Plant Circular RNA Database

Detail information of Zm00001d003309_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d003309_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007158
					
						Alias
						Zm02circ00042
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 39696490-39698883  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d003309						
					
						Parent gene annotation
						
							Copper amine oxidase family protein
							
						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
						Zm00001d003309_T002:6
Zm00001d003309_T001:6
Zm00001d003309_T003:4

General Information
CircRNA Name	Zm00001d003309_circ_g.2
ID in PlantcircBase	zma_circ_007158
Alias	Zm02circ00042
Organism	Zea mays
Position	chr2: 39696490-39698883 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d003309
Parent gene annotation	Copper amine oxidase family protein
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	Zm00001d003309_T002:6 Zm00001d003309_T001:6 Zm00001d003309_T003:4

			
						 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  
						
							TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATG
CGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgatgctatggagtatgctgaatgtgagg
ctactgtcaaaagttatcctccatttattgaagctatgaagagaagaggtgtggatgacatgga
tcttgtta

									
								

					

						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
						
							GATGCTATGGAGTATGCTGAATGTGAGGCTACTGTCAAAAGTTATCCTCCATTTATTGAAGCTA
TGAAGAGAAGAGGTGTGGATGACATGGATCTTGTTATGGTGGATGCTTGGTAATTTATATATAA
GGGCTTTCTTGGGCTAAAATTTTCCTATTTTGCTATGTTTCAACTTGCATCATCATATTTGTAA
ATTGAAAGGAAAGTTATTAAATTGTCAGGTGTGCTGGCTACTACAGCGAAGCTGATGCTCCTAG
TCGCAGACTTGGCAAGCCTTTGATATTTTGCAGAACTGAGAGTGATAGCCCCATGGAGAATGGT
TATGCTCGTCCTGTAGAAGGAATCCATGTTGTTGTTGATATGCAGAATAATGCTGTGATAGAGT
TTGAAGATAGGAAGTTGGTTCCTCTACCCCCTCCAGATCATTTGAGAAACTATACTCCTGGGGA
GACAAGAGGAGGTGTTGATCGAAGTGATGTAAAACCACTTATCATCAATCAGCCTGAGGGTCCA
AGTTTTCGAATTAATGGCTATTTTGTGGAATGGCAGAAGGTAATTGTTTGTTGAACTGCAGTGC
TAGTATTAACATAATGTCTTCTGAAATAAATAACACTTAATGGTTATGGCAGTGGAACTTCCGT
ATTGGCTTCACCCCCAAAGAGGGTTTGGTTATCTATTCTGTTGCTTATGTTGATGGTAGCCGTG
GACGTAGACCTATAGCACATAGGCTGAGCTTTGTTGAGATGGTTGTTCCTTATGGAGATCCAAG
TGAACCACATTATCGCAAGAATGCATTTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCAT
TCTCTTAAGAAGGTTATTTTATTCAGTTCTTGATGTGTATACTTTGACGTTCAAAATTTTTCTT
TGATTTGACTATGCTCTTTAACCTTTTTGTGCAGGGATGCGATTGCTTGGGCTACATAAAATAT
TTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGC
ATGAGGAGGATCATGGGATCCTTTGGAAACATCAAGACTGGAGAACTGGTTTAGCAGAAGTAAG
GCGGTCAAGGAGGCTCACTGTTTCATTTATCTGTACAGTTGCAAACTATGAGTATGGTTTTTAC
TGGCACTTCTATCAGGTAATATTTCATTTCCTCTTATAATGTTACAAAGTAAGTACCATTTACC
TACAATACCCAATATATATATTATCTATACAAGTTGATTACCGCTCACTGATGGGTTTTAGTGA
TTAAATGTTCTTAAAAATTTCTGAAGCTTTTTCCGCGATCATGTCTAAGCACATTTTTCTTAAA
AATGTTACTTCATTTCAAAGGAATTGAAATTTACTCAATAGAGTAGGTTATTTGGTTTGGAATT
TGACATTCCACCACTTTCCCAACTTATAGATATAAGCCTATAACACGCTCATAGGATGATGTGT
AGAAATTGATTTTATGTATATATTTCTATTTTCTACTCTGCAACTTATAACACGCTATTCGGCT
CACTACTCTATAGTAGAAATTTAACATATAAATATCTTCCACATATGGCCAACATTAATATACG
ATTAAATTATGTATACCATATTAGCTTAATTGTTCTATGCCTAAATTAGGATTATTAGAATGGA
ATTCAATTCTAAGGATCCAAACGGGGACTAAGAGGAAATAATTTTCTGAAGCTTCAAAGTTTTG
TAATTATTTGTTGATCCTCTTGGTTGCAGGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGG
AATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCT
GGTCTGTATGCACCAGTTCATCAGCATTTCTTTGTTGCCCGTATGGACATGGCTGTTGATTGCA
AACCTAATGAAGCTCATAACCAGGTTGGGGGTTGCCATCTATTTGCACCTTTTTTTTAATCAAT
CAAATCGCTCACAAAAATCGTTTGCAATCTGAATGGGACCACACAAAATTCAATTATATATTTA
CATTAGATACACGAAGGGCAGACCTGTTGCTGGGAAAAGGTTTGCCTCAATTTGCCCCTTCCTA
GGCCATAAGTGTATGCTTTGTAGACCTTAAGTGTGTAAAAGTAATTACCACTGCACATTGCATG
ATATCAATCTGTCTTCATCCAATGGAGATCCCTGTATTCCATATTGAAGCCATTGTGATTGATC
ATTTTTCGTGCAGGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
AATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCG
ACCCTTCATCTGCCCGCCACTGGATT
						
					

			
		

Sequences
Splice junction sequence	TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATG CGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgatgctatggagtatgctgaatgtgagg ctactgtcaaaagttatcctccatttattgaagctatgaagagaagaggtgtggatgacatgga tcttgtta
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	GATGCTATGGAGTATGCTGAATGTGAGGCTACTGTCAAAAGTTATCCTCCATTTATTGAAGCTA TGAAGAGAAGAGGTGTGGATGACATGGATCTTGTTATGGTGGATGCTTGGTAATTTATATATAA GGGCTTTCTTGGGCTAAAATTTTCCTATTTTGCTATGTTTCAACTTGCATCATCATATTTGTAA ATTGAAAGGAAAGTTATTAAATTGTCAGGTGTGCTGGCTACTACAGCGAAGCTGATGCTCCTAG TCGCAGACTTGGCAAGCCTTTGATATTTTGCAGAACTGAGAGTGATAGCCCCATGGAGAATGGT TATGCTCGTCCTGTAGAAGGAATCCATGTTGTTGTTGATATGCAGAATAATGCTGTGATAGAGT TTGAAGATAGGAAGTTGGTTCCTCTACCCCCTCCAGATCATTTGAGAAACTATACTCCTGGGGA GACAAGAGGAGGTGTTGATCGAAGTGATGTAAAACCACTTATCATCAATCAGCCTGAGGGTCCA AGTTTTCGAATTAATGGCTATTTTGTGGAATGGCAGAAGGTAATTGTTTGTTGAACTGCAGTGC TAGTATTAACATAATGTCTTCTGAAATAAATAACACTTAATGGTTATGGCAGTGGAACTTCCGT ATTGGCTTCACCCCCAAAGAGGGTTTGGTTATCTATTCTGTTGCTTATGTTGATGGTAGCCGTG GACGTAGACCTATAGCACATAGGCTGAGCTTTGTTGAGATGGTTGTTCCTTATGGAGATCCAAG TGAACCACATTATCGCAAGAATGCATTTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCAT TCTCTTAAGAAGGTTATTTTATTCAGTTCTTGATGTGTATACTTTGACGTTCAAAATTTTTCTT TGATTTGACTATGCTCTTTAACCTTTTTGTGCAGGGATGCGATTGCTTGGGCTACATAAAATAT TTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGC ATGAGGAGGATCATGGGATCCTTTGGAAACATCAAGACTGGAGAACTGGTTTAGCAGAAGTAAG GCGGTCAAGGAGGCTCACTGTTTCATTTATCTGTACAGTTGCAAACTATGAGTATGGTTTTTAC TGGCACTTCTATCAGGTAATATTTCATTTCCTCTTATAATGTTACAAAGTAAGTACCATTTACC TACAATACCCAATATATATATTATCTATACAAGTTGATTACCGCTCACTGATGGGTTTTAGTGA TTAAATGTTCTTAAAAATTTCTGAAGCTTTTTCCGCGATCATGTCTAAGCACATTTTTCTTAAA AATGTTACTTCATTTCAAAGGAATTGAAATTTACTCAATAGAGTAGGTTATTTGGTTTGGAATT TGACATTCCACCACTTTCCCAACTTATAGATATAAGCCTATAACACGCTCATAGGATGATGTGT AGAAATTGATTTTATGTATATATTTCTATTTTCTACTCTGCAACTTATAACACGCTATTCGGCT CACTACTCTATAGTAGAAATTTAACATATAAATATCTTCCACATATGGCCAACATTAATATACG ATTAAATTATGTATACCATATTAGCTTAATTGTTCTATGCCTAAATTAGGATTATTAGAATGGA ATTCAATTCTAAGGATCCAAACGGGGACTAAGAGGAAATAATTTTCTGAAGCTTCAAAGTTTTG TAATTATTTGTTGATCCTCTTGGTTGCAGGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGG AATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCT GGTCTGTATGCACCAGTTCATCAGCATTTCTTTGTTGCCCGTATGGACATGGCTGTTGATTGCA AACCTAATGAAGCTCATAACCAGGTTGGGGGTTGCCATCTATTTGCACCTTTTTTTTAATCAAT CAAATCGCTCACAAAAATCGTTTGCAATCTGAATGGGACCACACAAAATTCAATTATATATTTA CATTAGATACACGAAGGGCAGACCTGTTGCTGGGAAAAGGTTTGCCTCAATTTGCCCCTTCCTA GGCCATAAGTGTATGCTTTGTAGACCTTAAGTGTGTAAAAGTAATTACCACTGCACATTGCATG ATATCAATCTGTCTTCATCCAATGGAGATCCCTGTATTCCATATTGAAGCCATTGTGATTGATC ATTTTTCGTGCAGGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT AATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCG ACCCTTCATCTGCCCGCCACTGGATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.166346258

Conservation Information
Conserved circRNAs	NA
PMCS	0.166346258

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							39696497-39698880(+)
39698327-39696553(+)
39696838-39698865(-)
						
					

						Potential amino acid sequence
						
							MEYAECEATVKSYPPFIEAMKRRGVDDMDLVMVDAWCAGYYSEADAPSRRLGKPLIFCRTESDS
PMENGYARPVEGIHVVVDMQNNAVIEFEDRKLVPLPPPDHLRNYTPGETRGGVDRSDVKPLIIN
QPEGPSFRINGYFVEWQKWNFRIGFTPKEGLVIYSVAYVDGSRGRRPIAHRLSFVEMVVPYGDP
SEPHYRKNAFDAGEDGLGKNAHSLKKGCDCLGYIKYFDAHFTNFTGGVETIENCVCLHEEDHGI
LWKHQDWRTGLAEVRRSRRLTVSFICTVANYEYGFYWHFYQDGKIEAEVKLTGILSLGALMPGE
SRKYGTTIAPGLYAPVHQHFFVARMDMAVDCKPNEAHNQVVEVNVKVESAGTHNVHNNAFYAEE
KLLKSELQAMRDCDPSSARHWIDAMEYAECEATVKSYPPFIEAMKRRGVDDMDLVMVDAWCAGY
YSEADAPSRRLGKPLIFCRTESDSPMENGYARPVEGIHVVVDMQNNAVIEFEDRKLVPLPPPDH
LRNYTPGETRGGVDRSDVKPLIINQPEGPSFRINGYFVEWQKWNFRIGFTPKEGLVIYSVAYVD
GSRGRRPIAHRLSFVEMVVPYGDPSEPHYRKNAFDAGEDGLGKNAHSLKKGCDCLGYIKYFDAH
FTNFTGGVETIENCVCLHEEDHGILWKHQDWRTGLAEVRRSRRLTVSFICTVANYEYGFYWHFY
QDGKIEAEVKLTGILSLGALMPGESRKYGTTIAPGLYAPVHQHFFVARMDMAVDCKPNEAHNQV
VEVNVKVESAGTHNVHNNAFYAEEKLLKSELQAMRDCDPSSARHWIDAMEYAECEATVKSYPPF
IEAMKRRGVDDMDLVMVDAWCAGYYSEADAPSRRLGKPLIFCRTESDSPMENGYARPVEGIHVV
VDMQNNAVIEFEDRKLVPLPPPDHLRNYTPGETRGGVDRSDVKPLIINQPEGPSFRINGYFVEW
QKWNFRIGFTPKEGLVIYSVAYVDGSRGRRPIAHRLSFVEMVVPYGDPSEPHYRKNAFDAGEDG
LGKNAHSLKKGCDCLGYIKYFDAHFTNFTGGVETIENCVCLHEEDHGILWKHQDWRTGLAEVRR
SRRLTVSFICTVANYEYGFYWHFYQDGKIEAEVKLTGILSLGALMPGESRKYGTTIAPGLYAPV
HQHFFVARMDMAVDCKPNEAHNQVVEVNVKVESAGTHNVHNNAFYAEEKLLKSELQAMRDCDPS
SARHWIDAMEYAECEATVKSYPPFIEAMKRRGVDDMDLVMVDAWCAGYYSEADAPSRRLGKPLI
FCRTESDSPMENGYARPVEGIHVVVDMQNNAVIEFEDRKLVPLPPPDHLRNYTPGETRGGVDRS
DVKPLIINQPEGPSFRINGYFVEWQKWNFRIGFTPKEGLVIYSVAYVDGSRGRRPIAHRLSFVE
MVVPYGDPSEPHYRKNAFDAGEDGLGKNAHSLKKGCDCLGYIKYFDAHFTNFTGGVETIENCVC
LHEEDHGILWKHQDWRTGLAEVRRSRRLTVSFICTVANYEYGFYWHFYQDGKIEAEVKLTGILS
LGALMPGESRKYGTTIAPGLYAPVHQHFFVARMDMAVDCKPNEAHNQVVEVNVKVESAGTHNVH
NNAFYAEEKLLKSELQAMRDCDPSSARHWI(+)
MAQLLPLVCMHQFISISLLPVWTWLLIANLMKLITRWLRLMLKWKVQAHIMCIIMLSMLKRSCS
NLSCKQCVIATLHLPATGLMLWSMLNVRLLSKVILHLLKL*(+)
MDSFYRTSITILHGAITLSSAKYQRLAKSATRSISFAVVASTPSIHHNKIHVIHTSSLHSFNKW
RITFDSSLTFSILHSINPVAGR*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	39696497-39698880(+) 39698327-39696553(+) 39696838-39698865(-)
Potential amino acid sequence	MEYAECEATVKSYPPFIEAMKRRGVDDMDLVMVDAWCAGYYSEADAPSRRLGKPLIFCRTESDS PMENGYARPVEGIHVVVDMQNNAVIEFEDRKLVPLPPPDHLRNYTPGETRGGVDRSDVKPLIIN QPEGPSFRINGYFVEWQKWNFRIGFTPKEGLVIYSVAYVDGSRGRRPIAHRLSFVEMVVPYGDP SEPHYRKNAFDAGEDGLGKNAHSLKKGCDCLGYIKYFDAHFTNFTGGVETIENCVCLHEEDHGI LWKHQDWRTGLAEVRRSRRLTVSFICTVANYEYGFYWHFYQDGKIEAEVKLTGILSLGALMPGE SRKYGTTIAPGLYAPVHQHFFVARMDMAVDCKPNEAHNQVVEVNVKVESAGTHNVHNNAFYAEE KLLKSELQAMRDCDPSSARHWIDAMEYAECEATVKSYPPFIEAMKRRGVDDMDLVMVDAWCAGY YSEADAPSRRLGKPLIFCRTESDSPMENGYARPVEGIHVVVDMQNNAVIEFEDRKLVPLPPPDH LRNYTPGETRGGVDRSDVKPLIINQPEGPSFRINGYFVEWQKWNFRIGFTPKEGLVIYSVAYVD GSRGRRPIAHRLSFVEMVVPYGDPSEPHYRKNAFDAGEDGLGKNAHSLKKGCDCLGYIKYFDAH FTNFTGGVETIENCVCLHEEDHGILWKHQDWRTGLAEVRRSRRLTVSFICTVANYEYGFYWHFY QDGKIEAEVKLTGILSLGALMPGESRKYGTTIAPGLYAPVHQHFFVARMDMAVDCKPNEAHNQV VEVNVKVESAGTHNVHNNAFYAEEKLLKSELQAMRDCDPSSARHWIDAMEYAECEATVKSYPPF IEAMKRRGVDDMDLVMVDAWCAGYYSEADAPSRRLGKPLIFCRTESDSPMENGYARPVEGIHVV VDMQNNAVIEFEDRKLVPLPPPDHLRNYTPGETRGGVDRSDVKPLIINQPEGPSFRINGYFVEW QKWNFRIGFTPKEGLVIYSVAYVDGSRGRRPIAHRLSFVEMVVPYGDPSEPHYRKNAFDAGEDG LGKNAHSLKKGCDCLGYIKYFDAHFTNFTGGVETIENCVCLHEEDHGILWKHQDWRTGLAEVRR SRRLTVSFICTVANYEYGFYWHFYQDGKIEAEVKLTGILSLGALMPGESRKYGTTIAPGLYAPV HQHFFVARMDMAVDCKPNEAHNQVVEVNVKVESAGTHNVHNNAFYAEEKLLKSELQAMRDCDPS SARHWIDAMEYAECEATVKSYPPFIEAMKRRGVDDMDLVMVDAWCAGYYSEADAPSRRLGKPLI FCRTESDSPMENGYARPVEGIHVVVDMQNNAVIEFEDRKLVPLPPPDHLRNYTPGETRGGVDRS DVKPLIINQPEGPSFRINGYFVEWQKWNFRIGFTPKEGLVIYSVAYVDGSRGRRPIAHRLSFVE MVVPYGDPSEPHYRKNAFDAGEDGLGKNAHSLKKGCDCLGYIKYFDAHFTNFTGGVETIENCVC LHEEDHGILWKHQDWRTGLAEVRRSRRLTVSFICTVANYEYGFYWHFYQDGKIEAEVKLTGILS LGALMPGESRKYGTTIAPGLYAPVHQHFFVARMDMAVDCKPNEAHNQVVEVNVKVESAGTHNVH NNAFYAEEKLLKSELQAMRDCDPSSARHWI(+) MAQLLPLVCMHQFISISLLPVWTWLLIANLMKLITRWLRLMLKWKVQAHIMCIIMLSMLKRSCS NLSCKQCVIATLHLPATGLMLWSMLNVRLLSKVILHLLKL(+) MDSFYRTSITILHGAITLSSAKYQRLAKSATRSISFAVVASTPSIHHNKIHVIHTSSLHSFNKW RITFDSSLTFSILHSINPVAGR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d003309_circ_g.2

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