Plant Circular RNA Database

Detail information of Zm00001d050133_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d050133_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008046
					
						Alias
						zma_circ_0001812
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 68216243-68217298  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d050133						
					
						Parent gene annotation
						
							Homoserine dehydrogenase  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d050133_circ_g.1 Zm00001d050133_circ_g.2 Zm00001d050133_circ_g.3 Zm00001d050133_circ_g.5 Zm00001d050133_circ_ag.1 Zm00001d050134_circ_g.1 Zm00001d050134_circ_g.2 Zm00001d050134_circ_g.3 Zm00001d050134_circ_g.4 Zm00001d050134_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d050133_T001:3

General Information
CircRNA Name	Zm00001d050133_circ_g.4
ID in PlantcircBase	zma_circ_008046
Alias	zma_circ_0001812
Organism	Zea mays
Position	chr4: 68216243-68217298 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Zm00001d050133
Parent gene annotation	Homoserine dehydrogenase
Parent gene strand	-
Alternative splicing	Zm00001d050133_circ_g.1 Zm00001d050133_circ_g.2 Zm00001d050133_circ_g.3 Zm00001d050133_circ_g.5 Zm00001d050133_circ_ag.1 Zm00001d050134_circ_g.1 Zm00001d050134_circ_g.2 Zm00001d050134_circ_g.3 Zm00001d050134_circ_g.4 Zm00001d050134_circ_g.5
Support reads	NA
Tissues	leaf, 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	Zm00001d050133_T001:3

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: TTAGTGATGTTGTTGCTGAA
 R: TTTCTTGTTTGGAGTGATGA
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	Yes 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	F: TTAGTGATGTTGTTGCTGAA R: TTTCTTGTTTGGAGTGATGA 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  
						
							AAAAAAGTGATTCTCAGACAAATGATGAACAAACTTATCAAGATTGGCAGGTTCTGCTTCAGTT
TGTAGCTTCTCTTTCCACTGGGTCAAATCTACTCCTcttcctggcaacatcagtaccagacaga
tcatctcttggatctggttctgtgtatcctgctttttttgcttcagcaacaacatcactaaagg
ttcttgct

									
								

					

						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: 508
Transcript exons: 68216243-68216378,68216738-68216883,68217073-68217298
CTTCCTGGCAACATCAGTACCAGACAGATCATCTCTTGGATCTGGTTCTGTGTATCCTGCTTTT
TTTGCTTCAGCAACAACATCACTAAAGGTTCTTGCTCCTTCGAAGTTGTTAAAAATATAACTTA
ACGTTCCACTGAAAATCCCTTCAATGCGCAATATCTTGTCACCTGTCTCTAGGAGACCACGCAG
AGTGCTAATGATAGGGAGGCCAGCACCAACAGTTGCTTCATAGAAGTAATGAGTATATGATGCA
CGCTGAAGAGTTCTAAGTTTAAGATACCTGTCAAGTGGCCCTGAATTTGCTTTCTTGTTTGGAG
TGATGACATGGATTCCTTTCTTTAGCCAATCATAATAGTGAGATGCAACACTTGTATCTGCTGT
GCAATCTACCAAAACTCTGTTAGGAAAAAAGTGATTCTCAGACAAATGATGAACAAACTTATCA
AGATTGGCAGGTTCTGCTTCAGTTTGTAGCTTCTCTTTCCACTGGGTCAAATCTACTCCT
						
					

						Genomic sequence
						
							CTTCCTGGCAACATCAGTACCAGACAGATCATCTCTTGGATCTGGTTCTGTGTATCCTGCTTTT
TTTGCTTCAGCAACAACATCACTAAAGGTTCTTGCTCCTTCGAAGTTGTTAAAAATATAACTTA
ACGTTCCACTGCAATTAAACAAAGAGTTAAAACATATTAGTCGTAATAAACTTAATAAATGAAC
AAAAATGTACGAAGCAGTCATACAGGTTCAACAGGGGCAGTGAAAATATGGTATCAGAAAAATA
TCTGTGAATCCAATAAAAGACCTGTACTGTAAAGTTACTCCCTTGTATTCGTACTTATCTAAGG
ATCTGGTACATCCCTTGTGCTCATACAAAACATGTACTATAAAATTACTCTATTGTTCTCATAC
TTATCCAAGGATCTGGTGTATCCCCTTGTGCTCATTCGTAACAAAAGATCTGTAATATCACAAA
AAATACTAACATGTTCATGCCATCATTTAATCTGAAATTATACTGACCTGAAAATCCCTTCAAT
GCGCAATATCTTGTCACCTGTCTCTAGGAGACCACGCAGAGTGCTAATGATAGGGAGGCCAGCA
CCAACAGTTGCTTCATAGAAGTAATGAGTATATGATGCACGCTGAAGAGTTCTAAGTTTAAGAT
ACTGCAGGTCCGGGAGAATACAATAGTTAGTCAAAGAAAGCAACAGCATAGAGTCTAGCAACAT
ATTGGTTCAACCTATTTAATGTTCAGATAGCCTGTAACCATCTAACAGCCAAACCAAAACTACT
ATCAAACAAATGCAAAAACAGAGAACATTCTCAGCAAAAAACATGGTCAACAAAATTATTACCC
TGTCAAGTGGCCCTGAATTTGCTTTCTTGTTTGGAGTGATGACATGGATTCCTTTCTTTAGCCA
ATCATAATAGTGAGATGCAACACTTGTATCTGCTGTGCAATCTACCAAAACTCTGTTAGGAAAA
AAGTGATTCTCAGACAAATGATGAACAAACTTATCAAGATTGGCAGGTTCTGCTTCAGTTTGTA
GCTTCTCTTTCCACTGGGTCAAATCTACTCCT
						
					

			
		

Sequences
Splice junction sequence	AAAAAAGTGATTCTCAGACAAATGATGAACAAACTTATCAAGATTGGCAGGTTCTGCTTCAGTT TGTAGCTTCTCTTTCCACTGGGTCAAATCTACTCCTcttcctggcaacatcagtaccagacaga tcatctcttggatctggttctgtgtatcctgctttttttgcttcagcaacaacatcactaaagg ttcttgct
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: 508 Transcript exons: 68216243-68216378,68216738-68216883,68217073-68217298 CTTCCTGGCAACATCAGTACCAGACAGATCATCTCTTGGATCTGGTTCTGTGTATCCTGCTTTT TTTGCTTCAGCAACAACATCACTAAAGGTTCTTGCTCCTTCGAAGTTGTTAAAAATATAACTTA ACGTTCCACTGAAAATCCCTTCAATGCGCAATATCTTGTCACCTGTCTCTAGGAGACCACGCAG AGTGCTAATGATAGGGAGGCCAGCACCAACAGTTGCTTCATAGAAGTAATGAGTATATGATGCA CGCTGAAGAGTTCTAAGTTTAAGATACCTGTCAAGTGGCCCTGAATTTGCTTTCTTGTTTGGAG TGATGACATGGATTCCTTTCTTTAGCCAATCATAATAGTGAGATGCAACACTTGTATCTGCTGT GCAATCTACCAAAACTCTGTTAGGAAAAAAGTGATTCTCAGACAAATGATGAACAAACTTATCA AGATTGGCAGGTTCTGCTTCAGTTTGTAGCTTCTCTTTCCACTGGGTCAAATCTACTCCT
Genomic sequence	CTTCCTGGCAACATCAGTACCAGACAGATCATCTCTTGGATCTGGTTCTGTGTATCCTGCTTTT TTTGCTTCAGCAACAACATCACTAAAGGTTCTTGCTCCTTCGAAGTTGTTAAAAATATAACTTA ACGTTCCACTGCAATTAAACAAAGAGTTAAAACATATTAGTCGTAATAAACTTAATAAATGAAC AAAAATGTACGAAGCAGTCATACAGGTTCAACAGGGGCAGTGAAAATATGGTATCAGAAAAATA TCTGTGAATCCAATAAAAGACCTGTACTGTAAAGTTACTCCCTTGTATTCGTACTTATCTAAGG ATCTGGTACATCCCTTGTGCTCATACAAAACATGTACTATAAAATTACTCTATTGTTCTCATAC TTATCCAAGGATCTGGTGTATCCCCTTGTGCTCATTCGTAACAAAAGATCTGTAATATCACAAA AAATACTAACATGTTCATGCCATCATTTAATCTGAAATTATACTGACCTGAAAATCCCTTCAAT GCGCAATATCTTGTCACCTGTCTCTAGGAGACCACGCAGAGTGCTAATGATAGGGAGGCCAGCA CCAACAGTTGCTTCATAGAAGTAATGAGTATATGATGCACGCTGAAGAGTTCTAAGTTTAAGAT ACTGCAGGTCCGGGAGAATACAATAGTTAGTCAAAGAAAGCAACAGCATAGAGTCTAGCAACAT ATTGGTTCAACCTATTTAATGTTCAGATAGCCTGTAACCATCTAACAGCCAAACCAAAACTACT ATCAAACAAATGCAAAAACAGAGAACATTCTCAGCAAAAAACATGGTCAACAAAATTATTACCC TGTCAAGTGGCCCTGAATTTGCTTTCTTGTTTGGAGTGATGACATGGATTCCTTTCTTTAGCCA ATCATAATAGTGAGATGCAACACTTGTATCTGCTGTGCAATCTACCAAAACTCTGTTAGGAAAA AAGTGATTCTCAGACAAATGATGAACAAACTTATCAAGATTGGCAGGTTCTGCTTCAGTTTGTA GCTTCTCTTTCCACTGGGTCAAATCTACTCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.152256378

Conservation Information
Conserved circRNAs	NA
PMCS	0.152256378

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							68216327-68217259(-)
						
						Potential amino acid sequence
						
							MLLLKQKKQDTQNQIQEMICLVLMLPGRGVDLTQWKEKLQTEAEPANLDKFVHHLSENHFFPNR
VLVDCTADTSVASHYYDWLKKGIHVITPNKKANSGPLDRYLKLRTLQRASYTHYFYEATVGAGL
PIISTLRGLLETGDKILRIEGIFSGTLSYIFNNFEGARTFSDVVAEAKKAGYTEPDPRDDLSGT
DVARKRSRFDPVEREATN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						regulating the response to N deficiency

Functional Information
Coding potential	Y
Potential coding position	68216327-68217259(-)
Potential amino acid sequence	MLLLKQKKQDTQNQIQEMICLVLMLPGRGVDLTQWKEKLQTEAEPANLDKFVHHLSENHFFPNR VLVDCTADTSVASHYYDWLKKGIHVITPNKKANSGPLDRYLKLRTLQRASYTHYFYEATVGAGL PIISTLRGLLETGDKILRIEGIFSGTLSYIFNNFEGARTFSDVVAEAKKAGYTEPDPRDDLSGT DVARKRSRFDPVEREATN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	regulating the response to N deficiency

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d050133_circ_g.4

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