Plant Circular RNA Database

Detail information of Zm00001d018795_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d018795_circ_g.3
					

						ID in PlantcircBase
						zma_circ_009208
					

						Alias
						zma_circ_0002727
					

						Organism
						
							Zea mays						
					

						Position
						
							chr7: 5376561-5378219  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d018795						
					

						Parent gene annotation
						
							187-kDa microtubule-associated protein AIR9
							
					

						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  
						
							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
						Zm00001d018795_T031:5
Zm00001d018795_T022:5
Zm00001d018795_T056:5
Zm00001d018795_T093:5
Zm00001d018795_T073:5
Zm00001d018795_T059:3
Zm00001d018795_T051:5
Zm00001d018795_T036:5
Zm00001d018795_T080:6
Zm00001d018795_T082:5
Zm00001d018795_T025:5
Zm00001d018795_T014:5
Zm00001d018795_T071:5
Zm00001d018795_T066:5
Zm00001d018795_T040:5
Zm00001d018795_T077:5
Zm00001d018795_T075:5
Zm00001d018795_T062:5
Zm00001d018795_T005:5
Zm00001d018795_T033:5
Zm00001d018795_T072:5
Zm00001d018795_T045:4
Zm00001d018795_T085:5
Zm00001d018795_T098:5
Zm00001d018795_T064:5
Zm00001d018795_T002:5
Zm00001d018795_T050:4
Zm00001d018795_T057:4
Zm00001d018795_T096:5
Zm00001d018795_T023:5
Zm00001d018795_T028:5
Zm00001d018795_T043:5
Zm00001d018795_T034:5
Zm00001d018795_T095:5
Zm00001d018795_T018:5
Zm00001d018795_T009:5
Zm00001d018795_T048:4
Zm00001d018795_T019:5
Zm00001d018795_T069:5
Zm00001d018795_T088:5
Zm00001d018795_T029:5
Zm00001d018795_T016:5
Zm00001d018795_T101:3
Zm00001d018795_T076:5
Zm00001d018795_T086:5
Zm00001d018795_T011:5
Zm00001d018795_T091:5
Zm00001d018795_T099:5
Zm00001d018795_T039:5
Zm00001d018795_T007:5
Zm00001d018795_T047:5
Zm00001d018795_T053:5
Zm00001d018795_T004:5
Zm00001d018795_T079:5
Zm00001d018795_T074:5
Zm00001d018795_T060:5

					

			
		

General Information
CircRNA Name	Zm00001d018795_circ_g.3
ID in PlantcircBase	zma_circ_009208
Alias	zma_circ_0002727
Organism	Zea mays
Position	chr7: 5376561-5378219 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d018795
Parent gene annotation	187-kDa microtubule-associated protein AIR9
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	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	Zm00001d018795_T031:5 Zm00001d018795_T022:5 Zm00001d018795_T056:5 Zm00001d018795_T093:5 Zm00001d018795_T073:5 Zm00001d018795_T059:3 Zm00001d018795_T051:5 Zm00001d018795_T036:5 Zm00001d018795_T080:6 Zm00001d018795_T082:5 Zm00001d018795_T025:5 Zm00001d018795_T014:5 Zm00001d018795_T071:5 Zm00001d018795_T066:5 Zm00001d018795_T040:5 Zm00001d018795_T077:5 Zm00001d018795_T075:5 Zm00001d018795_T062:5 Zm00001d018795_T005:5 Zm00001d018795_T033:5 Zm00001d018795_T072:5 Zm00001d018795_T045:4 Zm00001d018795_T085:5 Zm00001d018795_T098:5 Zm00001d018795_T064:5 Zm00001d018795_T002:5 Zm00001d018795_T050:4 Zm00001d018795_T057:4 Zm00001d018795_T096:5 Zm00001d018795_T023:5 Zm00001d018795_T028:5 Zm00001d018795_T043:5 Zm00001d018795_T034:5 Zm00001d018795_T095:5 Zm00001d018795_T018:5 Zm00001d018795_T009:5 Zm00001d018795_T048:4 Zm00001d018795_T019:5 Zm00001d018795_T069:5 Zm00001d018795_T088:5 Zm00001d018795_T029:5 Zm00001d018795_T016:5 Zm00001d018795_T101:3 Zm00001d018795_T076:5 Zm00001d018795_T086:5 Zm00001d018795_T011:5 Zm00001d018795_T091:5 Zm00001d018795_T099:5 Zm00001d018795_T039:5 Zm00001d018795_T007:5 Zm00001d018795_T047:5 Zm00001d018795_T053:5 Zm00001d018795_T004:5 Zm00001d018795_T079:5 Zm00001d018795_T074:5 Zm00001d018795_T060:5

			
						 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  
						
							GGTGCTGTTGGATATTATATCGTTGCAAAGTTTACACCTGTGGCACCTGATGGTGAAGTCGGTG
AACCAGCCTATGCTACATCAGATGGCCTTGTGGAAAcaacaccatcagtcagcaatgtgcatgt
tctgggagatattgttgaagataacattatcgtagggaaaggaaaatacttcggtggcagagag
ggactaag

									
								

					

						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: 585
Transcript exons: 5376561-5376693,5377357-5377457,5377635-5377682,5377794-
5377978,5378102-5378219
CAACACCATCAGTCAGCAATGTGCATGTTCTGGGAGATATTGTTGAAGATAACATTATCGTAGG
GAAAGGAAAATACTTCGGTGGCAGAGAGGGACTAAGTAAAATCCGGTGGTTTAGAGAGAAGGAA
AATGGTGAATTTCTTCTTGTGCTATCAGACAGCATGGAGTATACACTAACCAAGGAGGACGTGG
GGAGACACCTCAAATTTGTATATATCCCTGTTAACCTTGAAGGTCAGGAGGGTGAATCTGCTTG
TGCGATAACAGATGTAGTTAAGAAAGCCCCTCCAAAAGTATTCAATCTAAAGATTGTTGGGGAA
TCTATGGAAGGAAGCAAGATATCTGCCAGTGCTACTGTTACAGGTGGAACTGAAGGGTCCAGCA
GGGTTCAATGGTACAAGGCATCTTCCTCTGAATTTAAGAATGAACATGAGCTTGAAGCCCTTAC
TCCGTCACGAGTTTCTAAGACATTCCGCATTCCTCTTGGTGCTGTTGGATATTATATCGTTGCA
AAGTTTACACCTGTGGCACCTGATGGTGAAGTCGGTGAACCAGCCTATGCTACATCAGATGGCC
TTGTGGAAA
						
					

						Genomic sequence
						
							CAACACCATCAGTCAGCAATGTGCATGTTCTGGGAGATATTGTTGAAGATAACATTATCGTAGG
GAAAGGAAAATACTTCGGTGGCAGAGAGGGACTAAGTAAAATCCGGTGGTTTAGAGAGAAGGAA
AATGGGTATGCACCATTACTTGCCATCCCTTAAGATTGAATACAGGAAAAGCTGTTCTATCTTC
TTAATATAATTGATGCACAGTTCTCCTATGCGTTTTAGAAAAAAAAACAGGAAAAACTTGTGGT
GTGGTGCCTATAATTTTCATCAACAGAAAATTCTTAAAATCATTGACATTATGATATATAAGGA
TAATCTGTTGCGTGCCATCAATCACACATTTCCATGAACACAATTCCTGAAAGTCTATAATGGT
TGAATAGAAGGGCATGCCTGGTGCAGTTGTGAGAGTTGTCTCACTGAGTCACCAGGTCGCGGGT
TCGAAGCAACCTCTCAGCATTTGTTGGGGAAGGCCTGCCTCGGTTTATCCCTTCCCCAGACCCC
ACTCATGTAGGAATCTCTGGCACTAGATCTGCCCTCTAATGGTTGAGTAATTGCAAATTAACAA
CTAAGAGCAACTGAGCCAACCTTTTCTCTGTTATATTGTTGAACAAAATATTGCAGCTCGTAAA
CTGAAAATCCTGGGGCGAGGTGTAACAAAAATATGCCATGTGCTAGAACATGATCGTAAACTGG
ATGAACACAAGTGCAAAATCCAAAGTAATCCATATACCTTCATGAATGAAGACACATTCTGTTT
TAATGGTTAATTATTTGTTTATATGCAGTGAATTTCTTCTTGTGCTATCAGACAGCATGGAGTA
TACACTAACCAAGGAGGACGTGGGGAGACACCTCAAATTTGTATATATCCCTGTTAACCTTGAA
GGTCTGAATGTCTGATAAACAGTCAGACATTAACAATGACATAAATTTGTATATATCCCTGTTA
ACCTTGAAGGTCTGAATGTCTGATAAACAGTCAGACATTAACAATGACATCTCTACTGCTTGTT
TACAAAAAAAAATATTATTTTGCGCTAACAAACACTGATGACTTCAACAGGTCAGGAGGGTGAA
TCTGCTTGTGCGATAACAGATGTAGTTAAGAAAGGTACTTATGTCTGACATTTGTGCCAATTAT
GTCATAAAAGTCTATTTTTATTTCGCTTTGGATATGACTGATCAGGTGTGATTACTTTGTTTTA
CCTTCTTGTTTGGCCAGCCCCTCCAAAAGTATTCAATCTAAAGATTGTTGGGGAATCTATGGAA
GGAAGCAAGATATCTGCCAGTGCTACTGTTACAGGTGGAACTGAAGGGTCCAGCAGGGTTCAAT
GGTACAAGGCATCTTCCTCTGAATTTAAGAATGAACATGAGCTTGAAGCCCTTACTCCGTCACG
AGTTTCTAAGGTTATGCCAATTTACTCTCTATTACTATCATTGATGCACTGCTCAAAGCTTAAG
CCATTTTTATTTGTTGTATATTTGGTTAACGTGATAAAACTAAATTGCAACCTTTTAATTTCTC
ACTAGACATTCCGCATTCCTCTTGGTGCTGTTGGATATTATATCGTTGCAAAGTTTACACCTGT
GGCACCTGATGGTGAAGTCGGTGAACCAGCCTATGCTACATCAGATGGCCTTGTGGAAA
						
					

			
		

Sequences
Splice junction sequence	GGTGCTGTTGGATATTATATCGTTGCAAAGTTTACACCTGTGGCACCTGATGGTGAAGTCGGTG AACCAGCCTATGCTACATCAGATGGCCTTGTGGAAAcaacaccatcagtcagcaatgtgcatgt tctgggagatattgttgaagataacattatcgtagggaaaggaaaatacttcggtggcagagag ggactaag
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: 585 Transcript exons: 5376561-5376693,5377357-5377457,5377635-5377682,5377794- 5377978,5378102-5378219 CAACACCATCAGTCAGCAATGTGCATGTTCTGGGAGATATTGTTGAAGATAACATTATCGTAGG GAAAGGAAAATACTTCGGTGGCAGAGAGGGACTAAGTAAAATCCGGTGGTTTAGAGAGAAGGAA AATGGTGAATTTCTTCTTGTGCTATCAGACAGCATGGAGTATACACTAACCAAGGAGGACGTGG GGAGACACCTCAAATTTGTATATATCCCTGTTAACCTTGAAGGTCAGGAGGGTGAATCTGCTTG TGCGATAACAGATGTAGTTAAGAAAGCCCCTCCAAAAGTATTCAATCTAAAGATTGTTGGGGAA TCTATGGAAGGAAGCAAGATATCTGCCAGTGCTACTGTTACAGGTGGAACTGAAGGGTCCAGCA GGGTTCAATGGTACAAGGCATCTTCCTCTGAATTTAAGAATGAACATGAGCTTGAAGCCCTTAC TCCGTCACGAGTTTCTAAGACATTCCGCATTCCTCTTGGTGCTGTTGGATATTATATCGTTGCA AAGTTTACACCTGTGGCACCTGATGGTGAAGTCGGTGAACCAGCCTATGCTACATCAGATGGCC TTGTGGAAA
Genomic sequence	CAACACCATCAGTCAGCAATGTGCATGTTCTGGGAGATATTGTTGAAGATAACATTATCGTAGG GAAAGGAAAATACTTCGGTGGCAGAGAGGGACTAAGTAAAATCCGGTGGTTTAGAGAGAAGGAA AATGGGTATGCACCATTACTTGCCATCCCTTAAGATTGAATACAGGAAAAGCTGTTCTATCTTC TTAATATAATTGATGCACAGTTCTCCTATGCGTTTTAGAAAAAAAAACAGGAAAAACTTGTGGT GTGGTGCCTATAATTTTCATCAACAGAAAATTCTTAAAATCATTGACATTATGATATATAAGGA TAATCTGTTGCGTGCCATCAATCACACATTTCCATGAACACAATTCCTGAAAGTCTATAATGGT TGAATAGAAGGGCATGCCTGGTGCAGTTGTGAGAGTTGTCTCACTGAGTCACCAGGTCGCGGGT TCGAAGCAACCTCTCAGCATTTGTTGGGGAAGGCCTGCCTCGGTTTATCCCTTCCCCAGACCCC ACTCATGTAGGAATCTCTGGCACTAGATCTGCCCTCTAATGGTTGAGTAATTGCAAATTAACAA CTAAGAGCAACTGAGCCAACCTTTTCTCTGTTATATTGTTGAACAAAATATTGCAGCTCGTAAA CTGAAAATCCTGGGGCGAGGTGTAACAAAAATATGCCATGTGCTAGAACATGATCGTAAACTGG ATGAACACAAGTGCAAAATCCAAAGTAATCCATATACCTTCATGAATGAAGACACATTCTGTTT TAATGGTTAATTATTTGTTTATATGCAGTGAATTTCTTCTTGTGCTATCAGACAGCATGGAGTA TACACTAACCAAGGAGGACGTGGGGAGACACCTCAAATTTGTATATATCCCTGTTAACCTTGAA GGTCTGAATGTCTGATAAACAGTCAGACATTAACAATGACATAAATTTGTATATATCCCTGTTA ACCTTGAAGGTCTGAATGTCTGATAAACAGTCAGACATTAACAATGACATCTCTACTGCTTGTT TACAAAAAAAAATATTATTTTGCGCTAACAAACACTGATGACTTCAACAGGTCAGGAGGGTGAA TCTGCTTGTGCGATAACAGATGTAGTTAAGAAAGGTACTTATGTCTGACATTTGTGCCAATTAT GTCATAAAAGTCTATTTTTATTTCGCTTTGGATATGACTGATCAGGTGTGATTACTTTGTTTTA CCTTCTTGTTTGGCCAGCCCCTCCAAAAGTATTCAATCTAAAGATTGTTGGGGAATCTATGGAA GGAAGCAAGATATCTGCCAGTGCTACTGTTACAGGTGGAACTGAAGGGTCCAGCAGGGTTCAAT GGTACAAGGCATCTTCCTCTGAATTTAAGAATGAACATGAGCTTGAAGCCCTTACTCCGTCACG AGTTTCTAAGGTTATGCCAATTTACTCTCTATTACTATCATTGATGCACTGCTCAAAGCTTAAG CCATTTTTATTTGTTGTATATTTGGTTAACGTGATAAAACTAAATTGCAACCTTTTAATTTCTC ACTAGACATTCCGCATTCCTCTTGGTGCTGTTGGATATTATATCGTTGCAAAGTTTACACCTGT GGCACCTGATGGTGAAGTCGGTGAACCAGCCTATGCTACATCAGATGGCCTTGTGGAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.145611902

Conservation Information
Conserved circRNAs	NA
PMCS	0.145611902

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5377936-5376620(+)
5377386-5378216(+)
5377388-5378193(-)
						
						Potential amino acid sequence
						
							MNMSLKPLLRHEFLRHSAFLLVLLDIISLQSLHLWHLMVKSVNQPMLHQMALWKQHHQSAMCMF
WEILLKITLS*(+)
MEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESMEGSKISASA
TVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKFTPVAPDGEV
GEPAYATSDGLVETTPSVSNVHVLGDIVEDNIIVGKGKYFGGREGLSKIRWFREKENGEFLLVL
SDSMEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESMEGSKIS
ASATVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKFTPVAPD
GEVGEPAYATSDGLVETTPSVSNVHVLGDIVEDNIIVGKGKYFGGREGLSKIRWFREKENGEFL
LVLSDSMEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESMEGS
KISASATVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKFTPV
APDGEVGEPAYATSDGLVETTPSVSNVHVLGDIVEDNIIVGKGKYFGGREGLSKIRWFREKENG
EFLLVLSDSMEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESM
EGSKISASATVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKF
TPVAPDGEVGEPAYATSDGLVE(+)
MLSDSTRRNSPFSFSLNHRILLSPSLPPKYFPFPTIMLSSTISPRTCTLLTDGVVSTRPSDVA*
(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5377936-5376620(+) 5377386-5378216(+) 5377388-5378193(-)
Potential amino acid sequence	MNMSLKPLLRHEFLRHSAFLLVLLDIISLQSLHLWHLMVKSVNQPMLHQMALWKQHHQSAMCMF WEILLKITLS(+) MEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESMEGSKISASA TVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKFTPVAPDGEV GEPAYATSDGLVETTPSVSNVHVLGDIVEDNIIVGKGKYFGGREGLSKIRWFREKENGEFLLVL SDSMEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESMEGSKIS ASATVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKFTPVAPD GEVGEPAYATSDGLVETTPSVSNVHVLGDIVEDNIIVGKGKYFGGREGLSKIRWFREKENGEFL LVLSDSMEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESMEGS KISASATVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKFTPV APDGEVGEPAYATSDGLVETTPSVSNVHVLGDIVEDNIIVGKGKYFGGREGLSKIRWFREKENG EFLLVLSDSMEYTLTKEDVGRHLKFVYIPVNLEGQEGESACAITDVVKKAPPKVFNLKIVGESM EGSKISASATVTGGTEGSSRVQWYKASSSEFKNEHELEALTPSRVSKTFRIPLGAVGYYIVAKF TPVAPDGEVGEPAYATSDGLVE(+) MLSDSTRRNSPFSFSLNHRILLSPSLPPKYFPFPTIMLSSTISPRTCTLLTDGVVSTRPSDVA (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d018795_circ_g.3

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