Plant Circular RNA Database

Detail information of Zm00001d008429_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d008429_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009539
					
						Alias
						zma_circ_0003011
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 8455598-8457066  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d008429						
					
						Parent gene annotation
						
							Paired amphipathic helix protein Sin3-like 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
						Zm00001d008429_T020:6
Zm00001d008429_T032:6
Zm00001d008429_T036:5
Zm00001d008429_T034:6
Zm00001d008429_T033:6
Zm00001d008429_T008:6
Zm00001d008429_T014:6
Zm00001d008429_T002:6
Zm00001d008429_T027:6
Zm00001d008429_T022:6
Zm00001d008429_T001:5
Zm00001d008429_T017:6
Zm00001d008429_T038:6
Zm00001d008429_T004:6
Zm00001d008429_T026:6
Zm00001d008429_T029:6
Zm00001d008429_T030:6
Zm00001d008429_T023:6
Zm00001d008429_T025:6
Zm00001d008429_T010:6
Zm00001d008429_T007:6
Zm00001d008429_T015:6
Zm00001d008429_T006:6
Zm00001d008429_T021:6
Zm00001d008429_T018:5
Zm00001d008429_T040:1
Zm00001d008429_T019:6
Zm00001d008429_T013:5
Zm00001d008429_T012:6
Zm00001d008429_T003:6
Zm00001d008429_T028:6
Zm00001d008429_T035:6
Zm00001d008429_T024:6

General Information
CircRNA Name	Zm00001d008429_circ_g.1
ID in PlantcircBase	zma_circ_009539
Alias	zma_circ_0003011
Organism	Zea mays
Position	chr8: 8455598-8457066 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d008429
Parent gene annotation	Paired amphipathic helix protein Sin3-like 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	Zm00001d008429_T020:6 Zm00001d008429_T032:6 Zm00001d008429_T036:5 Zm00001d008429_T034:6 Zm00001d008429_T033:6 Zm00001d008429_T008:6 Zm00001d008429_T014:6 Zm00001d008429_T002:6 Zm00001d008429_T027:6 Zm00001d008429_T022:6 Zm00001d008429_T001:5 Zm00001d008429_T017:6 Zm00001d008429_T038:6 Zm00001d008429_T004:6 Zm00001d008429_T026:6 Zm00001d008429_T029:6 Zm00001d008429_T030:6 Zm00001d008429_T023:6 Zm00001d008429_T025:6 Zm00001d008429_T010:6 Zm00001d008429_T007:6 Zm00001d008429_T015:6 Zm00001d008429_T006:6 Zm00001d008429_T021:6 Zm00001d008429_T018:5 Zm00001d008429_T040:1 Zm00001d008429_T019:6 Zm00001d008429_T013:5 Zm00001d008429_T012:6 Zm00001d008429_T003:6 Zm00001d008429_T028:6 Zm00001d008429_T035:6 Zm00001d008429_T024:6

			
						 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  
						
							TTGCATATAGATCAGGAGGGTTTGTATCCTTGGAATTCCTCCATTTCTTTTCAGCGGTAAAAGA
GTTAGTTTTTGCTGAAAGTAGTCTCTCATATAAGATcattttgtatgccaaatgatcctatgct
ttggataggaacctattgaagcgctgcacttttgcagcatatatttttgaaaactgcgaactgt
cagacaca

						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
						
							CATTTTGTATGCCAAATGATCCTATGCTTTGGATAGGAACCTATTGAAGCGCTGCACTTTTGCA
GCATATATTTTTGAAAACTGCGAACTGTCAGACACACTCCCACCCCGCAAAATTTTCCTTCTCT
TCCGAAGCCGGGACAAGAAATCTTCAGTGTCTAGGACATACGAGACCTGTATCCAATGCATTGC
CAGATATGCTTTATTCTCAACTACAATAAAGCATGCGATGTCCGGTCAAGATTGCATACCTTAG
AGGTCTTGCAGGATATCTTGCATTCGAGACCATTCACAACTTTGATACCATCCATTGCCTTCAA
AAAATCTGAAGGTTCATCATTATCTGAATATTTCCGCTTATTCCTGGAAGAGCAGCACACGATC
GGCACAAATAATGGAAACGGAATCAGGAGCTTCGTTGTGGGTTGGGGAAAAAATAATACCTTGC
AAGGTAGACGCCTTCAGATAATTTCTTGTCTGACGTACTACATAAATACTCGCCAAAAAGATAC
GAAGAAAAATTTGGATCAATTGATACTGCGGTAACTTCTGGCTTTTCGTGACCATATTCCATCA
GCTGAATAGACAACCTTGTCGGACTTGAGCACTGCCATTAACATCACAAACTAATTAATATCAT
TCCACAAAAAGAAAAGCATGATGAATTGACAACAGTACTGTTAGACTATTATATTTCTGTCTAA
ATTTTATGGGCCTAGAGCCCAGCCCATGTATTCTGATATATGTACTACTCAGCCTAACTTAATG
AATTAGGATTTCATTTCCTCTAACAAGTACACTACAACTGAAATATTTGTTGGTACACAAGACG
AGCTTGCCACATGTACAGGACTGAGTCAATAGAACACACAAAAAAAATTAGGCATGGATATCAT
CAGAAGCTGCATAAAATGATGCTTACACATTCAAATCGGTATATGCTCTCATCATGCAGTAGAA
CACGGGCATTTTCATGATAAACTAGGTCAAAAAACCTCCCGGGAGATCTTGATTTTTCATATAA
ATATAGCTGCAGAAGCTTATTGTCCATTTCATCTGTTGCTATTGCTTGAAGCTGGCATCAGGAA
GTTGAATAATGAATCTGTTATCCAGGCCATAAAAAAAGTGACAGTGCAAAGGGGTAAAGCATTT
TACCTGCTTCACAACTTTATAAATCAATTTATCTAAAGTAAAGAGAACATATGATTGAGTCCCA
ATAATAGCTCGGCAGTCGTCCTCAAATTTTGTGTTGTCAGAAGAACCATCGAGCAAGTTGTAAA
GCGCACTCATAAACCTTCATAGGAAAGACAGATCAGTTATTCATCATATATGGATATAATGTAA
ACACTGCAGAAATGCAAACATTACTTTGCATATAGATCAGGAGGGTTTGTATCCTTGGAATTCC
TCCATTTCTTTTCAGCGGTAAAAGAGTTAGTTTTTGCTGAAAGTAGTCTCTCATATAAGAT

Sequences
Splice junction sequence	TTGCATATAGATCAGGAGGGTTTGTATCCTTGGAATTCCTCCATTTCTTTTCAGCGGTAAAAGA GTTAGTTTTTGCTGAAAGTAGTCTCTCATATAAGATcattttgtatgccaaatgatcctatgct ttggataggaacctattgaagcgctgcacttttgcagcatatatttttgaaaactgcgaactgt cagacaca
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	CATTTTGTATGCCAAATGATCCTATGCTTTGGATAGGAACCTATTGAAGCGCTGCACTTTTGCA GCATATATTTTTGAAAACTGCGAACTGTCAGACACACTCCCACCCCGCAAAATTTTCCTTCTCT TCCGAAGCCGGGACAAGAAATCTTCAGTGTCTAGGACATACGAGACCTGTATCCAATGCATTGC CAGATATGCTTTATTCTCAACTACAATAAAGCATGCGATGTCCGGTCAAGATTGCATACCTTAG AGGTCTTGCAGGATATCTTGCATTCGAGACCATTCACAACTTTGATACCATCCATTGCCTTCAA AAAATCTGAAGGTTCATCATTATCTGAATATTTCCGCTTATTCCTGGAAGAGCAGCACACGATC GGCACAAATAATGGAAACGGAATCAGGAGCTTCGTTGTGGGTTGGGGAAAAAATAATACCTTGC AAGGTAGACGCCTTCAGATAATTTCTTGTCTGACGTACTACATAAATACTCGCCAAAAAGATAC GAAGAAAAATTTGGATCAATTGATACTGCGGTAACTTCTGGCTTTTCGTGACCATATTCCATCA GCTGAATAGACAACCTTGTCGGACTTGAGCACTGCCATTAACATCACAAACTAATTAATATCAT TCCACAAAAAGAAAAGCATGATGAATTGACAACAGTACTGTTAGACTATTATATTTCTGTCTAA ATTTTATGGGCCTAGAGCCCAGCCCATGTATTCTGATATATGTACTACTCAGCCTAACTTAATG AATTAGGATTTCATTTCCTCTAACAAGTACACTACAACTGAAATATTTGTTGGTACACAAGACG AGCTTGCCACATGTACAGGACTGAGTCAATAGAACACACAAAAAAAATTAGGCATGGATATCAT CAGAAGCTGCATAAAATGATGCTTACACATTCAAATCGGTATATGCTCTCATCATGCAGTAGAA CACGGGCATTTTCATGATAAACTAGGTCAAAAAACCTCCCGGGAGATCTTGATTTTTCATATAA ATATAGCTGCAGAAGCTTATTGTCCATTTCATCTGTTGCTATTGCTTGAAGCTGGCATCAGGAA GTTGAATAATGAATCTGTTATCCAGGCCATAAAAAAAGTGACAGTGCAAAGGGGTAAAGCATTT TACCTGCTTCACAACTTTATAAATCAATTTATCTAAAGTAAAGAGAACATATGATTGAGTCCCA ATAATAGCTCGGCAGTCGTCCTCAAATTTTGTGTTGTCAGAAGAACCATCGAGCAAGTTGTAAA GCGCACTCATAAACCTTCATAGGAAAGACAGATCAGTTATTCATCATATATGGATATAATGTAA ACACTGCAGAAATGCAAACATTACTTTGCATATAGATCAGGAGGGTTTGTATCCTTGGAATTCC TCCATTTCTTTTCAGCGGTAAAAGAGTTAGTTTTTGCTGAAAGTAGTCTCTCATATAAGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.189745711

Conservation Information
Conserved circRNAs	NA
PMCS	0.189745711

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8455602-8455621(-)
						
						Potential amino acid sequence
						
							MILYERLLSAKTNSFTAEKKWRNSKDTNPPDLYAKFMSALYNLLDGSSDNTKFEDDCRAIIGTQ
SYVLFTLDKLIYKVVKQLQAIATDEMDNKLLQLYLYEKSRSPGRFFDLVYHENARVLLHDESIY
RFECCSSPTRLSIQLMEYGHEKPEVTAVSIDPNFSSYLFGEYLCSTSDKKLSEGVYLARNKRKY
SDNDEPSDFLKAMDGIKVVNGLECKISCKTSKVSYVLDTEDFLSRLRKRRKILRGGSVSDSSQF
SKIYAAKVQRFNRFLSKA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8455602-8455621(-)
Potential amino acid sequence	MILYERLLSAKTNSFTAEKKWRNSKDTNPPDLYAKFMSALYNLLDGSSDNTKFEDDCRAIIGTQ SYVLFTLDKLIYKVVKQLQAIATDEMDNKLLQLYLYEKSRSPGRFFDLVYHENARVLLHDESIY RFECCSSPTRLSIQLMEYGHEKPEVTAVSIDPNFSSYLFGEYLCSTSDKKLSEGVYLARNKRKY SDNDEPSDFLKAMDGIKVVNGLECKISCKTSKVSYVLDTEDFLSRLRKRRKILRGGSVSDSSQF SKIYAAKVQRFNRFLSKA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d008429_circ_g.1

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