Plant Circular RNA Database

Detail information of Zm00001d029004_circ_g.6

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d029004_circ_g.6
					

						ID in PlantcircBase
						zma_circ_006514
					

						Alias
						Zm01circ00060
					

						Organism
						
							Zea mays						
					

						Position
						
							chr1: 54463464-54474913  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI2
					

						Parent gene
						
							Zm00001d029004						
					

						Parent gene annotation
						
							Guanine nucleotide exchange factor SPIKE 1
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d029004_circ_g.2 Zm00001d029004_circ_g.3 Zm00001d029004_circ_g.4 Zm00001d029004_circ_g.5 Zm00001d029004_circ_g.7 Zm00001d029004_circ_g.8 						
					

						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
						Zm00001d029004_T122:4
Zm00001d029004_T051:12
Zm00001d029004_T029:12
Zm00001d029004_T056:12
Zm00001d029004_T023:12
Zm00001d029004_T014:12
Zm00001d029004_T075:12
Zm00001d029004_T033:12
Zm00001d029004_T104:12
Zm00001d029004_T058:12
Zm00001d029004_T074:12
Zm00001d029004_T114:9
Zm00001d029004_T107:11
Zm00001d029004_T082:12
Zm00001d029004_T022:4
Zm00001d029004_T099:12
Zm00001d029004_T008:12
Zm00001d029004_T118:7
Zm00001d029004_T095:12
Zm00001d029004_T105:12
Zm00001d029004_T113:11
Zm00001d029004_T059:12
Zm00001d029004_T044:12
Zm00001d029004_T087:12
Zm00001d029004_T027:12
Zm00001d029004_T025:12
Zm00001d029004_T047:13
Zm00001d029004_T016:12
Zm00001d029004_T005:12
Zm00001d029004_T062:12
Zm00001d029004_T055:12
Zm00001d029004_T071:12
Zm00001d029004_T019:12
Zm00001d029004_T070:11
Zm00001d029004_T002:12
Zm00001d029004_T042:12
Zm00001d029004_T092:12
Zm00001d029004_T053:12
Zm00001d029004_T049:12
Zm00001d029004_T041:12
Zm00001d029004_T088:12
Zm00001d029004_T046:12
Zm00001d029004_T112:10
Zm00001d029004_T061:12
Zm00001d029004_T067:12
Zm00001d029004_T017:11
Zm00001d029004_T010:11
Zm00001d029004_T108:11
Zm00001d029004_T011:12
Zm00001d029004_T101:12
Zm00001d029004_T028:12
Zm00001d029004_T097:12
Zm00001d029004_T021:11
Zm00001d029004_T065:12
Zm00001d029004_T003:12
Zm00001d029004_T004:12
Zm00001d029004_T079:11
Zm00001d029004_T013:12
Zm00001d029004_T096:12
Zm00001d029004_T018:12
Zm00001d029004_T034:12
Zm00001d029004_T077:12
Zm00001d029004_T083:12
Zm00001d029004_T086:12
Zm00001d029004_T120:7
Zm00001d029004_T039:12
Zm00001d029004_T060:12
Zm00001d029004_T036:12

					

			
		

General Information
CircRNA Name	Zm00001d029004_circ_g.6
ID in PlantcircBase	zma_circ_006514
Alias	Zm01circ00060
Organism	Zea mays
Position	chr1: 54463464-54474913 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d029004
Parent gene annotation	Guanine nucleotide exchange factor SPIKE 1
Parent gene strand	+
Alternative splicing	Zm00001d029004_circ_g.2 Zm00001d029004_circ_g.3 Zm00001d029004_circ_g.4 Zm00001d029004_circ_g.5 Zm00001d029004_circ_g.7 Zm00001d029004_circ_g.8
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	Zm00001d029004_T122:4 Zm00001d029004_T051:12 Zm00001d029004_T029:12 Zm00001d029004_T056:12 Zm00001d029004_T023:12 Zm00001d029004_T014:12 Zm00001d029004_T075:12 Zm00001d029004_T033:12 Zm00001d029004_T104:12 Zm00001d029004_T058:12 Zm00001d029004_T074:12 Zm00001d029004_T114:9 Zm00001d029004_T107:11 Zm00001d029004_T082:12 Zm00001d029004_T022:4 Zm00001d029004_T099:12 Zm00001d029004_T008:12 Zm00001d029004_T118:7 Zm00001d029004_T095:12 Zm00001d029004_T105:12 Zm00001d029004_T113:11 Zm00001d029004_T059:12 Zm00001d029004_T044:12 Zm00001d029004_T087:12 Zm00001d029004_T027:12 Zm00001d029004_T025:12 Zm00001d029004_T047:13 Zm00001d029004_T016:12 Zm00001d029004_T005:12 Zm00001d029004_T062:12 Zm00001d029004_T055:12 Zm00001d029004_T071:12 Zm00001d029004_T019:12 Zm00001d029004_T070:11 Zm00001d029004_T002:12 Zm00001d029004_T042:12 Zm00001d029004_T092:12 Zm00001d029004_T053:12 Zm00001d029004_T049:12 Zm00001d029004_T041:12 Zm00001d029004_T088:12 Zm00001d029004_T046:12 Zm00001d029004_T112:10 Zm00001d029004_T061:12 Zm00001d029004_T067:12 Zm00001d029004_T017:11 Zm00001d029004_T010:11 Zm00001d029004_T108:11 Zm00001d029004_T011:12 Zm00001d029004_T101:12 Zm00001d029004_T028:12 Zm00001d029004_T097:12 Zm00001d029004_T021:11 Zm00001d029004_T065:12 Zm00001d029004_T003:12 Zm00001d029004_T004:12 Zm00001d029004_T079:11 Zm00001d029004_T013:12 Zm00001d029004_T096:12 Zm00001d029004_T018:12 Zm00001d029004_T034:12 Zm00001d029004_T077:12 Zm00001d029004_T083:12 Zm00001d029004_T086:12 Zm00001d029004_T120:7 Zm00001d029004_T039:12 Zm00001d029004_T060:12 Zm00001d029004_T036:12

			
						 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  
						
							GAGCCCAGATGTCGAGCATCCTGCATCCCCAAAGTACTCTGAACGATTGTCCCCATCGGTCAAC
ACATATTTGTCGGAGGCTTCGAGGCATGAAATAAGGgttactttcagatgtgtccttgccgatt
ttgagagagctcgttccacattacctgcaggaaagtggaaaggtttgcttcttgattttgtgtt
tctcggtg

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	GAGCCCAGATGTCGAGCATCCTGCATCCCCAAAGTACTCTGAACGATTGTCCCCATCGGTCAAC ACATATTTGTCGGAGGCTTCGAGGCATGAAATAAGGgttactttcagatgtgtccttgccgatt ttgagagagctcgttccacattacctgcaggaaagtggaaaggtttgcttcttgattttgtgtt tctcggtg
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	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
						0.021435221

Conservation Information
Conserved circRNAs	NA
PMCS	0.021435221

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							54463649-54463718(+)
						
						Potential amino acid sequence
						
							MDYLEDGKTVFRLRLRLCSSLFPINERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTA
LLQFLQPILNMLLHLIGDGGETLQVAAFRAMVNILTRVQQESSDGAERNRFLINYVDFAFDDFG
DRQAPVYPGLTTVWGSLARSKAKGYRVGPVYDDVLAMAWFFLELIVKSMGLEQSRLFYHNLPLG
EDVPPLQLKEGVFRCIMQLFDCLLTEVHERCKKGLSLAKRLNSTLAFFCYDLLSIIEPRQVFEL
VSLYMDKFAGVCQSVLHDCKLTFLQIICDHDLFVEMPGRDPSDRNYLSSVLIQEIFLTLDHDDL
SQRAKAARILVVLICKHEFDARYQKSEDKLYIAQLYFPLIGQILDEMPVFYNLNAIEKREVLVV
ILQIVRNLDDATLIKAWQQSIARTRLFFKLLEECIIHFEHNKTGDNMLLGASSRSPDVEHPASP
KYSERLSPSVNTYLSEASRHEIRVTFRCVLADFERARSTLPAGKWKGENGLSGRWENCFQVTFK
ALLFIVPN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	54463649-54463718(+)
Potential amino acid sequence	MDYLEDGKTVFRLRLRLCSSLFPINERIRDFFVEYDRHTLHTSPPWGSELLEAINSLKNVESTA LLQFLQPILNMLLHLIGDGGETLQVAAFRAMVNILTRVQQESSDGAERNRFLINYVDFAFDDFG DRQAPVYPGLTTVWGSLARSKAKGYRVGPVYDDVLAMAWFFLELIVKSMGLEQSRLFYHNLPLG EDVPPLQLKEGVFRCIMQLFDCLLTEVHERCKKGLSLAKRLNSTLAFFCYDLLSIIEPRQVFEL VSLYMDKFAGVCQSVLHDCKLTFLQIICDHDLFVEMPGRDPSDRNYLSSVLIQEIFLTLDHDDL SQRAKAARILVVLICKHEFDARYQKSEDKLYIAQLYFPLIGQILDEMPVFYNLNAIEKREVLVV ILQIVRNLDDATLIKAWQQSIARTRLFFKLLEECIIHFEHNKTGDNMLLGASSRSPDVEHPASP KYSERLSPSVNTYLSEASRHEIRVTFRCVLADFERARSTLPAGKWKGENGLSGRWENCFQVTFK ALLFIVPN*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d029004_circ_g.6

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