Plant Circular RNA Database

Detail information of Zm00001d024523_circ_g.2

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d024523_circ_g.2
					

						ID in PlantcircBase
						zma_circ_010224
					

						Alias
						zma_circ_0000174
					

						Organism
						
							Zea mays						
					

						Position
						
							chr10: 75996887-75997279  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d024523						
					

						Parent gene annotation
						
							Ramosa 1 enhancer locus 2; Ramosa1 enhancer locus2  
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d024523_circ_g.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  
						
							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
						Zm00001d024523_T009:2
Zm00001d024523_T038:2
Zm00001d024523_T045:2
Zm00001d024523_T028:2
Zm00001d024523_T005:2
Zm00001d024523_T011:2
Zm00001d024523_T026:2
Zm00001d024523_T051:2
Zm00001d024523_T055:2
Zm00001d024523_T034:2
Zm00001d024523_T054:2
Zm00001d024523_T023:2
Zm00001d024523_T037:2
Zm00001d024523_T060:2
Zm00001d024523_T058:2
Zm00001d024523_T033:2
Zm00001d024523_T047:2
Zm00001d024523_T015:2
Zm00001d024523_T013:2
Zm00001d024523_T061:2
Zm00001d024523_T004:2
Zm00001d024523_T022:2
Zm00001d024523_T019:2
Zm00001d024523_T036:2
Zm00001d024523_T002:2
Zm00001d024523_T044:2
Zm00001d024523_T049:2
Zm00001d024523_T031:2
Zm00001d024523_T017:2
Zm00001d024523_T029:2
Zm00001d024523_T052:2
Zm00001d024523_T048:2
Zm00001d024523_T027:2
Zm00001d024523_T025:1
Zm00001d024523_T057:2
Zm00001d024523_T040:2
Zm00001d024523_T043:2
Zm00001d024523_T035:2
Zm00001d024523_T024:2
Zm00001d024523_T046:2
Zm00001d024523_T010:2
Zm00001d024523_T030:2
Zm00001d024523_T056:2
Zm00001d024523_T059:2
Zm00001d024523_T039:2
Zm00001d024523_T050:2
Zm00001d024523_T016:2
Zm00001d024523_T041:2
Zm00001d024523_T020:2
Zm00001d024523_T001:2
Zm00001d024523_T006:2
Zm00001d024523_T018:2
Zm00001d024523_T003:2
Zm00001d024523_T032:2

					

			
		

General Information
CircRNA Name	Zm00001d024523_circ_g.2
ID in PlantcircBase	zma_circ_010224
Alias	zma_circ_0000174
Organism	Zea mays
Position	chr10: 75996887-75997279 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d024523
Parent gene annotation	Ramosa 1 enhancer locus 2; Ramosa1 enhancer locus2
Parent gene strand	-
Alternative splicing	Zm00001d024523_circ_g.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	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	Zm00001d024523_T009:2 Zm00001d024523_T038:2 Zm00001d024523_T045:2 Zm00001d024523_T028:2 Zm00001d024523_T005:2 Zm00001d024523_T011:2 Zm00001d024523_T026:2 Zm00001d024523_T051:2 Zm00001d024523_T055:2 Zm00001d024523_T034:2 Zm00001d024523_T054:2 Zm00001d024523_T023:2 Zm00001d024523_T037:2 Zm00001d024523_T060:2 Zm00001d024523_T058:2 Zm00001d024523_T033:2 Zm00001d024523_T047:2 Zm00001d024523_T015:2 Zm00001d024523_T013:2 Zm00001d024523_T061:2 Zm00001d024523_T004:2 Zm00001d024523_T022:2 Zm00001d024523_T019:2 Zm00001d024523_T036:2 Zm00001d024523_T002:2 Zm00001d024523_T044:2 Zm00001d024523_T049:2 Zm00001d024523_T031:2 Zm00001d024523_T017:2 Zm00001d024523_T029:2 Zm00001d024523_T052:2 Zm00001d024523_T048:2 Zm00001d024523_T027:2 Zm00001d024523_T025:1 Zm00001d024523_T057:2 Zm00001d024523_T040:2 Zm00001d024523_T043:2 Zm00001d024523_T035:2 Zm00001d024523_T024:2 Zm00001d024523_T046:2 Zm00001d024523_T010:2 Zm00001d024523_T030:2 Zm00001d024523_T056:2 Zm00001d024523_T059:2 Zm00001d024523_T039:2 Zm00001d024523_T050:2 Zm00001d024523_T016:2 Zm00001d024523_T041:2 Zm00001d024523_T020:2 Zm00001d024523_T001:2 Zm00001d024523_T006:2 Zm00001d024523_T018:2 Zm00001d024523_T003:2 Zm00001d024523_T032:2

			
						 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  
						
							CATTATCAACAATGTCAGCCAACTTCCAGGTTTTGACCTTTTCGGATTCATCTGTTATTCTTGG
CTTAACATCTGGAGTTCTGCTAGCATCCATAGGTGCcttgccgctaggatttctgtcgctccgt
tgccatttccacaacttatgaacagcattggagccaagagccaagagtgcaaccccattatttg
tatataac

						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: 261
Transcript exons: 75996887-75996997,75997130-75997279
CTTGCCGCTAGGATTTCTGTCGCTCCGTTGCCATTTCCACAACTTATGAACAGCATTGGAGCCA
AGAGCCAAGAGTGCAACCCCATTATTTGTATATAACAAACGGACAATTTTGCTTGGATTAGTGT
CTGTGTCTGTCAAATGCAGAGCTCGAAGATGTCCATTATCAACAATGTCAGCCAACTTCCAGGT
TTTGACCTTTTCGGATTCATCTGTTATTCTTGGCTTAACATCTGGAGTTCTGCTAGCATCCATA
GGTGC
						
						Genomic sequence
						
							CTTGCCGCTAGGATTTCTGTCGCTCCGTTGCCATTTCCACAACTTATGAACAGCATTGGAGCCA
AGAGCCAAGAGTGCAACCCCATTATTTGTATATAACAAACGGACAATCTGCGGAACAAAGAAAT
AAACGTAACCTACATCAGAGATTTTCATAACCTAGAACATCAATATAAAGACCAACTCATGTGT
CAGTTTGATTCTGCATGCATGATTAAACAACTTAATCACAATTCATCATACTTTGCTTGGATTA
GTGTCTGTGTCTGTCAAATGCAGAGCTCGAAGATGTCCATTATCAACAATGTCAGCCAACTTCC
AGGTTTTGACCTTTTCGGATTCATCTGTTATTCTTGGCTTAACATCTGGAGTTCTGCTAGCATC
CATAGGTGC

Sequences
Splice junction sequence	CATTATCAACAATGTCAGCCAACTTCCAGGTTTTGACCTTTTCGGATTCATCTGTTATTCTTGG CTTAACATCTGGAGTTCTGCTAGCATCCATAGGTGCcttgccgctaggatttctgtcgctccgt tgccatttccacaacttatgaacagcattggagccaagagccaagagtgcaaccccattatttg tatataac
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: 261 Transcript exons: 75996887-75996997,75997130-75997279 CTTGCCGCTAGGATTTCTGTCGCTCCGTTGCCATTTCCACAACTTATGAACAGCATTGGAGCCA AGAGCCAAGAGTGCAACCCCATTATTTGTATATAACAAACGGACAATTTTGCTTGGATTAGTGT CTGTGTCTGTCAAATGCAGAGCTCGAAGATGTCCATTATCAACAATGTCAGCCAACTTCCAGGT TTTGACCTTTTCGGATTCATCTGTTATTCTTGGCTTAACATCTGGAGTTCTGCTAGCATCCATA GGTGC
Genomic sequence	CTTGCCGCTAGGATTTCTGTCGCTCCGTTGCCATTTCCACAACTTATGAACAGCATTGGAGCCA AGAGCCAAGAGTGCAACCCCATTATTTGTATATAACAAACGGACAATCTGCGGAACAAAGAAAT AAACGTAACCTACATCAGAGATTTTCATAACCTAGAACATCAATATAAAGACCAACTCATGTGT CAGTTTGATTCTGCATGCATGATTAAACAACTTAATCACAATTCATCATACTTTGCTTGGATTA GTGTCTGTGTCTGTCAAATGCAGAGCTCGAAGATGTCCATTATCAACAATGTCAGCCAACTTCC AGGTTTTGACCTTTTCGGATTCATCTGTTATTCTTGGCTTAACATCTGGAGTTCTGCTAGCATC CATAGGTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.189845266

Conservation Information
Conserved circRNAs	NA
PMCS	0.189845266

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							75997161-75996982(+)
75997192-75996932(+)
75997275-75996889(-)
75996974-75997236(-)
						
						Potential amino acid sequence
						
							MQSSKMSIINNVSQLPGFDLFGFICYSWLNIWSSASIHRCLAARISVAPLPFPQLMNSIGAKSQ
ECNPIICI*(+)
MSANFQVLTFSDSSVILGLTSGVLLASIGALPLGFLSLRCHFHNL*(+)
MDASRTPDVKPRITDESEKVKTWKLADIVDNGHLRALHLTDTDTNPSKIVRLLYTNNGVALLAL
GSNAVHKLWKWQRSDRNPSGKAPMDASRTPDVKPRITDESEKVKTWKLADIVDNGHLRALHLTD
TDTNPSKIVRLLYTNNGVALLALGSNAVHKLWKWQRSDRNPSGKAPMDASRTPDVKPRITDESE
KVKTWKLADIVDNGHLRALHLTDTDTNPSKIVRLLYTNNGVALLALGSNAVHKLWKWQRSDRNP
SGKAPMDASRTPDVKPRITDESEKVKTWKLADIVDNGHLRALHLTDTDTNPSKIVRLLYTNNGV
ALLALGSNAVHKLWKWQRSDRNPSGK(-)
MGLHSWLLAPMLFISCGNGNGATEILAARHLWMLAELQMLSQE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	75997161-75996982(+) 75997192-75996932(+) 75997275-75996889(-) 75996974-75997236(-)
Potential amino acid sequence	MQSSKMSIINNVSQLPGFDLFGFICYSWLNIWSSASIHRCLAARISVAPLPFPQLMNSIGAKSQ ECNPIICI(+) MSANFQVLTFSDSSVILGLTSGVLLASIGALPLGFLSLRCHFHNL(+) MDASRTPDVKPRITDESEKVKTWKLADIVDNGHLRALHLTDTDTNPSKIVRLLYTNNGVALLAL GSNAVHKLWKWQRSDRNPSGKAPMDASRTPDVKPRITDESEKVKTWKLADIVDNGHLRALHLTD TDTNPSKIVRLLYTNNGVALLALGSNAVHKLWKWQRSDRNPSGKAPMDASRTPDVKPRITDESE KVKTWKLADIVDNGHLRALHLTDTDTNPSKIVRLLYTNNGVALLALGSNAVHKLWKWQRSDRNP SGKAPMDASRTPDVKPRITDESEKVKTWKLADIVDNGHLRALHLTDTDTNPSKIVRLLYTNNGV ALLALGSNAVHKLWKWQRSDRNPSGK(-) MGLHSWLLAPMLFISCGNGNGATEILAARHLWMLAELQMLSQE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d024523_circ_g.2

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