Plant Circular RNA Database

Detail information of Zm00001d029004_circ_g.5

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d029004_circ_g.5
					

						ID in PlantcircBase
						zma_circ_006513
					

						Alias
						zma_circ_0000667, GRMZM2G559436_C1
					

						Organism
						
							Zea mays						
					

						Position
						
							chr1: 54463464-54463803  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ, 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.6 Zm00001d029004_circ_g.7 Zm00001d029004_circ_g.8 						
					

						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
						Zm00001d029004_T096:2
Zm00001d029004_T028:2
Zm00001d029004_T019:2
Zm00001d029004_T107:2
Zm00001d029004_T023:2
Zm00001d029004_T053:2
Zm00001d029004_T029:2
Zm00001d029004_T097:2
Zm00001d029004_T059:2
Zm00001d029004_T056:2
Zm00001d029004_T075:2
Zm00001d029004_T105:2
Zm00001d029004_T005:2
Zm00001d029004_T033:2
Zm00001d029004_T055:2
Zm00001d029004_T058:2
Zm00001d029004_T070:2
Zm00001d029004_T074:2
Zm00001d029004_T036:2
Zm00001d029004_T082:2
Zm00001d029004_T041:2
Zm00001d029004_T003:2
Zm00001d029004_T042:2
Zm00001d029004_T067:2
Zm00001d029004_T060:2
Zm00001d029004_T061:2
Zm00001d029004_T099:2
Zm00001d029004_T077:2
Zm00001d029004_T011:2
Zm00001d029004_T004:2
Zm00001d029004_T046:2
Zm00001d029004_T044:2
Zm00001d029004_T101:2
Zm00001d029004_T079:2
Zm00001d029004_T021:2
Zm00001d029004_T002:2
Zm00001d029004_T049:2
Zm00001d029004_T095:2
Zm00001d029004_T016:2
Zm00001d029004_T062:2
Zm00001d029004_T008:2
Zm00001d029004_T022:2
Zm00001d029004_T014:2
Zm00001d029004_T018:2
Zm00001d029004_T108:2
Zm00001d029004_T025:2
Zm00001d029004_T087:2
Zm00001d029004_T034:2
Zm00001d029004_T104:2
Zm00001d029004_T065:2
Zm00001d029004_T051:2
Zm00001d029004_T017:2
Zm00001d029004_T083:2
Zm00001d029004_T010:2
Zm00001d029004_T013:2
Zm00001d029004_T047:2
Zm00001d029004_T092:2
Zm00001d029004_T027:2
Zm00001d029004_T088:2
Zm00001d029004_T071:2
Zm00001d029004_T086:2
Zm00001d029004_T039:2

					

			
		

General Information
CircRNA Name	Zm00001d029004_circ_g.5
ID in PlantcircBase	zma_circ_006513
Alias	zma_circ_0000667, GRMZM2G559436_C1
Organism	Zea mays
Position	chr1: 54463464-54463803 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, 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.6 Zm00001d029004_circ_g.7 Zm00001d029004_circ_g.8
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	Zm00001d029004_T096:2 Zm00001d029004_T028:2 Zm00001d029004_T019:2 Zm00001d029004_T107:2 Zm00001d029004_T023:2 Zm00001d029004_T053:2 Zm00001d029004_T029:2 Zm00001d029004_T097:2 Zm00001d029004_T059:2 Zm00001d029004_T056:2 Zm00001d029004_T075:2 Zm00001d029004_T105:2 Zm00001d029004_T005:2 Zm00001d029004_T033:2 Zm00001d029004_T055:2 Zm00001d029004_T058:2 Zm00001d029004_T070:2 Zm00001d029004_T074:2 Zm00001d029004_T036:2 Zm00001d029004_T082:2 Zm00001d029004_T041:2 Zm00001d029004_T003:2 Zm00001d029004_T042:2 Zm00001d029004_T067:2 Zm00001d029004_T060:2 Zm00001d029004_T061:2 Zm00001d029004_T099:2 Zm00001d029004_T077:2 Zm00001d029004_T011:2 Zm00001d029004_T004:2 Zm00001d029004_T046:2 Zm00001d029004_T044:2 Zm00001d029004_T101:2 Zm00001d029004_T079:2 Zm00001d029004_T021:2 Zm00001d029004_T002:2 Zm00001d029004_T049:2 Zm00001d029004_T095:2 Zm00001d029004_T016:2 Zm00001d029004_T062:2 Zm00001d029004_T008:2 Zm00001d029004_T022:2 Zm00001d029004_T014:2 Zm00001d029004_T018:2 Zm00001d029004_T108:2 Zm00001d029004_T025:2 Zm00001d029004_T087:2 Zm00001d029004_T034:2 Zm00001d029004_T104:2 Zm00001d029004_T065:2 Zm00001d029004_T051:2 Zm00001d029004_T017:2 Zm00001d029004_T083:2 Zm00001d029004_T010:2 Zm00001d029004_T013:2 Zm00001d029004_T047:2 Zm00001d029004_T092:2 Zm00001d029004_T027:2 Zm00001d029004_T088:2 Zm00001d029004_T071:2 Zm00001d029004_T086:2 Zm00001d029004_T039:2

			
						 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  
						
							TTCATTGTTCCCAATTAATGAAAGGATAAGGGACTTTTTTGTTGAGTATGATCGCCATACTCTA
CATACAAGTCCCCCATGGGGTTCTGAGCTTCTTGAGgttactttcagatgtgtccttgccgatt
ttgagagagctcgttccacattacctgcaggaaagtggaaaggtttgcttcttgattttgtgtt
tctcggtg

						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: 232
Transcript exons: 54463464-54463533,54463642-54463803
GTTACTTTCAGATGTGTCCTTGCCGATTTTGAGAGAGCTCGTTCCACATTACCTGCAGGAAAGT
GGAAAGGAGAGAATGGACTATCTGGAAGATGGGAAAACTGTTTTCAGGTTACGTTTAAGGCTCT
GCTCTTCATTGTTCCCAATTAATGAAAGGATAAGGGACTTTTTTGTTGAGTATGATCGCCATAC
TCTACATACAAGTCCCCCATGGGGTTCTGAGCTTCTTGAG
						
						Genomic sequence
						
							GTTACTTTCAGATGTGTCCTTGCCGATTTTGAGAGAGCTCGTTCCACATTACCTGCAGGAAAGT
GGAAAGGTTTGCTTCTTGATTTTGTGTTTCTCGGTGCCACCTTAGTTGCAGAAATTTCATTTAT
GGAATTATATCTGTGGTAAGATTCTTCTCTAATTTTCAGTTTTTATACAGGAGAGAATGGACTA
TCTGGAAGATGGGAAAACTGTTTTCAGGTTACGTTTAAGGCTCTGCTCTTCATTGTTCCCAATT
AATGAAAGGATAAGGGACTTTTTTGTTGAGTATGATCGCCATACTCTACATACAAGTCCCCCAT
GGGGTTCTGAGCTTCTTGAG

Sequences
Splice junction sequence	TTCATTGTTCCCAATTAATGAAAGGATAAGGGACTTTTTTGTTGAGTATGATCGCCATACTCTA CATACAAGTCCCCCATGGGGTTCTGAGCTTCTTGAGgttactttcagatgtgtccttgccgatt ttgagagagctcgttccacattacctgcaggaaagtggaaaggtttgcttcttgattttgtgtt tctcggtg
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: 232 Transcript exons: 54463464-54463533,54463642-54463803 GTTACTTTCAGATGTGTCCTTGCCGATTTTGAGAGAGCTCGTTCCACATTACCTGCAGGAAAGT GGAAAGGAGAGAATGGACTATCTGGAAGATGGGAAAACTGTTTTCAGGTTACGTTTAAGGCTCT GCTCTTCATTGTTCCCAATTAATGAAAGGATAAGGGACTTTTTTGTTGAGTATGATCGCCATAC TCTACATACAAGTCCCCCATGGGGTTCTGAGCTTCTTGAG
Genomic sequence	GTTACTTTCAGATGTGTCCTTGCCGATTTTGAGAGAGCTCGTTCCACATTACCTGCAGGAAAGT GGAAAGGTTTGCTTCTTGATTTTGTGTTTCTCGGTGCCACCTTAGTTGCAGAAATTTCATTTAT GGAATTATATCTGTGGTAAGATTCTTCTCTAATTTTCAGTTTTTATACAGGAGAGAATGGACTA TCTGGAAGATGGGAAAACTGTTTTCAGGTTACGTTTAAGGCTCTGCTCTTCATTGTTCCCAATT AATGAAAGGATAAGGGACTTTTTTGTTGAGTATGATCGCCATACTCTACATACAAGTCCCCCAT GGGGTTCTGAGCTTCTTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.34194455

Conservation Information
Conserved circRNAs	NA
PMCS	0.34194455

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							54463649-54463718(+)
54463752-54463718(+)
						
						Potential amino acid sequence
						
							MDYLEDGKTVFRLRLRLCSSLFPINERIRDFFVEYDRHTLHTSPPWGSELLEVTFRCVLADFER
ARSTLPAGKWKGENGLSGRWENCFQVTFKALLFIVPN*(+)
MIAILYIQVPHGVLSFLRLLSDVSLPILRELVPHYLQESGKERMDYLEDGKTVFRLRLRLCSSL
FPINERIRDFFVEYDRHTLHTSPPWGSELLEVTFRCVLADFERARSTLPAGKWKGENGLSGRWE
NCFQVTFKALLFIVPN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	54463649-54463718(+) 54463752-54463718(+)
Potential amino acid sequence	MDYLEDGKTVFRLRLRLCSSLFPINERIRDFFVEYDRHTLHTSPPWGSELLEVTFRCVLADFER ARSTLPAGKWKGENGLSGRWENCFQVTFKALLFIVPN(+) MIAILYIQVPHGVLSFLRLLSDVSLPILRELVPHYLQESGKERMDYLEDGKTVFRLRLRLCSSL FPINERIRDFFVEYDRHTLHTSPPWGSELLEVTFRCVLADFERARSTLPAGKWKGENGLSGRWE NCFQVTFKALLFIVPN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d029004_circ_g.5

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