Plant Circular RNA Database

Detail information of Zm00001d007357_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d007357_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007416
					
						Alias
						Zm02circ00114
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 229615188-229617181  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d007357						
					
						Parent gene annotation
						
							Protein AUXIN SIGNALING F-BOX 3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d007357_T004:3
Zm00001d007357_T001:2
Zm00001d007357_T006:2
Zm00001d007357_T003:2
Zm00001d007357_T002:2
Zm00001d007357_T005:2

General Information
CircRNA Name	Zm00001d007357_circ_g.1
ID in PlantcircBase	zma_circ_007416
Alias	Zm02circ00114
Organism	Zea mays
Position	chr2: 229615188-229617181 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d007357
Parent gene annotation	Protein AUXIN SIGNALING F-BOX 3
Parent gene strand	+
Alternative splicing	NA
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	Zm00001d007357_T004:3 Zm00001d007357_T001:2 Zm00001d007357_T006:2 Zm00001d007357_T003:2 Zm00001d007357_T002:2 Zm00001d007357_T005:2

			
						 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  
						
							CAGAAATCTTACATGCTTGAATCTCAGCTATGCTACATTGATTCAGAGTACCCAGCTTATCGGT
ATTATTCGTCATTGTAAGAAGCTCCATGTCTTATGGgcaacttttggggaactacacgtgtatg
gagttttattagtattccaggggcgtcacaatggcatactttcctgatgaagtagtagggtata
tccttggt

									
								

					

						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
						
							GCAACTTTTGGGGAACTACACGTGTATGGAGTTTTATTAGTATTCCAGGGGCGTCACAATGGCA
TACTTTCCTGATGAAGTAGTAGGGTATATCCTTGGTTATGTAACGTCGCATCAGGACCGCAACG
CGGTGTCCTTGGTCTGCCGGGCATGGTACGACATTGAGCGTCATGGCCGCCATTCAGTGCTTGT
AAGAAACTGTTATGCGGTGTGCCCAGAGCGTGTACACATGCGGTTTCCCAACATGCGTGCACTG
AGCTTGAAGGGCAAACCGCACTTTGCTGAATTCAACCTTGTCCCGGCGGGTTGGGGTGCCACTG
CAAATCCATGGGTGGATGCGTGCGCCCGTGCATGCCCAGGTCTTGAGGAGCTCCGGCTGAAGTT
TATGGTTGTGACTGATGAATGCCTCAAGTTGCTTTCTCTATCCTTTACCAACTTTAAATCACTT
GTCCTTGTTTGTTGTGAGGGGTTCAGTACTACCGGGCTTGCTAATATTGCCACCAATTGCAGGT
GAGAATTCTGAAAACTTAGGCATTATCATGTTTGGGAAAGTGCCTAGTGACCATTGTTTTAGTT
CATCTAGCATGCCCATTTAATTAACAAACAATCCATTTCAGTATTATGTTTGCAATCTTCATCC
TGCTGATGCTGAGTTTATTGTGTCTACACCATATTATACCAGATCATGTATGCCTTTCCATCTC
TGTATACTTCCTTGGTTATTGATTATTAAAAGTTATCTGCTGTGTGTTTATAGATAAAGACTTC
CCAATGCAAATAATTGACGCAATGCAAAATCTACGAAACAGAAGTTATCTACACTTCTAGTTTT
TTCCATAGCTTATCTGTATGATACTTGAATACTGAAATATTGTTTATGTTTACTTTGGTTTATA
TCCAAATACCATAATTGAGATCTTCAATGCTTGGCAGAGCATAAACTCTCAAACTTAGTATCTA
GGTTCCCGGGTCGATGGGATCGAGGAACGGGAACGTGGTAGTGGTACGCTACTAAACTAGGTTT
TAACACTACGGGAATGAGATTGTTCCCAGATTCCTGGAACGGAATGAACGTTCTTGGAACGAGG
AACATGGCCAAGTTCCACGTTCCCGGTTTCTAAGCTCTCGAACTAAAATCTTTGACAAAGATGG
TACAGTAGTTTCTAGTCTGCTTAGTACATGCCTATTGTCTAGTGCTTGAGTGATTGTATGAGTT
CCATTCCTTGTTTCTATCTCTCTAGCAAAGTACATACTGAAAAGGCATGATTGAGACATCTAGC
TAGAACAAATAGATTTCAATGATGGAAGAAAGCTCAAGCTGCAGTTATATAACATTATTGGCTT
CCAGTTTTGGCATCTTCTATTGTGTTAAGAAAACTTCATTTTAATTGACAAAGTGTCATCTTAC
TATTTAGTTTGCTAAAGAGATGTTACTCATGGTTAGTCCACAATATTTTACATTTTTACATATC
TTGTAGCTCTTCACTTTCAGGTTTCTTAAGGAACTAGACTTACAAAAGAGTTGTGTGAAACATC
AAGACCATCAGTGGATTAATTGTTTTCCCAAGTCTTCAACATCACTAGAATGCTTGAATTTTTC
CTGCTTGACTGGGGAGGTGAATGCTGTTGCACTGGAGGAACTTGTTGCAAGGAGTCCAAATCTT
AAAAGTTTAAGGCTGAATCTTGCAGTTCCATTTGATGTTTTGTCCAGAATCCTTTCTCGCACAC
CTAAGCTAGAGGATTTAGGCACAGGATCCTTTTTACAAGGCAATGACCCTGCTGCATATGCCAG
TTTATGTAGAGCTCTTGAGAACTGCACTTCACTGAAGAGTATATCTGGTTTTTGGGATGCTCCA
GGCTTTTATGTTCAAGGAATTTTGTCAAATTGCAAGATCAGAAATCTTACATGCTTGAATCTCA
GCTATGCTACATTGATTCAGAGTACCCAGCTTATCGGTATTATTCGTCATTGTAAGAAGCTCCA
TGTCTTATGG
						
					

			
		

Sequences
Splice junction sequence	CAGAAATCTTACATGCTTGAATCTCAGCTATGCTACATTGATTCAGAGTACCCAGCTTATCGGT ATTATTCGTCATTGTAAGAAGCTCCATGTCTTATGGgcaacttttggggaactacacgtgtatg gagttttattagtattccaggggcgtcacaatggcatactttcctgatgaagtagtagggtata tccttggt
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	GCAACTTTTGGGGAACTACACGTGTATGGAGTTTTATTAGTATTCCAGGGGCGTCACAATGGCA TACTTTCCTGATGAAGTAGTAGGGTATATCCTTGGTTATGTAACGTCGCATCAGGACCGCAACG CGGTGTCCTTGGTCTGCCGGGCATGGTACGACATTGAGCGTCATGGCCGCCATTCAGTGCTTGT AAGAAACTGTTATGCGGTGTGCCCAGAGCGTGTACACATGCGGTTTCCCAACATGCGTGCACTG AGCTTGAAGGGCAAACCGCACTTTGCTGAATTCAACCTTGTCCCGGCGGGTTGGGGTGCCACTG CAAATCCATGGGTGGATGCGTGCGCCCGTGCATGCCCAGGTCTTGAGGAGCTCCGGCTGAAGTT TATGGTTGTGACTGATGAATGCCTCAAGTTGCTTTCTCTATCCTTTACCAACTTTAAATCACTT GTCCTTGTTTGTTGTGAGGGGTTCAGTACTACCGGGCTTGCTAATATTGCCACCAATTGCAGGT GAGAATTCTGAAAACTTAGGCATTATCATGTTTGGGAAAGTGCCTAGTGACCATTGTTTTAGTT CATCTAGCATGCCCATTTAATTAACAAACAATCCATTTCAGTATTATGTTTGCAATCTTCATCC TGCTGATGCTGAGTTTATTGTGTCTACACCATATTATACCAGATCATGTATGCCTTTCCATCTC TGTATACTTCCTTGGTTATTGATTATTAAAAGTTATCTGCTGTGTGTTTATAGATAAAGACTTC CCAATGCAAATAATTGACGCAATGCAAAATCTACGAAACAGAAGTTATCTACACTTCTAGTTTT TTCCATAGCTTATCTGTATGATACTTGAATACTGAAATATTGTTTATGTTTACTTTGGTTTATA TCCAAATACCATAATTGAGATCTTCAATGCTTGGCAGAGCATAAACTCTCAAACTTAGTATCTA GGTTCCCGGGTCGATGGGATCGAGGAACGGGAACGTGGTAGTGGTACGCTACTAAACTAGGTTT TAACACTACGGGAATGAGATTGTTCCCAGATTCCTGGAACGGAATGAACGTTCTTGGAACGAGG AACATGGCCAAGTTCCACGTTCCCGGTTTCTAAGCTCTCGAACTAAAATCTTTGACAAAGATGG TACAGTAGTTTCTAGTCTGCTTAGTACATGCCTATTGTCTAGTGCTTGAGTGATTGTATGAGTT CCATTCCTTGTTTCTATCTCTCTAGCAAAGTACATACTGAAAAGGCATGATTGAGACATCTAGC TAGAACAAATAGATTTCAATGATGGAAGAAAGCTCAAGCTGCAGTTATATAACATTATTGGCTT CCAGTTTTGGCATCTTCTATTGTGTTAAGAAAACTTCATTTTAATTGACAAAGTGTCATCTTAC TATTTAGTTTGCTAAAGAGATGTTACTCATGGTTAGTCCACAATATTTTACATTTTTACATATC TTGTAGCTCTTCACTTTCAGGTTTCTTAAGGAACTAGACTTACAAAAGAGTTGTGTGAAACATC AAGACCATCAGTGGATTAATTGTTTTCCCAAGTCTTCAACATCACTAGAATGCTTGAATTTTTC CTGCTTGACTGGGGAGGTGAATGCTGTTGCACTGGAGGAACTTGTTGCAAGGAGTCCAAATCTT AAAAGTTTAAGGCTGAATCTTGCAGTTCCATTTGATGTTTTGTCCAGAATCCTTTCTCGCACAC CTAAGCTAGAGGATTTAGGCACAGGATCCTTTTTACAAGGCAATGACCCTGCTGCATATGCCAG TTTATGTAGAGCTCTTGAGAACTGCACTTCACTGAAGAGTATATCTGGTTTTTGGGATGCTCCA GGCTTTTATGTTCAAGGAATTTTGTCAAATTGCAAGATCAGAAATCTTACATGCTTGAATCTCA GCTATGCTACATTGATTCAGAGTACCCAGCTTATCGGTATTATTCGTCATTGTAAGAAGCTCCA TGTCTTATGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.044401534

Conservation Information
Conserved circRNAs	NA
PMCS	0.044401534

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							229617179-229615267(+)
229615247-229615259(+)
229615370-229617149(-)
						
						Potential amino acid sequence
						
							MGNFWGTTRVWSFISIPGASQWHTFLMK*(+)
MAYFPDEVVGYILGYVTSHQDRNAVSLVCRAWYDIERHGRHSVLVRNCYAVCPERVHMRFPNMR
ALSLKGKPHFAEFNLVPAGWGATANPWVDACARACPGLEELRLKFMVVTDECLKLLSLSFTNFK
SLVLVCCEGFSTTGLANIATNCRFLKELDLQKSCVKHQDHQWINCFPKSSTSLECLNFSCLTGE
VNAVALEELVARSPNLKSLRLNLAVPFDVLSRILSRTPKLEDLGTGSFLQGNDPAAYASLCRAL
ENCTSLKSISGFWDAPGFYVQGILSNCKIRNLTCLNLSYATLIQSTQLIGIIRHCKKLHVLWAT
FGELHVYGVLLVFQGRHNGILS*(+)
MAAMTLNVVPCPADQGHRVAVLMRRYITKDIPYYFIRKVCHCDAPGILIKLHTRVVPQKLPIRH
GASYNDE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	229617179-229615267(+) 229615247-229615259(+) 229615370-229617149(-)
Potential amino acid sequence	MGNFWGTTRVWSFISIPGASQWHTFLMK(+) MAYFPDEVVGYILGYVTSHQDRNAVSLVCRAWYDIERHGRHSVLVRNCYAVCPERVHMRFPNMR ALSLKGKPHFAEFNLVPAGWGATANPWVDACARACPGLEELRLKFMVVTDECLKLLSLSFTNFK SLVLVCCEGFSTTGLANIATNCRFLKELDLQKSCVKHQDHQWINCFPKSSTSLECLNFSCLTGE VNAVALEELVARSPNLKSLRLNLAVPFDVLSRILSRTPKLEDLGTGSFLQGNDPAAYASLCRAL ENCTSLKSISGFWDAPGFYVQGILSNCKIRNLTCLNLSYATLIQSTQLIGIIRHCKKLHVLWAT FGELHVYGVLLVFQGRHNGILS(+) MAAMTLNVVPCPADQGHRVAVLMRRYITKDIPYYFIRKVCHCDAPGILIKLHTRVVPQKLPIRH GASYNDE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d007357_circ_g.1

Address

Any questions?

Supported by