Plant Circular RNA Database

Detail information of Zm00001d011713_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d011713_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009755
					
						Alias
						Zm08circ00068, zma_circ_0002836, ZmciR329
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 159550035-159551404  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d011713						
					
						Parent gene annotation
						
							Myosin family protein with Dil domain
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d011713_circ_g.2 Zm00001d011713_circ_g.4 Zm00001d011713_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d011713_T005:4
Zm00001d011713_T004:4
Zm00001d011713_T010:4
Zm00001d011713_T006:4
Zm00001d011713_T003:4
Zm00001d011713_T012:4
Zm00001d011713_T013:4
Zm00001d011713_T007:4
Zm00001d011713_T014:4
Zm00001d011713_T009:4
Zm00001d011713_T016:4
Zm00001d011713_T015:4
Zm00001d011713_T008:4

General Information
CircRNA Name	Zm00001d011713_circ_g.3
ID in PlantcircBase	zma_circ_009755
Alias	Zm08circ00068, zma_circ_0002836, ZmciR329
Organism	Zea mays
Position	chr8: 159550035-159551404 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d011713
Parent gene annotation	Myosin family protein with Dil domain
Parent gene strand	-
Alternative splicing	Zm00001d011713_circ_g.2 Zm00001d011713_circ_g.4 Zm00001d011713_circ_g.5
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d011713_T005:4 Zm00001d011713_T004:4 Zm00001d011713_T010:4 Zm00001d011713_T006:4 Zm00001d011713_T003:4 Zm00001d011713_T012:4 Zm00001d011713_T013:4 Zm00001d011713_T007:4 Zm00001d011713_T014:4 Zm00001d011713_T009:4 Zm00001d011713_T016:4 Zm00001d011713_T015:4 Zm00001d011713_T008:4

			
						 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  
						
							ACTTCTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGC
AAAAGGGCCTCATATTCACTTACAGTCCCTTCTAGTctctgcaaagaatcttgaagaagcccat
ttctggcatcagcatcttcaagcttcctttgcagctctcctatttcaccctgagattcagctag
ttgtttca

									
								

					

						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: 672
Transcript exons: 159550035-159550202,159550355-159550522,159550853-159551
020,159551237-159551404
CTCTGCAAAGAATCTTGAAGAAGCCCATTTCTGGCATCAGCATCTTCAAGCTTCCTTTGCAGCT
CTCCTATTTCACCCTGAGATTCAGCTAGTTGTTTCATGATTGCATCCTTTTGCTGCCTTTCAGA
TCTCAACGAAGTTTCCAGTGCTGCCATATTTTCTTCATTTCTTTGGACAGTTTCTTGGAAGTGA
GCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGTCCTTGTTTCTATCCTCAGATTCAT
TGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGTTGTCAATAGAGCATCCTTCTCTCC
TAACCTTTCTTCAAGGCTTTGTATACTAGTCTGAAGCAGGGTGGATTTTTCATCAGTGTCCCCA
ACTTCTCTTTGAAGTTCTTCAATCTTTTCTCGCGCTTCATCTAATTCTATCAAATTTGCCTGAT
GCCGTTGCTTCTCAAATGTTAGTGAAGATTCCAAATTTTTTGTAGCTTCTTCAAATCTTTGAGC
AGCTTCATGGAGGAGATCATTTTGTTTCACAGCATCTTCGAGCTTGCTTACCAATGCTTCACTT
CTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGCAAAA
GGGCCTCATATTCACTTACAGTCCCTTCTAGT
						
					

						Genomic sequence
						
							CTCTGCAAAGAATCTTGAAGAAGCCCATTTCTGGCATCAGCATCTTCAAGCTTCCTTTGCAGCT
CTCCTATTTCACCCTGAGATTCAGCTAGTTGTTTCATGATTGCATCCTTTTGCTGCCTTTCAGA
TCTCAACGAAGTTTCCAGTGCTGCCATATTTTCTTCATTTCTAAACCATTGGGGAACAAAAGAT
AAGTTGAGAGAATAGTGACATGTAGATTTATTTATTAACAGCAAGATCATGACTGCGGAATCAG
GAATTAAATCAGAAATGAACCGCATCAAGCATTTTTAAGGCAAGTTAAACATTAAGCAACAGAC
CTTTGGACAGTTTCTTGGAAGTGAGCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGT
CCTTGTTTCTATCCTCAGATTCATTGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGT
TGTCAATAGAGCATCCTTCTCTCCTAACCTTTCTTCAAGGCTATGTCCACCCATCAAAGAAAGA
AATAACTATTAGTCTAACAAAAAGTGAGGGGTTAATCCTTCCCCCTTATCCATGCAAATAGATC
CATACATTGTACTTTTATAGTTTATTGACTCAAAGTATATTTTGTATTTTCTTGATAATATATT
CTTACAGCATGCTCTCTCTTGATGCATCCCCACAAAGAAAAAAGGAATTAACAGAGTTTTTATT
AAAATATTAAATATATAGTTTCAAAGGAAACATCACATAACAAATTTGCTCAAAAAAATGCAAT
GCATTATCACACGAAGTTAGAACTCTTGAAAAGGGGAAGAAAAGAAAAACCTTTGTATACTAGT
CTGAAGCAGGGTGGATTTTTCATCAGTGTCCCCAACTTCTCTTTGAAGTTCTTCAATCTTTTCT
CGCGCTTCATCTAATTCTATCAAATTTGCCTGATGCCGTTGCTTCTCAAATGTTAGTGAAGATT
CCAAATTTTTTGTAGCTTCTTCAAATCTGCATTCAACCACAAGATACAAACTATGTGGAACACA
TATAGAAATATGAAAAGATTAAAACTGTACAGCTCACAATAATTAATGCCACTGTGTTATTGGG
CCATTATTTGCTCTTAAAGAGTAGCTATGACCTTATAAATATGCAAATTAGGGATTATTGATGA
CACTACAATTTGCAGAGTTGGCCACATTACTTTCTGGAATAAACACTAACCTTTGAGCAGCTTC
ATGGAGGAGATCATTTTGTTTCACAGCATCTTCGAGCTTGCTTACCAATGCTTCACTTCTTGCT
TGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGCAAAAGGGCCT
CATATTCACTTACAGTCCCTTCTAGT
						
					

			
		

Sequences
Splice junction sequence	ACTTCTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGC AAAAGGGCCTCATATTCACTTACAGTCCCTTCTAGTctctgcaaagaatcttgaagaagcccat ttctggcatcagcatcttcaagcttcctttgcagctctcctatttcaccctgagattcagctag ttgtttca
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: 672 Transcript exons: 159550035-159550202,159550355-159550522,159550853-159551 020,159551237-159551404 CTCTGCAAAGAATCTTGAAGAAGCCCATTTCTGGCATCAGCATCTTCAAGCTTCCTTTGCAGCT CTCCTATTTCACCCTGAGATTCAGCTAGTTGTTTCATGATTGCATCCTTTTGCTGCCTTTCAGA TCTCAACGAAGTTTCCAGTGCTGCCATATTTTCTTCATTTCTTTGGACAGTTTCTTGGAAGTGA GCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGTCCTTGTTTCTATCCTCAGATTCAT TGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGTTGTCAATAGAGCATCCTTCTCTCC TAACCTTTCTTCAAGGCTTTGTATACTAGTCTGAAGCAGGGTGGATTTTTCATCAGTGTCCCCA ACTTCTCTTTGAAGTTCTTCAATCTTTTCTCGCGCTTCATCTAATTCTATCAAATTTGCCTGAT GCCGTTGCTTCTCAAATGTTAGTGAAGATTCCAAATTTTTTGTAGCTTCTTCAAATCTTTGAGC AGCTTCATGGAGGAGATCATTTTGTTTCACAGCATCTTCGAGCTTGCTTACCAATGCTTCACTT CTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGCAAAA GGGCCTCATATTCACTTACAGTCCCTTCTAGT
Genomic sequence	CTCTGCAAAGAATCTTGAAGAAGCCCATTTCTGGCATCAGCATCTTCAAGCTTCCTTTGCAGCT CTCCTATTTCACCCTGAGATTCAGCTAGTTGTTTCATGATTGCATCCTTTTGCTGCCTTTCAGA TCTCAACGAAGTTTCCAGTGCTGCCATATTTTCTTCATTTCTAAACCATTGGGGAACAAAAGAT AAGTTGAGAGAATAGTGACATGTAGATTTATTTATTAACAGCAAGATCATGACTGCGGAATCAG GAATTAAATCAGAAATGAACCGCATCAAGCATTTTTAAGGCAAGTTAAACATTAAGCAACAGAC CTTTGGACAGTTTCTTGGAAGTGAGCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGT CCTTGTTTCTATCCTCAGATTCATTGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGT TGTCAATAGAGCATCCTTCTCTCCTAACCTTTCTTCAAGGCTATGTCCACCCATCAAAGAAAGA AATAACTATTAGTCTAACAAAAAGTGAGGGGTTAATCCTTCCCCCTTATCCATGCAAATAGATC CATACATTGTACTTTTATAGTTTATTGACTCAAAGTATATTTTGTATTTTCTTGATAATATATT CTTACAGCATGCTCTCTCTTGATGCATCCCCACAAAGAAAAAAGGAATTAACAGAGTTTTTATT AAAATATTAAATATATAGTTTCAAAGGAAACATCACATAACAAATTTGCTCAAAAAAATGCAAT GCATTATCACACGAAGTTAGAACTCTTGAAAAGGGGAAGAAAAGAAAAACCTTTGTATACTAGT CTGAAGCAGGGTGGATTTTTCATCAGTGTCCCCAACTTCTCTTTGAAGTTCTTCAATCTTTTCT CGCGCTTCATCTAATTCTATCAAATTTGCCTGATGCCGTTGCTTCTCAAATGTTAGTGAAGATT CCAAATTTTTTGTAGCTTCTTCAAATCTGCATTCAACCACAAGATACAAACTATGTGGAACACA TATAGAAATATGAAAAGATTAAAACTGTACAGCTCACAATAATTAATGCCACTGTGTTATTGGG CCATTATTTGCTCTTAAAGAGTAGCTATGACCTTATAAATATGCAAATTAGGGATTATTGATGA CACTACAATTTGCAGAGTTGGCCACATTACTTTCTGGAATAAACACTAACCTTTGAGCAGCTTC ATGGAGGAGATCATTTTGTTTCACAGCATCTTCGAGCTTGCTTACCAATGCTTCACTTCTTGCT TGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGCAAAAGGGCCT CATATTCACTTACAGTCCCTTCTAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.196669064

Conservation Information
Conserved circRNAs	NA
PMCS	0.196669064

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							159550412-159550037(-)
						
						Potential amino acid sequence
						
							MKIEVAEKDIAHFQETVQRNEENMAALETSLRSERQQKDAIMKQLAESQGEIGELQRKLEDADA
RNGLLQDSLQRLEGTVSEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVKQNDLLHEA
AQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTSIQSLEERL
GEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRNEENMAALETSLR
SERQQKDAIMKQLAESQGEIGELQRKLEDADARNGLLQDSLQRLEGTVSEYEALLLTERQQNEA
ANAAVAESQARSEALVSKLEDAVKQNDLLHEAAQRFEEATKNLESSLTFEKQRHQANLIELDEA
REKIEELQREVGDTDEKSTLLQTSIQSLEERLGEKDALLTTERLESEATKKSLNESEDRNKDLL
MKIEVAEKDIAHFQETVQRNEENMAALETSLRSERQQKDAIMKQLAESQGEIGELQRKLEDADA
RNGLLQDSLQRLEGTVSEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVKQNDLLHEA
AQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTSIQSLEERL
GEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRNEENMAALETSLR
SERQQKDAIMKQLAESQGEIGELQRKLEDADARNGLLQDSLQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	159550412-159550037(-)
Potential amino acid sequence	MKIEVAEKDIAHFQETVQRNEENMAALETSLRSERQQKDAIMKQLAESQGEIGELQRKLEDADA RNGLLQDSLQRLEGTVSEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVKQNDLLHEA AQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTSIQSLEERL GEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRNEENMAALETSLR SERQQKDAIMKQLAESQGEIGELQRKLEDADARNGLLQDSLQRLEGTVSEYEALLLTERQQNEA ANAAVAESQARSEALVSKLEDAVKQNDLLHEAAQRFEEATKNLESSLTFEKQRHQANLIELDEA REKIEELQREVGDTDEKSTLLQTSIQSLEERLGEKDALLTTERLESEATKKSLNESEDRNKDLL MKIEVAEKDIAHFQETVQRNEENMAALETSLRSERQQKDAIMKQLAESQGEIGELQRKLEDADA RNGLLQDSLQRLEGTVSEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVKQNDLLHEA AQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTSIQSLEERL GEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRNEENMAALETSLR SERQQKDAIMKQLAESQGEIGELQRKLEDADARNGLLQDSLQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d011713_circ_g.3

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