Plant Circular RNA Database

Detail information of Zm00001d009364_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d009364_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009608
					
						Alias
						Zm08circ00027, zma_circ_0002693
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 59929412-59930576  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d009364						
					
						Parent gene annotation
						
							Protein kinase and PP2C-like domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d009364_circ_g.1 Zm00001d009364_circ_g.2 Zm00001d009364_circ_g.4 Zm00001d009364_circ_g.5 Zm00001d009364_circ_g.6 						
					
						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  
						
							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
						Zm00001d009364_T001:4

General Information
CircRNA Name	Zm00001d009364_circ_g.3
ID in PlantcircBase	zma_circ_009608
Alias	Zm08circ00027, zma_circ_0002693
Organism	Zea mays
Position	chr8: 59929412-59930576 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d009364
Parent gene annotation	Protein kinase and PP2C-like domain-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d009364_circ_g.1 Zm00001d009364_circ_g.2 Zm00001d009364_circ_g.4 Zm00001d009364_circ_g.5 Zm00001d009364_circ_g.6
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	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	Zm00001d009364_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  
						
							TGTTGCTAGTTGCCCAAATGAAAGAGAACGAGTAACAAAGGCGGGGACTGAAGTAAAATGGCAA
ATAGATACGTGGCGAGTGGGTTCAGCTGCTCTTCAGgcacacactgttcttgaaatgacatata
ctgaacaacaacttacagcagcaattgtttctcaaggattgcgtccagcacttgcccttcctga
atctggtg

									
								

					

						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: 918
Transcript exons: 59929412-59929934,59930017-59930086,59930165-59930384,59
930472-59930576
GCACACACTGTTCTTGAAATGACATATACTGAACAACAACTTACAGCAGCAATTGTTTCTCAAG
GATTGCGTCCAGCACTTGCCCTTCCTGAATCTGGTGCCCCACCAACTCTTTTGTCACTTATCCA
GCGTTGCTGGGATCCTGATCCTGAAAAGAGACCATCATTTGAAGATATAATTGATGAGCTAAAT
ATAGTTCAAAAGCATATAGTTTCAAATGCTTCTGTTCCATCATCTCCTGTCAGCAAGACTCAAA
ATGGTACCATAGAAGTGCACCATTATCAAGAAGCATTGAACTGGTTCAACCAGGGGGAGCTTTT
TGTTAAAGGATCAAGTAGATCAGACCTTAAGAATCTTTGGTCTGATTGTTTTGATCAATCTTCA
GAGTACCATCCAACATTAAGTTGGGGCTCTTTTGCAACGTGTGGTCGAAGGGAAACCATGGAAG
ACACCCATTTTGTACTTCCCCATGTGAGCGAAGAAAATGATGTTTTTGCCTTTGGCATTTTTGA
TGGCCATAGAGGTTCAGCAGCCGCTGAATTTTCTGTCCGAGCAGTTCCTGGATTTCTCAAGCAA
TTTGGTCAGGGTGCAAGCCCAACTGACGCTCTTTCAGAAGCGTTTGTAAGGACTGACATAGCAT
TTCGAGAAGAACTAATTCTTCACCGGAAGTCAAAAAGGATAATTCAAAAAGATTGGCATCCTGG
TTGCACGGCAATAACCGCCCTGATAGTGAGAAACAAGCTTTTTGTAGCAAATGCTGGTGATTGC
CGAGCAATCCTGAGCCGTAAGGGCAAACCATTTCTGTTGACCAAGGATCATGTTGCTAGTTGCC
CAAATGAAAGAGAACGAGTAACAAAGGCGGGGACTGAAGTAAAATGGCAAATAGATACGTGGCG
AGTGGGTTCAGCTGCTCTTCAG
						
					

						Genomic sequence
						
							GCACACACTGTTCTTGAAATGACATATACTGAACAACAACTTACAGCAGCAATTGTTTCTCAAG
GATTGCGTCCAGCACTTGCCCTTCCTGAATCTGGTGCCCCACCAACTCTTTTGTCACTTATCCA
GCGTTGCTGGGATCCTGATCCTGAAAAGAGACCATCATTTGAAGATATAATTGATGAGCTAAAT
ATAGTTCAAAAGCATATAGTTTCAAATGCTTCTGTTCCATCATCTCCTGTCAGCAAGACTCAAA
ATGGTACCATAGAAGTGCACCATTATCAAGAAGCATTGAACTGGTTCAACCAGGGGGAGCTTTT
TGTTAAAGGATCAAGTAGATCAGACCTTAAGAATCTTTGGTCTGATTGTTTTGATCAATCTTCA
GAGTACCATCCAACATTAAGTTGGGGCTCTTTTGCAACGTGTGGTCGAAGGGAAACCATGGAAG
ACACCCATTTTGTACTTCCCCATGTGAGCGAAGAAAATGATGTTTTTGCCTTTGGCATTTTTGA
TGGCCATAGAGGTTCGCTAATCAAAAAACATAGTTTGGTTGATCTTTGCTAGATTTTACATTAG
CATTTCTTAACAAAAAAAACTTTTCACAGGTTCAGCAGCCGCTGAATTTTCTGTCCGAGCAGTT
CCTGGATTTCTCAAGCAATTTGGTCAGGGTGCAAGGTTTGTCCGTTTGTATTGAATGCAAATGA
TCTAAAATGTTTGCCATGTTGTATCGATTTGAGTTCTGGCATTTTGCAGCCCAACTGACGCTCT
TTCAGAAGCGTTTGTAAGGACTGACATAGCATTTCGAGAAGAACTAATTCTTCACCGGAAGTCA
AAAAGGATAATTCAAAAAGATTGGCATCCTGGTTGCACGGCAATAACCGCCCTGATAGTGAGAA
ACAAGCTTTTTGTAGCAAATGCTGGTGATTGCCGAGCAATCCTGAGCCGTAAGGGCAAACCATT
TCTGTTGACCAAGGTTGTGATTAACCTTTCTATATCGTTACTACATTTTTTTGGTAGTATATCA
TCTCGTGCATAACTTTTTTTCCATTTGCTGTTATAGGATCATGTTGCTAGTTGCCCAAATGAAA
GAGAACGAGTAACAAAGGCGGGGACTGAAGTAAAATGGCAAATAGATACGTGGCGAGTGGGTTC
AGCTGCTCTTCAG
						
					

			
		

Sequences
Splice junction sequence	TGTTGCTAGTTGCCCAAATGAAAGAGAACGAGTAACAAAGGCGGGGACTGAAGTAAAATGGCAA ATAGATACGTGGCGAGTGGGTTCAGCTGCTCTTCAGgcacacactgttcttgaaatgacatata ctgaacaacaacttacagcagcaattgtttctcaaggattgcgtccagcacttgcccttcctga atctggtg
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: 918 Transcript exons: 59929412-59929934,59930017-59930086,59930165-59930384,59 930472-59930576 GCACACACTGTTCTTGAAATGACATATACTGAACAACAACTTACAGCAGCAATTGTTTCTCAAG GATTGCGTCCAGCACTTGCCCTTCCTGAATCTGGTGCCCCACCAACTCTTTTGTCACTTATCCA GCGTTGCTGGGATCCTGATCCTGAAAAGAGACCATCATTTGAAGATATAATTGATGAGCTAAAT ATAGTTCAAAAGCATATAGTTTCAAATGCTTCTGTTCCATCATCTCCTGTCAGCAAGACTCAAA ATGGTACCATAGAAGTGCACCATTATCAAGAAGCATTGAACTGGTTCAACCAGGGGGAGCTTTT TGTTAAAGGATCAAGTAGATCAGACCTTAAGAATCTTTGGTCTGATTGTTTTGATCAATCTTCA GAGTACCATCCAACATTAAGTTGGGGCTCTTTTGCAACGTGTGGTCGAAGGGAAACCATGGAAG ACACCCATTTTGTACTTCCCCATGTGAGCGAAGAAAATGATGTTTTTGCCTTTGGCATTTTTGA TGGCCATAGAGGTTCAGCAGCCGCTGAATTTTCTGTCCGAGCAGTTCCTGGATTTCTCAAGCAA TTTGGTCAGGGTGCAAGCCCAACTGACGCTCTTTCAGAAGCGTTTGTAAGGACTGACATAGCAT TTCGAGAAGAACTAATTCTTCACCGGAAGTCAAAAAGGATAATTCAAAAAGATTGGCATCCTGG TTGCACGGCAATAACCGCCCTGATAGTGAGAAACAAGCTTTTTGTAGCAAATGCTGGTGATTGC CGAGCAATCCTGAGCCGTAAGGGCAAACCATTTCTGTTGACCAAGGATCATGTTGCTAGTTGCC CAAATGAAAGAGAACGAGTAACAAAGGCGGGGACTGAAGTAAAATGGCAAATAGATACGTGGCG AGTGGGTTCAGCTGCTCTTCAG
Genomic sequence	GCACACACTGTTCTTGAAATGACATATACTGAACAACAACTTACAGCAGCAATTGTTTCTCAAG GATTGCGTCCAGCACTTGCCCTTCCTGAATCTGGTGCCCCACCAACTCTTTTGTCACTTATCCA GCGTTGCTGGGATCCTGATCCTGAAAAGAGACCATCATTTGAAGATATAATTGATGAGCTAAAT ATAGTTCAAAAGCATATAGTTTCAAATGCTTCTGTTCCATCATCTCCTGTCAGCAAGACTCAAA ATGGTACCATAGAAGTGCACCATTATCAAGAAGCATTGAACTGGTTCAACCAGGGGGAGCTTTT TGTTAAAGGATCAAGTAGATCAGACCTTAAGAATCTTTGGTCTGATTGTTTTGATCAATCTTCA GAGTACCATCCAACATTAAGTTGGGGCTCTTTTGCAACGTGTGGTCGAAGGGAAACCATGGAAG ACACCCATTTTGTACTTCCCCATGTGAGCGAAGAAAATGATGTTTTTGCCTTTGGCATTTTTGA TGGCCATAGAGGTTCGCTAATCAAAAAACATAGTTTGGTTGATCTTTGCTAGATTTTACATTAG CATTTCTTAACAAAAAAAACTTTTCACAGGTTCAGCAGCCGCTGAATTTTCTGTCCGAGCAGTT CCTGGATTTCTCAAGCAATTTGGTCAGGGTGCAAGGTTTGTCCGTTTGTATTGAATGCAAATGA TCTAAAATGTTTGCCATGTTGTATCGATTTGAGTTCTGGCATTTTGCAGCCCAACTGACGCTCT TTCAGAAGCGTTTGTAAGGACTGACATAGCATTTCGAGAAGAACTAATTCTTCACCGGAAGTCA AAAAGGATAATTCAAAAAGATTGGCATCCTGGTTGCACGGCAATAACCGCCCTGATAGTGAGAA ACAAGCTTTTTGTAGCAAATGCTGGTGATTGCCGAGCAATCCTGAGCCGTAAGGGCAAACCATT TCTGTTGACCAAGGTTGTGATTAACCTTTCTATATCGTTACTACATTTTTTTGGTAGTATATCA TCTCGTGCATAACTTTTTTTCCATTTGCTGTTATAGGATCATGTTGCTAGTTGCCCAAATGAAA GAGAACGAGTAACAAAGGCGGGGACTGAAGTAAAATGGCAAATAGATACGTGGCGAGTGGGTTC AGCTGCTCTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_002083 						
					
						PMCS
						0.212567795

Conservation Information
Conserved circRNAs	osa_circ_002083
PMCS	0.212567795

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							59929431-59930573(+)
59929438-59930484(-)
						
						Potential amino acid sequence
						
							MTYTEQQLTAAIVSQGLRPALALPESGAPPTLLSLIQRCWDPDPEKRPSFEDIIDELNIVQKHI
VSNASVPSSPVSKTQNGTIEVHHYQEALNWFNQGELFVKGSSRSDLKNLWSDCFDQSSEYHPTL
SWGSFATCGRRETMEDTHFVLPHVSEENDVFAFGIFDGHRGSAAAEFSVRAVPGFLKQFGQGAS
PTDALSEAFVRTDIAFREELILHRKSKRIIQKDWHPGCTAITALIVRNKLFVANAGDCRAILSR
KGKPFLLTKDHVASCPNERERVTKAGTEVKWQIDTWRVGSAALQAHTVLEMTYTEQQLTAAIVS
QGLRPALALPESGAPPTLLSLIQRCWDPDPEKRPSFEDIIDELNIVQKHIVSNASVPSSPVSKT
QNGTIEVHHYQEALNWFNQGELFVKGSSRSDLKNLWSDCFDQSSEYHPTLSWGSFATCGRRETM
EDTHFVLPHVSEENDVFAFGIFDGHRGSAAAEFSVRAVPGFLKQFGQGASPTDALSEAFVRTDI
AFREELILHRKSKRIIQKDWHPGCTAITALIVRNKLFVANAGDCRAILSRKGKPFLLTKDHVAS
CPNERERVTKAGTEVKWQIDTWRVGSAALQAHTVLEMTYTEQQLTAAIVSQGLRPALALPESGA
PPTLLSLIQRCWDPDPEKRPSFEDIIDELNIVQKHIVSNASVPSSPVSKTQNGTIEVHHYQEAL
NWFNQGELFVKGSSRSDLKNLWSDCFDQSSEYHPTLSWGSFATCGRRETMEDTHFVLPHVSEEN
DVFAFGIFDGHRGSAAAEFSVRAVPGFLKQFGQGASPTDALSEAFVRTDIAFREELILHRKSKR
IIQKDWHPGCTAITALIVRNKLFVANAGDCRAILSRKGKPFLLTKDHVASCPNERERVTKAGTE
VKWQIDTWRVGSAALQAHTVLEMTYTEQQLTAAIVSQGLRPALALPESGAPPTLLSLIQRCWDP
DPEKRPSFEDIIDELNIVQKHIVSNASVPSSPVSKTQNGTIEVHHYQEALNWFNQGELFVKGSS
RSDLKNLWSDCFDQSSEYHPTLSWGSFATCGRRETMEDTHFVLPHVSEENDVFAFGIFDGHRGS
AAAEFSVRAVPGFLKQFGQGASPTDALSEAFVRTDIAFREELILHRKSKRIIQKDWHPGCTAIT
ALIVRNKLFVANAGDCRAILSRKGKPFLLTKDHVASCPNERERVTKAGTEVKWQIDTWRVGSAA
LQ(+)
MSFQEQCVPEEQLNPLATYLFAILLQSPPLLLVLFHLGN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	59929431-59930573(+) 59929438-59930484(-)
Potential amino acid sequence	MTYTEQQLTAAIVSQGLRPALALPESGAPPTLLSLIQRCWDPDPEKRPSFEDIIDELNIVQKHI VSNASVPSSPVSKTQNGTIEVHHYQEALNWFNQGELFVKGSSRSDLKNLWSDCFDQSSEYHPTL SWGSFATCGRRETMEDTHFVLPHVSEENDVFAFGIFDGHRGSAAAEFSVRAVPGFLKQFGQGAS PTDALSEAFVRTDIAFREELILHRKSKRIIQKDWHPGCTAITALIVRNKLFVANAGDCRAILSR KGKPFLLTKDHVASCPNERERVTKAGTEVKWQIDTWRVGSAALQAHTVLEMTYTEQQLTAAIVS QGLRPALALPESGAPPTLLSLIQRCWDPDPEKRPSFEDIIDELNIVQKHIVSNASVPSSPVSKT QNGTIEVHHYQEALNWFNQGELFVKGSSRSDLKNLWSDCFDQSSEYHPTLSWGSFATCGRRETM EDTHFVLPHVSEENDVFAFGIFDGHRGSAAAEFSVRAVPGFLKQFGQGASPTDALSEAFVRTDI AFREELILHRKSKRIIQKDWHPGCTAITALIVRNKLFVANAGDCRAILSRKGKPFLLTKDHVAS CPNERERVTKAGTEVKWQIDTWRVGSAALQAHTVLEMTYTEQQLTAAIVSQGLRPALALPESGA PPTLLSLIQRCWDPDPEKRPSFEDIIDELNIVQKHIVSNASVPSSPVSKTQNGTIEVHHYQEAL NWFNQGELFVKGSSRSDLKNLWSDCFDQSSEYHPTLSWGSFATCGRRETMEDTHFVLPHVSEEN DVFAFGIFDGHRGSAAAEFSVRAVPGFLKQFGQGASPTDALSEAFVRTDIAFREELILHRKSKR IIQKDWHPGCTAITALIVRNKLFVANAGDCRAILSRKGKPFLLTKDHVASCPNERERVTKAGTE VKWQIDTWRVGSAALQAHTVLEMTYTEQQLTAAIVSQGLRPALALPESGAPPTLLSLIQRCWDP DPEKRPSFEDIIDELNIVQKHIVSNASVPSSPVSKTQNGTIEVHHYQEALNWFNQGELFVKGSS RSDLKNLWSDCFDQSSEYHPTLSWGSFATCGRRETMEDTHFVLPHVSEENDVFAFGIFDGHRGS AAAEFSVRAVPGFLKQFGQGASPTDALSEAFVRTDIAFREELILHRKSKRIIQKDWHPGCTAIT ALIVRNKLFVANAGDCRAILSRKGKPFLLTKDHVASCPNERERVTKAGTEVKWQIDTWRVGSAA LQ(+) MSFQEQCVPEEQLNPLATYLFAILLQSPPLLLVLFHLGN*(-)
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 Zm00001d009364_circ_g.3

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