Plant Circular RNA Database

Detail information of Zm00001d010456_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d010456_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009669
					
						Alias
						Zm08circ00044, zma_circ_0002742, ZmciR319
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 116058868-116060128  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d010456						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d010456_T002:4
Zm00001d010456_T001:4
Zm00001d010456_T003:2

General Information
CircRNA Name	Zm00001d010456_circ_g.1
ID in PlantcircBase	zma_circ_009669
Alias	Zm08circ00044, zma_circ_0002742, ZmciR319
Organism	Zea mays
Position	chr8: 116058868-116060128 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d010456
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	NA
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	Zm00001d010456_T002:4 Zm00001d010456_T001:4 Zm00001d010456_T003:2

			
						 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  
						
							CATCTAAAACAAAGTTCACTGCTGCTCTGTAGAAAGAATCACGAGCATTTTCAGTATCAAAGCA
GACCTTTACCCCCGATATCTTGCATAATTGCCGAAGcagaccaagagcctgtgcagctgttttt
aagttaccagcagtacaaacgctcctgtatagatatagaaggtgaaccctctcggcaacatgca
aattcttt

									
								

					

						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: 495
Transcript exons: 116058868-116058999,116059510-116059602,116059679-116059
838,116060019-116060128
CAGACCAAGAGCCTGTGCAGCTGTTTTTAAGTTACCAGCAGTACAAACGCTCCTGTATAGATAT
AGAAGGTGAACCCTCTCGGCAACATGCAAATTCTTTTCTAGTCCAGCAGCCACCATTTCCATCT
CTGCAGAATTGTCCTCTGGAGGAAATATGTAATGAATTCTACAAATCTTCACGAGTTCATCCAG
TGCTTCTGGCCGTTTTCCTTGAATCTCTAGAGCCCAGCATTGCAAGAAGCATGTCCGTGTACGA
GTAGCAACTGATGCACATACAAGAGTGGCAGCACGAAACTTGTCTAATCCAATATTGCTAGCAA
GGCCGGCGAGAAAATCCCTTGGATCCTCACCATTAAGTTTTGCTGCACCGATGTCTTTTGCTGC
TCTGCTGCAATCATCTAAAACAAAGTTCACTGCTGCTCTGTAGAAAGAATCACGAGCATTTTCA
GTATCAAAGCAGACCTTTACCCCCGATATCTTGCATAATTGCCGAAG
						
					

						Genomic sequence
						
							CAGACCAAGAGCCTGTGCAGCTGTTTTTAAGTTACCAGCAGTACAAACGCTCCTGTATAGATAT
AGAAGGTGAACCCTCTCGGCAACATGCAAATTCTTTTCTAGTCCAGCAGCCACCATTTCCATCT
CTGCCTGTAGGAAACAATAAAATGTGATTACGTTTGTATGGATAATCATACAGTAACAAAACCG
AATGCATACATGATGTTGGGTTTCTTCAGACAAATAACCATCTTGAGTACACGTTATAACTATA
TGCTCTCAGCTAAGTACCAGGGAAACTATTTAAAATAGGCATGAGAAAAATATCAATCAAACTG
GCACAAAAAATCTAAGCATTATATGAGGGCATGAGGCATCACCTGCTGCTCTAGGCCCCCAGGT
CTAAACATGCTACGTCCTAGCTCAGGCGCACAGGACATAAACAACTTACCTGGACTTGCTTCCT
AGCTTTAAATAAGAAAGAATTAACATTGCCTAATAGTTATATACTCCTACGCAGGTCCAGATGC
GCAATTTTGAACGCACACAGTTCAACCAGCACATCAAGACACACAGTACGTGAAGGGGTGAAAA
TTGAATTAAATGCAGAACAATTGTAATTCCAAAGGACAAGTTTCGAGCTTAAACGAAATGACAT
ACAGAATTGTCCTCTGGAGGAAATATGTAATGAATTCTACAAATCTTCACGAGTTCATCCAGTG
CTTCTGGCCGTTTTCCTTGAATCTCTAGAGCCTAGGGACAAAAAAAACATGGAATCAACATTGC
AAGAACATGGACTCTCCACAGCTATGTATAGATAAATGCATACCCAGCATTGCAAGAAGCATGT
CCGTGTACGAGTAGCAACTGATGCACATACAAGAGTGGCAGCACGAAACTTGTCTAATCCAATA
TTGCTAGCAAGGCCGGCGAGAAAATCCCTTGGATCCTCACCATTAAGTTTTGCTGCACCGATGT
CTTTTGCTGCTCTTTATTAAGAACAAAATATCAACGAGTCCAGATCAAGGATGGCAATTGTAAA
ATAAGAACAGCATGTACAAAGAAATACATAAAATTAAAAAAAATGTCTGACAGCAGAAATTTAC
AAATAGCTGATGAACAGAGTAACTGAAGGCAAAACAAATTCTTTGAACAAAAGCTATAAATACC
TGCTGCAATCATCTAAAACAAAGTTCACTGCTGCTCTGTAGAAAGAATCACGAGCATTTTCAGT
ATCAAAGCAGACCTTTACCCCCGATATCTTGCATAATTGCCGAAG
						
					

			
		

Sequences
Splice junction sequence	CATCTAAAACAAAGTTCACTGCTGCTCTGTAGAAAGAATCACGAGCATTTTCAGTATCAAAGCA GACCTTTACCCCCGATATCTTGCATAATTGCCGAAGcagaccaagagcctgtgcagctgttttt aagttaccagcagtacaaacgctcctgtatagatatagaaggtgaaccctctcggcaacatgca aattcttt
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: 495 Transcript exons: 116058868-116058999,116059510-116059602,116059679-116059 838,116060019-116060128 CAGACCAAGAGCCTGTGCAGCTGTTTTTAAGTTACCAGCAGTACAAACGCTCCTGTATAGATAT AGAAGGTGAACCCTCTCGGCAACATGCAAATTCTTTTCTAGTCCAGCAGCCACCATTTCCATCT CTGCAGAATTGTCCTCTGGAGGAAATATGTAATGAATTCTACAAATCTTCACGAGTTCATCCAG TGCTTCTGGCCGTTTTCCTTGAATCTCTAGAGCCCAGCATTGCAAGAAGCATGTCCGTGTACGA GTAGCAACTGATGCACATACAAGAGTGGCAGCACGAAACTTGTCTAATCCAATATTGCTAGCAA GGCCGGCGAGAAAATCCCTTGGATCCTCACCATTAAGTTTTGCTGCACCGATGTCTTTTGCTGC TCTGCTGCAATCATCTAAAACAAAGTTCACTGCTGCTCTGTAGAAAGAATCACGAGCATTTTCA GTATCAAAGCAGACCTTTACCCCCGATATCTTGCATAATTGCCGAAG
Genomic sequence	CAGACCAAGAGCCTGTGCAGCTGTTTTTAAGTTACCAGCAGTACAAACGCTCCTGTATAGATAT AGAAGGTGAACCCTCTCGGCAACATGCAAATTCTTTTCTAGTCCAGCAGCCACCATTTCCATCT CTGCCTGTAGGAAACAATAAAATGTGATTACGTTTGTATGGATAATCATACAGTAACAAAACCG AATGCATACATGATGTTGGGTTTCTTCAGACAAATAACCATCTTGAGTACACGTTATAACTATA TGCTCTCAGCTAAGTACCAGGGAAACTATTTAAAATAGGCATGAGAAAAATATCAATCAAACTG GCACAAAAAATCTAAGCATTATATGAGGGCATGAGGCATCACCTGCTGCTCTAGGCCCCCAGGT CTAAACATGCTACGTCCTAGCTCAGGCGCACAGGACATAAACAACTTACCTGGACTTGCTTCCT AGCTTTAAATAAGAAAGAATTAACATTGCCTAATAGTTATATACTCCTACGCAGGTCCAGATGC GCAATTTTGAACGCACACAGTTCAACCAGCACATCAAGACACACAGTACGTGAAGGGGTGAAAA TTGAATTAAATGCAGAACAATTGTAATTCCAAAGGACAAGTTTCGAGCTTAAACGAAATGACAT ACAGAATTGTCCTCTGGAGGAAATATGTAATGAATTCTACAAATCTTCACGAGTTCATCCAGTG CTTCTGGCCGTTTTCCTTGAATCTCTAGAGCCTAGGGACAAAAAAAACATGGAATCAACATTGC AAGAACATGGACTCTCCACAGCTATGTATAGATAAATGCATACCCAGCATTGCAAGAAGCATGT CCGTGTACGAGTAGCAACTGATGCACATACAAGAGTGGCAGCACGAAACTTGTCTAATCCAATA TTGCTAGCAAGGCCGGCGAGAAAATCCCTTGGATCCTCACCATTAAGTTTTGCTGCACCGATGT CTTTTGCTGCTCTTTATTAAGAACAAAATATCAACGAGTCCAGATCAAGGATGGCAATTGTAAA ATAAGAACAGCATGTACAAAGAAATACATAAAATTAAAAAAAATGTCTGACAGCAGAAATTTAC AAATAGCTGATGAACAGAGTAACTGAAGGCAAAACAAATTCTTTGAACAAAAGCTATAAATACC TGCTGCAATCATCTAAAACAAAGTTCACTGCTGCTCTGTAGAAAGAATCACGAGCATTTTCAGT ATCAAAGCAGACCTTTACCCCCGATATCTTGCATAATTGCCGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.158689367

Conservation Information
Conserved circRNAs	NA
PMCS	0.158689367

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							116058995-116058870(-)
						
						Potential amino acid sequence
						
							MEMVAAGLEKNLHVAERVHLLYLYRSVCTAGNLKTAAQALGLLRQLCKISGVKVCFDTENARDS
FYRAAVNFVLDDCSRAAKDIGAAKLNGEDPRDFLAGLASNIGLDKFRAATLVCASVATRTRTCF
LQCWALEIQGKRPEALDELVKICRIHYIFPPEDNSAEMEMVAAGLEKNLHVAERVHLLYLYRSV
CTAGNLKTAAQALGLLRQLCKISGVKVCFDTENARDSFYRAAVNFVLDDCSRAAKDIGAAKLNG
EDPRDFLAGLASNIGLDKFRAATLVCASVATRTRTCFLQCWALEIQGKRPEALDELVKICRIHY
IFPPEDNSAEMEMVAAGLEKNLHVAERVHLLYLYRSVCTAGNLKTAAQALGLLRQLCKISGVKV
CFDTENARDSFYRAAVNFVLDDCSRAAKDIGAAKLNGEDPRDFLAGLASNIGLDKFRAATLVCA
SVATRTRTCFLQCWALEIQGKRPEALDELVKICRIHYIFPPEDNSAEMEMVAAGLEKNLHVAER
VHLLYLYRSVCTAGNLKTAAQALGL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	116058995-116058870(-)
Potential amino acid sequence	MEMVAAGLEKNLHVAERVHLLYLYRSVCTAGNLKTAAQALGLLRQLCKISGVKVCFDTENARDS FYRAAVNFVLDDCSRAAKDIGAAKLNGEDPRDFLAGLASNIGLDKFRAATLVCASVATRTRTCF LQCWALEIQGKRPEALDELVKICRIHYIFPPEDNSAEMEMVAAGLEKNLHVAERVHLLYLYRSV CTAGNLKTAAQALGLLRQLCKISGVKVCFDTENARDSFYRAAVNFVLDDCSRAAKDIGAAKLNG EDPRDFLAGLASNIGLDKFRAATLVCASVATRTRTCFLQCWALEIQGKRPEALDELVKICRIHY IFPPEDNSAEMEMVAAGLEKNLHVAERVHLLYLYRSVCTAGNLKTAAQALGLLRQLCKISGVKV CFDTENARDSFYRAAVNFVLDDCSRAAKDIGAAKLNGEDPRDFLAGLASNIGLDKFRAATLVCA SVATRTRTCFLQCWALEIQGKRPEALDELVKICRIHYIFPPEDNSAEMEMVAAGLEKNLHVAER VHLLYLYRSVCTAGNLKTAAQALGL(-)
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 Zm00001d010456_circ_g.1

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