Plant Circular RNA Database

Detail information of Zm00001d047761_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d047761_circ_g.2
					
						ID in PlantcircBase
						zma_circ_010060
					
						Alias
						zma_circ_0003092
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 141198523-141199233  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d047761						
					
						Parent gene annotation
						
							Two-component response regulator-like APRR3
							
						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  
						
							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
						Zm00001d047761_T004:3
Zm00001d047761_T007:3
Zm00001d047761_T010:2
Zm00001d047761_T013:3
Zm00001d047761_T006:2
Zm00001d047761_T015:2
Zm00001d047761_T003:3
Zm00001d047761_T014:3
Zm00001d047761_T002:3
Zm00001d047761_T005:3
Zm00001d047761_T001:2
Zm00001d047761_T008:3
Zm00001d047761_T011:3
Zm00001d047761_T009:2
Zm00001d047761_T012:3

General Information
CircRNA Name	Zm00001d047761_circ_g.2
ID in PlantcircBase	zma_circ_010060
Alias	zma_circ_0003092
Organism	Zea mays
Position	chr9: 141198523-141199233 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d047761
Parent gene annotation	Two-component response regulator-like APRR3
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	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	Zm00001d047761_T004:3 Zm00001d047761_T007:3 Zm00001d047761_T010:2 Zm00001d047761_T013:3 Zm00001d047761_T006:2 Zm00001d047761_T015:2 Zm00001d047761_T003:3 Zm00001d047761_T014:3 Zm00001d047761_T002:3 Zm00001d047761_T005:3 Zm00001d047761_T001:2 Zm00001d047761_T008:3 Zm00001d047761_T011:3 Zm00001d047761_T009:2 Zm00001d047761_T012:3

			
						 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  
						
							CAGCAATCATGATGATGAAGAAAATGATGACGGCGACGATGACGACTTCAGTGTTGGACTCAAT
GCTAGGGATGGAAGTGACAATGGCAGTGGTACTCAAttattcctgctgaaaatggtttgcatgc
atggcgatatcttgaagatctgcagaacaacatcgaccttgtattgactgaggttttcatgcct
tgtctatc

						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
						
							TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGCAGAACAACATCGA
CCTTGTATTGACTGAGGTTTTCATGCCTTGTCTATCTGGTATCGGTCTGCTTAGCAAAATCACA
AGTCACAAAATTTGCAAAGACATTCCTGTGATTAGTAAGTAGATTTCCTCAACTACCCTAATGC
ACGTGAAATTTTATCTTGTTAATTGTTGGGTTTAAATACTTTTAGCTGCTACACTGATGTGTTT
TGCATGCAGTGATGTCTACGAATGATTCTATGAGTATGGTGTTTAAGTGTTTGTCGAAGGGAGC
AGTTGATTTCTTGGTAAAACCACTACGTAAGAATGAGCTTAAGAACCTTTGGCAGCATGTTTGG
AGGCGATGCCACAGTGTAAGCTGTTTGTTTTTGGTCTAGTTTTTTCTGGATATTTTATTCCACG
AAACATGAGGCGTGATTTCTTTGAGTCCTCACTGTGTTTCCTTTGTGATCACTCTGAGTTGAAT
TTGCCTCTTTGGTACTCAGTCCAGTGGAAGTGAAAGTGGCATCCAGACACAGAAGTGTGCCAAA
CTAAATACTGGCGACGAGTATGAGAACGGCAGTGACAGCAATCATGATGATGAAGAAAATGATG
ACGGCGACGATGACGACTTCAGTGTTGGACTCAATGCTAGGGATGGAAGTGACAATGGCAGTGG
TACTCAA

Sequences
Splice junction sequence	CAGCAATCATGATGATGAAGAAAATGATGACGGCGACGATGACGACTTCAGTGTTGGACTCAAT GCTAGGGATGGAAGTGACAATGGCAGTGGTACTCAAttattcctgctgaaaatggtttgcatgc atggcgatatcttgaagatctgcagaacaacatcgaccttgtattgactgaggttttcatgcct tgtctatc
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	TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGCAGAACAACATCGA CCTTGTATTGACTGAGGTTTTCATGCCTTGTCTATCTGGTATCGGTCTGCTTAGCAAAATCACA AGTCACAAAATTTGCAAAGACATTCCTGTGATTAGTAAGTAGATTTCCTCAACTACCCTAATGC ACGTGAAATTTTATCTTGTTAATTGTTGGGTTTAAATACTTTTAGCTGCTACACTGATGTGTTT TGCATGCAGTGATGTCTACGAATGATTCTATGAGTATGGTGTTTAAGTGTTTGTCGAAGGGAGC AGTTGATTTCTTGGTAAAACCACTACGTAAGAATGAGCTTAAGAACCTTTGGCAGCATGTTTGG AGGCGATGCCACAGTGTAAGCTGTTTGTTTTTGGTCTAGTTTTTTCTGGATATTTTATTCCACG AAACATGAGGCGTGATTTCTTTGAGTCCTCACTGTGTTTCCTTTGTGATCACTCTGAGTTGAAT TTGCCTCTTTGGTACTCAGTCCAGTGGAAGTGAAAGTGGCATCCAGACACAGAAGTGTGCCAAA CTAAATACTGGCGACGAGTATGAGAACGGCAGTGACAGCAATCATGATGATGAAGAAAATGATG ACGGCGACGATGACGACTTCAGTGTTGGACTCAATGCTAGGGATGGAAGTGACAATGGCAGTGG TACTCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.259825022

Conservation Information
Conserved circRNAs	NA
PMCS	0.259825022

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							141199119-141198532(+)
141198610-141198594(+)
141198612-141199201(-)
						
						Potential amino acid sequence
						
							MRTAVTAIMMMKKMMTATMTTSVLDSMLGMEVTMAVVLNYSC*(+)
MPCLSGIGLLSKITSHKICKDIPVIMMSTNDSMSMVFKCLSKGAVDFLVKPLRKNELKNLWQHV
WRRCHSSSGSESGIQTQKCAKLNTGDEYENGSDSNHDDEENDDGDDDDFSVGLNARDGSDNGSG
TQLFLLKMVCMHGDILKICRTTSTLY*(+)
MKTSVNTRSMLFCRSSRYRHACKPFSAGIIEYHCHCHFHP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	141199119-141198532(+) 141198610-141198594(+) 141198612-141199201(-)
Potential amino acid sequence	MRTAVTAIMMMKKMMTATMTTSVLDSMLGMEVTMAVVLNYSC(+) MPCLSGIGLLSKITSHKICKDIPVIMMSTNDSMSMVFKCLSKGAVDFLVKPLRKNELKNLWQHV WRRCHSSSGSESGIQTQKCAKLNTGDEYENGSDSNHDDEENDDGDDDDFSVGLNARDGSDNGSG TQLFLLKMVCMHGDILKICRTTSTLY(+) MKTSVNTRSMLFCRSSRYRHACKPFSAGIIEYHCHCHFHP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d047761_circ_g.2

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