Plant Circular RNA Database

Detail information of Zm00001d014425_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d014425_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008472
					
						Alias
						zma_circ_0002099
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 46343574-46344336  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d014425						
					
						Parent gene annotation
						
							Glycerol-3-phosphate acyltransferase  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d014425_circ_g.1 Zm00001d014425_circ_g.2 Zm00001d014425_circ_igg.1 						
					
						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  
						
							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
						Zm00001d014425_T017:3
Zm00001d014425_T014:3
Zm00001d014425_T003:3
Zm00001d014425_T012:3
Zm00001d014425_T004:3
Zm00001d014425_T018:3
Zm00001d014425_T007:2
Zm00001d014425_T001:3
Zm00001d014425_T015:3
Zm00001d014425_T013:2
Zm00001d014425_T002:3
Zm00001d014425_T016:3
Zm00001d014425_T011:3
Zm00001d014425_T008:3
Zm00001d014425_T009:2
Zm00001d014425_T005:3
Zm00001d014425_T006:3
Zm00001d014425_T010:2

General Information
CircRNA Name	Zm00001d014425_circ_g.3
ID in PlantcircBase	zma_circ_008472
Alias	zma_circ_0002099
Organism	Zea mays
Position	chr5: 46343574-46344336 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d014425
Parent gene annotation	Glycerol-3-phosphate acyltransferase
Parent gene strand	+
Alternative splicing	Zm00001d014425_circ_g.1 Zm00001d014425_circ_g.2 Zm00001d014425_circ_igg.1
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	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	Zm00001d014425_T017:3 Zm00001d014425_T014:3 Zm00001d014425_T003:3 Zm00001d014425_T012:3 Zm00001d014425_T004:3 Zm00001d014425_T018:3 Zm00001d014425_T007:2 Zm00001d014425_T001:3 Zm00001d014425_T015:3 Zm00001d014425_T013:2 Zm00001d014425_T002:3 Zm00001d014425_T016:3 Zm00001d014425_T011:3 Zm00001d014425_T008:3 Zm00001d014425_T009:2 Zm00001d014425_T005:3 Zm00001d014425_T006:3 Zm00001d014425_T010:2

			
						 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  
						
							TGGTGAGCAGAGGGTGATATCCTTCCATGGAGCAGGCTTGTCAGTAACTGAAGAAATAAACTAT
GGAGACATTACTGCTCATACCAAGAATGCTGATGAGtggtggttcacagttaatttggattgca
ccgagtggtggtagagaccgcccaaatccctcatcaggagaatggtacccggtaaatggtctta
tttttcca

						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: 313
Transcript exons: 46343574-46343652,46344011-46344130,46344223-46344336
TGGTGGTTCACAGTTAATTTGGATTGCACCGAGTGGTGGTAGAGACCGCCCAAATCCCTCATCA
GGAGAATGGTACCCGGCACCATTCGATTCATCTGCAGTGGACAATATGAGGAGGCTTCTGGAGC
ATGCTGGTGTTCCTGGGCACATATATCCACTATCATTGCTGTGCTATGAGGTTATGCCTCCACC
ACAACAGGTTGAGAAGGAGATTGGTGAGCAGAGGGTGATATCCTTCCATGGAGCAGGCTTGTCA
GTAACTGAAGAAATAAACTATGGAGACATTACTGCTCATACCAAGAATGCTGATGAG
						
						Genomic sequence
						
							TGGTGGTTCACAGTTAATTTGGATTGCACCGAGTGGTGGTAGAGACCGCCCAAATCCCTCATCA
GGAGAATGGTACCCGGTAAATGGTCTTATTTTTCCATTTTGACTTAGCTATGCATTATAGTTCA
TCTTCTCTTTCAATGTAACTGCATTGCTAAGACCGTGTTCAGCACACCCAAAACACTATTTTGC
ACTGTAGACTGAACTGTTCGCAGAGTGGAGTTTGAATATGAGTATGGGGATGGGTAAGCTCTAA
GCTGCTGGAGATAGCCTAACAAACAAATGAAATGAGATGGTACAGTAACAGTGTAGAGGTGTGA
GGTGTCTGACAAGAATGATCTGTTTTTTTTACCTAAGACATGCTTGAAAAGTCCGCTGCTTTTG
TAAGTATGTTCCCTTAGGTTTACTTTATCTGCTACATGCAAAAACAAGGGCAGGCACCATTCGA
TTCATCTGCAGTGGACAATATGAGGAGGCTTCTGGAGCATGCTGGTGTTCCTGGGCACATATAT
CCACTATCATTGCTGTGCTATGAGGTTATGCCTCCACCACAACAGGTACTGTACTTCATTAGTG
CTCATTGTACCTGTTTAAGTATTCTTGCTGTGGTAACCCTTTGAAATTTTTTCTTTCTCTTCGA
GTTGGATAGGTTGAGAAGGAGATTGGTGAGCAGAGGGTGATATCCTTCCATGGAGCAGGCTTGT
CAGTAACTGAAGAAATAAACTATGGAGACATTACTGCTCATACCAAGAATGCTGATGAG

Sequences
Splice junction sequence	TGGTGAGCAGAGGGTGATATCCTTCCATGGAGCAGGCTTGTCAGTAACTGAAGAAATAAACTAT GGAGACATTACTGCTCATACCAAGAATGCTGATGAGtggtggttcacagttaatttggattgca ccgagtggtggtagagaccgcccaaatccctcatcaggagaatggtacccggtaaatggtctta tttttcca
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: 313 Transcript exons: 46343574-46343652,46344011-46344130,46344223-46344336 TGGTGGTTCACAGTTAATTTGGATTGCACCGAGTGGTGGTAGAGACCGCCCAAATCCCTCATCA GGAGAATGGTACCCGGCACCATTCGATTCATCTGCAGTGGACAATATGAGGAGGCTTCTGGAGC ATGCTGGTGTTCCTGGGCACATATATCCACTATCATTGCTGTGCTATGAGGTTATGCCTCCACC ACAACAGGTTGAGAAGGAGATTGGTGAGCAGAGGGTGATATCCTTCCATGGAGCAGGCTTGTCA GTAACTGAAGAAATAAACTATGGAGACATTACTGCTCATACCAAGAATGCTGATGAG
Genomic sequence	TGGTGGTTCACAGTTAATTTGGATTGCACCGAGTGGTGGTAGAGACCGCCCAAATCCCTCATCA GGAGAATGGTACCCGGTAAATGGTCTTATTTTTCCATTTTGACTTAGCTATGCATTATAGTTCA TCTTCTCTTTCAATGTAACTGCATTGCTAAGACCGTGTTCAGCACACCCAAAACACTATTTTGC ACTGTAGACTGAACTGTTCGCAGAGTGGAGTTTGAATATGAGTATGGGGATGGGTAAGCTCTAA GCTGCTGGAGATAGCCTAACAAACAAATGAAATGAGATGGTACAGTAACAGTGTAGAGGTGTGA GGTGTCTGACAAGAATGATCTGTTTTTTTTACCTAAGACATGCTTGAAAAGTCCGCTGCTTTTG TAAGTATGTTCCCTTAGGTTTACTTTATCTGCTACATGCAAAAACAAGGGCAGGCACCATTCGA TTCATCTGCAGTGGACAATATGAGGAGGCTTCTGGAGCATGCTGGTGTTCCTGGGCACATATAT CCACTATCATTGCTGTGCTATGAGGTTATGCCTCCACCACAACAGGTACTGTACTTCATTAGTG CTCATTGTACCTGTTTAAGTATTCTTGCTGTGGTAACCCTTTGAAATTTTTTCTTTCTCTTCGA GTTGGATAGGTTGAGAAGGAGATTGGTGAGCAGAGGGTGATATCCTTCCATGGAGCAGGCTTGT CAGTAACTGAAGAAATAAACTATGGAGACATTACTGCTCATACCAAGAATGCTGATGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.144248474

Conservation Information
Conserved circRNAs	NA
PMCS	0.144248474

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							46343644-46343612(+)
46344300-46344041(+)
46344083-46344317(-)
						
						Potential amino acid sequence
						
							MVPGQAPFDSSAVDNMRRLLEHAGVPGHIYPLSLLCYEVMPPPQQVEKEIGEQRVISFHGAGLS
VTEEINYGDITAHTKNADEWWFTVNLDCTEWW*(+)
METLLLIPRMLMSGGSQLIWIAPSGGRDRPNPSSGEWYPGRHHSIHLQWTI*(+)
MCPGTPACSRSLLILSTADESNGACPGTILLMRDLGGLYHHSVQSKLTVNHHSSAFLV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	46343644-46343612(+) 46344300-46344041(+) 46344083-46344317(-)
Potential amino acid sequence	MVPGQAPFDSSAVDNMRRLLEHAGVPGHIYPLSLLCYEVMPPPQQVEKEIGEQRVISFHGAGLS VTEEINYGDITAHTKNADEWWFTVNLDCTEWW(+) METLLLIPRMLMSGGSQLIWIAPSGGRDRPNPSSGEWYPGRHHSIHLQWTI(+) MCPGTPACSRSLLILSTADESNGACPGTILLMRDLGGLYHHSVQSKLTVNHHSSAFLV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d014425_circ_g.3

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