Plant Circular RNA Database

Detail information of Zm00001d007597_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d007597_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007432
					
						Alias
						Zm02circ00119
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 235973319-235974539  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d007597						
					
						Parent gene annotation
						
							 ABC family1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d007597_circ_g.1 Zm00001d007597_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d007597_T001:4

General Information
CircRNA Name	Zm00001d007597_circ_g.2
ID in PlantcircBase	zma_circ_007432
Alias	Zm02circ00119
Organism	Zea mays
Position	chr2: 235973319-235974539 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d007597
Parent gene annotation	ABC family1
Parent gene strand	+
Alternative splicing	Zm00001d007597_circ_g.1 Zm00001d007597_circ_g.3
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d007597_T001:4

			
						 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  
						
							AGATTGGATACTTGATGATATCAAAGGTCTCCTTGGCCGTTGCAACTTCAGGGATGACATGCTG
GATAGAAAAGTTCAGTTTTTAAGTGGTGGAGAGAAGgaccctgatttgcttttgcttgatgagc
ctacgaatcatgtcgatttggataccattgagtggctggagatgtatctcaagacgcaggatgt
gccgatgg

									
								

					

						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: 819
Transcript exons: 235973319-235973660,235973787-235973927,235974049-235974
228,235974384-235974539
GACCCTGATTTGCTTTTGCTTGATGAGCCTACGAATCATGTCGATTTGGATACCATTGAGTGGC
TGGAGATGTATCTCAAGACGCAGGATGTGCCGATGGTCATTATATCTCATGACAGGGCGTTCCT
TGATCAGTTGTGCACAAAGATAGTGGAAACTGAATTTGGTGTGTCCAAGACATACAAGGGTAAC
TATTCAGAGTACATTCTAGCAAAGGCGGTAGCAGTGGAGGCACAGTATGCTGCGTGGGAGAAGC
AACAGAAGGAAATTGAACAGACAAAGGAGCTGATAAACAGACTTGGTGCTGGAGTTAATGCAGG
GCGTGCTTCCAGCGAGCAGAAGAAATTGGAGAAGCTTGAAAAAGAAGGGTTGATTGAGAAACCT
TTCCAAAGGAAGCAGCTAAAGATCAGATTCCCTGAGCGTGGAAGAAGTGGGAGAACTGTGTTGA
CGATAAACAATCTTCAATTCGGATTTGAGAATAAGACTTTGTTCAACAATGCTAATCTGATAGT
AGAGAGAGGTGAAAAGATAGCTATTATTGGGCCCAATGGTTGTGGGAAGAGCACACTGCTTAAA
CTTATGTTGGGGATGGAGAAGCCACAAGGTGGTGAGGTGCTTCTTGGGGAGCATAATGTGTTGC
CGAACTATTTTGAGCAGAATCAGGCAGAAGCTCTTGATTTAGAGAAGACCGTGTTAGACACTGT
AGCAGAAGCTGCGGAAGATTGGATACTTGATGATATCAAAGGTCTCCTTGGCCGTTGCAACTTC
AGGGATGACATGCTGGATAGAAAAGTTCAGTTTTTAAGTGGTGGAGAGAAG
						
					

						Genomic sequence
						
							GACCCTGATTTGCTTTTGCTTGATGAGCCTACGAATCATGTCGATTTGGATACCATTGAGTGGC
TGGAGATGTATCTCAAGACGCAGGATGTGCCGATGGTCATTATATCTCATGACAGGGCGTTCCT
TGATCAGTTGTGCACAAAGATAGTGGAAACTGAATTTGGTGTGTCCAAGACATACAAGGGTAAC
TATTCAGAGTACATTCTAGCAAAGGCGGTAGCAGTGGAGGCACAGTATGCTGCGTGGGAGAAGC
AACAGAAGGAAATTGAACAGACAAAGGAGCTGATAAACAGACTTGGTGCTGGAGTTAATGCAGG
GCGTGCTTCCAGCGAGCAGAAGGTAACTACTTGGATTGCTTATTGGGAAACCAATCACTGTGAC
CGAGTTGTAATTTTAGTTGCTATTTTTCTTCATATACTTCTACACACTTGTGTGTGACTAGTAA
CTTTTATCTTGTTTCAACAGAAATTGGAGAAGCTTGAAAAAGAAGGGTTGATTGAGAAACCTTT
CCAAAGGAAGCAGCTAAAGATCAGATTCCCTGAGCGTGGAAGAAGTGGGAGAACTGTGTTGACG
ATAAACAATCTTCAATTCGGATTTGAGAATAAGGTCAACAATGTTGTGCAAATGCTCATTTCTT
CCAAGATTTTATTTTTTTCGAATTTATACACTGTGATATTCTCTACATCAAACTTTTGCACATA
TCCTGATTGCTGTGTTGTGTGTCCAGACTTTGTTCAACAATGCTAATCTGATAGTAGAGAGAGG
TGAAAAGATAGCTATTATTGGGCCCAATGGTTGTGGGAAGAGCACACTGCTTAAACTTATGTTG
GGGATGGAGAAGCCACAAGGTGGTGAGGTGCTTCTTGGGGAGCATAATGTGTTGCCGAACTATT
TTGAGCAGAATCAGGTAAACCGAGCTACTCTGTTTGTTATCTTCTATTGTGGTTATTTCAGATA
AAATGTCACCATGGGGGGACTTGGTTATTAGTCATGTTCCTACTCAACAAATACAGTAAAGTTA
TCCCTTTCCTATTAGATTAATGGGCTATGATGTTTTACCAGGCAGAAGCTCTTGATTTAGAGAA
GACCGTGTTAGACACTGTAGCAGAAGCTGCGGAAGATTGGATACTTGATGATATCAAAGGTCTC
CTTGGCCGTTGCAACTTCAGGGATGACATGCTGGATAGAAAAGTTCAGTTTTTAAGTGGTGGAG
AGAAG
						
					

			
		

Sequences
Splice junction sequence	AGATTGGATACTTGATGATATCAAAGGTCTCCTTGGCCGTTGCAACTTCAGGGATGACATGCTG GATAGAAAAGTTCAGTTTTTAAGTGGTGGAGAGAAGgaccctgatttgcttttgcttgatgagc ctacgaatcatgtcgatttggataccattgagtggctggagatgtatctcaagacgcaggatgt gccgatgg
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: 819 Transcript exons: 235973319-235973660,235973787-235973927,235974049-235974 228,235974384-235974539 GACCCTGATTTGCTTTTGCTTGATGAGCCTACGAATCATGTCGATTTGGATACCATTGAGTGGC TGGAGATGTATCTCAAGACGCAGGATGTGCCGATGGTCATTATATCTCATGACAGGGCGTTCCT TGATCAGTTGTGCACAAAGATAGTGGAAACTGAATTTGGTGTGTCCAAGACATACAAGGGTAAC TATTCAGAGTACATTCTAGCAAAGGCGGTAGCAGTGGAGGCACAGTATGCTGCGTGGGAGAAGC AACAGAAGGAAATTGAACAGACAAAGGAGCTGATAAACAGACTTGGTGCTGGAGTTAATGCAGG GCGTGCTTCCAGCGAGCAGAAGAAATTGGAGAAGCTTGAAAAAGAAGGGTTGATTGAGAAACCT TTCCAAAGGAAGCAGCTAAAGATCAGATTCCCTGAGCGTGGAAGAAGTGGGAGAACTGTGTTGA CGATAAACAATCTTCAATTCGGATTTGAGAATAAGACTTTGTTCAACAATGCTAATCTGATAGT AGAGAGAGGTGAAAAGATAGCTATTATTGGGCCCAATGGTTGTGGGAAGAGCACACTGCTTAAA CTTATGTTGGGGATGGAGAAGCCACAAGGTGGTGAGGTGCTTCTTGGGGAGCATAATGTGTTGC CGAACTATTTTGAGCAGAATCAGGCAGAAGCTCTTGATTTAGAGAAGACCGTGTTAGACACTGT AGCAGAAGCTGCGGAAGATTGGATACTTGATGATATCAAAGGTCTCCTTGGCCGTTGCAACTTC AGGGATGACATGCTGGATAGAAAAGTTCAGTTTTTAAGTGGTGGAGAGAAG
Genomic sequence	GACCCTGATTTGCTTTTGCTTGATGAGCCTACGAATCATGTCGATTTGGATACCATTGAGTGGC TGGAGATGTATCTCAAGACGCAGGATGTGCCGATGGTCATTATATCTCATGACAGGGCGTTCCT TGATCAGTTGTGCACAAAGATAGTGGAAACTGAATTTGGTGTGTCCAAGACATACAAGGGTAAC TATTCAGAGTACATTCTAGCAAAGGCGGTAGCAGTGGAGGCACAGTATGCTGCGTGGGAGAAGC AACAGAAGGAAATTGAACAGACAAAGGAGCTGATAAACAGACTTGGTGCTGGAGTTAATGCAGG GCGTGCTTCCAGCGAGCAGAAGGTAACTACTTGGATTGCTTATTGGGAAACCAATCACTGTGAC CGAGTTGTAATTTTAGTTGCTATTTTTCTTCATATACTTCTACACACTTGTGTGTGACTAGTAA CTTTTATCTTGTTTCAACAGAAATTGGAGAAGCTTGAAAAAGAAGGGTTGATTGAGAAACCTTT CCAAAGGAAGCAGCTAAAGATCAGATTCCCTGAGCGTGGAAGAAGTGGGAGAACTGTGTTGACG ATAAACAATCTTCAATTCGGATTTGAGAATAAGGTCAACAATGTTGTGCAAATGCTCATTTCTT CCAAGATTTTATTTTTTTCGAATTTATACACTGTGATATTCTCTACATCAAACTTTTGCACATA TCCTGATTGCTGTGTTGTGTGTCCAGACTTTGTTCAACAATGCTAATCTGATAGTAGAGAGAGG TGAAAAGATAGCTATTATTGGGCCCAATGGTTGTGGGAAGAGCACACTGCTTAAACTTATGTTG GGGATGGAGAAGCCACAAGGTGGTGAGGTGCTTCTTGGGGAGCATAATGTGTTGCCGAACTATT TTGAGCAGAATCAGGTAAACCGAGCTACTCTGTTTGTTATCTTCTATTGTGGTTATTTCAGATA AAATGTCACCATGGGGGGACTTGGTTATTAGTCATGTTCCTACTCAACAAATACAGTAAAGTTA TCCCTTTCCTATTAGATTAATGGGCTATGATGTTTTACCAGGCAGAAGCTCTTGATTTAGAGAA GACCGTGTTAGACACTGTAGCAGAAGCTGCGGAAGATTGGATACTTGATGATATCAAAGGTCTC CTTGGCCGTTGCAACTTCAGGGATGACATGCTGGATAGAAAAGTTCAGTTTTTAAGTGGTGGAG AGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24744209

Conservation Information
Conserved circRNAs	NA
PMCS	0.24744209

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							235973389-235974536(+)
235973434-235974524(-)
						
						Potential amino acid sequence
						
							MYLKTQDVPMVIISHDRAFLDQLCTKIVETEFGVSKTYKGNYSEYILAKAVAVEAQYAAWEKQQ
KEIEQTKELINRLGAGVNAGRASSEQKKLEKLEKEGLIEKPFQRKQLKIRFPERGRSGRTVLTI
NNLQFGFENKTLFNNANLIVERGEKIAIIGPNGCGKSTLLKLMLGMEKPQGGEVLLGEHNVLPN
YFEQNQAEALDLEKTVLDTVAEAAEDWILDDIKGLLGRCNFRDDMLDRKVQFLSGGEKDPDLLL
LDEPTNHVDLDTIEWLEMYLKTQDVPMVIISHDRAFLDQLCTKIVETEFGVSKTYKGNYSEYIL
AKAVAVEAQYAAWEKQQKEIEQTKELINRLGAGVNAGRASSEQKKLEKLEKEGLIEKPFQRKQL
KIRFPERGRSGRTVLTINNLQFGFENKTLFNNANLIVERGEKIAIIGPNGCGKSTLLKLMLGME
KPQGGEVLLGEHNVLPNYFEQNQAEALDLEKTVLDTVAEAAEDWILDDIKGLLGRCNFRDDMLD
RKVQFLSGGEKDPDLLLLDEPTNHVDLDTIEWLEMYLKTQDVPMVIISHDRAFLDQLCTKIVET
EFGVSKTYKGNYSEYILAKAVAVEAQYAAWEKQQKEIEQTKELINRLGAGVNAGRASSEQKKLE
KLEKEGLIEKPFQRKQLKIRFPERGRSGRTVLTINNLQFGFENKTLFNNANLIVERGEKIAIIG
PNGCGKSTLLKLMLGMEKPQGGEVLLGEHNVLPNYFEQNQAEALDLEKTVLDTVAEAAEDWILD
DIKGLLGRCNFRDDMLDRKVQFLSGGEKDPDLLLLDEPTNHVDLDTIEWLEMYLKTQDVPMVII
SHDRAFLDQLCTKIVETEFGVSKTYKGNYSEYILAKAVAVEAQYAAWEKQQKEIEQTKELINRL
GAGVNAGRASSEQKKLEKLEKEGLIEKPFQRKQLKIRFPERGRSGRTVLTINNLQFGFENKTLF
NNANLIVERGEKIAIIGPNGCGKSTLLKLMLGMEKPQGGEVLLGEHNVLPNYFEQNQAEALDLE
KTVLDTVAEAAEDWILDDIKGLLGRCNFRDDMLDRKVQFLSGGEK(+)
MRYNDHRHILRLEIHLQPLNGIQIDMIRRLIKQKQIRVLLSTT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	235973389-235974536(+) 235973434-235974524(-)
Potential amino acid sequence	MYLKTQDVPMVIISHDRAFLDQLCTKIVETEFGVSKTYKGNYSEYILAKAVAVEAQYAAWEKQQ KEIEQTKELINRLGAGVNAGRASSEQKKLEKLEKEGLIEKPFQRKQLKIRFPERGRSGRTVLTI NNLQFGFENKTLFNNANLIVERGEKIAIIGPNGCGKSTLLKLMLGMEKPQGGEVLLGEHNVLPN YFEQNQAEALDLEKTVLDTVAEAAEDWILDDIKGLLGRCNFRDDMLDRKVQFLSGGEKDPDLLL LDEPTNHVDLDTIEWLEMYLKTQDVPMVIISHDRAFLDQLCTKIVETEFGVSKTYKGNYSEYIL AKAVAVEAQYAAWEKQQKEIEQTKELINRLGAGVNAGRASSEQKKLEKLEKEGLIEKPFQRKQL KIRFPERGRSGRTVLTINNLQFGFENKTLFNNANLIVERGEKIAIIGPNGCGKSTLLKLMLGME KPQGGEVLLGEHNVLPNYFEQNQAEALDLEKTVLDTVAEAAEDWILDDIKGLLGRCNFRDDMLD RKVQFLSGGEKDPDLLLLDEPTNHVDLDTIEWLEMYLKTQDVPMVIISHDRAFLDQLCTKIVET EFGVSKTYKGNYSEYILAKAVAVEAQYAAWEKQQKEIEQTKELINRLGAGVNAGRASSEQKKLE KLEKEGLIEKPFQRKQLKIRFPERGRSGRTVLTINNLQFGFENKTLFNNANLIVERGEKIAIIG PNGCGKSTLLKLMLGMEKPQGGEVLLGEHNVLPNYFEQNQAEALDLEKTVLDTVAEAAEDWILD DIKGLLGRCNFRDDMLDRKVQFLSGGEKDPDLLLLDEPTNHVDLDTIEWLEMYLKTQDVPMVII SHDRAFLDQLCTKIVETEFGVSKTYKGNYSEYILAKAVAVEAQYAAWEKQQKEIEQTKELINRL GAGVNAGRASSEQKKLEKLEKEGLIEKPFQRKQLKIRFPERGRSGRTVLTINNLQFGFENKTLF NNANLIVERGEKIAIIGPNGCGKSTLLKLMLGMEKPQGGEVLLGEHNVLPNYFEQNQAEALDLE KTVLDTVAEAAEDWILDDIKGLLGRCNFRDDMLDRKVQFLSGGEK(+) MRYNDHRHILRLEIHLQPLNGIQIDMIRRLIKQKQIRVLLSTT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d007597_circ_g.2

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