Plant Circular RNA Database

Detail information of Zm00001d027472_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d027472_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006371
					
						Alias
						zma_circ_0000680
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 6085739-6088396  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d027472						
					
						Parent gene annotation
						
							Callose synthase 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d027472_circ_g.2 Zm00001d027472_circ_g.3 Zm00001d027472_circ_g.4 Zm00001d027472_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
						Zm00001d027472_T001:4
Zm00001d027472_T003:4
Zm00001d027472_T002:5

General Information
CircRNA Name	Zm00001d027472_circ_g.1
ID in PlantcircBase	zma_circ_006371
Alias	zma_circ_0000680
Organism	Zea mays
Position	chr1: 6085739-6088396 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d027472
Parent gene annotation	Callose synthase 3
Parent gene strand	-
Alternative splicing	Zm00001d027472_circ_g.2 Zm00001d027472_circ_g.3 Zm00001d027472_circ_g.4 Zm00001d027472_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	Zm00001d027472_T001:4 Zm00001d027472_T003:4 Zm00001d027472_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  
						
							TGTACCTAAGGTGGTCGTCAAATATATCTCTTGTTACAACCTCCAGCATATCTTGAAAAATCTT
TATTACAGCACTCCTGTCTTTCTCATCATTCTCCTTctgttcgagctagtgtttggcctctgta
tgaggcccatagacgaagttcctcctttagttcttcgctttcttcgctctctttaagttcttcc
tccaatcc

									
								

					

						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: 628
Transcript exons: 6085739-6085867,6085962-6086071,6086699-6086850,6086976-
6087117,6088302-6088396
CTGTTCGAGCTAGTGTTTGGCCTCTGTATGAGGCCCATAGACGAAGTTCCTCCTTTAGTTCTTC
GCTTTCTTCGCTCTCTTTAAGTTCTTCCTCCAATCCAACCCTTTCCTTAAAGTTTTTCCATTCA
TCTGGATAAATTTTTTGCAGGTAGAATAGGGTGGAAACTCCATCTTCATTTTCTTCCTCAAGTT
CTTTTATAGAGAAAAGAACTGGTTCATTGTAATAAGGGGTCAATGCGGAAAACGAGAGCATGTT
TCGGACTTTGGGTGCATCAGGCATATCCATAAATAAGGAGTTGGTAAAAAATGTAAGACGCCTT
CTGGCTTCTAGGTTTGAAGGAACATCCATAGCAGATTCCTTCACCGTAAGTAGCAGTTCCAGCC
TTTTTATCTTTTCTAGCCAAGCATCTGTGGTCGTGACTTGTAGAGGAAACTTGATAGCTCCAGA
TGGTTGAAACAACTGATACTCTTTATCCCACGTGGTTGTGCCATCATGCTTTTGATATGAGCCT
CCATGACTTGACTCTAAAATACTAAGGTGGTCGTCAAATATATCTCTTGTTACAACCTCCAGCA
TATCTTGAAAAATCTTTATTACAGCACTCCTGTCTTTCTCATCATTCTCCTT
						
					

						Genomic sequence
						
							CTGTTCGAGCTAGTGTTTGGCCTCTGTATGAGGCCCATAGACGAAGTTCCTCCTTTAGTTCTTC
GCTTTCTTCGCTCTCTTTAAGTTCTTCCTCCAATCCAACCCTTTCCTTAAAGTTTTTCCATTCA
TCTACATGTATAAGCATAACATGACAAAGTTAATGCCAGATGTTCTTGAACACACTTTATGTTA
ATACATGAATAGGATAAAGTTGTGCCTCAACCTGGATAAATTTTTTGCAGGTAGAATAGGGTGG
AAACTCCATCTTCATTTTCTTCCTCAAGTTCTTTTATAGAGAAAAGAACTGGTTCATTGTAATA
AGGGGTCAATGCGCTGCAGAGAGAGGCAAAATATCATCACCTATAGATTCCAACAGCAAGTTTA
TGACAGGGAAAAGAGTCAACAGGAGAAAGAATTTCAAAATGCAAAGGAAAATATAATCATTTCT
GTATGTGCTCTACTATGCTTCTGTTTTGCAACTTTCAGACAACGTAGCAGTAAATTATTTCAGT
AAATTGACTACAACTAAGGAAAAAAAATGCCTCCAGGAAAGGTATTCAAATTAACAGAGTAACT
GCTCGAGAAGAGTTAGAGAGACAAGTATCATAAGAACACTGGGCATATGACAGTATAAAAGTGA
TATGATATGAGCTTCAGAAATATTTTTTTTTCGAAAAACGCAGGAGAGCTGCGCATCATTATAT
TAAGAAGGGGAAATTAAGGTCCAAGAGGACCAGTACAAAAAACCACCCTATGGTGGCCAGCAAC
AAGCATAAATAAAACTATCCATAGGACTAAGATACAAAAAGACGACCAAGGAAAAAATTAAGTC
GGGCCTGCTGCGCCTAGAGCAGCAGCAAGCCCAAGGCTTCCGAGGTGTTTGGCACCAGCCAGCA
CCCATAAGGATAGCTCGTCGACGAAGCTTCAGAAATAATGACCGAGTTATTCACAGGTACTTAC
GAAAACGAGAGCATGTTTCGGACTTTGGGTGCATCAGGCATATCCATAAATAAGGAGTTGGTAA
AAAATGTAAGACGCCTTCTGGCTTCTAGGTTTGAAGGAACATCCATAGCAGATTCCTTCACCGT
AAGTAGCAGTTCCAGCCTTTTTATCTGCAGTGAAACGAATCATATAAGCAACAAAGCATTTAGA
CGTATGCCCCTTGTCCAGCAAAAACACTGCACAGGAAAGTCAACATGCATTCAATTTTGCACAA
GTTTAATTATAGCTCAATAACCTTTTCTAGCCAAGCATCTGTGGTCGTGACTTGTAGAGGAAAC
TTGATAGCTCCAGATGGTTGAAACAACTGATACTCTTTATCCCACGTGGTTGTGCCATCATGCT
TTTGATATGAGCCTCCATGACTTGACTCTAAAATACTGCCATGTTGCGGAAAAATGATTAGCTA
CAGAAAGTCAAGCAGAAGCCTACCCAACTTGCTTTGGACACAAAGGCTTTGTTGTTACTACTGT
CGTAGAAAGCCAGGGCTAAAGAAAGCATGAGACAGATATCAGCATCAAGATTTAATCTTATTTT
TGTGATTGCTTGCACATTCATCATGTTTCTGGAGGGACCGCAAAAATGCATGAATTCAGTATTC
CTAAGACATTGTTTTAGCATAAACCATTGGATTCTAGAACAATAGCTCATGATCAAAGCGACCA
CAGGCTATTTTGATAGTTGCGCTTGCGGAAATCTTTGGCACAAAGTCCCTCCTTGTTTTCAGCT
TTTGGGTGATATGGATGATGCTTGAAACTCAATACTGCAAATAATTTAACAGAAACAGCTGCAT
ATGGTTATTACCTGAAATGGGCATTGTCCACAGGATGTGAAACATTAAGTTAGCAAAATCAGCA
TCCCACTGTTATGGCAAGTAGAGTGCCGAACAGATTAGATTGTTTTGTTAGGAAAATAGATTAG
ATTGGTTTGGTTTGTTAGGAAAGAGAGATTAGATTGGTTTGGTAGGATAAAGAAAGAGATAAGT
TAGATTGATTTGGTTAAGATATTTCTTTAGGGTTCAAGTAAGGCTCTCTATATAAGGAGAGATG
GCGAAAGGGCCTCTAGCTGAATTGGTTAGGTGGTCTGAGTAGCACTCCTCAGGTCCTGAGTATA
AATCCTAGTGTGAGCGAATTTCAGGCTGAGGTTAAAAAAGGCCACTCACTGGTTCCCCTGGTTG
TGTGCACACGAGATGGACTGACCTATGGGAGACGGATCCTCGTGTACGGGCTGGGCAGACTCAA
AGCACGAGTAAAGATCTGGCCTATACGGGGCAGACCCTCTGCACCGGGGGGGGGCATGTTTCGT
GACCTTTCTTGGTCGGGGCTCTGAATGCGCTTTTTCTTGATATAATACCATGGGGCCGGTCTTC
CCCTACAGGCGAGTTTTTTTATATAAGAAGAGATGTATCAATCTAATCGAGCAAAAATTAGGAA
GAAATCCTAACCAAATCAATCTAACTTATCTCTTTCCTAACAAACCAAATCAATCTAATTTGTC
CGACACTCTACTTGCCATAACACCCACTTGGTAATATATGTACAAGCTTATAAAACAATATATG
TACCTAAGGTGGTCGTCAAATATATCTCTTGTTACAACCTCCAGCATATCTTGAAAAATCTTTA
TTACAGCACTCCTGTCTTTCTCATCATTCTCCTT
						
					

			
		

Sequences
Splice junction sequence	TGTACCTAAGGTGGTCGTCAAATATATCTCTTGTTACAACCTCCAGCATATCTTGAAAAATCTT TATTACAGCACTCCTGTCTTTCTCATCATTCTCCTTctgttcgagctagtgtttggcctctgta tgaggcccatagacgaagttcctcctttagttcttcgctttcttcgctctctttaagttcttcc tccaatcc
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: 628 Transcript exons: 6085739-6085867,6085962-6086071,6086699-6086850,6086976- 6087117,6088302-6088396 CTGTTCGAGCTAGTGTTTGGCCTCTGTATGAGGCCCATAGACGAAGTTCCTCCTTTAGTTCTTC GCTTTCTTCGCTCTCTTTAAGTTCTTCCTCCAATCCAACCCTTTCCTTAAAGTTTTTCCATTCA TCTGGATAAATTTTTTGCAGGTAGAATAGGGTGGAAACTCCATCTTCATTTTCTTCCTCAAGTT CTTTTATAGAGAAAAGAACTGGTTCATTGTAATAAGGGGTCAATGCGGAAAACGAGAGCATGTT TCGGACTTTGGGTGCATCAGGCATATCCATAAATAAGGAGTTGGTAAAAAATGTAAGACGCCTT CTGGCTTCTAGGTTTGAAGGAACATCCATAGCAGATTCCTTCACCGTAAGTAGCAGTTCCAGCC TTTTTATCTTTTCTAGCCAAGCATCTGTGGTCGTGACTTGTAGAGGAAACTTGATAGCTCCAGA TGGTTGAAACAACTGATACTCTTTATCCCACGTGGTTGTGCCATCATGCTTTTGATATGAGCCT CCATGACTTGACTCTAAAATACTAAGGTGGTCGTCAAATATATCTCTTGTTACAACCTCCAGCA TATCTTGAAAAATCTTTATTACAGCACTCCTGTCTTTCTCATCATTCTCCTT
Genomic sequence	CTGTTCGAGCTAGTGTTTGGCCTCTGTATGAGGCCCATAGACGAAGTTCCTCCTTTAGTTCTTC GCTTTCTTCGCTCTCTTTAAGTTCTTCCTCCAATCCAACCCTTTCCTTAAAGTTTTTCCATTCA TCTACATGTATAAGCATAACATGACAAAGTTAATGCCAGATGTTCTTGAACACACTTTATGTTA ATACATGAATAGGATAAAGTTGTGCCTCAACCTGGATAAATTTTTTGCAGGTAGAATAGGGTGG AAACTCCATCTTCATTTTCTTCCTCAAGTTCTTTTATAGAGAAAAGAACTGGTTCATTGTAATA AGGGGTCAATGCGCTGCAGAGAGAGGCAAAATATCATCACCTATAGATTCCAACAGCAAGTTTA TGACAGGGAAAAGAGTCAACAGGAGAAAGAATTTCAAAATGCAAAGGAAAATATAATCATTTCT GTATGTGCTCTACTATGCTTCTGTTTTGCAACTTTCAGACAACGTAGCAGTAAATTATTTCAGT AAATTGACTACAACTAAGGAAAAAAAATGCCTCCAGGAAAGGTATTCAAATTAACAGAGTAACT GCTCGAGAAGAGTTAGAGAGACAAGTATCATAAGAACACTGGGCATATGACAGTATAAAAGTGA TATGATATGAGCTTCAGAAATATTTTTTTTTCGAAAAACGCAGGAGAGCTGCGCATCATTATAT TAAGAAGGGGAAATTAAGGTCCAAGAGGACCAGTACAAAAAACCACCCTATGGTGGCCAGCAAC AAGCATAAATAAAACTATCCATAGGACTAAGATACAAAAAGACGACCAAGGAAAAAATTAAGTC GGGCCTGCTGCGCCTAGAGCAGCAGCAAGCCCAAGGCTTCCGAGGTGTTTGGCACCAGCCAGCA CCCATAAGGATAGCTCGTCGACGAAGCTTCAGAAATAATGACCGAGTTATTCACAGGTACTTAC GAAAACGAGAGCATGTTTCGGACTTTGGGTGCATCAGGCATATCCATAAATAAGGAGTTGGTAA AAAATGTAAGACGCCTTCTGGCTTCTAGGTTTGAAGGAACATCCATAGCAGATTCCTTCACCGT AAGTAGCAGTTCCAGCCTTTTTATCTGCAGTGAAACGAATCATATAAGCAACAAAGCATTTAGA CGTATGCCCCTTGTCCAGCAAAAACACTGCACAGGAAAGTCAACATGCATTCAATTTTGCACAA GTTTAATTATAGCTCAATAACCTTTTCTAGCCAAGCATCTGTGGTCGTGACTTGTAGAGGAAAC TTGATAGCTCCAGATGGTTGAAACAACTGATACTCTTTATCCCACGTGGTTGTGCCATCATGCT TTTGATATGAGCCTCCATGACTTGACTCTAAAATACTGCCATGTTGCGGAAAAATGATTAGCTA CAGAAAGTCAAGCAGAAGCCTACCCAACTTGCTTTGGACACAAAGGCTTTGTTGTTACTACTGT CGTAGAAAGCCAGGGCTAAAGAAAGCATGAGACAGATATCAGCATCAAGATTTAATCTTATTTT TGTGATTGCTTGCACATTCATCATGTTTCTGGAGGGACCGCAAAAATGCATGAATTCAGTATTC CTAAGACATTGTTTTAGCATAAACCATTGGATTCTAGAACAATAGCTCATGATCAAAGCGACCA CAGGCTATTTTGATAGTTGCGCTTGCGGAAATCTTTGGCACAAAGTCCCTCCTTGTTTTCAGCT TTTGGGTGATATGGATGATGCTTGAAACTCAATACTGCAAATAATTTAACAGAAACAGCTGCAT ATGGTTATTACCTGAAATGGGCATTGTCCACAGGATGTGAAACATTAAGTTAGCAAAATCAGCA TCCCACTGTTATGGCAAGTAGAGTGCCGAACAGATTAGATTGTTTTGTTAGGAAAATAGATTAG ATTGGTTTGGTTTGTTAGGAAAGAGAGATTAGATTGGTTTGGTAGGATAAAGAAAGAGATAAGT TAGATTGATTTGGTTAAGATATTTCTTTAGGGTTCAAGTAAGGCTCTCTATATAAGGAGAGATG GCGAAAGGGCCTCTAGCTGAATTGGTTAGGTGGTCTGAGTAGCACTCCTCAGGTCCTGAGTATA AATCCTAGTGTGAGCGAATTTCAGGCTGAGGTTAAAAAAGGCCACTCACTGGTTCCCCTGGTTG TGTGCACACGAGATGGACTGACCTATGGGAGACGGATCCTCGTGTACGGGCTGGGCAGACTCAA AGCACGAGTAAAGATCTGGCCTATACGGGGCAGACCCTCTGCACCGGGGGGGGGCATGTTTCGT GACCTTTCTTGGTCGGGGCTCTGAATGCGCTTTTTCTTGATATAATACCATGGGGCCGGTCTTC CCCTACAGGCGAGTTTTTTTATATAAGAAGAGATGTATCAATCTAATCGAGCAAAAATTAGGAA GAAATCCTAACCAAATCAATCTAACTTATCTCTTTCCTAACAAACCAAATCAATCTAATTTGTC CGACACTCTACTTGCCATAACACCCACTTGGTAATATATGTACAAGCTTATAAAACAATATATG TACCTAAGGTGGTCGTCAAATATATCTCTTGTTACAACCTCCAGCATATCTTGAAAAATCTTTA TTACAGCACTCCTGTCTTTCTCATCATTCTCCTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.062183627

Conservation Information
Conserved circRNAs	NA
PMCS	0.062183627

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6088347-6088388(-)
6085778-6088365(-)
						
						Potential amino acid sequence
						
							MLEVVTRDIFDDHLSILESSHGGSYQKHDGTTTWDKEYQLFQPSGAIKFPLQVTTTDAWLEKIK
RLELLLTVKESAMDVPSNLEARRRLTFFTNSLFMDMPDAPKVRNMLSFSALTPYYNEPVLFSIK
ELEEENEDGVSTLFYLQKIYPDEWKNFKERVGLEEELKESEESEELKEELRLWASYRGQTLART
EGE*(-)
MGLIQRPNTSSNRRRMMRKTGVL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6088347-6088388(-) 6085778-6088365(-)
Potential amino acid sequence	MLEVVTRDIFDDHLSILESSHGGSYQKHDGTTTWDKEYQLFQPSGAIKFPLQVTTTDAWLEKIK RLELLLTVKESAMDVPSNLEARRRLTFFTNSLFMDMPDAPKVRNMLSFSALTPYYNEPVLFSIK ELEEENEDGVSTLFYLQKIYPDEWKNFKERVGLEEELKESEESEELKEELRLWASYRGQTLART EGE(-) MGLIQRPNTSSNRRRMMRKTGVL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d027472_circ_g.1

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