Plant Circular RNA Database

Detail information of Zm00001d015446_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d015446_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008617
					
						Alias
						zma_circ_0002249, GRMZM5G893864_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 90511610-90512813  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d015446						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 9 plasma membrane-type
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d015446_circ_g.1 Zm00001d015446_circ_g.3 						
					
						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
						Zm00001d015446_T013:4
Zm00001d015446_T030:4
Zm00001d015446_T002:4
Zm00001d015446_T010:4
Zm00001d015446_T027:4
Zm00001d015446_T020:4
Zm00001d015446_T024:4
Zm00001d015446_T016:4
Zm00001d015446_T026:4
Zm00001d015446_T028:4
Zm00001d015446_T015:3
Zm00001d015446_T018:4
Zm00001d015446_T022:4
Zm00001d015446_T009:4
Zm00001d015446_T017:4
Zm00001d015446_T006:4
Zm00001d015446_T001:4
Zm00001d015446_T004:4
Zm00001d015446_T008:4
Zm00001d015446_T005:4

General Information
CircRNA Name	Zm00001d015446_circ_g.2
ID in PlantcircBase	zma_circ_008617
Alias	zma_circ_0002249, GRMZM5G893864_C1
Organism	Zea mays
Position	chr5: 90511610-90512813 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d015446
Parent gene annotation	Calcium-transporting ATPase 9 plasma membrane-type
Parent gene strand	-
Alternative splicing	Zm00001d015446_circ_g.1 Zm00001d015446_circ_g.3
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	Zm00001d015446_T013:4 Zm00001d015446_T030:4 Zm00001d015446_T002:4 Zm00001d015446_T010:4 Zm00001d015446_T027:4 Zm00001d015446_T020:4 Zm00001d015446_T024:4 Zm00001d015446_T016:4 Zm00001d015446_T026:4 Zm00001d015446_T028:4 Zm00001d015446_T015:3 Zm00001d015446_T018:4 Zm00001d015446_T022:4 Zm00001d015446_T009:4 Zm00001d015446_T017:4 Zm00001d015446_T006:4 Zm00001d015446_T001:4 Zm00001d015446_T004:4 Zm00001d015446_T008:4 Zm00001d015446_T005:4

			
						 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  
						
							CATCATTCGTTCCATCACCAGTAACAGCTACAACATGGCCTATTTTCTTAAGAGCTTTTACTAG
GAGAAGTTTGTCATTAGGAGAGGATCGTGCCATCACctccgtccaactggtggccgcctcataa
gttgatctgttggtggttcagtagccaaagcaagagcaccgagtgtgtccatgatgagattaac
ccagagaa

									
								

					

						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: 455
Transcript exons: 90511610-90511710,90512218-90512355,90512450-90512548,90
512697-90512813
CTCCGTCCAACTGGTGGCCGCCTCATAAGTTGATCTGTTGGTGGTTCAGTAGCCAAAGCAAGAG
CACCGAGTGTGTCCATGATGAGATTAACCCAGAGAAGCTGAACAGCATTTAGAGGAACATTTCC
TGAGGAAACAGCAGCAACAACATTGATGACAAGAGCTGCAACATTTACGGTAAGCTGGAACTGA
ATAAACTTTTGGATATTTGCATAAACAGAGCGACCCCAGCGAACCACCTTCACAACAGAAGAAA
AATTGTCATCCAGAATTATTATGTCTGAGCTCTCTTTGGCTACTTCTGTTCCTTGGATGCCCAT
AGAAAGACCAATATCTGCCTCATGCAATGCAGGAGCATCATTCGTTCCATCACCAGTAACAGCT
ACAACATGGCCTATTTTCTTAAGAGCTTTTACTAGGAGAAGTTTGTCATTAGGAGAGGATCGTG
CCATCAC
						
					

						Genomic sequence
						
							CTCCGTCCAACTGGTGGCCGCCTCATAAGTTGATCTGTTGGTGGTTCAGTAGCCAAAGCAAGAG
CACCGAGTGTGTCCATGATGAGATTAACCCAGAGAAGCTGTATAAAAAACAAAAGGAAGCTAAT
ATTTGTTGGTGTCCAACTTTCAAATAGAAGCTTAATACTTTAACTACACTTTGTTCATTAACAA
CTTGGTTTGGTCCGTGGCAAGTTGGCAATACTGTCACAGTACTTATCATTGACAGAAAGTGCAG
TTATCAGGGTGATCCAATCCTCTTTCCATGGACCAAACCAAATGCAAGATTTTTTTATGGGTGG
TGACTAGAGATAAGTACTGGACTGCAGGCAGGTTATCCCAGAGATCTCCCCGTTCCAAGCAATG
TATTATTTGTGACCAAGGAGACAGTGCAGCATATCCTCCTAATTGTGTTTTTGCTAGGCAATTT
CGGCATAATTTGCTAGCCCTCTTGGGTTTGAGCAAACTGTACGTAGAAGGAACAAGAGCCCTCT
TGGGTTAAAAACTTAAAATACCAATACAGACGAATAGATGTTATTTAATATAGCAGTGATTATT
TAAAAAATCATACTACATATGTTTATCCAAACCTGAACAGCATTTAGAGGAACATTTCCTGAGG
AAACAGCAGCAACAACATTGATGACAAGAGCTGCAACATTTACGGTAAGCTGGAACTGAATAAA
CTTTTGGATATTTGCATAAACAGAGCGACCCCAGCGAACCACCTAGAATATAAAAGATAAAGAA
CATGTAAGACAACGTTGTATTAGGCATGTGCGCGTATTATCAAGATCCTTAGATTCTAAAAATA
GGCCAAACCTTCACAACAGAAGAAAAATTGTCATCCAGAATTATTATGTCTGAGCTCTCTTTGG
CTACTTCTGTTCCTTGGATGCCCATAGAAAGACCAATATCTGCCTGATAAGTGGGAATAATGAT
AAGATTGAGAAGGGGAAGAAACCTCAACATGTTAGAAGTGCTGTATTACCAAATAGTGCTTCAT
ATAATCACATGCATGTTGAATTCTTGTATTCATTTAAAATATGAACTCCCAAATTGAATGTACC
TCATGCAATGCAGGAGCATCATTCGTTCCATCACCAGTAACAGCTACAACATGGCCTATTTTCT
TAAGAGCTTTTACTAGGAGAAGTTTGTCATTAGGAGAGGATCGTGCCATCAC
						
					

			
		

Sequences
Splice junction sequence	CATCATTCGTTCCATCACCAGTAACAGCTACAACATGGCCTATTTTCTTAAGAGCTTTTACTAG GAGAAGTTTGTCATTAGGAGAGGATCGTGCCATCACctccgtccaactggtggccgcctcataa gttgatctgttggtggttcagtagccaaagcaagagcaccgagtgtgtccatgatgagattaac ccagagaa
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: 455 Transcript exons: 90511610-90511710,90512218-90512355,90512450-90512548,90 512697-90512813 CTCCGTCCAACTGGTGGCCGCCTCATAAGTTGATCTGTTGGTGGTTCAGTAGCCAAAGCAAGAG CACCGAGTGTGTCCATGATGAGATTAACCCAGAGAAGCTGAACAGCATTTAGAGGAACATTTCC TGAGGAAACAGCAGCAACAACATTGATGACAAGAGCTGCAACATTTACGGTAAGCTGGAACTGA ATAAACTTTTGGATATTTGCATAAACAGAGCGACCCCAGCGAACCACCTTCACAACAGAAGAAA AATTGTCATCCAGAATTATTATGTCTGAGCTCTCTTTGGCTACTTCTGTTCCTTGGATGCCCAT AGAAAGACCAATATCTGCCTCATGCAATGCAGGAGCATCATTCGTTCCATCACCAGTAACAGCT ACAACATGGCCTATTTTCTTAAGAGCTTTTACTAGGAGAAGTTTGTCATTAGGAGAGGATCGTG CCATCAC
Genomic sequence	CTCCGTCCAACTGGTGGCCGCCTCATAAGTTGATCTGTTGGTGGTTCAGTAGCCAAAGCAAGAG CACCGAGTGTGTCCATGATGAGATTAACCCAGAGAAGCTGTATAAAAAACAAAAGGAAGCTAAT ATTTGTTGGTGTCCAACTTTCAAATAGAAGCTTAATACTTTAACTACACTTTGTTCATTAACAA CTTGGTTTGGTCCGTGGCAAGTTGGCAATACTGTCACAGTACTTATCATTGACAGAAAGTGCAG TTATCAGGGTGATCCAATCCTCTTTCCATGGACCAAACCAAATGCAAGATTTTTTTATGGGTGG TGACTAGAGATAAGTACTGGACTGCAGGCAGGTTATCCCAGAGATCTCCCCGTTCCAAGCAATG TATTATTTGTGACCAAGGAGACAGTGCAGCATATCCTCCTAATTGTGTTTTTGCTAGGCAATTT CGGCATAATTTGCTAGCCCTCTTGGGTTTGAGCAAACTGTACGTAGAAGGAACAAGAGCCCTCT TGGGTTAAAAACTTAAAATACCAATACAGACGAATAGATGTTATTTAATATAGCAGTGATTATT TAAAAAATCATACTACATATGTTTATCCAAACCTGAACAGCATTTAGAGGAACATTTCCTGAGG AAACAGCAGCAACAACATTGATGACAAGAGCTGCAACATTTACGGTAAGCTGGAACTGAATAAA CTTTTGGATATTTGCATAAACAGAGCGACCCCAGCGAACCACCTAGAATATAAAAGATAAAGAA CATGTAAGACAACGTTGTATTAGGCATGTGCGCGTATTATCAAGATCCTTAGATTCTAAAAATA GGCCAAACCTTCACAACAGAAGAAAAATTGTCATCCAGAATTATTATGTCTGAGCTCTCTTTGG CTACTTCTGTTCCTTGGATGCCCATAGAAAGACCAATATCTGCCTGATAAGTGGGAATAATGAT AAGATTGAGAAGGGGAAGAAACCTCAACATGTTAGAAGTGCTGTATTACCAAATAGTGCTTCAT ATAATCACATGCATGTTGAATTCTTGTATTCATTTAAAATATGAACTCCCAAATTGAATGTACC TCATGCAATGCAGGAGCATCATTCGTTCCATCACCAGTAACAGCTACAACATGGCCTATTTTCT TAAGAGCTTTTACTAGGAGAAGTTTGTCATTAGGAGAGGATCGTGCCATCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.153626103

Conservation Information
Conserved circRNAs	NA
PMCS	0.153626103

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							90512488-90511634(+)
90512812-90512812(-)
						
						Potential amino acid sequence
						
							MSELSLATSVPWMPIERPISASCNAGASFVPSPVTATTWPIFLRAFTRRSLSLGEDRAITSVQL
VAAS*(+)
MARSSPNDKLLLVKALKKIGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDD
NFSSVVKVVRWGRSVYANIQKFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQLLWVNLIMDTL
GALALATEPPTDQLMRRPPVGRR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	90512488-90511634(+) 90512812-90512812(-)
Potential amino acid sequence	MSELSLATSVPWMPIERPISASCNAGASFVPSPVTATTWPIFLRAFTRRSLSLGEDRAITSVQL VAAS(+) MARSSPNDKLLLVKALKKIGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDD NFSSVVKVVRWGRSVYANIQKFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQLLWVNLIMDTL GALALATEPPTDQLMRRPPVGRR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d015446_circ_g.2

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