Plant Circular RNA Database

Detail information of Zm00001d025156_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d025156_circ_g.1
					
						ID in PlantcircBase
						zma_circ_010292
					
						Alias
						Zm10circ00045, zma_circ_0003226, ZmciR424
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 106850135-106851046  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d025156						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025156_circ_g.2 						
					
						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
						Zm00001d025156_T001:4

General Information
CircRNA Name	Zm00001d025156_circ_g.1
ID in PlantcircBase	zma_circ_010292
Alias	Zm10circ00045, zma_circ_0003226, ZmciR424
Organism	Zea mays
Position	chr10: 106850135-106851046 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d025156
Parent gene annotation	Phospholipid-transporting ATPase 2
Parent gene strand	-
Alternative splicing	Zm00001d025156_circ_g.2
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	Zm00001d025156_T001:4

			
						 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  
						
							GACTCACCTTGACTTTTCCTAGCTGCTCTACTGACAAGTTAGCAGAAATTGGAGGAATGGTTCT
TGTTTTCAAGTCAGTTTCACCATCCAAAGCAGCAGTctttatggagattggaatcattatggag
cacaacagctcaaagcgtaacgggataatcaagaaatcataccatgggccctctacctccatag
gatacata

									
								

					

						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: 546
Transcript exons: 106850135-106850245,106850436-106850602,106850715-106850
889,106850954-106851046
CTTTATGGAGATTGGAATCATTATGGAGCACAACAGCTCAAAGCGTAACGGGATAATCAAGAAA
TCATACCATGGGCCCTCTACCTCCATAGGATACATAAGATACCATTGCTTAAGCCCCTGAGTGT
CCTTCCAAGTATTCCCAAAATAACCCAGAACAAGTACAACAACAACTTGGAACATGAATATTGC
AATAGTGAGCTTGTCTATTATTACATCAGCAGCAGTGAACTTGGGCTCCGCAGCTCCCCTACTT
ATTCCAGATTTTGTTTCATTGCCTGTGTAAACTGCAACTCCACAAGCCCATTCAGTGTATCGAA
GGTAACATGACTGAAGAAGTGTATTGTTGATAGTCAAAGGACTTTTTTCATTGTCAATTATAGG
GAGGAACAAGCGCATGTTAGCATCAAACCTCCGTATGTCATTGTCTGGGTTGGGGCACTCAATT
ACACCCTTGACTTTTCCTAGCTGCTCTACTGACAAGTTAGCAGAAATTGGAGGAATGGTTCTTG
TTTTCAAGTCAGTTTCACCATCCAAAGCAGCAGT
						
					

						Genomic sequence
						
							CTTTATGGAGATTGGAATCATTATGGAGCACAACAGCTCAAAGCGTAACGGGATAATCAAGAAA
TCATACCATGGGCCCTCTACCTCCATAGGATACATAAGATACCATTGCTACATAAATAAAATGA
CATATCAGGTCACAGAATACAAATGGCATAATTATATGTTCAATTTCTTATAAATGCAACCATC
TACATCACAAAATACAATAGCAAGTGCCCATGAGAGGGTACAACGACATGCATGCAAATTACAG
TAAATTTTCTTCGCCAAAACACTGATAATCAAAAAGAGATAGCACCTTAAGCCCCTGAGTGTCC
TTCCAAGTATTCCCAAAATAACCCAGAACAAGTACAACAACAACTTGGAACATGAATATTGCAA
TAGTGAGCTTGTCTATTATTACATCAGCAGCAGTGAACTTGGGCTCCGCAGCTCCCCTACTTAT
TCCAGATTTTGTTTCATTGCCTGCAATGGATGGTTGGTGAGTTAACCATGCACTACAATGTCTT
CAGGTCTGCTACATGCAAAACAAATGCTCTGGCACAATAAGGCATCATGTATCATATTCTGTAT
TTACCTGTGTAAACTGCAACTCCACAAGCCCATTCAGTGTATCGAAGGTAACATGACTGAAGAA
GTGTATTGTTGATAGTCAAAGGACTTTTTTCATTGTCAATTATAGGGAGGAACAAGCGCATGTT
AGCATCAAACCTCCGTATGTCATTGTCTGGGTTGGGGCACTCAATTACACCCTGCACAAATTAA
ACAGAAGTAATCAGAAAACAAAAAAAGAAATAGAAGTGTGGAAAGACTCACCTTGACTTTTCCT
AGCTGCTCTACTGACAAGTTAGCAGAAATTGGAGGAATGGTTCTTGTTTTCAAGTCAGTTTCAC
CATCCAAAGCAGCAGT
						
					

			
		

Sequences
Splice junction sequence	GACTCACCTTGACTTTTCCTAGCTGCTCTACTGACAAGTTAGCAGAAATTGGAGGAATGGTTCT TGTTTTCAAGTCAGTTTCACCATCCAAAGCAGCAGTctttatggagattggaatcattatggag cacaacagctcaaagcgtaacgggataatcaagaaatcataccatgggccctctacctccatag gatacata
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: 546 Transcript exons: 106850135-106850245,106850436-106850602,106850715-106850 889,106850954-106851046 CTTTATGGAGATTGGAATCATTATGGAGCACAACAGCTCAAAGCGTAACGGGATAATCAAGAAA TCATACCATGGGCCCTCTACCTCCATAGGATACATAAGATACCATTGCTTAAGCCCCTGAGTGT CCTTCCAAGTATTCCCAAAATAACCCAGAACAAGTACAACAACAACTTGGAACATGAATATTGC AATAGTGAGCTTGTCTATTATTACATCAGCAGCAGTGAACTTGGGCTCCGCAGCTCCCCTACTT ATTCCAGATTTTGTTTCATTGCCTGTGTAAACTGCAACTCCACAAGCCCATTCAGTGTATCGAA GGTAACATGACTGAAGAAGTGTATTGTTGATAGTCAAAGGACTTTTTTCATTGTCAATTATAGG GAGGAACAAGCGCATGTTAGCATCAAACCTCCGTATGTCATTGTCTGGGTTGGGGCACTCAATT ACACCCTTGACTTTTCCTAGCTGCTCTACTGACAAGTTAGCAGAAATTGGAGGAATGGTTCTTG TTTTCAAGTCAGTTTCACCATCCAAAGCAGCAGT
Genomic sequence	CTTTATGGAGATTGGAATCATTATGGAGCACAACAGCTCAAAGCGTAACGGGATAATCAAGAAA TCATACCATGGGCCCTCTACCTCCATAGGATACATAAGATACCATTGCTACATAAATAAAATGA CATATCAGGTCACAGAATACAAATGGCATAATTATATGTTCAATTTCTTATAAATGCAACCATC TACATCACAAAATACAATAGCAAGTGCCCATGAGAGGGTACAACGACATGCATGCAAATTACAG TAAATTTTCTTCGCCAAAACACTGATAATCAAAAAGAGATAGCACCTTAAGCCCCTGAGTGTCC TTCCAAGTATTCCCAAAATAACCCAGAACAAGTACAACAACAACTTGGAACATGAATATTGCAA TAGTGAGCTTGTCTATTATTACATCAGCAGCAGTGAACTTGGGCTCCGCAGCTCCCCTACTTAT TCCAGATTTTGTTTCATTGCCTGCAATGGATGGTTGGTGAGTTAACCATGCACTACAATGTCTT CAGGTCTGCTACATGCAAAACAAATGCTCTGGCACAATAAGGCATCATGTATCATATTCTGTAT TTACCTGTGTAAACTGCAACTCCACAAGCCCATTCAGTGTATCGAAGGTAACATGACTGAAGAA GTGTATTGTTGATAGTCAAAGGACTTTTTTCATTGTCAATTATAGGGAGGAACAAGCGCATGTT AGCATCAAACCTCCGTATGTCATTGTCTGGGTTGGGGCACTCAATTACACCCTGCACAAATTAA ACAGAAGTAATCAGAAAACAAAAAAAGAAATAGAAGTGTGGAAAGACTCACCTTGACTTTTCCT AGCTGCTCTACTGACAAGTTAGCAGAAATTGGAGGAATGGTTCTTGTTTTCAAGTCAGTTTCAC CATCCAAAGCAGCAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.208155778

Conservation Information
Conserved circRNAs	NA
PMCS	0.208155778

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							106850835-106850445(+)
106850837-106850137(-)
						
						Potential amino acid sequence
						
							MLASNLRMSLSGLGHSITPLTFPSCSTDKLAEIGGMVLVFKSVSPSKAAVFMEIGIIMEHNSSK
RNGIIKKSYHGPSTSIGYIRYHCLSP*(+)
MRLFLPIIDNEKSPLTINNTLLQSCYLRYTEWACGVAVYTGNETKSGISRGAAEPKFTAADVII
DKLTIAIFMFQVVVVLVLGYFGNTWKDTQGLKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMI
PISIKTAALDGETDLKTRTIPPISANLSVEQLGKVKGVIECPNPDNDIRRFDANMRLFLPIIDN
EKSPLTINNTLLQSCYLRYTEWACGVAVYTGNETKSGISRGAAEPKFTAADVIIDKLTIAIFMF
QVVVVLVLGYFGNTWKDTQGLKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMIPISIKTAALD
GETDLKTRTIPPISANLSVEQLGKVKGVIECPNPDNDIRRFDANMRLFLPIIDNEKSPLTINNT
LLQSCYLRYTEWACGVAVYTGNETKSGISRGAAEPKFTAADVIIDKLTIAIFMFQVVVVLVLGY
FGNTWKDTQGLKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMIPISIKTAALDGETDLKTRTI
PPISANLSVEQLGKVKGVIECPNPDNDIRRFDANMRLFLPIIDNEKSPLTINNTLLQSCYLRYT
EWACGVAVYTGNETKSGISRGAAEPKFTAADVIIDKLTIAIFMFQVVVVLVLGYFGNTWKDTQG
LKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMIPISIK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	106850835-106850445(+) 106850837-106850137(-)
Potential amino acid sequence	MLASNLRMSLSGLGHSITPLTFPSCSTDKLAEIGGMVLVFKSVSPSKAAVFMEIGIIMEHNSSK RNGIIKKSYHGPSTSIGYIRYHCLSP*(+) MRLFLPIIDNEKSPLTINNTLLQSCYLRYTEWACGVAVYTGNETKSGISRGAAEPKFTAADVII DKLTIAIFMFQVVVVLVLGYFGNTWKDTQGLKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMI PISIKTAALDGETDLKTRTIPPISANLSVEQLGKVKGVIECPNPDNDIRRFDANMRLFLPIIDN EKSPLTINNTLLQSCYLRYTEWACGVAVYTGNETKSGISRGAAEPKFTAADVIIDKLTIAIFMF QVVVVLVLGYFGNTWKDTQGLKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMIPISIKTAALD GETDLKTRTIPPISANLSVEQLGKVKGVIECPNPDNDIRRFDANMRLFLPIIDNEKSPLTINNT LLQSCYLRYTEWACGVAVYTGNETKSGISRGAAEPKFTAADVIIDKLTIAIFMFQVVVVLVLGY FGNTWKDTQGLKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMIPISIKTAALDGETDLKTRTI PPISANLSVEQLGKVKGVIECPNPDNDIRRFDANMRLFLPIIDNEKSPLTINNTLLQSCYLRYT EWACGVAVYTGNETKSGISRGAAEPKFTAADVIIDKLTIAIFMFQVVVVLVLGYFGNTWKDTQG LKQWYLMYPMEVEGPWYDFLIIPLRFELLCSIMIPISIK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d025156_circ_g.1

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