Plant Circular RNA Database

Detail information of Zm00001d045887_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d045887_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009928
					
						Alias
						zma_circ_0003212, GRMZM2G395842_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 45733231-45734236  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d045887						
					
						Parent gene annotation
						
							E3 ubiquitin-protein ligase makorin
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d045887_circ_g.1 Zm00001d045887_circ_g.3 						
					
						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
						Zm00001d045887_T003:2
Zm00001d045887_T006:2
Zm00001d045887_T004:2
Zm00001d045887_T005:2
Zm00001d045887_T001:2
Zm00001d045887_T002:2

General Information
CircRNA Name	Zm00001d045887_circ_g.2
ID in PlantcircBase	zma_circ_009928
Alias	zma_circ_0003212, GRMZM2G395842_C1
Organism	Zea mays
Position	chr9: 45733231-45734236 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d045887
Parent gene annotation	E3 ubiquitin-protein ligase makorin
Parent gene strand	+
Alternative splicing	Zm00001d045887_circ_g.1 Zm00001d045887_circ_g.3
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	Zm00001d045887_T003:2 Zm00001d045887_T006:2 Zm00001d045887_T004:2 Zm00001d045887_T005:2 Zm00001d045887_T001:2 Zm00001d045887_T002:2

			
						 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  
						
							TATGTCGGAAACTTTCATACTATGTCATTCCAAGTGTTCTTTGGTACTTCTCAAAGGAAGAGAA
AGAGGAGATCACTGAAAGCTACAAATCCAAGCTCAAagttctttgcaagttcttcatgcatgga
gcttgcttgaaaggagagtactgtgaattctcccacgactggagtgatcaagcaaataatgtaa
cgtattag

									
								

					

						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: 903
Transcript exons: 45733231-45733318,45733422-45734236
AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCAC
GACTGGAGTGATCAAGCAAATAATGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTA
GCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCCCAAC
GTCAAGTACTTCAAGACGTGCATCTACTTCTCTTCAACTTTCAAGTTACAATCATCCACCTCAT
ATGGTGCACCAAACAGATTCAAGCAACCAAAGACATCAGATATCTGTGGATGTGTTGGCACATT
CTGCCAGTAAGCCTGCATGGAGAAATGATTTTCAGCATGATATTGTTTCAGATGATGGAATTGA
CTGGTCTTCTAATCAAAATTTGATAAACCAGACATCATTGAAACCTGTGGATCTCCCTATTTGT
TCTTTTGCTGCTGCTGGTAATTGTCCTTATGGGGAAGGGTGCCCTCAAATGCATGGAGATCTGT
GTGCAACCTGTGGAAAACTGTGCTTGCATCCTTATCGTCCTGATGAGAGGGAGGAGCATATCAA
GTTATGTGAGAAAAATCACAAACGCCTTGTAGCTCTGAAACGCAGCCAAGAAATAGAATGCAGT
GTATGTTTGGATCGTGTGCTTTCAAAGCCTACTGCTGCTGAAAGGAAGTTTGGACTCTTATCCG
AATGTGATCATCCTTTCTGTATTGAATGCATTAGAAATTGGCGTAGCAATTCTCCTGCATCTGG
TATGGATGTGAACTCAGCATTGAGGGCTTGTCCAATATGTCGGAAACTTTCATACTATGTCATT
CCAAGTGTTCTTTGGTACTTCTCAAAGGAAGAGAAAGAGGAGATCACTGAAAGCTACAAATCCA
AGCTCAA
						
					

						Genomic sequence
						
							AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCAC
GACTGGAGTGATCAAGCAAATAATGTAACGTATTAGTAACATTCCATGCAGTTTAGTCTTACAT
ATGGAGTTACAGTCATAAGTGCATATCCTCTGCTGTATCTTACTGTTACACTTTTCACCTCAGG
TTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAA
AGTTTCTCGTAACCCCACAGTGCCACCACCACGCCCAACGTCAAGTACTTCAAGACGTGCATCT
ACTTCTCTTCAACTTTCAAGTTACAATCATCCACCTCATATGGTGCACCAAACAGATTCAAGCA
ACCAAAGACATCAGATATCTGTGGATGTGTTGGCACATTCTGCCAGTAAGCCTGCATGGAGAAA
TGATTTTCAGCATGATATTGTTTCAGATGATGGAATTGACTGGTCTTCTAATCAAAATTTGATA
AACCAGACATCATTGAAACCTGTGGATCTCCCTATTTGTTCTTTTGCTGCTGCTGGTAATTGTC
CTTATGGGGAAGGGTGCCCTCAAATGCATGGAGATCTGTGTGCAACCTGTGGAAAACTGTGCTT
GCATCCTTATCGTCCTGATGAGAGGGAGGAGCATATCAAGTTATGTGAGAAAAATCACAAACGC
CTTGTAGCTCTGAAACGCAGCCAAGAAATAGAATGCAGTGTATGTTTGGATCGTGTGCTTTCAA
AGCCTACTGCTGCTGAAAGGAAGTTTGGACTCTTATCCGAATGTGATCATCCTTTCTGTATTGA
ATGCATTAGAAATTGGCGTAGCAATTCTCCTGCATCTGGTATGGATGTGAACTCAGCATTGAGG
GCTTGTCCAATATGTCGGAAACTTTCATACTATGTCATTCCAAGTGTTCTTTGGTACTTCTCAA
AGGAAGAGAAAGAGGAGATCACTGAAAGCTACAAATCCAAGCTCAA
						
					

			
		

Sequences
Splice junction sequence	TATGTCGGAAACTTTCATACTATGTCATTCCAAGTGTTCTTTGGTACTTCTCAAAGGAAGAGAA AGAGGAGATCACTGAAAGCTACAAATCCAAGCTCAAagttctttgcaagttcttcatgcatgga gcttgcttgaaaggagagtactgtgaattctcccacgactggagtgatcaagcaaataatgtaa cgtattag
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: 903 Transcript exons: 45733231-45733318,45733422-45734236 AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCAC GACTGGAGTGATCAAGCAAATAATGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTA GCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCCCAAC GTCAAGTACTTCAAGACGTGCATCTACTTCTCTTCAACTTTCAAGTTACAATCATCCACCTCAT ATGGTGCACCAAACAGATTCAAGCAACCAAAGACATCAGATATCTGTGGATGTGTTGGCACATT CTGCCAGTAAGCCTGCATGGAGAAATGATTTTCAGCATGATATTGTTTCAGATGATGGAATTGA CTGGTCTTCTAATCAAAATTTGATAAACCAGACATCATTGAAACCTGTGGATCTCCCTATTTGT TCTTTTGCTGCTGCTGGTAATTGTCCTTATGGGGAAGGGTGCCCTCAAATGCATGGAGATCTGT GTGCAACCTGTGGAAAACTGTGCTTGCATCCTTATCGTCCTGATGAGAGGGAGGAGCATATCAA GTTATGTGAGAAAAATCACAAACGCCTTGTAGCTCTGAAACGCAGCCAAGAAATAGAATGCAGT GTATGTTTGGATCGTGTGCTTTCAAAGCCTACTGCTGCTGAAAGGAAGTTTGGACTCTTATCCG AATGTGATCATCCTTTCTGTATTGAATGCATTAGAAATTGGCGTAGCAATTCTCCTGCATCTGG TATGGATGTGAACTCAGCATTGAGGGCTTGTCCAATATGTCGGAAACTTTCATACTATGTCATT CCAAGTGTTCTTTGGTACTTCTCAAAGGAAGAGAAAGAGGAGATCACTGAAAGCTACAAATCCA AGCTCAA
Genomic sequence	AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCAC GACTGGAGTGATCAAGCAAATAATGTAACGTATTAGTAACATTCCATGCAGTTTAGTCTTACAT ATGGAGTTACAGTCATAAGTGCATATCCTCTGCTGTATCTTACTGTTACACTTTTCACCTCAGG TTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAA AGTTTCTCGTAACCCCACAGTGCCACCACCACGCCCAACGTCAAGTACTTCAAGACGTGCATCT ACTTCTCTTCAACTTTCAAGTTACAATCATCCACCTCATATGGTGCACCAAACAGATTCAAGCA ACCAAAGACATCAGATATCTGTGGATGTGTTGGCACATTCTGCCAGTAAGCCTGCATGGAGAAA TGATTTTCAGCATGATATTGTTTCAGATGATGGAATTGACTGGTCTTCTAATCAAAATTTGATA AACCAGACATCATTGAAACCTGTGGATCTCCCTATTTGTTCTTTTGCTGCTGCTGGTAATTGTC CTTATGGGGAAGGGTGCCCTCAAATGCATGGAGATCTGTGTGCAACCTGTGGAAAACTGTGCTT GCATCCTTATCGTCCTGATGAGAGGGAGGAGCATATCAAGTTATGTGAGAAAAATCACAAACGC CTTGTAGCTCTGAAACGCAGCCAAGAAATAGAATGCAGTGTATGTTTGGATCGTGTGCTTTCAA AGCCTACTGCTGCTGAAAGGAAGTTTGGACTCTTATCCGAATGTGATCATCCTTTCTGTATTGA ATGCATTAGAAATTGGCGTAGCAATTCTCCTGCATCTGGTATGGATGTGAACTCAGCATTGAGG GCTTGTCCAATATGTCGGAAACTTTCATACTATGTCATTCCAAGTGTTCTTTGGTACTTCTCAA AGGAAGAGAAAGAGGAGATCACTGAAAGCTACAAATCCAAGCTCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.384004109

Conservation Information
Conserved circRNAs	NA
PMCS	0.384004109

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							45733251-45734233(+)
45734159-45733265(+)
45733483-45734189(-)
						
					

						Potential amino acid sequence
						
							MHGACLKGEYCEFSHDWSDQANNVCTFYQKGACSYGSRCRYDHVKVSRNPTVPPPRPTSSTSRR
ASTSLQLSSYNHPPHMVHQTDSSNQRHQISVDVLAHSASKPAWRNDFQHDIVSDDGIDWSSNQN
LINQTSLKPVDLPICSFAAAGNCPYGEGCPQMHGDLCATCGKLCLHPYRPDEREEHIKLCEKNH
KRLVALKRSQEIECSVCLDRVLSKPTAAERKFGLLSECDHPFCIECIRNWRSNSPASGMDVNSA
LRACPICRKLSYYVIPSVLWYFSKEEKEEITESYKSKLKVLCKFFMHGACLKGEYCEFSHDWSD
QANNVCTFYQKGACSYGSRCRYDHVKVSRNPTVPPPRPTSSTSRRASTSLQLSSYNHPPHMVHQ
TDSSNQRHQISVDVLAHSASKPAWRNDFQHDIVSDDGIDWSSNQNLINQTSLKPVDLPICSFAA
AGNCPYGEGCPQMHGDLCATCGKLCLHPYRPDEREEHIKLCEKNHKRLVALKRSQEIECSVCLD
RVLSKPTAAERKFGLLSECDHPFCIECIRNWRSNSPASGMDVNSALRACPICRKLSYYVIPSVL
WYFSKEEKEEITESYKSKLKVLCKFFMHGACLKGEYCEFSHDWSDQANNVCTFYQKGACSYGSR
CRYDHVKVSRNPTVPPPRPTSSTSRRASTSLQLSSYNHPPHMVHQTDSSNQRHQISVDVLAHSA
SKPAWRNDFQHDIVSDDGIDWSSNQNLINQTSLKPVDLPICSFAAAGNCPYGEGCPQMHGDLCA
TCGKLCLHPYRPDEREEHIKLCEKNHKRLVALKRSQEIECSVCLDRVLSKPTAAERKFGLLSEC
DHPFCIECIRNWRSNSPASGMDVNSALRACPICRKLSYYVIPSVLWYFSKEEKEEITESYKSKL
KVLCKFFMHGACLKGEYCEFSHDWSDQANNVCTFYQKGACSYGSRCRYDHVKVSRNPTVPPPRP
TSSTSRRASTSLQLSSYNHPPHMVHQTDSSNQRHQISVDVLAHSASKPAWRNDFQHDIVSDDGI
DWSSNQNLINQTSLKPVDLPICSFAAAGNCPYGEGCPQMHGDLCATCGKLCLHPYRPDEREEHI
KLCEKNHKRLVALKRSQEIECSVCLDRVLSKPTAAERKFGLLSECDHPFCIECIRNWRSNSPAS
GMDVNSALRACPICRKLSYYVIPSVLWYFSKEEKEEITESYKSKL(+)
MSFQVFFGTSQRKRKRRSLKATNPSSKFFASSSCMELA*(+)
MVISATATIRACTFLVECANIICLITPVVGEFTVLSFQASSMHEELAKNFELGFVAFSDLLFLF
L*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	45733251-45734233(+) 45734159-45733265(+) 45733483-45734189(-)
Potential amino acid sequence	MHGACLKGEYCEFSHDWSDQANNVCTFYQKGACSYGSRCRYDHVKVSRNPTVPPPRPTSSTSRR ASTSLQLSSYNHPPHMVHQTDSSNQRHQISVDVLAHSASKPAWRNDFQHDIVSDDGIDWSSNQN LINQTSLKPVDLPICSFAAAGNCPYGEGCPQMHGDLCATCGKLCLHPYRPDEREEHIKLCEKNH KRLVALKRSQEIECSVCLDRVLSKPTAAERKFGLLSECDHPFCIECIRNWRSNSPASGMDVNSA LRACPICRKLSYYVIPSVLWYFSKEEKEEITESYKSKLKVLCKFFMHGACLKGEYCEFSHDWSD QANNVCTFYQKGACSYGSRCRYDHVKVSRNPTVPPPRPTSSTSRRASTSLQLSSYNHPPHMVHQ TDSSNQRHQISVDVLAHSASKPAWRNDFQHDIVSDDGIDWSSNQNLINQTSLKPVDLPICSFAA AGNCPYGEGCPQMHGDLCATCGKLCLHPYRPDEREEHIKLCEKNHKRLVALKRSQEIECSVCLD RVLSKPTAAERKFGLLSECDHPFCIECIRNWRSNSPASGMDVNSALRACPICRKLSYYVIPSVL WYFSKEEKEEITESYKSKLKVLCKFFMHGACLKGEYCEFSHDWSDQANNVCTFYQKGACSYGSR CRYDHVKVSRNPTVPPPRPTSSTSRRASTSLQLSSYNHPPHMVHQTDSSNQRHQISVDVLAHSA SKPAWRNDFQHDIVSDDGIDWSSNQNLINQTSLKPVDLPICSFAAAGNCPYGEGCPQMHGDLCA TCGKLCLHPYRPDEREEHIKLCEKNHKRLVALKRSQEIECSVCLDRVLSKPTAAERKFGLLSEC DHPFCIECIRNWRSNSPASGMDVNSALRACPICRKLSYYVIPSVLWYFSKEEKEEITESYKSKL KVLCKFFMHGACLKGEYCEFSHDWSDQANNVCTFYQKGACSYGSRCRYDHVKVSRNPTVPPPRP TSSTSRRASTSLQLSSYNHPPHMVHQTDSSNQRHQISVDVLAHSASKPAWRNDFQHDIVSDDGI DWSSNQNLINQTSLKPVDLPICSFAAAGNCPYGEGCPQMHGDLCATCGKLCLHPYRPDEREEHI KLCEKNHKRLVALKRSQEIECSVCLDRVLSKPTAAERKFGLLSECDHPFCIECIRNWRSNSPAS GMDVNSALRACPICRKLSYYVIPSVLWYFSKEEKEEITESYKSKL(+) MSFQVFFGTSQRKRKRRSLKATNPSSKFFASSSCMELA(+) MVISATATIRACTFLVECANIICLITPVVGEFTVLSFQASSMHEELAKNFELGFVAFSDLLFLF L(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d045887_circ_g.2

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