Plant Circular RNA Database

Detail information of Zm00001d040166_circ_g.9

			
						 General Information
					
						CircRNA Name
						Zm00001d040166_circ_g.9
					
						ID in PlantcircBase
						zma_circ_007537
					
						Alias
						Zm03circ00019, zma_circ_0001038
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 30128346-30140465  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d040166						
					
						Parent gene annotation
						
							ataxia-telangiectasia mutated
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d040166_circ_g.10 Zm00001d040166_circ_g.11 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d040166_T047:7
Zm00001d040166_T048:7
Zm00001d040166_T052:7
Zm00001d040166_T044:7
Zm00001d040166_T056:7
Zm00001d040166_T014:7
Zm00001d040166_T042:7
Zm00001d040166_T037:7
Zm00001d040166_T055:7
Zm00001d040166_T045:4
Zm00001d040166_T046:7
Zm00001d040166_T013:7
Zm00001d040166_T015:7
Zm00001d040166_T054:2
Zm00001d040166_T049:7
Zm00001d040166_T005:7
Zm00001d040166_T012:7
Zm00001d040166_T040:7
Zm00001d040166_T041:7
Zm00001d040166_T053:7
Zm00001d040166_T051:7

General Information
CircRNA Name	Zm00001d040166_circ_g.9
ID in PlantcircBase	zma_circ_007537
Alias	Zm03circ00019, zma_circ_0001038
Organism	Zea mays
Position	chr3: 30128346-30140465 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d040166
Parent gene annotation	ataxia-telangiectasia mutated
Parent gene strand	-
Alternative splicing	Zm00001d040166_circ_g.10 Zm00001d040166_circ_g.11
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d040166_T047:7 Zm00001d040166_T048:7 Zm00001d040166_T052:7 Zm00001d040166_T044:7 Zm00001d040166_T056:7 Zm00001d040166_T014:7 Zm00001d040166_T042:7 Zm00001d040166_T037:7 Zm00001d040166_T055:7 Zm00001d040166_T045:4 Zm00001d040166_T046:7 Zm00001d040166_T013:7 Zm00001d040166_T015:7 Zm00001d040166_T054:2 Zm00001d040166_T049:7 Zm00001d040166_T005:7 Zm00001d040166_T012:7 Zm00001d040166_T040:7 Zm00001d040166_T041:7 Zm00001d040166_T053:7 Zm00001d040166_T051:7

			
						 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  
						
							TTCAATTACGAGAACAGATTGTGGACCAACAGCTAAGACTTCTCTAGCTGTAACTGGAGAAATA
TTTGAGAACTTCACCATCTTGGCACCAATGCTTGAGattgtgtccacaaatccatcaacaacca
ttctgactgaaagtgcaacattcttcttggaaaaatatggaatttgtggcccatgagcagatga
agaaacag

						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: 777
Transcript exons: 30128346-30128470,30129199-30129384,30129718-30129840,30
131282-30131356,30131528-30131591,30131708-30131754,3014
0309-30140465
ATTGTGTCCACAAATCCATCAACAACCATTCTGACTGAAAGTGCAACATTCTTCTTGGAAAAAT
ATGGAATTTGTGGCCCATGAGCAGATGAAGAAACAGAGAGCAAAAAGGCAACGATCGCAACCAT
GTGTTTTTTAATGAGATCATCACGCTCAAGTTCAGAAATTTCACCAAGCTGCAAAACTGATTCA
CATAAGACAGTTTCAGCTAAGTCCTTCTCTGGCCCTGTGCCACATCTGACAGCAATGCACATTC
CAAAGATTGGAACGAAGTATCTCTTGATAATGATTGACAAAGGTTGAGATAAAATCTTCGATAT
CCAATTCATATCAGCACCATCACCCCTGAGAATGAGGAAAGGGAGAAGCCATGAACTACAATGT
TCAACAAAGTTGTTTGGCTCAGCAGATCCATAACCAAACATTTCTTGCACCTCAACAAGTGAAA
TTAGATTCATCTCACAAGCAACCCATCGAAAAAGAATCGGGCCCATCACTTGGTCCAGATACTT
GCTTCTTGAAGCATAACCAAGCCTCCTTGAAATGGAATCAAATAACGCAAAAGCTAATTCTCGC
TGAGAAGGCTCTATAGCAGCCGCAGCAGAAATCATGAACAAACACTCAACTTCAACATCCTCGC
TATGCACAGCCAAATGAGCTAGTGTAATGAGAGCAGTTTCAATTACGAGAACAGATTGTGGACC
AACAGCTAAGACTTCTCTAGCTGTAACTGGAGAAATATTTGAGAACTTCACCATCTTGGCACCA
ATGCTTGAG
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	TTCAATTACGAGAACAGATTGTGGACCAACAGCTAAGACTTCTCTAGCTGTAACTGGAGAAATA TTTGAGAACTTCACCATCTTGGCACCAATGCTTGAGattgtgtccacaaatccatcaacaacca ttctgactgaaagtgcaacattcttcttggaaaaatatggaatttgtggcccatgagcagatga agaaacag
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: 777 Transcript exons: 30128346-30128470,30129199-30129384,30129718-30129840,30 131282-30131356,30131528-30131591,30131708-30131754,3014 0309-30140465 ATTGTGTCCACAAATCCATCAACAACCATTCTGACTGAAAGTGCAACATTCTTCTTGGAAAAAT ATGGAATTTGTGGCCCATGAGCAGATGAAGAAACAGAGAGCAAAAAGGCAACGATCGCAACCAT GTGTTTTTTAATGAGATCATCACGCTCAAGTTCAGAAATTTCACCAAGCTGCAAAACTGATTCA CATAAGACAGTTTCAGCTAAGTCCTTCTCTGGCCCTGTGCCACATCTGACAGCAATGCACATTC CAAAGATTGGAACGAAGTATCTCTTGATAATGATTGACAAAGGTTGAGATAAAATCTTCGATAT CCAATTCATATCAGCACCATCACCCCTGAGAATGAGGAAAGGGAGAAGCCATGAACTACAATGT TCAACAAAGTTGTTTGGCTCAGCAGATCCATAACCAAACATTTCTTGCACCTCAACAAGTGAAA TTAGATTCATCTCACAAGCAACCCATCGAAAAAGAATCGGGCCCATCACTTGGTCCAGATACTT GCTTCTTGAAGCATAACCAAGCCTCCTTGAAATGGAATCAAATAACGCAAAAGCTAATTCTCGC TGAGAAGGCTCTATAGCAGCCGCAGCAGAAATCATGAACAAACACTCAACTTCAACATCCTCGC TATGCACAGCCAAATGAGCTAGTGTAATGAGAGCAGTTTCAATTACGAGAACAGATTGTGGACC AACAGCTAAGACTTCTCTAGCTGTAACTGGAGAAATATTTGAGAACTTCACCATCTTGGCACCA ATGCTTGAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.233639676

Conservation Information
Conserved circRNAs	NA
PMCS	0.233639676

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30140356-30128426(+)
30140448-30128348(-)
30129223-30140442(-)
						
						Potential amino acid sequence
						
							MRAVSITRTDCGPTAKTSLAVTGEIFENFTILAPMLEIVSTNPSTTILTESATFFLEKYGICGP
*(+)
MVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAAAIEPSQREL
AFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAEPNNFVEHCS
SWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDLAETVLCESV
LQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVDGFVDTISSI
GAKMVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAAAIEPSQ
RELAFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAEPNNFVE
HCSSWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDLAETVLC
ESVLQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVDGFVDTI
SSIGAKMVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAAAIE
PSQRELAFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAEPNN
FVEHCSSWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDLAET
VLCESVLQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVDGFV
DTISSIGAKMVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAA
AIEPSQRELAFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAE
PNNFVEHCSSWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDL
AETVLCESVLQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVD
GFVDT(-)
MISLKNTWLRSLPFCSLFLHLLMGHKFHIFPRRMLHFQSEWLLMDLWTQSQALVPRW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30140356-30128426(+) 30140448-30128348(-) 30129223-30140442(-)
Potential amino acid sequence	MRAVSITRTDCGPTAKTSLAVTGEIFENFTILAPMLEIVSTNPSTTILTESATFFLEKYGICGP (+) MVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAAAIEPSQREL AFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAEPNNFVEHCS SWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDLAETVLCESV LQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVDGFVDTISSI GAKMVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAAAIEPSQ RELAFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAEPNNFVE HCSSWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDLAETVLC ESVLQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVDGFVDTI SSIGAKMVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAAAIE PSQRELAFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAEPNN FVEHCSSWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDLAET VLCESVLQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVDGFV DTISSIGAKMVKFSNISPVTAREVLAVGPQSVLVIETALITLAHLAVHSEDVEVECLFMISAAA AIEPSQRELAFALFDSISRRLGYASRSKYLDQVMGPILFRWVACEMNLISLVEVQEMFGYGSAE PNNFVEHCSSWLLPFLILRGDGADMNWISKILSQPLSIIIKRYFVPIFGMCIAVRCGTGPEKDL AETVLCESVLQLGEISELERDDLIKKHMVAIVAFLLSVSSSAHGPQIPYFSKKNVALSVRMVVD GFVDT(-) MISLKNTWLRSLPFCSLFLHLLMGHKFHIFPRRMLHFQSEWLLMDLWTQSQALVPRW(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d040166_circ_g.9

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