Plant Circular RNA Database

Detail information of Zm00001d014297_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d014297_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008455
					
						Alias
						zma_circ_0002080
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 40029526-40031682  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d014297						
					
						Parent gene annotation
						
							 histidine kinase3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d014297_circ_g.1 Zm00001d014297_circ_g.2 						
					
						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
						Zm00001d014297_T007:7
Zm00001d014297_T017:7
Zm00001d014297_T013:7
Zm00001d014297_T004:7
Zm00001d014297_T009:7
Zm00001d014297_T010:7
Zm00001d014297_T001:7
Zm00001d014297_T022:5
Zm00001d014297_T012:7
Zm00001d014297_T014:7
Zm00001d014297_T020:6
Zm00001d014297_T015:7
Zm00001d014297_T011:7
Zm00001d014297_T024:5
Zm00001d014297_T008:7
Zm00001d014297_T016:7
Zm00001d014297_T006:7
Zm00001d014297_T019:7

General Information
CircRNA Name	Zm00001d014297_circ_g.3
ID in PlantcircBase	zma_circ_008455
Alias	zma_circ_0002080
Organism	Zea mays
Position	chr5: 40029526-40031682 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d014297
Parent gene annotation	histidine kinase3
Parent gene strand	+
Alternative splicing	Zm00001d014297_circ_g.1 Zm00001d014297_circ_g.2
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	Zm00001d014297_T007:7 Zm00001d014297_T017:7 Zm00001d014297_T013:7 Zm00001d014297_T004:7 Zm00001d014297_T009:7 Zm00001d014297_T010:7 Zm00001d014297_T001:7 Zm00001d014297_T022:5 Zm00001d014297_T012:7 Zm00001d014297_T014:7 Zm00001d014297_T020:6 Zm00001d014297_T015:7 Zm00001d014297_T011:7 Zm00001d014297_T024:5 Zm00001d014297_T008:7 Zm00001d014297_T016:7 Zm00001d014297_T006:7 Zm00001d014297_T019:7

			
						 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  
						
							GTTGGCCGTGCTTGTATCTGACCAAGTTCCTGATGTCCTAATTGGGGATCCATGGCGGTTCCGG
CAGATCATTACGAACCTTGTGGGGAATTCTATGAAGaaaacatttgaggacttcacagcaagga
caacatttgaaaggccattgatgagtggtgtcgcctatgcattgaaggtattacacaatgaaag
acaacagt

									
								

					

						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: 1227
Transcript exons: 40029526-40029801,40030233-40030402,40030498-40030710,40
030798-40030984,40031091-40031142,40031258-40031487,4003
1584-40031682
AAAACATTTGAGGACTTCACAGCAAGGACAACATTTGAAAGGCCATTGATGAGTGGTGTCGCCT
ATGCATTGAAGGTATTACACAATGAAAGACAACAGTTTGAGGAACAACATGGATGGAAGATTAA
GAAGATGGAAGATGGAGATCAGTCCCTTGTTCATGACTACAACCTTGAAAAGCTTGAACCATCA
CCAGTTCAAGATGAGTATGCGCCTGTTATTTTCTCTCAGGAAACTGTGAAGCACATTATATCTG
TAGATATGATGTCTGGGAAGGAAGATCATGACAATATATTACGTTCCTGGTCAACAGGTAAAGG
GGCCCTAACATCCCCTTTTAAGCTTCTGAAGTCCAACCATCTCGGTGTGGTGCTTACATTCACT
GTATATAAATATGATCTGCCTCCAAATGCAACACCACAGGAGCGTATTCATGCTACATTGGGCT
ATCTTGGTGCCTCATTTGATGTCCCTTCTCTGGTTGATAAACTCCTAGAACAACTCGCTAGCAA
ACGAAAGATAGTAGTTAATTTATATGACACCACAAATCATACCTCTCCTATTGAAATGTATGGT
TCTGATTTTACTCCATCTGGTGATCTGCATATTAGTAGCATTGATTTTGGAGACCCAACACGCA
AACATGAGATGCATTGCAGATTTAAACATGAACCTTCACTGCCATGGTCTGCAATAATAATATC
AACAGCTGTAGCTATAATTGTTTTGCTTGTTGGACATATTATTTATGCAACTCTGAACTCCCTT
GAAAAGGCTGAACATGATTATAGAGTAATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATA
TAGCAAAATCTCAGTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTT
AGGTATGCTGCAGATGCTAATGGACACTGAACTTGATACAACTCAGCAGGATTTTGTAGTCACC
GCTCAAGAAAGTGGAAAGGTATTAATAAACTTAATAAATGAAGTCCTTGATCTGGCTAAGATAG
AGTCAGGAAGGATTGAGCTGGAAGCAGTGCCTTTTGATGTCCGTGATATTCTTGACAATGTGAT
ATCTCTTTTCTACGATAAATCACAAGCTAAAGGCATAGAGTTGGCCGTGCTTGTATCTGACCAA
GTTCCTGATGTCCTAATTGGGGATCCATGGCGGTTCCGGCAGATCATTACGAACCTTGTGGGGA
ATTCTATGAAG
						
					

						Genomic sequence
						
							AAAACATTTGAGGACTTCACAGCAAGGACAACATTTGAAAGGCCATTGATGAGTGGTGTCGCCT
ATGCATTGAAGGTATTACACAATGAAAGACAACAGTTTGAGGAACAACATGGATGGAAGATTAA
GAAGATGGAAGATGGAGATCAGTCCCTTGTTCATGACTACAACCTTGAAAAGCTTGAACCATCA
CCAGTTCAAGATGAGTATGCGCCTGTTATTTTCTCTCAGGAAACTGTGAAGCACATTATATCTG
TAGATATGATGTCTGGGAAGGTAGTAGGATATTCGTAAGCCTTTACAGTAAATACTTACTATTT
TATCTATCCTGAGTTCCTTACTACTATTTTTGTTATAAAACGAAGAAATTTCTGGCTCTTCTTC
TAACTTTCAATATTATTAGGATTAAACATGTGTAGAACTTCTCGGTCAAAAAAGACACTTTAGA
ACTTATATTTTTATTTTAATTAGAATTTGATGTATAAAAATTAATCATTTTTACAATGAGTGTT
ATAGTAATATAAGTTGTTATGTGTCTTGTTCAATGTGTTAATTACTATAGCATGTTCCATAGAA
ATACTGTGCAGGCTGTTACTAATTCTCTCTTATTCTGTCTTTGTGGAAATTACATAATTACTAA
ACCTCATAGTAATAATAATAATAACTAAGACTCCATTTTTCTGCTAACATTACAACCTTGATTT
CAGGAAGATCATGACAATATATTACGTTCCTGGTCAACAGGTAAAGGGGCCCTAACATCCCCTT
TTAAGCTTCTGAAGTCCAACCATCTCGGTGTGGTGCTTACATTCACTGTATATAAATATGATCT
GCCTCCAAATGCAACACCACAGGAGCGTATTCATGCTACATTGGGGTAAAATGTTTTGCAAAGT
TTCAAGTTGAAGCTATATAGGAATACACTATTTTTTCTTTAGGAGACTTAACCTTGTGGTTATT
GACACTTTGCAGCTATCTTGGTGCCTCATTTGATGTCCCTTCTCTGGTTGATAAACTCCTAGAA
CAACTCGCTAGCAAACGAAAGATAGTAGTTAATTTATATGACACCACAAATCATACCTCTCCTA
TTGAAATGTATGGTTCTGATTTTACTCCATCTGGTGATCTGCATATTAGTAGCATTGATTTTGG
AGACCCAACACGCAAACATGAGATGCATTGCAGGTAGAAAACTTTTTTTTGATGCGAATTATAC
AATGCTTTTGTTCTTCAGATATGCTCAGTGCTTTCTCTTTCAAACTTCTCTTTCAGATTTAAAC
ATGAACCTTCACTGCCATGGTCTGCAATAATAATATCAACAGCTGTAGCTATAATTGTTTTGCT
TGTTGGACATATTATTTATGCAACTCTGAACTCCCTTGAAAAGGCTGAACATGATTATAGAGTA
ATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATATAGCAAAATCTCAGGTTCATTCTACCT
CTTCCAGTGTCTTCATCCTATGCATTGGTTTGTTATCTCATTTGTTCTACTTTTCTCTTTTTGT
CGGCTGAGTCATTATTGATTGTCTTGCAGTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCC
AATGAATGGTGTTTTAGGTCTGTACTTCTGATATTTCTTTTTTGTCTATTAATACATACCGCAG
TTATTTGTGTTTATGTTTTAATCAAAGACAACTAAATAAATTTTGAAAAGGATTTCTTCTTGAA
TTAGGTATGCTGCAGATGCTAATGGACACTGAACTTGATACAACTCAGCAGGATTTTGTAGTCA
CCGCTCAAGAAAGTGGAAAGGTATTAATAAACTTAATAAATGAAGTCCTTGATCTGGCTAAGAT
AGAGTCAGGAAGGATTGAGCTGGAAGCAGTGCCTTTTGATGTCCGTGATATTCTTGACAATGTG
ATATCTCTTTTCTACGATAAATCACAAGCTAAAGGCATAGAGGTGAGTCCTAATTTAGAACTTG
TATTGTTTGCTAAGCTCTGAATATTGTTTGTGCCATGGGACCTAAAATAATGTGTAATTCTTTT
TTGAGGGTAGTTGGCCGTGCTTGTATCTGACCAAGTTCCTGATGTCCTAATTGGGGATCCATGG
CGGTTCCGGCAGATCATTACGAACCTTGTGGGGAATTCTATGAAG
						
					

			
		

Sequences
Splice junction sequence	GTTGGCCGTGCTTGTATCTGACCAAGTTCCTGATGTCCTAATTGGGGATCCATGGCGGTTCCGG CAGATCATTACGAACCTTGTGGGGAATTCTATGAAGaaaacatttgaggacttcacagcaagga caacatttgaaaggccattgatgagtggtgtcgcctatgcattgaaggtattacacaatgaaag acaacagt
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: 1227 Transcript exons: 40029526-40029801,40030233-40030402,40030498-40030710,40 030798-40030984,40031091-40031142,40031258-40031487,4003 1584-40031682 AAAACATTTGAGGACTTCACAGCAAGGACAACATTTGAAAGGCCATTGATGAGTGGTGTCGCCT ATGCATTGAAGGTATTACACAATGAAAGACAACAGTTTGAGGAACAACATGGATGGAAGATTAA GAAGATGGAAGATGGAGATCAGTCCCTTGTTCATGACTACAACCTTGAAAAGCTTGAACCATCA CCAGTTCAAGATGAGTATGCGCCTGTTATTTTCTCTCAGGAAACTGTGAAGCACATTATATCTG TAGATATGATGTCTGGGAAGGAAGATCATGACAATATATTACGTTCCTGGTCAACAGGTAAAGG GGCCCTAACATCCCCTTTTAAGCTTCTGAAGTCCAACCATCTCGGTGTGGTGCTTACATTCACT GTATATAAATATGATCTGCCTCCAAATGCAACACCACAGGAGCGTATTCATGCTACATTGGGCT ATCTTGGTGCCTCATTTGATGTCCCTTCTCTGGTTGATAAACTCCTAGAACAACTCGCTAGCAA ACGAAAGATAGTAGTTAATTTATATGACACCACAAATCATACCTCTCCTATTGAAATGTATGGT TCTGATTTTACTCCATCTGGTGATCTGCATATTAGTAGCATTGATTTTGGAGACCCAACACGCA AACATGAGATGCATTGCAGATTTAAACATGAACCTTCACTGCCATGGTCTGCAATAATAATATC AACAGCTGTAGCTATAATTGTTTTGCTTGTTGGACATATTATTTATGCAACTCTGAACTCCCTT GAAAAGGCTGAACATGATTATAGAGTAATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATA TAGCAAAATCTCAGTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTT AGGTATGCTGCAGATGCTAATGGACACTGAACTTGATACAACTCAGCAGGATTTTGTAGTCACC GCTCAAGAAAGTGGAAAGGTATTAATAAACTTAATAAATGAAGTCCTTGATCTGGCTAAGATAG AGTCAGGAAGGATTGAGCTGGAAGCAGTGCCTTTTGATGTCCGTGATATTCTTGACAATGTGAT ATCTCTTTTCTACGATAAATCACAAGCTAAAGGCATAGAGTTGGCCGTGCTTGTATCTGACCAA GTTCCTGATGTCCTAATTGGGGATCCATGGCGGTTCCGGCAGATCATTACGAACCTTGTGGGGA ATTCTATGAAG
Genomic sequence	AAAACATTTGAGGACTTCACAGCAAGGACAACATTTGAAAGGCCATTGATGAGTGGTGTCGCCT ATGCATTGAAGGTATTACACAATGAAAGACAACAGTTTGAGGAACAACATGGATGGAAGATTAA GAAGATGGAAGATGGAGATCAGTCCCTTGTTCATGACTACAACCTTGAAAAGCTTGAACCATCA CCAGTTCAAGATGAGTATGCGCCTGTTATTTTCTCTCAGGAAACTGTGAAGCACATTATATCTG TAGATATGATGTCTGGGAAGGTAGTAGGATATTCGTAAGCCTTTACAGTAAATACTTACTATTT TATCTATCCTGAGTTCCTTACTACTATTTTTGTTATAAAACGAAGAAATTTCTGGCTCTTCTTC TAACTTTCAATATTATTAGGATTAAACATGTGTAGAACTTCTCGGTCAAAAAAGACACTTTAGA ACTTATATTTTTATTTTAATTAGAATTTGATGTATAAAAATTAATCATTTTTACAATGAGTGTT ATAGTAATATAAGTTGTTATGTGTCTTGTTCAATGTGTTAATTACTATAGCATGTTCCATAGAA ATACTGTGCAGGCTGTTACTAATTCTCTCTTATTCTGTCTTTGTGGAAATTACATAATTACTAA ACCTCATAGTAATAATAATAATAACTAAGACTCCATTTTTCTGCTAACATTACAACCTTGATTT CAGGAAGATCATGACAATATATTACGTTCCTGGTCAACAGGTAAAGGGGCCCTAACATCCCCTT TTAAGCTTCTGAAGTCCAACCATCTCGGTGTGGTGCTTACATTCACTGTATATAAATATGATCT GCCTCCAAATGCAACACCACAGGAGCGTATTCATGCTACATTGGGGTAAAATGTTTTGCAAAGT TTCAAGTTGAAGCTATATAGGAATACACTATTTTTTCTTTAGGAGACTTAACCTTGTGGTTATT GACACTTTGCAGCTATCTTGGTGCCTCATTTGATGTCCCTTCTCTGGTTGATAAACTCCTAGAA CAACTCGCTAGCAAACGAAAGATAGTAGTTAATTTATATGACACCACAAATCATACCTCTCCTA TTGAAATGTATGGTTCTGATTTTACTCCATCTGGTGATCTGCATATTAGTAGCATTGATTTTGG AGACCCAACACGCAAACATGAGATGCATTGCAGGTAGAAAACTTTTTTTTGATGCGAATTATAC AATGCTTTTGTTCTTCAGATATGCTCAGTGCTTTCTCTTTCAAACTTCTCTTTCAGATTTAAAC ATGAACCTTCACTGCCATGGTCTGCAATAATAATATCAACAGCTGTAGCTATAATTGTTTTGCT TGTTGGACATATTATTTATGCAACTCTGAACTCCCTTGAAAAGGCTGAACATGATTATAGAGTA ATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATATAGCAAAATCTCAGGTTCATTCTACCT CTTCCAGTGTCTTCATCCTATGCATTGGTTTGTTATCTCATTTGTTCTACTTTTCTCTTTTTGT CGGCTGAGTCATTATTGATTGTCTTGCAGTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCC AATGAATGGTGTTTTAGGTCTGTACTTCTGATATTTCTTTTTTGTCTATTAATACATACCGCAG TTATTTGTGTTTATGTTTTAATCAAAGACAACTAAATAAATTTTGAAAAGGATTTCTTCTTGAA TTAGGTATGCTGCAGATGCTAATGGACACTGAACTTGATACAACTCAGCAGGATTTTGTAGTCA CCGCTCAAGAAAGTGGAAAGGTATTAATAAACTTAATAAATGAAGTCCTTGATCTGGCTAAGAT AGAGTCAGGAAGGATTGAGCTGGAAGCAGTGCCTTTTGATGTCCGTGATATTCTTGACAATGTG ATATCTCTTTTCTACGATAAATCACAAGCTAAAGGCATAGAGGTGAGTCCTAATTTAGAACTTG TATTGTTTGCTAAGCTCTGAATATTGTTTGTGCCATGGGACCTAAAATAATGTGTAATTCTTTT TTGAGGGTAGTTGGCCGTGCTTGTATCTGACCAAGTTCCTGATGTCCTAATTGGGGATCCATGG CGGTTCCGGCAGATCATTACGAACCTTGTGGGGAATTCTATGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.093706664

Conservation Information
Conserved circRNAs	NA
PMCS	0.093706664

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							40030620-40030281(+)
						
						Potential amino acid sequence
						
							MYGSDFTPSGDLHISSIDFGDPTRKHEMHCRFKHEPSLPWSAIIISTAVAIIVLLVGHIIYATL
NSLEKAEHDYRVMRELKGQAEAADIAKSQFLATVSHEIRTPMNGVLGMLQMLMDTELDTTQQDF
VVTAQESGKVLINLINEVLDLAKIESGRIELEAVPFDVRDILDNVISLFYDKSQAKGIELAVLV
SDQVPDVLIGDPWRFRQIITNLVGNSMKKTFEDFTARTTFERPLMSGVAYALKVLHNERQQFEE
QHGWKIKKMEDGDQSLVHDYNLEKLEPSPVQDEYAPVIFSQETVKHIISVDMMTIYYVPGQQVK
GP*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	40030620-40030281(+)
Potential amino acid sequence	MYGSDFTPSGDLHISSIDFGDPTRKHEMHCRFKHEPSLPWSAIIISTAVAIIVLLVGHIIYATL NSLEKAEHDYRVMRELKGQAEAADIAKSQFLATVSHEIRTPMNGVLGMLQMLMDTELDTTQQDF VVTAQESGKVLINLINEVLDLAKIESGRIELEAVPFDVRDILDNVISLFYDKSQAKGIELAVLV SDQVPDVLIGDPWRFRQIITNLVGNSMKKTFEDFTARTTFERPLMSGVAYALKVLHNERQQFEE QHGWKIKKMEDGDQSLVHDYNLEKLEPSPVQDEYAPVIFSQETVKHIISVDMMTIYYVPGQQVK GP*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d014297_circ_g.3

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