Plant Circular RNA Database

Detail information of Zm00001d024009_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d024009_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010190
					
						Alias
						zma_circ_0000138, GRMZM2G009443_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 36529707-36530291  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d024009						
					
						Parent gene annotation
						
							Chaperone protein ClpC1 chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d024009_circ_g.1 Zm00001d024009_circ_g.2 Zm00001d024009_circ_g.4 Zm00001d024009_circ_g.5 						
					
						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
						Zm00001d024009_T003:1
Zm00001d024009_T002:1
Zm00001d024009_T001:1

General Information
CircRNA Name	Zm00001d024009_circ_g.3
ID in PlantcircBase	zma_circ_010190
Alias	zma_circ_0000138, GRMZM2G009443_C1
Organism	Zea mays
Position	chr10: 36529707-36530291 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d024009
Parent gene annotation	Chaperone protein ClpC1 chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d024009_circ_g.1 Zm00001d024009_circ_g.2 Zm00001d024009_circ_g.4 Zm00001d024009_circ_g.5
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	Zm00001d024009_T003:1 Zm00001d024009_T002:1 Zm00001d024009_T001:1

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F:CGTGTGGAGGTGGAGAAGAT
 R:AGACCCACAAATGCTGACATC
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	Yes 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	F:CGTGTGGAGGTGGAGAAGAT R:AGACCCACAAATGCTGACATC 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  
						
							ATTATTGGCCGCGGCAATGGTTTTGTTGCTGTTGAAATACCATTCACACCACGTGCGAAACGTG
TTTTGGAGCTCTCCTTGGAGGAAGCTCGCCAATTAGgtcaagtgacggtatttgtgaccatggc
agggaccttactccagtcagttgccctgggaacaccatttgggggtcgcatgagaacccattgt
tggaggtc

						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: 585
Transcript exons: 36529707-36530291
GTCAAGTGACGGTATTTGTGACCATGGCAGGGACCTTACTCCAGTCAGTTGCCCTGGGAACACC
ATTTGGGGGTCGCATGAGAACCCATTGTTGGAGGTCCCATGGCACCAGGAGGCCTGCCTCTATG
TTGGCAGTGTCACTTAGCCGCCCTGTCAAGATGTCAGCATTTGTGGGTCTAAGATCAGTGCATA
GCTTCTCGGTCACACCGACGGTGTCCAATTCCAGGTCGGCAGTTGCATCTTACAGGTCATCGCG
ACAGACAAGACGATCTCGTTTTGTCACTCAGGCAATGTTTGAGAGGTTCACGGAGAAAGCTATT
AAGGTCATCATGCTTGCGCAAGAGGAAGCAAGGCGCCTGGGCCACAACTTTGTTGGAACTGAGC
AGATCCTCTTGGGTCTGATTGGAGAGGGCACTGGTATTGCAGCTAAGGTGCTCAAGTCCATGGG
AATAAATCTTAAGGATGCACGTGTGGAGGTGGAGAAGATTATTGGCCGCGGCAATGGTTTTGTT
GCTGTTGAAATACCATTCACACCACGTGCGAAACGTGTTTTGGAGCTCTCCTTGGAGGAAGCTC
GCCAATTAG
						
						Genomic sequence
						
							GTCAAGTGACGGTATTTGTGACCATGGCAGGGACCTTACTCCAGTCAGTTGCCCTGGGAACACC
ATTTGGGGGTCGCATGAGAACCCATTGTTGGAGGTCCCATGGCACCAGGAGGCCTGCCTCTATG
TTGGCAGTGTCACTTAGCCGCCCTGTCAAGATGTCAGCATTTGTGGGTCTAAGATCAGTGCATA
GCTTCTCGGTCACACCGACGGTGTCCAATTCCAGGTCGGCAGTTGCATCTTACAGGTCATCGCG
ACAGACAAGACGATCTCGTTTTGTCACTCAGGCAATGTTTGAGAGGTTCACGGAGAAAGCTATT
AAGGTCATCATGCTTGCGCAAGAGGAAGCAAGGCGCCTGGGCCACAACTTTGTTGGAACTGAGC
AGATCCTCTTGGGTCTGATTGGAGAGGGCACTGGTATTGCAGCTAAGGTGCTCAAGTCCATGGG
AATAAATCTTAAGGATGCACGTGTGGAGGTGGAGAAGATTATTGGCCGCGGCAATGGTTTTGTT
GCTGTTGAAATACCATTCACACCACGTGCGAAACGTGTTTTGGAGCTCTCCTTGGAGGAAGCTC
GCCAATTAG

Sequences
Splice junction sequence	ATTATTGGCCGCGGCAATGGTTTTGTTGCTGTTGAAATACCATTCACACCACGTGCGAAACGTG TTTTGGAGCTCTCCTTGGAGGAAGCTCGCCAATTAGgtcaagtgacggtatttgtgaccatggc agggaccttactccagtcagttgccctgggaacaccatttgggggtcgcatgagaacccattgt tggaggtc
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: 585 Transcript exons: 36529707-36530291 GTCAAGTGACGGTATTTGTGACCATGGCAGGGACCTTACTCCAGTCAGTTGCCCTGGGAACACC ATTTGGGGGTCGCATGAGAACCCATTGTTGGAGGTCCCATGGCACCAGGAGGCCTGCCTCTATG TTGGCAGTGTCACTTAGCCGCCCTGTCAAGATGTCAGCATTTGTGGGTCTAAGATCAGTGCATA GCTTCTCGGTCACACCGACGGTGTCCAATTCCAGGTCGGCAGTTGCATCTTACAGGTCATCGCG ACAGACAAGACGATCTCGTTTTGTCACTCAGGCAATGTTTGAGAGGTTCACGGAGAAAGCTATT AAGGTCATCATGCTTGCGCAAGAGGAAGCAAGGCGCCTGGGCCACAACTTTGTTGGAACTGAGC AGATCCTCTTGGGTCTGATTGGAGAGGGCACTGGTATTGCAGCTAAGGTGCTCAAGTCCATGGG AATAAATCTTAAGGATGCACGTGTGGAGGTGGAGAAGATTATTGGCCGCGGCAATGGTTTTGTT GCTGTTGAAATACCATTCACACCACGTGCGAAACGTGTTTTGGAGCTCTCCTTGGAGGAAGCTC GCCAATTAG
Genomic sequence	GTCAAGTGACGGTATTTGTGACCATGGCAGGGACCTTACTCCAGTCAGTTGCCCTGGGAACACC ATTTGGGGGTCGCATGAGAACCCATTGTTGGAGGTCCCATGGCACCAGGAGGCCTGCCTCTATG TTGGCAGTGTCACTTAGCCGCCCTGTCAAGATGTCAGCATTTGTGGGTCTAAGATCAGTGCATA GCTTCTCGGTCACACCGACGGTGTCCAATTCCAGGTCGGCAGTTGCATCTTACAGGTCATCGCG ACAGACAAGACGATCTCGTTTTGTCACTCAGGCAATGTTTGAGAGGTTCACGGAGAAAGCTATT AAGGTCATCATGCTTGCGCAAGAGGAAGCAAGGCGCCTGGGCCACAACTTTGTTGGAACTGAGC AGATCCTCTTGGGTCTGATTGGAGAGGGCACTGGTATTGCAGCTAAGGTGCTCAAGTCCATGGG AATAAATCTTAAGGATGCACGTGTGGAGGTGGAGAAGATTATTGGCCGCGGCAATGGTTTTGTT GCTGTTGAAATACCATTCACACCACGTGCGAAACGTGTTTTGGAGCTCTCCTTGGAGGAAGCTC GCCAATTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.420559312

Conservation Information
Conserved circRNAs	NA
PMCS	0.420559312

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							36529731-36530288(+)
36529774-36530237(-)
						
						Potential amino acid sequence
						
							MAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSVHSFSVTPTV
SNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLGLIG
EGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEEARQLGQVTV
FVTMAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSVHSFSVT
PTVSNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLG
LIGEGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEEARQLGQ
VTVFVTMAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSVHSF
SVTPTVSNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQI
LLGLIGEGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEEARQ
LGQVTVFVTMAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSV
HSFSVTPTVSNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGT
EQILLGLIGEGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEE
ARQL(+)
MVFPGQLTGVRSLPWSQIPSLDLIGELPPRRAPKHVSHVV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	36529731-36530288(+) 36529774-36530237(-)
Potential amino acid sequence	MAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSVHSFSVTPTV SNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLGLIG EGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEEARQLGQVTV FVTMAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSVHSFSVT PTVSNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLG LIGEGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEEARQLGQ VTVFVTMAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSVHSF SVTPTVSNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQI LLGLIGEGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEEARQ LGQVTVFVTMAGTLLQSVALGTPFGGRMRTHCWRSHGTRRPASMLAVSLSRPVKMSAFVGLRSV HSFSVTPTVSNSRSAVASYRSSRQTRRSRFVTQAMFERFTEKAIKVIMLAQEEARRLGHNFVGT EQILLGLIGEGTGIAAKVLKSMGINLKDARVEVEKIIGRGNGFVAVEIPFTPRAKRVLELSLEE ARQL(+) MVFPGQLTGVRSLPWSQIPSLDLIGELPPRRAPKHVSHVV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d024009_circ_g.3

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