Plant Circular RNA Database

Detail information of Zm00001d031502_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d031502_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006713
					
						Alias
						zma_circ_0000342
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 192123991-192125556  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d031502						
					
						Parent gene annotation
						
							RanBP2-type zinc finger protein 
							
						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  
						
							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
						Zm00001d031502_T024:5
Zm00001d031502_T022:5
Zm00001d031502_T026:5
Zm00001d031502_T001:3
Zm00001d031502_T012:5
Zm00001d031502_T009:5
Zm00001d031502_T010:5
Zm00001d031502_T027:5
Zm00001d031502_T004:5
Zm00001d031502_T023:5
Zm00001d031502_T011:5
Zm00001d031502_T017:5
Zm00001d031502_T006:5
Zm00001d031502_T016:4
Zm00001d031502_T021:4
Zm00001d031502_T002:5
Zm00001d031502_T020:5
Zm00001d031502_T018:5
Zm00001d031502_T005:3
Zm00001d031502_T013:5
Zm00001d031502_T015:4
Zm00001d031502_T007:5
Zm00001d031502_T014:5
Zm00001d031502_T025:4
Zm00001d031502_T008:5
Zm00001d031502_T003:3
Zm00001d031502_T019:4

General Information
CircRNA Name	Zm00001d031502_circ_g.1
ID in PlantcircBase	zma_circ_006713
Alias	zma_circ_0000342
Organism	Zea mays
Position	chr1: 192123991-192125556 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d031502
Parent gene annotation	RanBP2-type zinc finger protein
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	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	Zm00001d031502_T024:5 Zm00001d031502_T022:5 Zm00001d031502_T026:5 Zm00001d031502_T001:3 Zm00001d031502_T012:5 Zm00001d031502_T009:5 Zm00001d031502_T010:5 Zm00001d031502_T027:5 Zm00001d031502_T004:5 Zm00001d031502_T023:5 Zm00001d031502_T011:5 Zm00001d031502_T017:5 Zm00001d031502_T006:5 Zm00001d031502_T016:4 Zm00001d031502_T021:4 Zm00001d031502_T002:5 Zm00001d031502_T020:5 Zm00001d031502_T018:5 Zm00001d031502_T005:3 Zm00001d031502_T013:5 Zm00001d031502_T015:4 Zm00001d031502_T007:5 Zm00001d031502_T014:5 Zm00001d031502_T025:4 Zm00001d031502_T008:5 Zm00001d031502_T003:3 Zm00001d031502_T019:4

			
						 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  
						
							TAATAGGTATACAGAAGAATAATCACAAGAGCACATACCATTGGACCAGGACCAGCAGGTATTG
GCCCATACCTGTCCATGGGAATTCCATACATTCCACctgattgtcctgatctgtcgctgaacca
ttcacattgtttgtttgtgatggcttttctgctccacattggggacgattgcattttgttcgga
aaggataa

									
								

					

						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
						
							CTGATTGTCCTGATCTGTCGCTGAACCATTCACATTGTTTGTTTGTGATGGCTTTTCTGCTCCA
CATTGGGGACGATTGCATTTTGTTCGGAAAGGATAATTTATGTTATTGCACTGCTCACACTTCC
AACTGCCCTCTGGCATCTTTGCTTCTATCAATTAGAGGTTGGGGTGTGAGTTCGAACAGAATTG
ATGGAACAATAAACTACATAGACCATTAGATAAAGTAGCCCATAATTTATGTGCGAAAATCCAA
AGAAAACACACTAATTCCTTCAAAGAAATGTCTAGTGATAACAAATATTACAAAAAAATTTGTA
ATTCAGGGACATTTGTTATACGCAAAGAAGATTGGATGAGGAAGGAGCACTAAACCCTTATCAT
GTGGAAACTTACTTGAGCCCCTTAAACCATCAGACTTAGATCCCTGCACAAAGAGTTGATGCAC
AAGCAATCAGTAAGTAAAAGGGGATTAGTTGATGAACAATCGATCTCTATAAACTACAGATAGA
AGCCCAAGCATTAGAAATGAAGATTTAGATTTGGATGAAAGAGAAGTACTTCTACACAAAATAT
AGCCAAAACTTGTTTGCTTTTACTTCACAATATTATTCTGGTTTAGCTTGATAATACAAGAGGG
AGGATTGGAGGAAGTTGTATTGATTTTTTCCTAGAGTAAGAATACCTAAAAAATAGTAAGGAAC
AGGACTAAAGAGAAGGTCATCAACAAGTACTCAGATCCTGATGTGTAGGCTATGGCAGGGCAAA
CTAGAGGATGTATCCAGATGTGCATAAGCATGGTTTCACCAAACAGTTTACAGCAGTAGTATAA
AGTGAAACCATGTACACTCCAAGCACACAAATAATCTTGTGGCAGCAAAGTCAACTTCAAGCAC
AATTGCGAAGTTATAAAAGTACACTTCAACAGAAGTAAAGAATCATTTACTAACACAATTACAA
TTTTTAAAAATGATCTTAATTTAAATACATAAAAGAAGCAATATCAGATCGCTTATAATAGCAA
GATGAGACAGAAGTTGCAAACCTGGTTTGCAGGTCTAGGTGTGTTGCACTTTCTCATATTACAG
ACTGTGCGAAAGCCAAAGTTGATGTTATGGCAATTTGGACACTCCCAATCATTATCACGGCCAG
CTCCTTCATCAAAAGTTCAGGAGAATAGGCAAATAATTAATCAAGTGCTAACCACATTAATATA
AATAAGTCAAAATAAAAATTCAATGAGACATACCTGCAGGCTTCTTCTGAGAACCTTCATCAGA
ATATGAGCCAGCCCTTGTGCCCTTTCAGGTTCAGGAAATATAGATTTAAGGAATCATAACAGTT
AATCCATGTAGACACAATCACAGAAATCATAAATACCAAACAAAAAATGTAATAGAGTAACAGA
ACAACAAACATGTTGAAAGTTCTTCATGTAAGGCAACAGTAGTTAAATTAGCATGAGGTAATAG
GTATACAGAAGAATAATCACAAGAGCACATACCATTGGACCAGGACCAGCAGGTATTGGCCCAT
ACCTGTCCATGGGAATTCCATACATTCCAC
						
					

			
		

Sequences
Splice junction sequence	TAATAGGTATACAGAAGAATAATCACAAGAGCACATACCATTGGACCAGGACCAGCAGGTATTG GCCCATACCTGTCCATGGGAATTCCATACATTCCACctgattgtcctgatctgtcgctgaacca ttcacattgtttgtttgtgatggcttttctgctccacattggggacgattgcattttgttcgga aaggataa
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	CTGATTGTCCTGATCTGTCGCTGAACCATTCACATTGTTTGTTTGTGATGGCTTTTCTGCTCCA CATTGGGGACGATTGCATTTTGTTCGGAAAGGATAATTTATGTTATTGCACTGCTCACACTTCC AACTGCCCTCTGGCATCTTTGCTTCTATCAATTAGAGGTTGGGGTGTGAGTTCGAACAGAATTG ATGGAACAATAAACTACATAGACCATTAGATAAAGTAGCCCATAATTTATGTGCGAAAATCCAA AGAAAACACACTAATTCCTTCAAAGAAATGTCTAGTGATAACAAATATTACAAAAAAATTTGTA ATTCAGGGACATTTGTTATACGCAAAGAAGATTGGATGAGGAAGGAGCACTAAACCCTTATCAT GTGGAAACTTACTTGAGCCCCTTAAACCATCAGACTTAGATCCCTGCACAAAGAGTTGATGCAC AAGCAATCAGTAAGTAAAAGGGGATTAGTTGATGAACAATCGATCTCTATAAACTACAGATAGA AGCCCAAGCATTAGAAATGAAGATTTAGATTTGGATGAAAGAGAAGTACTTCTACACAAAATAT AGCCAAAACTTGTTTGCTTTTACTTCACAATATTATTCTGGTTTAGCTTGATAATACAAGAGGG AGGATTGGAGGAAGTTGTATTGATTTTTTCCTAGAGTAAGAATACCTAAAAAATAGTAAGGAAC AGGACTAAAGAGAAGGTCATCAACAAGTACTCAGATCCTGATGTGTAGGCTATGGCAGGGCAAA CTAGAGGATGTATCCAGATGTGCATAAGCATGGTTTCACCAAACAGTTTACAGCAGTAGTATAA AGTGAAACCATGTACACTCCAAGCACACAAATAATCTTGTGGCAGCAAAGTCAACTTCAAGCAC AATTGCGAAGTTATAAAAGTACACTTCAACAGAAGTAAAGAATCATTTACTAACACAATTACAA TTTTTAAAAATGATCTTAATTTAAATACATAAAAGAAGCAATATCAGATCGCTTATAATAGCAA GATGAGACAGAAGTTGCAAACCTGGTTTGCAGGTCTAGGTGTGTTGCACTTTCTCATATTACAG ACTGTGCGAAAGCCAAAGTTGATGTTATGGCAATTTGGACACTCCCAATCATTATCACGGCCAG CTCCTTCATCAAAAGTTCAGGAGAATAGGCAAATAATTAATCAAGTGCTAACCACATTAATATA AATAAGTCAAAATAAAAATTCAATGAGACATACCTGCAGGCTTCTTCTGAGAACCTTCATCAGA ATATGAGCCAGCCCTTGTGCCCTTTCAGGTTCAGGAAATATAGATTTAAGGAATCATAACAGTT AATCCATGTAGACACAATCACAGAAATCATAAATACCAAACAAAAAATGTAATAGAGTAACAGA ACAACAAACATGTTGAAAGTTCTTCATGTAAGGCAACAGTAGTTAAATTAGCATGAGGTAATAG GTATACAGAAGAATAATCACAAGAGCACATACCATTGGACCAGGACCAGCAGGTATTGGCCCAT ACCTGTCCATGGGAATTCCATACATTCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.017570456

Conservation Information
Conserved circRNAs	NA
PMCS	0.017570456

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							192125536-192124410(+)
192125274-192124011(+)
192124021-192125268(-)
192124074-192125070(-)
192125553-192125070(-)
						
						Potential amino acid sequence
						
							MGIPYIPPDCPDLSLNHSHCLFVMAFLLHIGDDCILFGKDNLCYCTAHTSNCPLASLLLSPLNH
QT*(+)
MSQPLCPLDQDQQVLAHTCPWEFHTFHLIVLICR*(+)
MVQRQIRTIRWNVWNSHGQVWANTCWSWSNGHKGWLIF*(-)
MQSSPMWSRKAITNKQCEWFSDRSGQSGGMYGIPMDRYGPIPAGPGPMGTRAGSYSDEGSQKKP
AGAGRDNDWECPNCHNINFGFRTVCNMRKCNTPRPANQGSKSDGLRGSKAKMPEGSWKCEQCNN
INYPFRTKCNRPQCGAEKPSQTNNVNGSATDQDNQVECMEFPWTGMGQYLLVLVQWAQGLAHIL
MKVLRRSLQELAVIMIGSVQIAITSTLAFAQSVI*(-)
MYGIPMDRYGPIPAGPGPMGTRAGSYSDEGSQKKPAGAGRDNDWECPNCHNINFGFRTVCNMRK
CNTPRPANQGSKSDGLRGSKAKMPEGSWKCEQCNNINYPFRTKCNRPQCGAEKPSQTNNVNGSA
TDQDNQVECMEFPWTGMGQYLLVLVQWAQGLAHILMKVLRRSLQELAVIMIGSVQIAITSTLAF
AQSVI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	192125536-192124410(+) 192125274-192124011(+) 192124021-192125268(-) 192124074-192125070(-) 192125553-192125070(-)
Potential amino acid sequence	MGIPYIPPDCPDLSLNHSHCLFVMAFLLHIGDDCILFGKDNLCYCTAHTSNCPLASLLLSPLNH QT(+) MSQPLCPLDQDQQVLAHTCPWEFHTFHLIVLICR(+) MVQRQIRTIRWNVWNSHGQVWANTCWSWSNGHKGWLIF(-) MQSSPMWSRKAITNKQCEWFSDRSGQSGGMYGIPMDRYGPIPAGPGPMGTRAGSYSDEGSQKKP AGAGRDNDWECPNCHNINFGFRTVCNMRKCNTPRPANQGSKSDGLRGSKAKMPEGSWKCEQCNN INYPFRTKCNRPQCGAEKPSQTNNVNGSATDQDNQVECMEFPWTGMGQYLLVLVQWAQGLAHIL MKVLRRSLQELAVIMIGSVQIAITSTLAFAQSVI(-) MYGIPMDRYGPIPAGPGPMGTRAGSYSDEGSQKKPAGAGRDNDWECPNCHNINFGFRTVCNMRK CNTPRPANQGSKSDGLRGSKAKMPEGSWKCEQCNNINYPFRTKCNRPQCGAEKPSQTNNVNGSA TDQDNQVECMEFPWTGMGQYLLVLVQWAQGLAHILMKVLRRSLQELAVIMIGSVQIAITSTLAF AQSVI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d031502_circ_g.1

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