Plant Circular RNA Database

Detail information of Zm00001d046039_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d046039_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009941
					
						Alias
						zma_circ_0003222
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 58118766-58119185  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d046039						
					
						Parent gene annotation
						
							HEAT repeat-containing protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d046039_circ_g.1 Zm00001d046039_circ_g.3 Zm00001d046039_circ_g.4 						
					
						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
						Zm00001d046039_T035:2
Zm00001d046039_T018:2
Zm00001d046039_T025:2
Zm00001d046039_T005:2
Zm00001d046039_T022:2
Zm00001d046039_T024:2
Zm00001d046039_T015:2
Zm00001d046039_T033:2
Zm00001d046039_T036:2
Zm00001d046039_T008:2
Zm00001d046039_T037:2
Zm00001d046039_T021:2
Zm00001d046039_T066:2
Zm00001d046039_T013:2
Zm00001d046039_T001:2
Zm00001d046039_T052:2
Zm00001d046039_T038:2
Zm00001d046039_T030:2
Zm00001d046039_T039:2
Zm00001d046039_T004:2
Zm00001d046039_T014:2
Zm00001d046039_T016:2
Zm00001d046039_T012:2
Zm00001d046039_T031:2
Zm00001d046039_T027:2
Zm00001d046039_T003:2
Zm00001d046039_T006:2
Zm00001d046039_T017:2
Zm00001d046039_T007:2
Zm00001d046039_T029:2
Zm00001d046039_T010:2
Zm00001d046039_T032:2
Zm00001d046039_T023:2
Zm00001d046039_T011:2
Zm00001d046039_T002:2
Zm00001d046039_T040:2

General Information
CircRNA Name	Zm00001d046039_circ_g.2
ID in PlantcircBase	zma_circ_009941
Alias	zma_circ_0003222
Organism	Zea mays
Position	chr9: 58118766-58119185 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d046039
Parent gene annotation	HEAT repeat-containing protein
Parent gene strand	-
Alternative splicing	Zm00001d046039_circ_g.1 Zm00001d046039_circ_g.3 Zm00001d046039_circ_g.4
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	Zm00001d046039_T035:2 Zm00001d046039_T018:2 Zm00001d046039_T025:2 Zm00001d046039_T005:2 Zm00001d046039_T022:2 Zm00001d046039_T024:2 Zm00001d046039_T015:2 Zm00001d046039_T033:2 Zm00001d046039_T036:2 Zm00001d046039_T008:2 Zm00001d046039_T037:2 Zm00001d046039_T021:2 Zm00001d046039_T066:2 Zm00001d046039_T013:2 Zm00001d046039_T001:2 Zm00001d046039_T052:2 Zm00001d046039_T038:2 Zm00001d046039_T030:2 Zm00001d046039_T039:2 Zm00001d046039_T004:2 Zm00001d046039_T014:2 Zm00001d046039_T016:2 Zm00001d046039_T012:2 Zm00001d046039_T031:2 Zm00001d046039_T027:2 Zm00001d046039_T003:2 Zm00001d046039_T006:2 Zm00001d046039_T017:2 Zm00001d046039_T007:2 Zm00001d046039_T029:2 Zm00001d046039_T010:2 Zm00001d046039_T032:2 Zm00001d046039_T023:2 Zm00001d046039_T011:2 Zm00001d046039_T002:2 Zm00001d046039_T040:2

			
						 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  
						
							GATATAGTAGGCCCTCTATGTCACTTAACGGGCGTGTTATCAGAGAAAACAAGCGACTAAGAGC
TAGTCTATCCCCACCAATTATGCTGCTCGTCATAACattgatttttgagtgcaaaccaaaactt
atagaaacataatccttgagtgctcgaatccagtattttcctaatagagttgaactgtttacaa
gtgaaggt

						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
						
							ATTGATTTTTGAGTGCAAACCAAAACTTATAGAAACATAATCCTTGAGTGCTCGAATCCAGTAT
TTTCCTAATAGAGTTGAACTGTTTACAAGTGAAGGTGCCAATTGCTGGTATTCATTAGGAGCAT
TTTCCCTCATCCTCAAGAATTGATAGGTGTTACACTTGACTGCTGCATGGGCAGTTAGAAGGCG
AACTTTTATCTGTCACTTACAAAACCTAGGTTAGATACTTAGGACACTAAGATATCCAAAACAA
ACTGAGTAAATGTGACAGTTTTAGAACTGAAATACCTTGCACACTACCCAGTCAGCAAAAGATG
GATATAGTAGGCCCTCTATGTCACTTAACGGGCGTGTTATCAGAGAAAACAAGCGACTAAGAGC
TAGTCTATCCCCACCAATTATGCTGCTCGTCATAAC

Sequences
Splice junction sequence	GATATAGTAGGCCCTCTATGTCACTTAACGGGCGTGTTATCAGAGAAAACAAGCGACTAAGAGC TAGTCTATCCCCACCAATTATGCTGCTCGTCATAACattgatttttgagtgcaaaccaaaactt atagaaacataatccttgagtgctcgaatccagtattttcctaatagagttgaactgtttacaa gtgaaggt
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	ATTGATTTTTGAGTGCAAACCAAAACTTATAGAAACATAATCCTTGAGTGCTCGAATCCAGTAT TTTCCTAATAGAGTTGAACTGTTTACAAGTGAAGGTGCCAATTGCTGGTATTCATTAGGAGCAT TTTCCCTCATCCTCAAGAATTGATAGGTGTTACACTTGACTGCTGCATGGGCAGTTAGAAGGCG AACTTTTATCTGTCACTTACAAAACCTAGGTTAGATACTTAGGACACTAAGATATCCAAAACAA ACTGAGTAAATGTGACAGTTTTAGAACTGAAATACCTTGCACACTACCCAGTCAGCAAAAGATG GATATAGTAGGCCCTCTATGTCACTTAACGGGCGTGTTATCAGAGAAAACAAGCGACTAAGAGC TAGTCTATCCCCACCAATTATGCTGCTCGTCATAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.223518532

Conservation Information
Conserved circRNAs	NA
PMCS	0.223518532

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58119104-58118802(+)
58119184-58118768(-)
						
						Potential amino acid sequence
						
							MSLNGRVIRENKRLRASLSPPIMLLVITLIFECKPKLIET*(+)
MTSSIIGGDRLALSRLFSLITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAVKCNTYQFLRM
RENAPNEYQQLAPSLVNSSTLLGKYWIRALKDYVSISFGLHSKINVMTSSIIGGDRLALSRLFS
LITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAVKCNTYQFLRMRENAPNEYQQLAPSLVNS
STLLGKYWIRALKDYVSISFGLHSKINVMTSSIIGGDRLALSRLFSLITRPLSDIEGLLYPSFA
DWVVCKIKVRLLTAHAAVKCNTYQFLRMRENAPNEYQQLAPSLVNSSTLLGKYWIRALKDYVSI
SFGLHSKINVMTSSIIGGDRLALSRLFSLITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAV
KCNTYQFLRMRENAPNEYQQLAPSLVNSSTLLGKYWIRALKDYVSISFGLHSKIN(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	58119104-58118802(+) 58119184-58118768(-)
Potential amino acid sequence	MSLNGRVIRENKRLRASLSPPIMLLVITLIFECKPKLIET*(+) MTSSIIGGDRLALSRLFSLITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAVKCNTYQFLRM RENAPNEYQQLAPSLVNSSTLLGKYWIRALKDYVSISFGLHSKINVMTSSIIGGDRLALSRLFS LITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAVKCNTYQFLRMRENAPNEYQQLAPSLVNS STLLGKYWIRALKDYVSISFGLHSKINVMTSSIIGGDRLALSRLFSLITRPLSDIEGLLYPSFA DWVVCKIKVRLLTAHAAVKCNTYQFLRMRENAPNEYQQLAPSLVNSSTLLGKYWIRALKDYVSI SFGLHSKINVMTSSIIGGDRLALSRLFSLITRPLSDIEGLLYPSFADWVVCKIKVRLLTAHAAV KCNTYQFLRMRENAPNEYQQLAPSLVNSSTLLGKYWIRALKDYVSISFGLHSKIN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d046039_circ_g.2

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