Plant Circular RNA Database

Detail information of Zm00001d032980_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d032980_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006846
					
						Alias
						zma_circ_0000464
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 245696390-245698102  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d032980						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase 3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d032980_circ_g.4 						
					
						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
						Zm00001d032980_T023:6
Zm00001d032980_T001:6
Zm00001d032980_T016:6
Zm00001d032980_T003:6
Zm00001d032980_T046:6
Zm00001d032980_T015:6
Zm00001d032980_T011:6
Zm00001d032980_T004:6
Zm00001d032980_T045:6
Zm00001d032980_T048:6
Zm00001d032980_T039:6
Zm00001d032980_T049:6
Zm00001d032980_T031:6
Zm00001d032980_T036:6
Zm00001d032980_T033:6
Zm00001d032980_T021:6
Zm00001d032980_T043:6
Zm00001d032980_T040:6
Zm00001d032980_T026:6
Zm00001d032980_T034:6
Zm00001d032980_T027:5
Zm00001d032980_T009:6
Zm00001d032980_T020:6
Zm00001d032980_T008:6
Zm00001d032980_T030:6
Zm00001d032980_T006:6
Zm00001d032980_T018:6

General Information
CircRNA Name	Zm00001d032980_circ_g.3
ID in PlantcircBase	zma_circ_006846
Alias	zma_circ_0000464
Organism	Zea mays
Position	chr1: 245696390-245698102 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d032980
Parent gene annotation	Phospholipid-transporting ATPase 3
Parent gene strand	+
Alternative splicing	Zm00001d032980_circ_g.4
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	Zm00001d032980_T023:6 Zm00001d032980_T001:6 Zm00001d032980_T016:6 Zm00001d032980_T003:6 Zm00001d032980_T046:6 Zm00001d032980_T015:6 Zm00001d032980_T011:6 Zm00001d032980_T004:6 Zm00001d032980_T045:6 Zm00001d032980_T048:6 Zm00001d032980_T039:6 Zm00001d032980_T049:6 Zm00001d032980_T031:6 Zm00001d032980_T036:6 Zm00001d032980_T033:6 Zm00001d032980_T021:6 Zm00001d032980_T043:6 Zm00001d032980_T040:6 Zm00001d032980_T026:6 Zm00001d032980_T034:6 Zm00001d032980_T027:5 Zm00001d032980_T009:6 Zm00001d032980_T020:6 Zm00001d032980_T008:6 Zm00001d032980_T030:6 Zm00001d032980_T006:6 Zm00001d032980_T018:6

			
						 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  
						
							AGGGTGAGGAGACTCCGGAAAAGATAAGTTACCAGGCTGCCTCACCTGATGAGGCTGCACTTGT
GTCTGCTGCTAAAAATTTTGGTTTCTTCTTTTATAGtggcatatttattaatgaaaaatacttt
tatcttggattgcgtgggcatgtggaggatcagttcaatcctaaaaacagatttgtggtatata
ctgttttg

									
								

					

						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: 684
Transcript exons: 245696390-245696474,245696550-245696627,245696708-245696
824,245697474-245697629,245697718-245697822,245697960-24
5698102
TGGCATATTTATTAATGAAAAATACTTTTATCTTGGATTGCGTGGGCATGTGGAGGATCAGTTC
AATCCTAAAAACAGATTTGTGGTGACCATTTTAACCATGTTTACTCTGATAACTCTATACTCAA
CGATCATCCCCATTTCCCTTTACGTGTCCATTGAGATGATCAAATTCATACAGTGCACACAATT
CATTAATAACGATCTTCATATGTACCATGCTGAGAGTAACACCCCTGCTTTGGCACGGACTTCT
AATCTTAATGAGGAGCTTGGACAGGTTGAATATATATTTTCTGACAAAACTGGCACACTTACAA
GAAATCTGATGGAATTCTTTAAATGCTCAATTGGTGGAGAAATGTATGGAACTGGCATCACAGA
GATTGAGAAAGGAGGAGCAGAACGGGCTGGAATTAGAATCGATGATGATGAGGGCAAAAGATCT
GCTAACGCGGTCCATGAAAAAGGATTCAATTTTGATGACGCTAGAATCATGCGCGGTGCATGGA
GAAACGAACCTAATCCTGAGGCTTGCAAGGAATTCTTTAGATGCCTTGCAATCTGTCATACAGT
TCTTCCAGAGGGTGAGGAGACTCCGGAAAAGATAAGTTACCAGGCTGCCTCACCTGATGAGGCT
GCACTTGTGTCTGCTGCTAAAAATTTTGGTTTCTTCTTTTATAG
						
					

						Genomic sequence
						
							TGGCATATTTATTAATGAAAAATACTTTTATCTTGGATTGCGTGGGCATGTGGAGGATCAGTTC
AATCCTAAAAACAGATTTGTGGTATATACTGTTTTGGACAATTTTAGTTGTATCTAAATTCATA
CATGTAGCTCTAAAACACTATCACTTGCACAGGTGACCATTTTAACCATGTTTACTCTGATAAC
TCTATACTCAACGATCATCCCCATTTCCCTTTACGTGTCCATTGAGGTATTTTGTTCAACTTGT
TTATTTAGGATGACCTAACCTATGTTCGGGCTATTAGAGCTTATGTTTCCTTTGGCTGCCAGAT
GATCAAATTCATACAGTGCACACAATTCATTAATAACGATCTTCATATGTACCATGCTGAGAGT
AACACCCCTGCTTTGGCACGGACTTCTAATCTTAATGAGGAGCTTGGACAGGTAATTTCTTCCT
CTTGCCCCTTATCCTGTTTTCAATTTGAAGAAAACTCCTATTTGGTCACTCAACTAGGAGTGTG
GGACTATCTATTCAATGCTAAAGGGTTGAGTTTGTATTGGTGTAGATTACATCTTTGTAGCGTC
ACTCTTTCCACAAGTTAGATAATTTGCACCATTTTGTGGAGAAGTGAGTTTTATTTTTATTTTT
TGGGGGTTGGTTGGTTGTTGCCCTCTAAGCATAAATATGGAAGGGAACGTATCTGGTGCTCAAA
GGGGTACGGTGTTCATGTACACATTTGAAATCTGGTGCATCCATCTTGCATTCAACGACACCAG
CTAATTTTACGAAGAACCCCTCCCACCAGGGGAGGAAGGTGGAAGGGGTTCTTCATAAAATTGG
TGCTGCTGTTAGATGCAAAATGGATGTTCCAGATTTAAAATGTGCACGTGAGCACTGTACCCCT
TTGAGCACCAGATATGTTGCCAATATGGAAATGCCTTTTGGCTTTTCTGTCCATATTGTGGGGA
TAATCAATATAATCTGTATTAACTGAATGCTTGAGATCTTGTCAGATTTTGAAGATTACAGATA
TAAACGTTTTGTACATTTCGCCTTACTTTAGATTTAACTCATCATCAACATTATTGTTAGGTTG
AATATATATTTTCTGACAAAACTGGCACACTTACAAGAAATCTGATGGAATTCTTTAAATGCTC
AATTGGTGGAGAAATGTATGGAACTGGCATCACAGAGATTGAGAAAGGAGGAGCAGAACGGGCT
GGAATTAGAATCGATGATGATGAGGTGTGGTGTTTGTTGTTGAAGTCGATAAATTGTACCATTA
CGTCTGCAAATATAGCAATCTTTACATTTCTTTTTTTTACTTTCATAGGGCAAAAGATCTGCTA
ACGCGGTCCATGAAAAAGGATTCAATTTTGATGACGCTAGAATCATGCGCGGTGCATGGAGAAA
CGAACCTAATCCTGAGGCTTGCAAGGTAGGTGTTTGGAGATTTTTTAAATAAGTTTGGGTCTTC
AGCATGAAAAGATATTTTTATTCGTCTCTTGTTACGATGATGTAAAATTCTAGTTTGTTCTGAA
AATCAATCTTTTGATTTTCTGATTTTATTTTTAGGAATTCTTTAGATGCCTTGCAATCTGTCAT
ACAGTTCTTCCAGAGGGTGAGGAGACTCCGGAAAAGATAAGTTACCAGGCTGCCTCACCTGATG
AGGCTGCACTTGTGTCTGCTGCTAAAAATTTTGGTTTCTTCTTTTATAG
						
					

			
		

Sequences
Splice junction sequence	AGGGTGAGGAGACTCCGGAAAAGATAAGTTACCAGGCTGCCTCACCTGATGAGGCTGCACTTGT GTCTGCTGCTAAAAATTTTGGTTTCTTCTTTTATAGtggcatatttattaatgaaaaatacttt tatcttggattgcgtgggcatgtggaggatcagttcaatcctaaaaacagatttgtggtatata ctgttttg
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: 684 Transcript exons: 245696390-245696474,245696550-245696627,245696708-245696 824,245697474-245697629,245697718-245697822,245697960-24 5698102 TGGCATATTTATTAATGAAAAATACTTTTATCTTGGATTGCGTGGGCATGTGGAGGATCAGTTC AATCCTAAAAACAGATTTGTGGTGACCATTTTAACCATGTTTACTCTGATAACTCTATACTCAA CGATCATCCCCATTTCCCTTTACGTGTCCATTGAGATGATCAAATTCATACAGTGCACACAATT CATTAATAACGATCTTCATATGTACCATGCTGAGAGTAACACCCCTGCTTTGGCACGGACTTCT AATCTTAATGAGGAGCTTGGACAGGTTGAATATATATTTTCTGACAAAACTGGCACACTTACAA GAAATCTGATGGAATTCTTTAAATGCTCAATTGGTGGAGAAATGTATGGAACTGGCATCACAGA GATTGAGAAAGGAGGAGCAGAACGGGCTGGAATTAGAATCGATGATGATGAGGGCAAAAGATCT GCTAACGCGGTCCATGAAAAAGGATTCAATTTTGATGACGCTAGAATCATGCGCGGTGCATGGA GAAACGAACCTAATCCTGAGGCTTGCAAGGAATTCTTTAGATGCCTTGCAATCTGTCATACAGT TCTTCCAGAGGGTGAGGAGACTCCGGAAAAGATAAGTTACCAGGCTGCCTCACCTGATGAGGCT GCACTTGTGTCTGCTGCTAAAAATTTTGGTTTCTTCTTTTATAG
Genomic sequence	TGGCATATTTATTAATGAAAAATACTTTTATCTTGGATTGCGTGGGCATGTGGAGGATCAGTTC AATCCTAAAAACAGATTTGTGGTATATACTGTTTTGGACAATTTTAGTTGTATCTAAATTCATA CATGTAGCTCTAAAACACTATCACTTGCACAGGTGACCATTTTAACCATGTTTACTCTGATAAC TCTATACTCAACGATCATCCCCATTTCCCTTTACGTGTCCATTGAGGTATTTTGTTCAACTTGT TTATTTAGGATGACCTAACCTATGTTCGGGCTATTAGAGCTTATGTTTCCTTTGGCTGCCAGAT GATCAAATTCATACAGTGCACACAATTCATTAATAACGATCTTCATATGTACCATGCTGAGAGT AACACCCCTGCTTTGGCACGGACTTCTAATCTTAATGAGGAGCTTGGACAGGTAATTTCTTCCT CTTGCCCCTTATCCTGTTTTCAATTTGAAGAAAACTCCTATTTGGTCACTCAACTAGGAGTGTG GGACTATCTATTCAATGCTAAAGGGTTGAGTTTGTATTGGTGTAGATTACATCTTTGTAGCGTC ACTCTTTCCACAAGTTAGATAATTTGCACCATTTTGTGGAGAAGTGAGTTTTATTTTTATTTTT TGGGGGTTGGTTGGTTGTTGCCCTCTAAGCATAAATATGGAAGGGAACGTATCTGGTGCTCAAA GGGGTACGGTGTTCATGTACACATTTGAAATCTGGTGCATCCATCTTGCATTCAACGACACCAG CTAATTTTACGAAGAACCCCTCCCACCAGGGGAGGAAGGTGGAAGGGGTTCTTCATAAAATTGG TGCTGCTGTTAGATGCAAAATGGATGTTCCAGATTTAAAATGTGCACGTGAGCACTGTACCCCT TTGAGCACCAGATATGTTGCCAATATGGAAATGCCTTTTGGCTTTTCTGTCCATATTGTGGGGA TAATCAATATAATCTGTATTAACTGAATGCTTGAGATCTTGTCAGATTTTGAAGATTACAGATA TAAACGTTTTGTACATTTCGCCTTACTTTAGATTTAACTCATCATCAACATTATTGTTAGGTTG AATATATATTTTCTGACAAAACTGGCACACTTACAAGAAATCTGATGGAATTCTTTAAATGCTC AATTGGTGGAGAAATGTATGGAACTGGCATCACAGAGATTGAGAAAGGAGGAGCAGAACGGGCT GGAATTAGAATCGATGATGATGAGGTGTGGTGTTTGTTGTTGAAGTCGATAAATTGTACCATTA CGTCTGCAAATATAGCAATCTTTACATTTCTTTTTTTTACTTTCATAGGGCAAAAGATCTGCTA ACGCGGTCCATGAAAAAGGATTCAATTTTGATGACGCTAGAATCATGCGCGGTGCATGGAGAAA CGAACCTAATCCTGAGGCTTGCAAGGTAGGTGTTTGGAGATTTTTTAAATAAGTTTGGGTCTTC AGCATGAAAAGATATTTTTATTCGTCTCTTGTTACGATGATGTAAAATTCTAGTTTGTTCTGAA AATCAATCTTTTGATTTTCTGATTTTATTTTTAGGAATTCTTTAGATGCCTTGCAATCTGTCAT ACAGTTCTTCCAGAGGGTGAGGAGACTCCGGAAAAGATAAGTTACCAGGCTGCCTCACCTGATG AGGCTGCACTTGTGTCTGCTGCTAAAAATTTTGGTTTCTTCTTTTATAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.097399857

Conservation Information
Conserved circRNAs	NA
PMCS	0.097399857

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							245696566-245698099(+)
245698052-245696550(+)
245696440-245698046(-)
						
						Potential amino acid sequence
						
							MFTLITLYSTIIPISLYVSIEMIKFIQCTQFINNDLHMYHAESNTPALARTSNLNEELGQVEYI
FSDKTGTLTRNLMEFFKCSIGGEMYGTGITEIEKGGAERAGIRIDDDEGKRSANAVHEKGFNFD
DARIMRGAWRNEPNPEACKEFFRCLAICHTVLPEGEETPEKISYQAASPDEAALVSAAKNFGFF
FYSGIFINEKYFYLGLRGHVEDQFNPKNRFVVTILTMFTLITLYSTIIPISLYVSIEMIKFIQC
TQFINNDLHMYHAESNTPALARTSNLNEELGQVEYIFSDKTGTLTRNLMEFFKCSIGGEMYGTG
ITEIEKGGAERAGIRIDDDEGKRSANAVHEKGFNFDDARIMRGAWRNEPNPEACKEFFRCLAIC
HTVLPEGEETPEKISYQAASPDEAALVSAAKNFGFFFYSGIFINEKYFYLGLRGHVEDQFNPKN
RFVVTILTMFTLITLYSTIIPISLYVSIEMIKFIQCTQFINNDLHMYHAESNTPALARTSNLNE
ELGQVEYIFSDKTGTLTRNLMEFFKCSIGGEMYGTGITEIEKGGAERAGIRIDDDEGKRSANAV
HEKGFNFDDARIMRGAWRNEPNPEACKEFFRCLAICHTVLPEGEETPEKISYQAASPDEAALVS
AAKNFGFFFYSGIFINEKYFYLGLRGHVEDQFNPKNRFVVTILTMFTLITLYSTIIPISLYVSI
EMIKFIQCTQFINNDLHMYHAESNTPALARTSNLNEELGQVEYIFSDKTGTLTRNLMEFFKCSI
GGEMYGTGITEIEKGGAERAGIRIDDDEGKRSANAVHEKGFNFDDARIMRGAWRNEPNPEACKE
FFRCLAICHTVLPEGEETPEKISYQAASPDEAALVSAAKNFGFFFY(+)
MRLHLCLLLKILVSSFIVAYLLMKNTFILDCVGMWRISSILKTDLW*(+)
MPTQSKIKVFFINKYATIKEETKIFSSRHKCSLIR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	245696566-245698099(+) 245698052-245696550(+) 245696440-245698046(-)
Potential amino acid sequence	MFTLITLYSTIIPISLYVSIEMIKFIQCTQFINNDLHMYHAESNTPALARTSNLNEELGQVEYI FSDKTGTLTRNLMEFFKCSIGGEMYGTGITEIEKGGAERAGIRIDDDEGKRSANAVHEKGFNFD DARIMRGAWRNEPNPEACKEFFRCLAICHTVLPEGEETPEKISYQAASPDEAALVSAAKNFGFF FYSGIFINEKYFYLGLRGHVEDQFNPKNRFVVTILTMFTLITLYSTIIPISLYVSIEMIKFIQC TQFINNDLHMYHAESNTPALARTSNLNEELGQVEYIFSDKTGTLTRNLMEFFKCSIGGEMYGTG ITEIEKGGAERAGIRIDDDEGKRSANAVHEKGFNFDDARIMRGAWRNEPNPEACKEFFRCLAIC HTVLPEGEETPEKISYQAASPDEAALVSAAKNFGFFFYSGIFINEKYFYLGLRGHVEDQFNPKN RFVVTILTMFTLITLYSTIIPISLYVSIEMIKFIQCTQFINNDLHMYHAESNTPALARTSNLNE ELGQVEYIFSDKTGTLTRNLMEFFKCSIGGEMYGTGITEIEKGGAERAGIRIDDDEGKRSANAV HEKGFNFDDARIMRGAWRNEPNPEACKEFFRCLAICHTVLPEGEETPEKISYQAASPDEAALVS AAKNFGFFFYSGIFINEKYFYLGLRGHVEDQFNPKNRFVVTILTMFTLITLYSTIIPISLYVSI EMIKFIQCTQFINNDLHMYHAESNTPALARTSNLNEELGQVEYIFSDKTGTLTRNLMEFFKCSI GGEMYGTGITEIEKGGAERAGIRIDDDEGKRSANAVHEKGFNFDDARIMRGAWRNEPNPEACKE FFRCLAICHTVLPEGEETPEKISYQAASPDEAALVSAAKNFGFFFY(+) MRLHLCLLLKILVSSFIVAYLLMKNTFILDCVGMWRISSILKTDLW(+) MPTQSKIKVFFINKYATIKEETKIFSSRHKCSLIR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d032980_circ_g.3

Address

Any questions?

Supported by