Plant Circular RNA Database

Detail information of Zm00001d018795_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d018795_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009206
					
						Alias
						Zm07circ00003
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 5366589-5367509  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d018795						
					
						Parent gene annotation
						
							187-kDa microtubule-associated protein AIR9
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d018795_circ_g.2 						
					
						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
						Zm00001d018795_T040:2
Zm00001d018795_T014:2
Zm00001d018795_T066:2
Zm00001d018795_T056:2
Zm00001d018795_T029:2
Zm00001d018795_T022:2
Zm00001d018795_T050:2
Zm00001d018795_T018:2
Zm00001d018795_T036:2
Zm00001d018795_T019:2
Zm00001d018795_T073:2
Zm00001d018795_T048:2
Zm00001d018795_T082:2
Zm00001d018795_T075:2
Zm00001d018795_T016:2
Zm00001d018795_T034:2
Zm00001d018795_T085:1
Zm00001d018795_T074:2
Zm00001d018795_T083:2
Zm00001d018795_T028:2
Zm00001d018795_T053:2
Zm00001d018795_T004:2
Zm00001d018795_T011:2
Zm00001d018795_T069:2
Zm00001d018795_T072:2
Zm00001d018795_T076:2
Zm00001d018795_T047:2
Zm00001d018795_T039:2
Zm00001d018795_T043:2
Zm00001d018795_T005:2
Zm00001d018795_T009:2
Zm00001d018795_T025:2
Zm00001d018795_T051:2
Zm00001d018795_T045:2
Zm00001d018795_T033:2
Zm00001d018795_T077:2
Zm00001d018795_T064:2
Zm00001d018795_T079:2
Zm00001d018795_T059:2
Zm00001d018795_T023:2
Zm00001d018795_T007:2
Zm00001d018795_T002:2
Zm00001d018795_T057:2
Zm00001d018795_T060:2
Zm00001d018795_T062:2
Zm00001d018795_T080:2
Zm00001d018795_T031:2
Zm00001d018795_T071:2

General Information
CircRNA Name	Zm00001d018795_circ_g.1
ID in PlantcircBase	zma_circ_009206
Alias	Zm07circ00003
Organism	Zea mays
Position	chr7: 5366589-5367509 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d018795
Parent gene annotation	187-kDa microtubule-associated protein AIR9
Parent gene strand	+
Alternative splicing	Zm00001d018795_circ_g.2
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	Zm00001d018795_T040:2 Zm00001d018795_T014:2 Zm00001d018795_T066:2 Zm00001d018795_T056:2 Zm00001d018795_T029:2 Zm00001d018795_T022:2 Zm00001d018795_T050:2 Zm00001d018795_T018:2 Zm00001d018795_T036:2 Zm00001d018795_T019:2 Zm00001d018795_T073:2 Zm00001d018795_T048:2 Zm00001d018795_T082:2 Zm00001d018795_T075:2 Zm00001d018795_T016:2 Zm00001d018795_T034:2 Zm00001d018795_T085:1 Zm00001d018795_T074:2 Zm00001d018795_T083:2 Zm00001d018795_T028:2 Zm00001d018795_T053:2 Zm00001d018795_T004:2 Zm00001d018795_T011:2 Zm00001d018795_T069:2 Zm00001d018795_T072:2 Zm00001d018795_T076:2 Zm00001d018795_T047:2 Zm00001d018795_T039:2 Zm00001d018795_T043:2 Zm00001d018795_T005:2 Zm00001d018795_T009:2 Zm00001d018795_T025:2 Zm00001d018795_T051:2 Zm00001d018795_T045:2 Zm00001d018795_T033:2 Zm00001d018795_T077:2 Zm00001d018795_T064:2 Zm00001d018795_T079:2 Zm00001d018795_T059:2 Zm00001d018795_T023:2 Zm00001d018795_T007:2 Zm00001d018795_T002:2 Zm00001d018795_T057:2 Zm00001d018795_T060:2 Zm00001d018795_T062:2 Zm00001d018795_T080:2 Zm00001d018795_T031:2 Zm00001d018795_T071:2

			
						 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  
						
							TTATCTGCTCAACACCTTTTTTTCTGTACTGCAGAGGCTGGATTCAAGAGGTCATCGAGTTCGT
AGTCTCAAGCAGCTGAGGTTATCACATGCTCTTGAGgtcaccaacgcccatgcttctatgaccg
agagactccgggcttgaccaggacggatttgagcgaatatcttgaggttcatattgttgctgga
ggggaatg

						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
						
							GTCACCAACGCCCATGCTTCTATGACCGAGAGACTCCGGGCTTGACCAGGACGGATTTGAGCGA
ATATCTTGAGGTTCATATTGTTGCTGGAGGGGAATGGAAACTCCATCAGAGGCCTTGAAGCCGG
CGGAGGCTAAACCGGCGAAGCCACGGCCAGTGGCGCCCACGGGCAGGTTCGCCTTGGGGACTGC
TTCGTCCATTAAAAAGCGAGCTGATGGTTCGGCTCCGGCGGAGGTGGGTGTGCCCCGGTCTTCC
TTGATGAAGTCTACCTCGTCGCTGAACGCCAGTTCGGCGACGAGAAGAAGCAGCACGGGGACTG
CTGGGAAGCAACAGGACAATGGGAGCTCAGCTGCTGCTAAGAAGTCTAGTCCTACGCTGTCGGA
TGGCGCGAGGAAGACTAAACTGGTGTCAGCTCCCGCTGCTGGCTCAAAACCAGCAGTGGAGAAG
AAAACATCCTTGGTCGAGAGGACAGGTGCCGATTTGGCCAGGAAGCCTGCTGTTAAGGCATCCC
CAACTTCAACACTGAAGAAGGTCCAGTCAAAGACAGAGAGCTCCAATGGCAGCAGTGGCAGCAC
CAGGAGAGTGTCCTCCAATGCTTCTGTGCCATCGCCACGTTCCGTCACAAGCAATGCAGCAAGG
AAACTGGGTACTCAAGCATCATCTGCTGCGTCTAATCGGCGGAAGAGCTCAACCGCAGATAGCC
GTGATTCGAGATTCATGATGCTGCCACAGGTGGATTTGAAGGCTAGCGATGAAGTGGTTAGTGC
GATTCGTTTTCATTTCTTTTAACATTCCAGGTAACAACATGATTTGGTGGGTTTTATCTGCTCA
ACACCTTTTTTTCTGTACTGCAGAGGCTGGATTCAAGAGGTCATCGAGTTCGTAGTCTCAAGCA
GCTGAGGTTATCACATGCTCTTGAG

Sequences
Splice junction sequence	TTATCTGCTCAACACCTTTTTTTCTGTACTGCAGAGGCTGGATTCAAGAGGTCATCGAGTTCGT AGTCTCAAGCAGCTGAGGTTATCACATGCTCTTGAGgtcaccaacgcccatgcttctatgaccg agagactccgggcttgaccaggacggatttgagcgaatatcttgaggttcatattgttgctgga ggggaatg
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	GTCACCAACGCCCATGCTTCTATGACCGAGAGACTCCGGGCTTGACCAGGACGGATTTGAGCGA ATATCTTGAGGTTCATATTGTTGCTGGAGGGGAATGGAAACTCCATCAGAGGCCTTGAAGCCGG CGGAGGCTAAACCGGCGAAGCCACGGCCAGTGGCGCCCACGGGCAGGTTCGCCTTGGGGACTGC TTCGTCCATTAAAAAGCGAGCTGATGGTTCGGCTCCGGCGGAGGTGGGTGTGCCCCGGTCTTCC TTGATGAAGTCTACCTCGTCGCTGAACGCCAGTTCGGCGACGAGAAGAAGCAGCACGGGGACTG CTGGGAAGCAACAGGACAATGGGAGCTCAGCTGCTGCTAAGAAGTCTAGTCCTACGCTGTCGGA TGGCGCGAGGAAGACTAAACTGGTGTCAGCTCCCGCTGCTGGCTCAAAACCAGCAGTGGAGAAG AAAACATCCTTGGTCGAGAGGACAGGTGCCGATTTGGCCAGGAAGCCTGCTGTTAAGGCATCCC CAACTTCAACACTGAAGAAGGTCCAGTCAAAGACAGAGAGCTCCAATGGCAGCAGTGGCAGCAC CAGGAGAGTGTCCTCCAATGCTTCTGTGCCATCGCCACGTTCCGTCACAAGCAATGCAGCAAGG AAACTGGGTACTCAAGCATCATCTGCTGCGTCTAATCGGCGGAAGAGCTCAACCGCAGATAGCC GTGATTCGAGATTCATGATGCTGCCACAGGTGGATTTGAAGGCTAGCGATGAAGTGGTTAGTGC GATTCGTTTTCATTTCTTTTAACATTCCAGGTAACAACATGATTTGGTGGGTTTTATCTGCTCA ACACCTTTTTTTCTGTACTGCAGAGGCTGGATTCAAGAGGTCATCGAGTTCGTAGTCTCAAGCA GCTGAGGTTATCACATGCTCTTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.162870177

Conservation Information
Conserved circRNAs	NA
PMCS	0.162870177

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5366687-5366630(+)
5366791-5367497(-)
5366700-5367463(-)
						
						Potential amino acid sequence
						
							METPSEALKPAEAKPAKPRPVAPTGRFALGTASSIKKRADGSAPAEVGVPRSSLMKSTSSLNAS
SATRRSSTGTAGKQQDNGSSAAAKKSSPTLSDGARKTKLVSAPAAGSKPAVEKKTSLVERTGAD
LARKPAVKASPTSTLKKVQSKTESSNGSSGSTRRVSSNASVPSPRSVTSNAARKLGTQASSAAS
NRRKSSTADSRDSRFMMLPQVDLKASDEVRLDSRGHRVRSLKQLRLSHALEVTNAHASMTERLR
A*(+)
MDEAVPKANLPVGATGRGFAGLASAGFKASDGVSIPLQQQYEPQDIRSNPSWSSPESLGHRSMG
VGDLKSM*(-)
MEFPFPSSNNMNLKIFAQIRPGQARSLSVIEAWALVTSRACDNLSCLRLRTR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5366687-5366630(+) 5366791-5367497(-) 5366700-5367463(-)
Potential amino acid sequence	METPSEALKPAEAKPAKPRPVAPTGRFALGTASSIKKRADGSAPAEVGVPRSSLMKSTSSLNAS SATRRSSTGTAGKQQDNGSSAAAKKSSPTLSDGARKTKLVSAPAAGSKPAVEKKTSLVERTGAD LARKPAVKASPTSTLKKVQSKTESSNGSSGSTRRVSSNASVPSPRSVTSNAARKLGTQASSAAS NRRKSSTADSRDSRFMMLPQVDLKASDEVRLDSRGHRVRSLKQLRLSHALEVTNAHASMTERLR A(+) MDEAVPKANLPVGATGRGFAGLASAGFKASDGVSIPLQQQYEPQDIRSNPSWSSPESLGHRSMG VGDLKSM(-) MEFPFPSSNNMNLKIFAQIRPGQARSLSVIEAWALVTSRACDNLSCLRLRTR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d018795_circ_g.1

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