Plant Circular RNA Database

Detail information of Zm00001d047717_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d047717_circ_g.1
					
						ID in PlantcircBase
						zma_circ_010054
					
						Alias
						Zm09circ00063, zma_circ_0003034
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 139873718-139875255  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d047717						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d047717_circ_g.2 Zm00001d047717_circ_g.3 						
					
						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
						Zm00001d047717_T001:6
Zm00001d047717_T026:5
Zm00001d047717_T010:6
Zm00001d047717_T016:6
Zm00001d047717_T022:6
Zm00001d047717_T007:6
Zm00001d047717_T030:6
Zm00001d047717_T003:6
Zm00001d047717_T014:6
Zm00001d047717_T011:6
Zm00001d047717_T004:6
Zm00001d047717_T017:6
Zm00001d047717_T031:6
Zm00001d047717_T006:5
Zm00001d047717_T019:5
Zm00001d047717_T028:6
Zm00001d047717_T025:6
Zm00001d047717_T023:6
Zm00001d047717_T018:5

General Information
CircRNA Name	Zm00001d047717_circ_g.1
ID in PlantcircBase	zma_circ_010054
Alias	Zm09circ00063, zma_circ_0003034
Organism	Zea mays
Position	chr9: 139873718-139875255 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d047717
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Zm00001d047717_circ_g.2 Zm00001d047717_circ_g.3
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	Zm00001d047717_T001:6 Zm00001d047717_T026:5 Zm00001d047717_T010:6 Zm00001d047717_T016:6 Zm00001d047717_T022:6 Zm00001d047717_T007:6 Zm00001d047717_T030:6 Zm00001d047717_T003:6 Zm00001d047717_T014:6 Zm00001d047717_T011:6 Zm00001d047717_T004:6 Zm00001d047717_T017:6 Zm00001d047717_T031:6 Zm00001d047717_T006:5 Zm00001d047717_T019:5 Zm00001d047717_T028:6 Zm00001d047717_T025:6 Zm00001d047717_T023:6 Zm00001d047717_T018:5

			
						 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  
						
							TGAATGGGAGTATTATTACCGTACTATTTGAAGTCTCATCTTTGTAGCCAGTACCTTTCTCACG
GTTCAGTGATCTCTTCCTCTCAATGCATATCGTGAGctagaaaagatttcagtgttgacgccat
ggtgacatatagtcgatccatttttgtcttcatttccttgaagccaccatacatggtcttattc
aggatatc

									
								

					

						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
						
							CTAGAAAAGATTTCAGTGTTGACGCCATGGTGACATATAGTCGATCCATTTTTGTCTTCATTTC
CTTGAAGCCACCATACATGGTCTTATTCAGGATATCAGCTGATGATTTGAAAGCTGTACACACC
ATTTGTTCAAGGAGCTGCTGTGGCCTTAAAGTTTCAAGGTAATGAAGCACCTGCGAATCACATA
TAAAAAGTTCAATAAGTAGCACACTACTATTTTACCGATAGTAAGAGCTAAGATGCTATCTAAT
ATTCATGAAGAATTGAATGTCATGGTTCTTCTTTTAAAAGTGATCATCCAGCTAAATGAATGTG
TGGCTTAAGTTGTGGAAAAGCCAAAACGACTTGCAATTTGTAATGGAGAGAGTAACTTTCTAAC
ACAAAATGCCGCCAACCATCCTATAAGTAATAAGATGATGAAATTACCAGCACATGGGTAGTAC
CTTTTCTCCTTCCCGAACAGGGTCAAGCAAAGACTTCTGTTCAGAAACAGGCAATGGCAGAGCA
TCATTCCAGATTTTGCGCCACACATTCCCATGTTGGGACATACGGTGAGAAAGCTTTCCTTTGG
GAGGCCAGCCTGCATTACCATCTGTTTTGTCCTCGCTCAACCATTCACCAGGTGAATGCCACCG
AATAAAATCTTCAAAGACAGCATCTGGGTTTGCAGCTTTAAAAGCAGACATATCTAATCAAGGA
GCAGAGCTTCCTAATTAGTAGCAAATGAAAAAGTTCCACAATACATGCAACAAAGAGGAAAAGT
AGAATAACTTCTTCAAAAGCTTTGGTCATTGCTCATAAATTAGATGAAGTAAAAGAAAATTCCT
GAAGATAGACTCGAGAAACATTAACAAGTTATGTAACAAGTGAAATGTCATGTTGTTCCCACAA
AATCTTACCGGAACATAATATATCCCTTTCCAGCTGTCCAGATAGACCCTGTAGGAACAGATGA
ACGCTATGTAATTTCTTGTAAATTTGATCTTATTTAGGTAGATAGGTCCAGCATGCAATAGAGC
CAGTAGTACATATAATCCAATTAACAGACATACTGTAGTTCTTTGGATAAACCTATGAATCAGA
AAGGGATTTCATCCTTTCATGCATACAACAGCAAGTTTAAGAACTTACAATGGCATTGCCAAAA
GCTTCAGCTGCATGGAGCCTTTCTTCATGCATATCTTCGGTCATCAAAGGTGCATCCTAAGGAA
CTAATGGAAACATAAGGGGGTGCATGTGGATCACAATATTAAACCTGAAGAAAAGGGCAAACAG
AACCTGAGTATATGGAGCATGCATTTCCTGAAACGTATTCAGGAGCATCATTTTAGGCACAACA
CCAGCTGATCCTTTCCTAGACTTGTTCACTGCCTGCTATTAATTATGAGTTAGCAACTTTAACA
TTAAATTGTTTTTTATTTCCAAATAGACATTGAATGGGAGTATTATTACCGTACTATTTGAAGT
CTCATCTTTGTAGCCAGTACCTTTCTCACGGTTCAGTGATCTCTTCCTCTCAATGCATATCGTG
AG
						
					

			
		

Sequences
Splice junction sequence	TGAATGGGAGTATTATTACCGTACTATTTGAAGTCTCATCTTTGTAGCCAGTACCTTTCTCACG GTTCAGTGATCTCTTCCTCTCAATGCATATCGTGAGctagaaaagatttcagtgttgacgccat ggtgacatatagtcgatccatttttgtcttcatttccttgaagccaccatacatggtcttattc aggatatc
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	CTAGAAAAGATTTCAGTGTTGACGCCATGGTGACATATAGTCGATCCATTTTTGTCTTCATTTC CTTGAAGCCACCATACATGGTCTTATTCAGGATATCAGCTGATGATTTGAAAGCTGTACACACC ATTTGTTCAAGGAGCTGCTGTGGCCTTAAAGTTTCAAGGTAATGAAGCACCTGCGAATCACATA TAAAAAGTTCAATAAGTAGCACACTACTATTTTACCGATAGTAAGAGCTAAGATGCTATCTAAT ATTCATGAAGAATTGAATGTCATGGTTCTTCTTTTAAAAGTGATCATCCAGCTAAATGAATGTG TGGCTTAAGTTGTGGAAAAGCCAAAACGACTTGCAATTTGTAATGGAGAGAGTAACTTTCTAAC ACAAAATGCCGCCAACCATCCTATAAGTAATAAGATGATGAAATTACCAGCACATGGGTAGTAC CTTTTCTCCTTCCCGAACAGGGTCAAGCAAAGACTTCTGTTCAGAAACAGGCAATGGCAGAGCA TCATTCCAGATTTTGCGCCACACATTCCCATGTTGGGACATACGGTGAGAAAGCTTTCCTTTGG GAGGCCAGCCTGCATTACCATCTGTTTTGTCCTCGCTCAACCATTCACCAGGTGAATGCCACCG AATAAAATCTTCAAAGACAGCATCTGGGTTTGCAGCTTTAAAAGCAGACATATCTAATCAAGGA GCAGAGCTTCCTAATTAGTAGCAAATGAAAAAGTTCCACAATACATGCAACAAAGAGGAAAAGT AGAATAACTTCTTCAAAAGCTTTGGTCATTGCTCATAAATTAGATGAAGTAAAAGAAAATTCCT GAAGATAGACTCGAGAAACATTAACAAGTTATGTAACAAGTGAAATGTCATGTTGTTCCCACAA AATCTTACCGGAACATAATATATCCCTTTCCAGCTGTCCAGATAGACCCTGTAGGAACAGATGA ACGCTATGTAATTTCTTGTAAATTTGATCTTATTTAGGTAGATAGGTCCAGCATGCAATAGAGC CAGTAGTACATATAATCCAATTAACAGACATACTGTAGTTCTTTGGATAAACCTATGAATCAGA AAGGGATTTCATCCTTTCATGCATACAACAGCAAGTTTAAGAACTTACAATGGCATTGCCAAAA GCTTCAGCTGCATGGAGCCTTTCTTCATGCATATCTTCGGTCATCAAAGGTGCATCCTAAGGAA CTAATGGAAACATAAGGGGGTGCATGTGGATCACAATATTAAACCTGAAGAAAAGGGCAAACAG AACCTGAGTATATGGAGCATGCATTTCCTGAAACGTATTCAGGAGCATCATTTTAGGCACAACA CCAGCTGATCCTTTCCTAGACTTGTTCACTGCCTGCTATTAATTATGAGTTAGCAACTTTAACA TTAAATTGTTTTTTATTTCCAAATAGACATTGAATGGGAGTATTATTACCGTACTATTTGAAGT CTCATCTTTGTAGCCAGTACCTTTCTCACGGTTCAGTGATCTCTTCCTCTCAATGCATATCGTG AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.18004578

Conservation Information
Conserved circRNAs	NA
PMCS	0.18004578

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							139875050-139875241(-)
						
						Potential amino acid sequence
						
							MMLLNTFQEMHAPYTQDAPLMTEDMHEERLHAAEAFGNAIGLSGQLERDILCSDMSAFKAANPD
AVFEDFIRWHSPGEWLSEDKTDGNAGWPPKGKLSHRMSQHGNVWRKIWNDALPLPVSEQKSLLD
PVREGEKVLHYLETLRPQQLLEQMVCTAFKSSADILNKTMYGGFKEMKTKMDRLYVTMASTLKS
FLAHDMH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	139875050-139875241(-)
Potential amino acid sequence	MMLLNTFQEMHAPYTQDAPLMTEDMHEERLHAAEAFGNAIGLSGQLERDILCSDMSAFKAANPD AVFEDFIRWHSPGEWLSEDKTDGNAGWPPKGKLSHRMSQHGNVWRKIWNDALPLPVSEQKSLLD PVREGEKVLHYLETLRPQQLLEQMVCTAFKSSADILNKTMYGGFKEMKTKMDRLYVTMASTLKS FLAHDMH*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d047717_circ_g.1

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