Plant Circular RNA Database

Detail information of Zm00001d027474_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d027474_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006375
					
						Alias
						zma_circ_0000684, ZmciR88
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 6143858-6145398  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d027474						
					
						Parent gene annotation
						
							Callose synthase 3
							
						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
						Zm00001d027472_T002:6
Zm00001d027472_T002:6
Zm00001d027474_T001:6

General Information
CircRNA Name	Zm00001d027474_circ_g.1
ID in PlantcircBase	zma_circ_006375
Alias	zma_circ_0000684, ZmciR88
Organism	Zea mays
Position	chr1: 6143858-6145398 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d027474
Parent gene annotation	Callose synthase 3
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	Zm00001d027472_T002:6 Zm00001d027472_T002:6 Zm00001d027474_T001:6

			
						 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  
						
							TGGCATAAAACGCAAGTTTGCAGCTTCACCCCAAATGAGAAGGTACAAGCCCATATACAGTAAT
TTTCGTTGTTGCATCTCCTGCTGAATTGTTGGCAACcttgtccaagatttagtatagcagaagt
gataaagatactcaaaaccttcttgaaaacagcataatcaaaaatactggctagtgaacctccg
tcccaagc

									
								

					

						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: 650
Transcript exons: 6143858-6143972,6144154-6144267,6144371-6144449,6144510-
6144586,6144685-6144822,6145272-6145398
CTTGTCCAAGATTTAGTATAGCAGAAGTGATAAAGATACTCAAAACCTTCTTGAAAACAGCATA
ATCAAAAATACTGGCTAGTGAACCTCCGTCCCAAGCGAGAATTATCATAACCTGAAGAGCTAAA
ATAAAGAAGCTCCAGAGTCTGTCAAAACTTCTGAATATGTGCCAAAATGAGCGTAGCTCAACGA
AGTTGACCTTTCCCTTCTGTTTGCTGATCCTTGTGCTTTCATTTCTTTCATCAGGCTGACAAAA
GAAGTCAGCATCAGCTCGCATAGGCCAACCAAGCCGAAAGCAGTCAGCAGACCAGAAGTACTCA
TTAAGATCATCATAGTTTCTCCACTCAGAATGATTCCCTTTCTCTCTTTTGCTCCTTTCAGCTT
CCTTTGCTATGGTATGGTAAATCGGTGTAACAACTTTCTTCAGAAAGGCTTCTTTCTCACCACC
ATAGGCCGGCTTCACATATTCACCCGTCAAGGCACTGACATTTCCAGCTAACATACCATACATT
TCAAATGCCATATGATGATATATGTAGCAAATGCACTCTGGCATAAAACGCAAGTTTGCAGCTT
CACCCCAAATGAGAAGGTACAAGCCCATATACAGTAATTTTCGTTGTTGCATCTCCTGCTGAAT
TGTTGGCAAC
						
					

						Genomic sequence
						
							CTTGTCCAAGATTTAGTATAGCAGAAGTGATAAAGATACTCAAAACCTTCTTGAAAACAGCATA
ATCAAAAATACTGGCTAGTGAACCTCCGTCCCAAGCGAGAATTATCATAACCTACATGAAACAA
TCAAAATTAAATTAAAAACCTCAAATAACAGATTAGCTATACAACATCCAGCTAAGATGTTAAG
TACCTTCCTGTAGAGTGTTTATTAAAAAATGCACTGAACCCTTCAAACGTCCAAAATAATGCAG
CAAATGCTTATTGCAGAAGAAGGTAAATATAAATAAATACCTGAAGAGCTAAAATAAAGAAGCT
CCAGAGTCTGTCAAAACTTCTGAATATGTGCCAAAATGAGCGTAGCTCAACGAAGTTGACCTTT
CCCTTCTGTTTGCTGATCCTTGTGCTCTGAACAGCTCATTACATTAGATGTTGCTAGCCCAACA
AAAACACGAAGATACCATGATGATATATGGTAAAATCCTAAGCTAAAAAACATAATCCAACTCA
CTTCATTTCTTTCATCAGGCTGACAAAAGAAGTCAGCATCAGCTCGCATAGGCCAACCAAGCCG
AAAGCAGTCAGCAGACCTGCAATTTAACAATATAAAATCTAAAGAGCAAACAAATAAACTAAGA
AAAAACTAGTACCAGAAGTACTCATTAAGATCATCATAGTTTCTCCACTCAGAATGATTCCCTT
TCTCTCTTTTGCTCCTTTCAGCTTCCTGAAAAGTTGTAGTGAAAAACTGAAGTTCAGCACCAGA
AGAAGAATAAAGCTCAACCGACACAACTGAATAACAGTCAAGAGCTGAGAGCAAACCACCTTTG
CTATGGTATGGTAAATCGGTGTAACAACTTTCTTCAGAAAGGCTTCTTTCTCACCACCATAGGC
CGGCTTCACATATTCACCCGTCAAGGCACTGACATTTCCAGCTAACATACCATACATTTCAAAT
GCCATCTATGACAATAACCAGAACTGTCAGGACCATCTTCGTTACGCTTTTAACATCCAAGACA
AGTACTTGCAAAACAAATGTATGACTCATGCATTTTTCTTAAGAACAAATCTGTAGCCTTCTTA
ATTCACCTATTGAACTCTGAGAGCATTCCATGGATACAATATTAATTTTTCGCATAAAACTTGA
TAGGGTCCATTATATATGTCCGTAATAGAGCGTATAGTCACAGTAGATTGTGCTAAAATTTTAA
TATTAGCTACCTTTAAAATGTCGTATTTACCAAATTAGTTACATGAATGAACTCATCCAGTTGA
TGCCGCTCGAGTGTTCAAAATTTAACTATTCATCCTTAAGAACATTTCTTAAGTATTGATCTTA
ATATGCTTATTTATTTAAGAAAGAAAAAATGAATTAATGTAAGGGAGTTCATGTGTTGTTTAGA
TCGTACATGATGATATATGTAGCAAATGCACTCTGGCATAAAACGCAAGTTTGCAGCTTCACCC
CAAATGAGAAGGTACAAGCCCATATACAGTAATTTTCGTTGTTGCATCTCCTGCTGAATTGTTG
GCAAC
						
					

			
		

Sequences
Splice junction sequence	TGGCATAAAACGCAAGTTTGCAGCTTCACCCCAAATGAGAAGGTACAAGCCCATATACAGTAAT TTTCGTTGTTGCATCTCCTGCTGAATTGTTGGCAACcttgtccaagatttagtatagcagaagt gataaagatactcaaaaccttcttgaaaacagcataatcaaaaatactggctagtgaacctccg tcccaagc
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: 650 Transcript exons: 6143858-6143972,6144154-6144267,6144371-6144449,6144510- 6144586,6144685-6144822,6145272-6145398 CTTGTCCAAGATTTAGTATAGCAGAAGTGATAAAGATACTCAAAACCTTCTTGAAAACAGCATA ATCAAAAATACTGGCTAGTGAACCTCCGTCCCAAGCGAGAATTATCATAACCTGAAGAGCTAAA ATAAAGAAGCTCCAGAGTCTGTCAAAACTTCTGAATATGTGCCAAAATGAGCGTAGCTCAACGA AGTTGACCTTTCCCTTCTGTTTGCTGATCCTTGTGCTTTCATTTCTTTCATCAGGCTGACAAAA GAAGTCAGCATCAGCTCGCATAGGCCAACCAAGCCGAAAGCAGTCAGCAGACCAGAAGTACTCA TTAAGATCATCATAGTTTCTCCACTCAGAATGATTCCCTTTCTCTCTTTTGCTCCTTTCAGCTT CCTTTGCTATGGTATGGTAAATCGGTGTAACAACTTTCTTCAGAAAGGCTTCTTTCTCACCACC ATAGGCCGGCTTCACATATTCACCCGTCAAGGCACTGACATTTCCAGCTAACATACCATACATT TCAAATGCCATATGATGATATATGTAGCAAATGCACTCTGGCATAAAACGCAAGTTTGCAGCTT CACCCCAAATGAGAAGGTACAAGCCCATATACAGTAATTTTCGTTGTTGCATCTCCTGCTGAAT TGTTGGCAAC
Genomic sequence	CTTGTCCAAGATTTAGTATAGCAGAAGTGATAAAGATACTCAAAACCTTCTTGAAAACAGCATA ATCAAAAATACTGGCTAGTGAACCTCCGTCCCAAGCGAGAATTATCATAACCTACATGAAACAA TCAAAATTAAATTAAAAACCTCAAATAACAGATTAGCTATACAACATCCAGCTAAGATGTTAAG TACCTTCCTGTAGAGTGTTTATTAAAAAATGCACTGAACCCTTCAAACGTCCAAAATAATGCAG CAAATGCTTATTGCAGAAGAAGGTAAATATAAATAAATACCTGAAGAGCTAAAATAAAGAAGCT CCAGAGTCTGTCAAAACTTCTGAATATGTGCCAAAATGAGCGTAGCTCAACGAAGTTGACCTTT CCCTTCTGTTTGCTGATCCTTGTGCTCTGAACAGCTCATTACATTAGATGTTGCTAGCCCAACA AAAACACGAAGATACCATGATGATATATGGTAAAATCCTAAGCTAAAAAACATAATCCAACTCA CTTCATTTCTTTCATCAGGCTGACAAAAGAAGTCAGCATCAGCTCGCATAGGCCAACCAAGCCG AAAGCAGTCAGCAGACCTGCAATTTAACAATATAAAATCTAAAGAGCAAACAAATAAACTAAGA AAAAACTAGTACCAGAAGTACTCATTAAGATCATCATAGTTTCTCCACTCAGAATGATTCCCTT TCTCTCTTTTGCTCCTTTCAGCTTCCTGAAAAGTTGTAGTGAAAAACTGAAGTTCAGCACCAGA AGAAGAATAAAGCTCAACCGACACAACTGAATAACAGTCAAGAGCTGAGAGCAAACCACCTTTG CTATGGTATGGTAAATCGGTGTAACAACTTTCTTCAGAAAGGCTTCTTTCTCACCACCATAGGC CGGCTTCACATATTCACCCGTCAAGGCACTGACATTTCCAGCTAACATACCATACATTTCAAAT GCCATCTATGACAATAACCAGAACTGTCAGGACCATCTTCGTTACGCTTTTAACATCCAAGACA AGTACTTGCAAAACAAATGTATGACTCATGCATTTTTCTTAAGAACAAATCTGTAGCCTTCTTA ATTCACCTATTGAACTCTGAGAGCATTCCATGGATACAATATTAATTTTTCGCATAAAACTTGA TAGGGTCCATTATATATGTCCGTAATAGAGCGTATAGTCACAGTAGATTGTGCTAAAATTTTAA TATTAGCTACCTTTAAAATGTCGTATTTACCAAATTAGTTACATGAATGAACTCATCCAGTTGA TGCCGCTCGAGTGTTCAAAATTTAACTATTCATCCTTAAGAACATTTCTTAAGTATTGATCTTA ATATGCTTATTTATTTAAGAAAGAAAAAATGAATTAATGTAAGGGAGTTCATGTGTTGTTTAGA TCGTACATGATGATATATGTAGCAAATGCACTCTGGCATAAAACGCAAGTTTGCAGCTTCACCC CAAATGAGAAGGTACAAGCCCATATACAGTAATTTTCGTTGTTGCATCTCCTGCTGAATTGTTG GCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.129108443

Conservation Information
Conserved circRNAs	NA
PMCS	0.129108443

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6145378-6144797(-)
						
						Potential amino acid sequence
						
							MQQRKLLYMGLYLLIWGEAANLRFMPECICYIYHHMAFEMYGMLAGNVSALTGEYVKPAYGGEK
EAFLKKVVTPIYHTIAKEAERSKREKGNHSEWRNYDDLNESADCFRLGWPMRADADFFCQPDER
NESTRISKQKGKVNFVELRSFWHIFRSFDRLWSFFILALQVMIILAWDGGSLASIFDYAVFKKV
LSIFITSAILNLGQGCQQFSRRCNNENYCIWACTFSFGVKLQTCVLCQSAFATYIIIWHLKCMV
C*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	6145378-6144797(-)
Potential amino acid sequence	MQQRKLLYMGLYLLIWGEAANLRFMPECICYIYHHMAFEMYGMLAGNVSALTGEYVKPAYGGEK EAFLKKVVTPIYHTIAKEAERSKREKGNHSEWRNYDDLNESADCFRLGWPMRADADFFCQPDER NESTRISKQKGKVNFVELRSFWHIFRSFDRLWSFFILALQVMIILAWDGGSLASIFDYAVFKKV LSIFITSAILNLGQGCQQFSRRCNNENYCIWACTFSFGVKLQTCVLCQSAFATYIIIWHLKCMV C*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d027474_circ_g.1

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