Plant Circular RNA Database

Detail information of Zm00001d039319_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d039319_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007459
					
						Alias
						zma_circ_0001217
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 1694814-1697104  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d039319						
					
						Parent gene annotation
						
							GTP binding;GTP binding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d039319_circ_g.1 						
					
						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
						Zm00001d039319_T004:4
Zm00001d039319_T002:4
Zm00001d039319_T005:4
Zm00001d039319_T001:5
Zm00001d039319_T003:4
Zm00001d039319_T007:3
Zm00001d039319_T006:4

General Information
CircRNA Name	Zm00001d039319_circ_g.2
ID in PlantcircBase	zma_circ_007459
Alias	zma_circ_0001217
Organism	Zea mays
Position	chr3: 1694814-1697104 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d039319
Parent gene annotation	GTP binding;GTP binding
Parent gene strand	-
Alternative splicing	Zm00001d039319_circ_g.1
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	Zm00001d039319_T004:4 Zm00001d039319_T002:4 Zm00001d039319_T005:4 Zm00001d039319_T001:5 Zm00001d039319_T003:4 Zm00001d039319_T007:3 Zm00001d039319_T006:4

			
						 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  
						
							AGCATTACCTGCATCATTCAGATCCATAAAAAACCTAAATACTGGACTATTTTCAGTCTTCTTC
GACGGTGATAGCATCCTTTTGAACCACATAGGAGTCcatctaattccatcatttgttgccactg
caatattcaagttttgcgcactaaaaacaggaaccccatcaagttttttccttctgcccctttg
tggaagtg

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CATCTAATTCCATCATTTGTTGCCACTGCAATATTCAAGTTTTGCGCACTAAAAACAGGAACCC
CATCAAGTTTTTTCCTTCTGCCCCTTTGTGGAAGTGACTTCAATAGCTTATTGGCAGCCTGGAC
CTGAAAGGGAAACGATATAATCTCTAATGGCATGCTTAAGTTATAGGTAGGCTGAGAAATTTTA
GCACAGACCTGCTTTTCATTTGGAACAAACTGGAACATGTGAGGCTTTTCCTGCAGAAAATTTA
TTTTTAATCTTACAAATAGAACATGAGTGCAAGTCATACATAACAAATAATGCGGACTAAAAAT
GCTGGTGTTACTCCCTCCATCCCGGAATGATATATTCATGTAAAAGTCAAACTTTACGAATTTT
GGCCAACAATTATTCAAATTATATAAAATTTTAAGGCATAGAAAAATGCTGTGATGGATTTATA
TTCGAATTGCCTCTGATCTGATATCGGAACTCTTTAGCAAACGAAAACATACAGTAAGAGGAAT
TAATGGTCAAAATCTAATTTGTTTGACTTTTCCTGATATGATTATCATTCCAAGACAGATGGAG
AATATTACTCCCACCGTCCCAAATTAAAATTCGTTTTAGACATTTATTAGATTCATACAATGAT
TAATGTATATGTTTGGTATATATGTCTAGATTCATCATCATCTATTTGAATATAGACATAAAAT
TCAAGTGCTAAAGCGAACACTAATATGGGACGGAGGGACCGAGGGAGTATAAAAAATGGAAAAG
AAAAGGATATAATAATACAGTGTCAAACAAGTACGAATTGTAGACACGAGTCATAACAGGCTGA
ATATGCCAAGAAGTTAATGTTAACAATAGATAAAAATGTAGACATGTCACTGAGTTGCCTGAAA
GCAATGAGACAATAGAAATTTTACCAAGAACCTCAGATAACTGAAAATCACACATCCTTTAATA
ATGCTATGCAATGCAACCATTTGCCACTATCAGTTATCACTATCCTATATTGGCGGCTAGAGAA
AAATTAGTTTGCATTCGACAGATGCAATTTTAAGACTAAGGGTCTGTTTGGTTTCCTACCTAAG
GCGCTACAATCTGCCTAACCTTAGGCGCTCAAATTGAATAACTAAGCTTAGGCAGAAAAGTTAG
ACATGTTGTGGCGCTTCAGGCAGCAAACCAAACAGCCCCTGATTCCTCATTTTTAAAGGGTACA
AAAGCCTCTACAAAATCATGTAAGAATGAAGTAAATGATATGACCTCTATATCTGTGACTCATG
TCCTGTGTCATATCTAAACTACCCCTATTTGCTTTGGATTAGGAAACTTTGTTATTTTTAATGT
GACTAAAACAACTCTGACACTGACGAGTTACTTGATCCCATATAGGAGAACCTAGAATTGTGTG
TTACCATAGCCATACAATAAAGAAATACCAGACACTAAAGCTCAGCAGTGACACAAAATATAAA
GCTAAAAGAAAATCAAGAGAAACTAAAAAATATATCAGAACTGACTTATCATAAAAAATGAAAA
TAAAATTATTTTCCTTGAAAAACTGCCACAACTAACCTTGAAATGTTCATATGCTACATCAAGG
CGACAAGCCCCCACCATGCCGCTTGGCACATTTAGTCGCTTTACATAGGATACTGGAAATGATA
GACCACATTAGCTGAAGTGCTGAACATCCTTTCAGACTCACTAAATAAGCTGGAGATGACTAAA
TTTGCAGAACATTGTTATAGAAAAGGTACTGCCGAGAAATCAAGTGTCTTTAGACAATATTACG
AGTAAATCCTGCTTAGAAATAAATCATCTTTTCTTGGTACAAGATATTGCAACCTACCACCATC
AAAAGAAAGTGTAAACTACATCCAGAGAACTAGGAACCAAAGTGGGTGTTTTTTAACCTGCCCA
ATAGGTCAATAAGCAACTGTGGACCTTTTTGTCTTGCCAGAGCTGGTCACAGTCCATTTCAGAA
TTAACTATACATGTTTAGCGGTTCCAAAAGATAGGGATGCTTTGCACTCAGGTTTGGGTTCAGG
ACATTTATTGACCTAGAAATCCAAAGACGAGAACTGGATTCAGGAAATTTTTATTGTCCCTGAC
TGAATGGTTTGAACAGACTTTAAATAACAGCTAAGGTCACAAGCATCAAACAGAGAAGAACAAC
AAAAGGTATAGAGACAGCATTACCTGCATCATTCAGATCCATAAAAAACCTAAATACTGGACTA
TTTTCAGTCTTCTTCGACGGTGATAGCATCCTTTTGAACCACATAGGAGTC
						
					

			
		

Sequences
Splice junction sequence	AGCATTACCTGCATCATTCAGATCCATAAAAAACCTAAATACTGGACTATTTTCAGTCTTCTTC GACGGTGATAGCATCCTTTTGAACCACATAGGAGTCcatctaattccatcatttgttgccactg caatattcaagttttgcgcactaaaaacaggaaccccatcaagttttttccttctgcccctttg tggaagtg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CATCTAATTCCATCATTTGTTGCCACTGCAATATTCAAGTTTTGCGCACTAAAAACAGGAACCC CATCAAGTTTTTTCCTTCTGCCCCTTTGTGGAAGTGACTTCAATAGCTTATTGGCAGCCTGGAC CTGAAAGGGAAACGATATAATCTCTAATGGCATGCTTAAGTTATAGGTAGGCTGAGAAATTTTA GCACAGACCTGCTTTTCATTTGGAACAAACTGGAACATGTGAGGCTTTTCCTGCAGAAAATTTA TTTTTAATCTTACAAATAGAACATGAGTGCAAGTCATACATAACAAATAATGCGGACTAAAAAT GCTGGTGTTACTCCCTCCATCCCGGAATGATATATTCATGTAAAAGTCAAACTTTACGAATTTT GGCCAACAATTATTCAAATTATATAAAATTTTAAGGCATAGAAAAATGCTGTGATGGATTTATA TTCGAATTGCCTCTGATCTGATATCGGAACTCTTTAGCAAACGAAAACATACAGTAAGAGGAAT TAATGGTCAAAATCTAATTTGTTTGACTTTTCCTGATATGATTATCATTCCAAGACAGATGGAG AATATTACTCCCACCGTCCCAAATTAAAATTCGTTTTAGACATTTATTAGATTCATACAATGAT TAATGTATATGTTTGGTATATATGTCTAGATTCATCATCATCTATTTGAATATAGACATAAAAT TCAAGTGCTAAAGCGAACACTAATATGGGACGGAGGGACCGAGGGAGTATAAAAAATGGAAAAG AAAAGGATATAATAATACAGTGTCAAACAAGTACGAATTGTAGACACGAGTCATAACAGGCTGA ATATGCCAAGAAGTTAATGTTAACAATAGATAAAAATGTAGACATGTCACTGAGTTGCCTGAAA GCAATGAGACAATAGAAATTTTACCAAGAACCTCAGATAACTGAAAATCACACATCCTTTAATA ATGCTATGCAATGCAACCATTTGCCACTATCAGTTATCACTATCCTATATTGGCGGCTAGAGAA AAATTAGTTTGCATTCGACAGATGCAATTTTAAGACTAAGGGTCTGTTTGGTTTCCTACCTAAG GCGCTACAATCTGCCTAACCTTAGGCGCTCAAATTGAATAACTAAGCTTAGGCAGAAAAGTTAG ACATGTTGTGGCGCTTCAGGCAGCAAACCAAACAGCCCCTGATTCCTCATTTTTAAAGGGTACA AAAGCCTCTACAAAATCATGTAAGAATGAAGTAAATGATATGACCTCTATATCTGTGACTCATG TCCTGTGTCATATCTAAACTACCCCTATTTGCTTTGGATTAGGAAACTTTGTTATTTTTAATGT GACTAAAACAACTCTGACACTGACGAGTTACTTGATCCCATATAGGAGAACCTAGAATTGTGTG TTACCATAGCCATACAATAAAGAAATACCAGACACTAAAGCTCAGCAGTGACACAAAATATAAA GCTAAAAGAAAATCAAGAGAAACTAAAAAATATATCAGAACTGACTTATCATAAAAAATGAAAA TAAAATTATTTTCCTTGAAAAACTGCCACAACTAACCTTGAAATGTTCATATGCTACATCAAGG CGACAAGCCCCCACCATGCCGCTTGGCACATTTAGTCGCTTTACATAGGATACTGGAAATGATA GACCACATTAGCTGAAGTGCTGAACATCCTTTCAGACTCACTAAATAAGCTGGAGATGACTAAA TTTGCAGAACATTGTTATAGAAAAGGTACTGCCGAGAAATCAAGTGTCTTTAGACAATATTACG AGTAAATCCTGCTTAGAAATAAATCATCTTTTCTTGGTACAAGATATTGCAACCTACCACCATC AAAAGAAAGTGTAAACTACATCCAGAGAACTAGGAACCAAAGTGGGTGTTTTTTAACCTGCCCA ATAGGTCAATAAGCAACTGTGGACCTTTTTGTCTTGCCAGAGCTGGTCACAGTCCATTTCAGAA TTAACTATACATGTTTAGCGGTTCCAAAAGATAGGGATGCTTTGCACTCAGGTTTGGGTTCAGG ACATTTATTGACCTAGAAATCCAAAGACGAGAACTGGATTCAGGAAATTTTTATTGTCCCTGAC TGAATGGTTTGAACAGACTTTAAATAACAGCTAAGGTCACAAGCATCAAACAGAGAAGAACAAC AAAAGGTATAGAGACAGCATTACCTGCATCATTCAGATCCATAAAAAACCTAAATACTGGACTA TTTTCAGTCTTCTTCGACGGTGATAGCATCCTTTTGAACCACATAGGAGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_000910 						
					
						PMCS
						0.036210108

Conservation Information
Conserved circRNAs	osa_circ_000910
PMCS	0.036210108

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1697099-1694816(-)
1694831-1697024(-)
						
						Potential amino acid sequence
						
							MWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVPSGMVGACRL
DVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNIAVATNDGIR
WTPMWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVPSGMVGA
CRLDVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNIAVATND
GIRWTPMWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVPSGM
VGACRLDVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNIAVA
TNDGIRWTPMWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVP
SGMVGACRLDVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNI
AVATNDGIR(-)
MMELDGLLCGSKGCYHRRRRLKIVQYLGFLWI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1697099-1694816(-) 1694831-1697024(-)
Potential amino acid sequence	MWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVPSGMVGACRL DVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNIAVATNDGIR WTPMWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVPSGMVGA CRLDVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNIAVATND GIRWTPMWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVPSGM VGACRLDVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNIAVA TNDGIRWTPMWFKRMLSPSKKTENSPVFRFFMDLNDAVRDNKNFLNPVLVFGFLVSYVKRLNVP SGMVGACRLDVAYEHFKEKPHMFQFVPNEKQVQAANKLLKSLPQRGRRKKLDGVPVFSAQNLNI AVATNDGIR(-) MMELDGLLCGSKGCYHRRRRLKIVQYLGFLWI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d039319_circ_g.2

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