Plant Circular RNA Database

Detail information of Zm00001d019115_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d019115_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009237
					
						Alias
						zma_circ_0002667
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 17579255-17581833  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d019115						
					
						Parent gene annotation
						
							Cleavage and polyadenylation specificity factor (CPSF) A subunit
 protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d019115_T007:5
Zm00001d019115_T029:2
Zm00001d019115_T010:4
Zm00001d019115_T024:4
Zm00001d019115_T046:3
Zm00001d019115_T009:4
Zm00001d019115_T027:5
Zm00001d019115_T045:4
Zm00001d019115_T021:3
Zm00001d019115_T026:3
Zm00001d019115_T033:4
Zm00001d019115_T001:3
Zm00001d019115_T017:2
Zm00001d019115_T008:4
Zm00001d019115_T039:5
Zm00001d019115_T034:4
Zm00001d019115_T047:3
Zm00001d019115_T003:4
Zm00001d019115_T041:2
Zm00001d019115_T013:4
Zm00001d019115_T018:2
Zm00001d019115_T036:4
Zm00001d019115_T048:4
Zm00001d019115_T006:5
Zm00001d019115_T031:4
Zm00001d019115_T004:4
Zm00001d019115_T042:2
Zm00001d019115_T005:4
Zm00001d019115_T044:4
Zm00001d019115_T002:4
Zm00001d019115_T020:4
Zm00001d019115_T051:4

General Information
CircRNA Name	Zm00001d019115_circ_g.1
ID in PlantcircBase	zma_circ_009237
Alias	zma_circ_0002667
Organism	Zea mays
Position	chr7: 17579255-17581833 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d019115
Parent gene annotation	Cleavage and polyadenylation specificity factor (CPSF) A subunit protein
Parent gene strand	-
Alternative splicing	NA
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	Zm00001d019115_T007:5 Zm00001d019115_T029:2 Zm00001d019115_T010:4 Zm00001d019115_T024:4 Zm00001d019115_T046:3 Zm00001d019115_T009:4 Zm00001d019115_T027:5 Zm00001d019115_T045:4 Zm00001d019115_T021:3 Zm00001d019115_T026:3 Zm00001d019115_T033:4 Zm00001d019115_T001:3 Zm00001d019115_T017:2 Zm00001d019115_T008:4 Zm00001d019115_T039:5 Zm00001d019115_T034:4 Zm00001d019115_T047:3 Zm00001d019115_T003:4 Zm00001d019115_T041:2 Zm00001d019115_T013:4 Zm00001d019115_T018:2 Zm00001d019115_T036:4 Zm00001d019115_T048:4 Zm00001d019115_T006:5 Zm00001d019115_T031:4 Zm00001d019115_T004:4 Zm00001d019115_T042:2 Zm00001d019115_T005:4 Zm00001d019115_T044:4 Zm00001d019115_T002:4 Zm00001d019115_T020:4 Zm00001d019115_T051:4

			
						 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  
						
							CCAACAGTGTTCTGCTTTCATTATGGTATAGCACTTTCCTTGGAGTCCCTCCAATTGAAAACTT
TTGTGCATTCAATCGCTTCCCATGAACCAGTTCAACcttccaatctggtgcatgataatacaga
tatgctcccacgtcgatctgataccacagcagtttcacaatttaaaagagcaatatcacccacc
aatctatg

									
								

					

						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: 463
Transcript exons: 17579255-17579393,17579501-17579656,17581666-17581833
CTTCCAATCTGGTGCATGATAATACAGATATGCTCCCACGTCGATCTGATACCACAGCAGTTTC
ACAATTTAAAAGAGCAATATCACCCACCAATCTATGAGCAGGATCAGAATAGACCAATTCCAAC
TTCCTATGACTCTCATTATAAGAATAGAAGAGAACACCATCACGACAATCACCAACAGCAATTC
GTGATGCAAATGTCTTCAGGCAAGTTATTGTAAATCGTGTCCTACCAACAGCACACTTTTTTAT
TCTGTGGGGATTTTCATTTGTGAAACCAAATACATAAATCCCATTTTGTGGATCTACTTGTACA
ACATCTGAAGAAGACGATGCACCATTTAGCCCAGTTCTCAGTACCAACAGTGTTCTGCTTTCAT
TATGGTATAGCACTTTCCTTGGAGTCCCTCCAATTGAAAACTTTTGTGCATTCAATCGCTTCCC
ATGAACCAGTTCAAC
						
					

						Genomic sequence
						
							CTTCCAATCTGGTGCATGATAATACAGATATGCTCCCACGTCGATCTGATACCACAGCAGTTTC
ACAATTTAAAAGAGCAATATCACCCACCAATCTATGAGCAGGATCAGAATAGACCAATTCCAAC
TTCCTATGACTCTGATAAAAATCAGAAAATGAAGAGCCAAGATTAGAACTAACAATAGAAAGAG
CTTCCATCACAAATCCATAAAGAACGTGTCATTTTAATCAGACCCAAGTATTACCTCATTATAA
GAATAGAAGAGAACACCATCACGACAATCACCAACAGCAATTCGTGATGCAAATGTCTTCAGGC
AAGTTATTGTAAATCGTGTCCTACCAACAGCACACTTTTTTATTCTGTGGGGATTTTCATTTGT
GAAACCAAATACATAAATCTGTCAAAAATAAGTAAACAAATGTTAGCTTCCATAAGCAATTGCA
GTCAACTAAACAAGGCCAAAGGGTATTAATTCATTAGCATCGCAAAGATATGAAACAAGAAATG
AATAAAAAATGCCCGTTTTGAAGCTTGGTGGCCAAAAAAGACAAGGACTAGAGAGTTCCATAAA
CAAAGATGCCCGTTTTGGAGCTTGGTGGCCAAAAGATCAGACCTGGGCTATAGTTTGATGGCCA
AAATAGACTTGTTCCTTCTTTGCAATTGAACAATGAACACAATGAGAGCTGCATATTATATTAC
TATTGCATTAAGAAGCTAAGCCATAAATCTGGGCATCTCATTTGATAATGTCCAAAGATCATGA
GGGCAAGGACACACAACATCCTTATTCTCCAACATAAATGTTGACTTCGTGCGGGAAAGGGCGC
TGCCACGGAGACACGTAGGAAAGGGATGTGCAGCCGCAAAGGCATGTGAGGGCAGCAGAAGAAT
CACTGGCCATTTCAGACTCGTGAAATATAGTAGATTAATTGATTGTGATGGGCAAGGTATACAA
ATATAGGCAACATCATCTATACTGGATTGATTGGTTGCAGTGGGTATGGTACACAGATATAGGC
AAGATCCCGGGGGGTTTATAGAAACATATCCGTCAGGGGAAAACCTTGCCTGTCAAAGAAACAA
TCATTATGCAGCTGGGCCCAAAATCTGATGGCACAGTACAAAACCCTATGCCCATACTGGGCAA
GCCCACTAAGGGCCTTAGCCACTATTCTGTCATTACTAATTCCCTTTTAGATAATTTGTCATAG
GAGAGTTCAGCTCCCTTTAAGGAATTTTTTTAAAGAAAATATAGTAAAAACAGCATATAGGCAT
CATACCATATTACCAGCAGCTGCCAACACATAACGATCTAGATAGGGACACAGAGCAAGAACTG
CGCCATTCAATATATATTGAGTCAATGATCTCAATTGCCCTGTCATTTGTTCAGCTTGGATCTG
GTTGCAGCTAAACTCATCAGGACTGCTGCACATGCTGTTACTAGAAAATTCCTCAGTTGTATAT
CCAACAATCTCGTGGAAAGGAGAACCAGAATGTGAAGAGGGATTAAAACTAAAAGTTGGAATAA
ACGAACTGCTCTCACGAGGACTTTCAACGGCCTCCAAGCTTAAAACAATCAGGCGTCCCTTGAT
GCTGCTTCATCAATAAAGAGTAGTCAGTCTTAAGGTATGTTTGGTTCATTACCTCAGTTGCCAC
ACTTTGCCTAACTTTTTTGCCTAAGGTTAGTTATTCAATTCGAACGACTAACCTTAGGCAAAGT
GTGGCACATTTAGCCACAAACCAAACAGGCCCTTTTAATCTTAGCTTCCTTCAACTAAAACCAC
AGATGATCATTGGTAACAATCAATCAATAAGAATCAGACAGGTATCTAAATATAGATTGCAGAC
TGATGAAGCTCTGTATGAGAAAAATAAAAACTACATGTCTTATGGTTTCAGATGTTTCATAGAA
ATCTAAACCCTAAACATAGGAAACATTTATATAGAACTTGATACTGTGCAAACCAAAACCAGGC
CAAATTAAAAAAAAAACTTAAACTTGGTAATTTTTCTGGCTCAGCATAACATCTAAGCACTGCA
TGGTATCATGATATGATTTTGTGAATACATTAAGACCTTGACACACTTTATAATAAAAATGCAA
TAACTAAGTCTAGATGAAAGGTAAATATATTCTCACTGGTTACACTCCACACAACCACAAAAAA
AAGTAGTTGCAAATCAAAGAAAATATTGCTAATGAATCATGGAGATATTAGAAATAAACCGTAT
TATTATAAACAAAAGATCAGGCGTGCACCTTTCTGCTTCACCATTTGACATCATCGGCCGTCCA
GCAGACTTAGTGGTCCCAACAATTAAAACTTGATCATTTCCTATTTTTGCAATTTGCATGCATT
TCGCTGTTTCGCCAGGTTCACATTTATATCTGGAAAGTAATACCCCATTTTGTGGATCTACTTG
TACAACATCTGAAGAAGACGATGCACCATTTAGCCCAGTTCTCAGTACCAACAGTGTTCTGCTT
TCATTATGGTATAGCACTTTCCTTGGAGTCCCTCCAATTGAAAACTTTTGTGCATTCAATCGCT
TCCCATGAACCAGTTCAAC
						
					

			
		

Sequences
Splice junction sequence	CCAACAGTGTTCTGCTTTCATTATGGTATAGCACTTTCCTTGGAGTCCCTCCAATTGAAAACTT TTGTGCATTCAATCGCTTCCCATGAACCAGTTCAACcttccaatctggtgcatgataatacaga tatgctcccacgtcgatctgataccacagcagtttcacaatttaaaagagcaatatcacccacc aatctatg
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: 463 Transcript exons: 17579255-17579393,17579501-17579656,17581666-17581833 CTTCCAATCTGGTGCATGATAATACAGATATGCTCCCACGTCGATCTGATACCACAGCAGTTTC ACAATTTAAAAGAGCAATATCACCCACCAATCTATGAGCAGGATCAGAATAGACCAATTCCAAC TTCCTATGACTCTCATTATAAGAATAGAAGAGAACACCATCACGACAATCACCAACAGCAATTC GTGATGCAAATGTCTTCAGGCAAGTTATTGTAAATCGTGTCCTACCAACAGCACACTTTTTTAT TCTGTGGGGATTTTCATTTGTGAAACCAAATACATAAATCCCATTTTGTGGATCTACTTGTACA ACATCTGAAGAAGACGATGCACCATTTAGCCCAGTTCTCAGTACCAACAGTGTTCTGCTTTCAT TATGGTATAGCACTTTCCTTGGAGTCCCTCCAATTGAAAACTTTTGTGCATTCAATCGCTTCCC ATGAACCAGTTCAAC
Genomic sequence	CTTCCAATCTGGTGCATGATAATACAGATATGCTCCCACGTCGATCTGATACCACAGCAGTTTC ACAATTTAAAAGAGCAATATCACCCACCAATCTATGAGCAGGATCAGAATAGACCAATTCCAAC TTCCTATGACTCTGATAAAAATCAGAAAATGAAGAGCCAAGATTAGAACTAACAATAGAAAGAG CTTCCATCACAAATCCATAAAGAACGTGTCATTTTAATCAGACCCAAGTATTACCTCATTATAA GAATAGAAGAGAACACCATCACGACAATCACCAACAGCAATTCGTGATGCAAATGTCTTCAGGC AAGTTATTGTAAATCGTGTCCTACCAACAGCACACTTTTTTATTCTGTGGGGATTTTCATTTGT GAAACCAAATACATAAATCTGTCAAAAATAAGTAAACAAATGTTAGCTTCCATAAGCAATTGCA GTCAACTAAACAAGGCCAAAGGGTATTAATTCATTAGCATCGCAAAGATATGAAACAAGAAATG AATAAAAAATGCCCGTTTTGAAGCTTGGTGGCCAAAAAAGACAAGGACTAGAGAGTTCCATAAA CAAAGATGCCCGTTTTGGAGCTTGGTGGCCAAAAGATCAGACCTGGGCTATAGTTTGATGGCCA AAATAGACTTGTTCCTTCTTTGCAATTGAACAATGAACACAATGAGAGCTGCATATTATATTAC TATTGCATTAAGAAGCTAAGCCATAAATCTGGGCATCTCATTTGATAATGTCCAAAGATCATGA GGGCAAGGACACACAACATCCTTATTCTCCAACATAAATGTTGACTTCGTGCGGGAAAGGGCGC TGCCACGGAGACACGTAGGAAAGGGATGTGCAGCCGCAAAGGCATGTGAGGGCAGCAGAAGAAT CACTGGCCATTTCAGACTCGTGAAATATAGTAGATTAATTGATTGTGATGGGCAAGGTATACAA ATATAGGCAACATCATCTATACTGGATTGATTGGTTGCAGTGGGTATGGTACACAGATATAGGC AAGATCCCGGGGGGTTTATAGAAACATATCCGTCAGGGGAAAACCTTGCCTGTCAAAGAAACAA TCATTATGCAGCTGGGCCCAAAATCTGATGGCACAGTACAAAACCCTATGCCCATACTGGGCAA GCCCACTAAGGGCCTTAGCCACTATTCTGTCATTACTAATTCCCTTTTAGATAATTTGTCATAG GAGAGTTCAGCTCCCTTTAAGGAATTTTTTTAAAGAAAATATAGTAAAAACAGCATATAGGCAT CATACCATATTACCAGCAGCTGCCAACACATAACGATCTAGATAGGGACACAGAGCAAGAACTG CGCCATTCAATATATATTGAGTCAATGATCTCAATTGCCCTGTCATTTGTTCAGCTTGGATCTG GTTGCAGCTAAACTCATCAGGACTGCTGCACATGCTGTTACTAGAAAATTCCTCAGTTGTATAT CCAACAATCTCGTGGAAAGGAGAACCAGAATGTGAAGAGGGATTAAAACTAAAAGTTGGAATAA ACGAACTGCTCTCACGAGGACTTTCAACGGCCTCCAAGCTTAAAACAATCAGGCGTCCCTTGAT GCTGCTTCATCAATAAAGAGTAGTCAGTCTTAAGGTATGTTTGGTTCATTACCTCAGTTGCCAC ACTTTGCCTAACTTTTTTGCCTAAGGTTAGTTATTCAATTCGAACGACTAACCTTAGGCAAAGT GTGGCACATTTAGCCACAAACCAAACAGGCCCTTTTAATCTTAGCTTCCTTCAACTAAAACCAC AGATGATCATTGGTAACAATCAATCAATAAGAATCAGACAGGTATCTAAATATAGATTGCAGAC TGATGAAGCTCTGTATGAGAAAAATAAAAACTACATGTCTTATGGTTTCAGATGTTTCATAGAA ATCTAAACCCTAAACATAGGAAACATTTATATAGAACTTGATACTGTGCAAACCAAAACCAGGC CAAATTAAAAAAAAAACTTAAACTTGGTAATTTTTCTGGCTCAGCATAACATCTAAGCACTGCA TGGTATCATGATATGATTTTGTGAATACATTAAGACCTTGACACACTTTATAATAAAAATGCAA TAACTAAGTCTAGATGAAAGGTAAATATATTCTCACTGGTTACACTCCACACAACCACAAAAAA AAGTAGTTGCAAATCAAAGAAAATATTGCTAATGAATCATGGAGATATTAGAAATAAACCGTAT TATTATAAACAAAAGATCAGGCGTGCACCTTTCTGCTTCACCATTTGACATCATCGGCCGTCCA GCAGACTTAGTGGTCCCAACAATTAAAACTTGATCATTTCCTATTTTTGCAATTTGCATGCATT TCGCTGTTTCGCCAGGTTCACATTTATATCTGGAAAGTAATACCCCATTTTGTGGATCTACTTG TACAACATCTGAAGAAGACGATGCACCATTTAGCCCAGTTCTCAGTACCAACAGTGTTCTGCTT TCATTATGGTATAGCACTTTCCTTGGAGTCCCTCCAATTGAAAACTTTTGTGCATTCAATCGCT TCCCATGAACCAGTTCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.151628184

Conservation Information
Conserved circRNAs	NA
PMCS	0.151628184

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17581708-17579352(+)
17581820-17579583(+)
						
						Potential amino acid sequence
						
							MHHLAQFSVPTVFCFHYGIALSLESLQLKTFVHSIASHEPVQPSNLVHDNTDMLPRRSDTTAVS
QFKRAISPTNL*(+)
MNQFNLPIWCMIIQICSHVDLIPQQFHNLKEQYHPPIYEQDQNRPIPTSYDSHYKNRREHHHDN
HQQQFVMQMSSGKLL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17581708-17579352(+) 17581820-17579583(+)
Potential amino acid sequence	MHHLAQFSVPTVFCFHYGIALSLESLQLKTFVHSIASHEPVQPSNLVHDNTDMLPRRSDTTAVS QFKRAISPTNL(+) MNQFNLPIWCMIIQICSHVDLIPQQFHNLKEQYHPPIYEQDQNRPIPTSYDSHYKNRREHHHDN HQQQFVMQMSSGKLL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d019115_circ_g.1

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