAATCAAGCACAAAATGTACCTTGCAATTGTAGCAGCTCTCCTTTCTTAATGCCTGGCTTAGAA
GACTTCGATGTCCCACAAGGAATATCATCCAG
						
					

			
		

Sequences
Splice junction sequence	CACAAAATCAAGCACAAAATGTACCTTGCAATTGTAGCAGCTCTCCTTTCTTAATGCCTGGCTT AGAAGACTTCGATGTCCCACAAGGAATATCATCCAGctccatgcgatatccagctcttgatgca cacattgcatgataatacgtagagcacttgtagcattgtgtgcaggcaccatgcatttgcttgc atatgacg
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: 555 Transcript exons: 26173426-26173530,26173641-26173786,26174033-26174157,26 174284-26174386,26174470-26174545 CTCCATGCGATATCCAGCTCTTGATGCACACATTGCATGATAATACGTAGAGCACTTGTAGCAT TGTGTGCAGGCACCATGCATTTGCTTGCATATGACGCAAGTCTTCTTAAAGTACTCTGCAGGGA TGCTCATTATTCCCATAGCTGGCTCCATGGTCTCCTCAACCGGAAAAGAGACTTTAGGCTGAAA CCAGGCACATGTAACATGAACCCACAGTCCATCAACATCTGTTGGCTTGAGAGCACCCCCTTTG ACAGGACATAGGCAGCATTCTCTTTTCTGTTGGGAGAATTCACATGCTCGACAAAGCCATATTG TAAGATCTTGTACAGCTCGTGCTCCATAGCACTCTTGGTGAACAGCTATTTGGCACCTGTTGCA AATTATAATTTTGTTGTAGTCCCAATCCTCAACCCATCGACAAACAGCACAGCGTTCCGTTGTC CATTTAGCACAGACAGGACTGTAAGCATTAGCTTGCAATTGTAGCAGCTCTCCTTTCTTAATGC CTGGCTTAGAAGACTTCGATGTCCCACAAGGAATATCATCCAG
Genomic sequence	CTCCATGCGATATCCAGCTCTTGATGCACACATTGCATGATAATACGTAGAGCACTTGTAGCAT TGTGTGCAGGCACCATGCATTTGCTTGCATATGACGCAAGTCTGCAGTTAAGATGAAAAAAATG CAAATATTAGGTTAAATTTGAATGGAAAGCACAGAAATTAAGATTTTGGATGCAGATTGTGTAA AAATATCAATTAAAAATCTCAACCTTCTTAAAGTACTCTGCAGGGATGCTCATTATTCCCATAG CTGGCTCCATGGTCTCCTCAACCGGAAAAGAGACTTTAGGCTGAAACCAGGCACATGTAACATG AACCCACAGTCCATCAACATCTGTTGGCTTGAGAGCACCCCCTATGTTAATGGAGGTAGTACAA GTTAATAGCTTCAAACAACAATAACAGACAGGACATCTCATACAAACTTAAGACGGCAATAGAA TATATAGTAAGCACGGAACAAAGTTTTATCATGCTACAAGCGTCACTGACAAGCATCACTACAA TGAGGATTATTTGAAGAAGAAAAATCTTTAATGGCTGGTAAACATAGTAAAACGGAAGAGCATA TTAGGCTACAAAATCCAATTATAAGCAATACCTTTGACAGGACATAGGCAGCATTCTCTTTTCT GTTGGGAGAATTCACATGCTCGACAAAGCCATATTGTAAGATCTTGTACAGCTCGTGCTCCATA GCACTCTTGGTGAACAGCTATTTGGCACCTGAGTAAATAAATATCAGAGTGGTAATGCAATCAA TGCAAGTCAAACATCTACATAAAGGTCACCTTAACATACAGTGAAATATCAAATTAAGGGTGCT AAACAAAACCAGTCCAGCAAGAATACCTGTTGCAAATTATAATTTTGTTGTAGTCCCAATCCTC AACCCATCGACAAACAGCACAGCGTTCCGTTGTCCATTTAGCACAGACAGGACTGTAAGCATTA GCTGCAGACATCAAAGTAATCAATTACATAAGGTCATGTTGCAACTGCCAGCTACACAAACACA AAATCAAGCACAAAATGTACCTTGCAATTGTAGCAGCTCTCCTTTCTTAATGCCTGGCTTAGAA GACTTCGATGTCCCACAAGGAATATCATCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.189990202

Conservation Information
Conserved circRNAs	NA
PMCS	0.189990202

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26174500-26173462(+)
26174522-26173472(+)
26173693-26173428(-)
26173507-26174296(-)
26173521-26174540(-)
						
						Potential amino acid sequence
						
							MPGLEDFDVPQGISSSSMRYPALDAHIA*(+)
MSHKEYHPAPCDIQLLMHTLHDNT*(+)
MEPAMGIMSIPAEYFKKTCVICKQMHGACTQCYKCSTYYHAMCASRAGYRMELDDIPCGTSKSS
KPGIKKGELLQLQANAYSPVCAKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGARAVQ
DLTIWLCRACEFSQQKRECCLCPVKGGALKPTDVDGLWVHVTCAWFQPKVSFPVEETMEPAMGI
MSIPAEYFKKTCVICKQMHGACTQCYKCSTYYHAMCASRAGYRMELDDIPCGTSKSSKPGIKKG
ELLQLQANAYSPVCAKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGARAVQDLTIWLC
RACEFSQQKRECCLCPVKGGALKPTDVDGLWVHVTCAWFQPKVSFPVEETMEPAMGIMSIPAEY
FKKTCVICKQMHGACTQCYKCSTYYHAMCASRAGYRMELDDIPCGTSKSSKPGIKKGELLQLQA
NAYSPVCAKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGARAVQDLTIWLCRACEFSQ
QKRECCLCPVKGGALKPTDVDGLWVHVTCAWFQPKVSFPVEETMEPAMGIMSIPAEYFKKTCVI
CKQMHGACTQCYKCSTYYHAMCASRAGYRME(-)
MVPAHNATSALRIIMQCVHQELDIAWSWMIFLVGHRSLLSQALRKESCYNCKLMLTVLSVLNGQ
RNAVLFVDGLRIGTTTKL*(-)
MQANAWCLHTMLQVLYVLSCNVCIKSWISHGAG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	26174500-26173462(+) 26174522-26173472(+) 26173693-26173428(-) 26173507-26174296(-) 26173521-26174540(-)
Potential amino acid sequence	MPGLEDFDVPQGISSSSMRYPALDAHIA(+) MSHKEYHPAPCDIQLLMHTLHDNT(+) MEPAMGIMSIPAEYFKKTCVICKQMHGACTQCYKCSTYYHAMCASRAGYRMELDDIPCGTSKSS KPGIKKGELLQLQANAYSPVCAKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGARAVQ DLTIWLCRACEFSQQKRECCLCPVKGGALKPTDVDGLWVHVTCAWFQPKVSFPVEETMEPAMGI MSIPAEYFKKTCVICKQMHGACTQCYKCSTYYHAMCASRAGYRMELDDIPCGTSKSSKPGIKKG ELLQLQANAYSPVCAKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGARAVQDLTIWLC RACEFSQQKRECCLCPVKGGALKPTDVDGLWVHVTCAWFQPKVSFPVEETMEPAMGIMSIPAEY FKKTCVICKQMHGACTQCYKCSTYYHAMCASRAGYRMELDDIPCGTSKSSKPGIKKGELLQLQA NAYSPVCAKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGARAVQDLTIWLCRACEFSQ QKRECCLCPVKGGALKPTDVDGLWVHVTCAWFQPKVSFPVEETMEPAMGIMSIPAEYFKKTCVI CKQMHGACTQCYKCSTYYHAMCASRAGYRME(-) MVPAHNATSALRIIMQCVHQELDIAWSWMIFLVGHRSLLSQALRKESCYNCKLMLTVLSVLNGQ RNAVLFVDGLRIGTTTKL(-) MQANAWCLHTMLQVLYVLSCNVCIKSWISHGAG(-)
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 Zm00001d008941_circ_g.2

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