Plant Circular RNA Database

Detail information of Zm00001d004012_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d004012_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007202
					
						Alias
						Zm02circ00060, zma_circ_0000750
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 75644144-75646557  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d004012						
					
						Parent gene annotation
						
							Dynamin-related protein 3A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d004012_T001:6

General Information
CircRNA Name	Zm00001d004012_circ_g.1
ID in PlantcircBase	zma_circ_007202
Alias	Zm02circ00060, zma_circ_0000750
Organism	Zea mays
Position	chr2: 75644144-75646557 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d004012
Parent gene annotation	Dynamin-related protein 3A
Parent gene strand	+
Alternative splicing	NA
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	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	Zm00001d004012_T001:6

			
						 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  
						
							TGTCACAAATATGCTTCCAGGCTTGAAAACTCGCATAAATGCTCAGTTGGTAGCAGTTGCGAAG
GAACACGCTGCCTATGGTGATACTGTAGAATCAGTGcttgaaacggacaaagaagctggagata
ataaaggggtttctgagaagcaaattcgtctgaaaatcttctcaccaaatgtcctagacatcac
cttggttg

									
								

					

						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: 657
Transcript exons: 75644144-75644426,75644526-75644554,75644641-75644742,75
645068-75645136,75645234-75645293,75646444-75646557
CTTGAAACGGACAAAGAAGCTGGAGATAATAAAGGGGTTTCTGAGAAGCAAATTCGTCTGAAAA
TCTTCTCACCAAATGTCCTAGACATCACCTTGGTTGACCTCCCTGGAATAACACGGGTACCAGT
TGGAGACCAGCCCAGTGATATTGAGTCAAGAATAAGAGCAATGATCATGCAATACATTAAACAT
CCAAGTTGTATTATCTTGGCTGTTTCTCCTGCAAATGCTGATTTAGCTAATTCTGATGCTCTCC
AACTGGCAAGGCTTGCTGATCCTGATGGGTCTCGTACAATTGGTGTTATCACCAAGTTAGATAT
CATGGACAGGGGCACTGATGCTCGTAACTTCTTGCTGGGAAATGTGATTCCACTCAAGTTTGGT
TATGTAGGTGTTGTCAATCGCAGCCAAGAGGATATCAACTTCAATCGAAGTGTCAAAGACGCGC
TAGCTTTTGAGGAAAAGTACTTCTTGACTCTACCTGCTTACCATGGTCTTGCACATTGTTGTGG
TGTTCCTCAATTGGCTAAAAAGCTAAATATGATTCTACTAAAGCATGTCACAAATATGCTTCCA
GGCTTGAAAACTCGCATAAATGCTCAGTTGGTAGCAGTTGCGAAGGAACACGCTGCCTATGGTG
ATACTGTAGAATCAGTG
						
					

						Genomic sequence
						
							CTTGAAACGGACAAAGAAGCTGGAGATAATAAAGGGGTTTCTGAGAAGCAAATTCGTCTGAAAA
TCTTCTCACCAAATGTCCTAGACATCACCTTGGTTGACCTCCCTGGAATAACACGGGTACCAGT
TGGAGACCAGCCCAGTGATATTGAGTCAAGAATAAGAGCAATGATCATGCAATACATTAAACAT
CCAAGTTGTATTATCTTGGCTGTTTCTCCTGCAAATGCTGATTTAGCTAATTCTGATGCTCTCC
AACTGGCAAGGCTTGCTGATCCTGATGGTACTTAATCTACTTAAATAATGCATTTGATTACTAT
TTTCGTTGTAGTAGACAGCTAGCTAAGTGTAAACCTTTAACTGCTGGTTGTTTTACTGGCAGGG
TCTCGTACAATTGGTGTTATCACCAAGGTATTTATTTACTGTACACAGCTAATGTTGTATAGTT
CTTTGATCACTGTATGGTCATTTTGATAACCTCATCTCAATGTCTTTAGTTAGATATCATGGAC
AGGGGCACTGATGCTCGTAACTTCTTGCTGGGAAATGTGATTCCACTCAAGTTTGGTTATGTAG
GTGTTGTCAATCGCAGCCAAGAGGTATATTCTTTGCCGAACCACATGCCTTGTAATATTCTATA
GCCTTCCAATGCCAGCTTGATTGAGATAAAAAGCGTTGTTATTGTTGGTTCGTTGGTTCTATGA
CCTCACATAATGCTAGATTGATGTCTGCAACCATAAGGAACAAACAATGGAGATCATTATGTTG
TATTAATGAGAAATGAATTTTCTGATATTAGAAGTATTGGTTTGCTTTTACGTTTTGTTCTTTT
TACGATCTTGATCTTAGAAGCAGGGTTTTGGTACCTGCTTAGTTGTTTTCTGAAGTTTTATGTT
TTTACTTTTAACTAGCTGATTGCAACAGGATATCAACTTCAATCGAAGTGTCAAAGACGCGCTA
GCTTTTGAGGAAAAGTACTTCTTGACTCTACCTGTATGTCAGGAAATTAAATTCTATCTGTGCA
ACATATTGTACTCTAGATCGGAGCACAATTGCTTAAAAAATTGGTTCTTCGTTTTGTGCTTAAC
AGGCTTACCATGGTCTTGCACATTGTTGTGGTGTTCCTCAATTGGCTAAAAAGCTAAATATGGT
ATATTACTGTTAAATTTCTGCTCATTATACTTTGCCTCTGTATACTATGTTTCTTTCCATCCTC
TGGATTTTATCTGTTAATATCCTGCAGAAACATTATACCCTTGAGGCAAAGTTGATGTTGATAT
AAAGACATGTGTCTTGGGTTTTTCTTTGATAGCTTTAAAGGAACTTGGGGGTTATTTGGAAGGC
TACCTAGACACAAGATATATGAGAATATTTACATTATTCGTTGTGGGCCTTTCTGCAAAACATG
CATCTTCTTCGTTGGGCACCTACTGTGCAGCCATGGCCGGCTCCTCAGCGCTCGGGGCTATGTG
AAGGAGGAGGTCAGGCCGGGCGACCGTGGGGAGAGGGAGGCGAGGCTGGGTGATGACAGCTTGG
CCTGTTGCTCGGCATGGCATGGGCCACTGCTCGTGGTGGGGGATGGCGCAGAGCAGTGGGCGTG
TGCAGCGATGGTGGACCAGTGCGAAGGAGCGAGAGGGAGAGCGAGTTTTGCGAGCTGCACTGCA
AACACGGAGGCGGCATGATGCTTGCGGCCCCTGTGGTGCTGACCATAGAGCATGAGAGGTCCAA
CCGGTGGAAAATCGACTCGCCGTGGAAGAAATGGGCGTGCGAGCTCGCGGTACATGATTCCTGA
GTTTTAGTGCAAATAGTGATTGTTTCTATTGTGAGCAACAGGGAGAGTCAGAGATAATCAAACC
ATCTGGGTGGGATTCTCACTTATTCCCACCGAGAATCTGATTTTAAGCATATCCAAACAGGGCC
CTAATATGATGAAGAATGAATCAGTCTCAACTAGTTCAAGATAATGACTGGAAGTTAAATTCTC
ATGCCTCATGCTTATATTGAAATGAGCAATGCTATATGGCATAGTCAGGTACACAGTAAAAATA
CAGTAAAACTCTTGAAGCTAGGTTATAATTAGCACACAATGCTTACTGAATTTATTATGATGTT
TGATATTTTAACTTCAAGATTTAAGGCTTTGGTACTGCTTCTTTACCAACTGTGGTTATTCTCT
ATGTAGACACCTTCGTTTACCCTTATGAAGTTGTGATGTACTGATGTTTCTACAAATAATATTA
GTATGTTTCTAATGATTTATCTGTTCAACTTATTATGATTTATCATGTTTTTTTTTGTAGATTC
TACTAAAGCATGTCACAAATATGCTTCCAGGCTTGAAAACTCGCATAAATGCTCAGTTGGTAGC
AGTTGCGAAGGAACACGCTGCCTATGGTGATACTGTAGAATCAGTG
						
					

			
		

Sequences
Splice junction sequence	TGTCACAAATATGCTTCCAGGCTTGAAAACTCGCATAAATGCTCAGTTGGTAGCAGTTGCGAAG GAACACGCTGCCTATGGTGATACTGTAGAATCAGTGcttgaaacggacaaagaagctggagata ataaaggggtttctgagaagcaaattcgtctgaaaatcttctcaccaaatgtcctagacatcac cttggttg
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: 657 Transcript exons: 75644144-75644426,75644526-75644554,75644641-75644742,75 645068-75645136,75645234-75645293,75646444-75646557 CTTGAAACGGACAAAGAAGCTGGAGATAATAAAGGGGTTTCTGAGAAGCAAATTCGTCTGAAAA TCTTCTCACCAAATGTCCTAGACATCACCTTGGTTGACCTCCCTGGAATAACACGGGTACCAGT TGGAGACCAGCCCAGTGATATTGAGTCAAGAATAAGAGCAATGATCATGCAATACATTAAACAT CCAAGTTGTATTATCTTGGCTGTTTCTCCTGCAAATGCTGATTTAGCTAATTCTGATGCTCTCC AACTGGCAAGGCTTGCTGATCCTGATGGGTCTCGTACAATTGGTGTTATCACCAAGTTAGATAT CATGGACAGGGGCACTGATGCTCGTAACTTCTTGCTGGGAAATGTGATTCCACTCAAGTTTGGT TATGTAGGTGTTGTCAATCGCAGCCAAGAGGATATCAACTTCAATCGAAGTGTCAAAGACGCGC TAGCTTTTGAGGAAAAGTACTTCTTGACTCTACCTGCTTACCATGGTCTTGCACATTGTTGTGG TGTTCCTCAATTGGCTAAAAAGCTAAATATGATTCTACTAAAGCATGTCACAAATATGCTTCCA GGCTTGAAAACTCGCATAAATGCTCAGTTGGTAGCAGTTGCGAAGGAACACGCTGCCTATGGTG ATACTGTAGAATCAGTG
Genomic sequence	CTTGAAACGGACAAAGAAGCTGGAGATAATAAAGGGGTTTCTGAGAAGCAAATTCGTCTGAAAA TCTTCTCACCAAATGTCCTAGACATCACCTTGGTTGACCTCCCTGGAATAACACGGGTACCAGT TGGAGACCAGCCCAGTGATATTGAGTCAAGAATAAGAGCAATGATCATGCAATACATTAAACAT CCAAGTTGTATTATCTTGGCTGTTTCTCCTGCAAATGCTGATTTAGCTAATTCTGATGCTCTCC AACTGGCAAGGCTTGCTGATCCTGATGGTACTTAATCTACTTAAATAATGCATTTGATTACTAT TTTCGTTGTAGTAGACAGCTAGCTAAGTGTAAACCTTTAACTGCTGGTTGTTTTACTGGCAGGG TCTCGTACAATTGGTGTTATCACCAAGGTATTTATTTACTGTACACAGCTAATGTTGTATAGTT CTTTGATCACTGTATGGTCATTTTGATAACCTCATCTCAATGTCTTTAGTTAGATATCATGGAC AGGGGCACTGATGCTCGTAACTTCTTGCTGGGAAATGTGATTCCACTCAAGTTTGGTTATGTAG GTGTTGTCAATCGCAGCCAAGAGGTATATTCTTTGCCGAACCACATGCCTTGTAATATTCTATA GCCTTCCAATGCCAGCTTGATTGAGATAAAAAGCGTTGTTATTGTTGGTTCGTTGGTTCTATGA CCTCACATAATGCTAGATTGATGTCTGCAACCATAAGGAACAAACAATGGAGATCATTATGTTG TATTAATGAGAAATGAATTTTCTGATATTAGAAGTATTGGTTTGCTTTTACGTTTTGTTCTTTT TACGATCTTGATCTTAGAAGCAGGGTTTTGGTACCTGCTTAGTTGTTTTCTGAAGTTTTATGTT TTTACTTTTAACTAGCTGATTGCAACAGGATATCAACTTCAATCGAAGTGTCAAAGACGCGCTA GCTTTTGAGGAAAAGTACTTCTTGACTCTACCTGTATGTCAGGAAATTAAATTCTATCTGTGCA ACATATTGTACTCTAGATCGGAGCACAATTGCTTAAAAAATTGGTTCTTCGTTTTGTGCTTAAC AGGCTTACCATGGTCTTGCACATTGTTGTGGTGTTCCTCAATTGGCTAAAAAGCTAAATATGGT ATATTACTGTTAAATTTCTGCTCATTATACTTTGCCTCTGTATACTATGTTTCTTTCCATCCTC TGGATTTTATCTGTTAATATCCTGCAGAAACATTATACCCTTGAGGCAAAGTTGATGTTGATAT AAAGACATGTGTCTTGGGTTTTTCTTTGATAGCTTTAAAGGAACTTGGGGGTTATTTGGAAGGC TACCTAGACACAAGATATATGAGAATATTTACATTATTCGTTGTGGGCCTTTCTGCAAAACATG CATCTTCTTCGTTGGGCACCTACTGTGCAGCCATGGCCGGCTCCTCAGCGCTCGGGGCTATGTG AAGGAGGAGGTCAGGCCGGGCGACCGTGGGGAGAGGGAGGCGAGGCTGGGTGATGACAGCTTGG CCTGTTGCTCGGCATGGCATGGGCCACTGCTCGTGGTGGGGGATGGCGCAGAGCAGTGGGCGTG TGCAGCGATGGTGGACCAGTGCGAAGGAGCGAGAGGGAGAGCGAGTTTTGCGAGCTGCACTGCA AACACGGAGGCGGCATGATGCTTGCGGCCCCTGTGGTGCTGACCATAGAGCATGAGAGGTCCAA CCGGTGGAAAATCGACTCGCCGTGGAAGAAATGGGCGTGCGAGCTCGCGGTACATGATTCCTGA GTTTTAGTGCAAATAGTGATTGTTTCTATTGTGAGCAACAGGGAGAGTCAGAGATAATCAAACC ATCTGGGTGGGATTCTCACTTATTCCCACCGAGAATCTGATTTTAAGCATATCCAAACAGGGCC CTAATATGATGAAGAATGAATCAGTCTCAACTAGTTCAAGATAATGACTGGAAGTTAAATTCTC ATGCCTCATGCTTATATTGAAATGAGCAATGCTATATGGCATAGTCAGGTACACAGTAAAAATA CAGTAAAACTCTTGAAGCTAGGTTATAATTAGCACACAATGCTTACTGAATTTATTATGATGTT TGATATTTTAACTTCAAGATTTAAGGCTTTGGTACTGCTTCTTTACCAACTGTGGTTATTCTCT ATGTAGACACCTTCGTTTACCCTTATGAAGTTGTGATGTACTGATGTTTCTACAAATAATATTA GTATGTTTCTAATGATTTATCTGTTCAACTTATTATGATTTATCATGTTTTTTTTTGTAGATTC TACTAAAGCATGTCACAAATATGCTTCCAGGCTTGAAAACTCGCATAAATGCTCAGTTGGTAGC AGTTGCGAAGGAACACGCTGCCTATGGTGATACTGTAGAATCAGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.133725231

Conservation Information
Conserved circRNAs	NA
PMCS	0.133725231

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							75644313-75646554(+)
75644653-75646535(-)
						
						Potential amino acid sequence
						
							MIMQYIKHPSCIILAVSPANADLANSDALQLARLADPDGSRTIGVITKLDIMDRGTDARNFLLG
NVIPLKFGYVGVVNRSQEDINFNRSVKDALAFEEKYFLTLPAYHGLAHCCGVPQLAKKLNMILL
KHVTNMLPGLKTRINAQLVAVAKEHAAYGDTVESVLETDKEAGDNKGVSEKQIRLKIFSPNVLD
ITLVDLPGITRVPVGDQPSDIESRIRAMIMQYIKHPSCIILAVSPANADLANSDALQLARLADP
DGSRTIGVITKLDIMDRGTDARNFLLGNVIPLKFGYVGVVNRSQEDINFNRSVKDALAFEEKYF
LTLPAYHGLAHCCGVPQLAKKLNMILLKHVTNMLPGLKTRINAQLVAVAKEHAAYGDTVESVLE
TDKEAGDNKGVSEKQIRLKIFSPNVLDITLVDLPGITRVPVGDQPSDIESRIRAMIMQYIKHPS
CIILAVSPANADLANSDALQLARLADPDGSRTIGVITKLDIMDRGTDARNFLLGNVIPLKFGYV
GVVNRSQEDINFNRSVKDALAFEEKYFLTLPAYHGLAHCCGVPQLAKKLNMILLKHVTNMLPGL
KTRINAQLVAVAKEHAAYGDTVESVLETDKEAGDNKGVSEKQIRLKIFSPNVLDITLVDLPGIT
RVPVGDQPSDIESRIRAMIMQYIKHPSCIILAVSPANADLANSDALQLARLADPDGSRTIGVIT
KLDIMDRGTDARNFLLGNVIPLKFGYVGVVNRSQEDINFNRSVKDALAFEEKYFLTLPAYHGLA
HCCGVPQLAKKLNMILLKHVTNMLPGLKTRINAQLVAVAKEHAAYGDTVESV(+)
MISNLVITPIVRDPSGSASLASWRASELAKSAFAGETAKIIQLGCLMYCMIIALILDSISLGWS
PTGTRVIPGRSTKVMSRTFGEKIFRRICFSETPLLSPASLSVSSTDSTVSP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	75644313-75646554(+) 75644653-75646535(-)
Potential amino acid sequence	MIMQYIKHPSCIILAVSPANADLANSDALQLARLADPDGSRTIGVITKLDIMDRGTDARNFLLG NVIPLKFGYVGVVNRSQEDINFNRSVKDALAFEEKYFLTLPAYHGLAHCCGVPQLAKKLNMILL KHVTNMLPGLKTRINAQLVAVAKEHAAYGDTVESVLETDKEAGDNKGVSEKQIRLKIFSPNVLD ITLVDLPGITRVPVGDQPSDIESRIRAMIMQYIKHPSCIILAVSPANADLANSDALQLARLADP DGSRTIGVITKLDIMDRGTDARNFLLGNVIPLKFGYVGVVNRSQEDINFNRSVKDALAFEEKYF LTLPAYHGLAHCCGVPQLAKKLNMILLKHVTNMLPGLKTRINAQLVAVAKEHAAYGDTVESVLE TDKEAGDNKGVSEKQIRLKIFSPNVLDITLVDLPGITRVPVGDQPSDIESRIRAMIMQYIKHPS CIILAVSPANADLANSDALQLARLADPDGSRTIGVITKLDIMDRGTDARNFLLGNVIPLKFGYV GVVNRSQEDINFNRSVKDALAFEEKYFLTLPAYHGLAHCCGVPQLAKKLNMILLKHVTNMLPGL KTRINAQLVAVAKEHAAYGDTVESVLETDKEAGDNKGVSEKQIRLKIFSPNVLDITLVDLPGIT RVPVGDQPSDIESRIRAMIMQYIKHPSCIILAVSPANADLANSDALQLARLADPDGSRTIGVIT KLDIMDRGTDARNFLLGNVIPLKFGYVGVVNRSQEDINFNRSVKDALAFEEKYFLTLPAYHGLA HCCGVPQLAKKLNMILLKHVTNMLPGLKTRINAQLVAVAKEHAAYGDTVESV(+) MISNLVITPIVRDPSGSASLASWRASELAKSAFAGETAKIIQLGCLMYCMIIALILDSISLGWS PTGTRVIPGRSTKVMSRTFGEKIFRRICFSETPLLSPASLSVSSTDSTVSP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d004012_circ_g.1

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