Plant Circular RNA Database

Detail information of Zm00001d018560_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d018560_circ_g.1
					
						ID in PlantcircBase
						zma_circ_008854
					
						Alias
						Zm05circ00143, zma_circ_0002088
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 223233042-223234480  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d018560						
					
						Parent gene annotation
						
							Callose synthase 3
							
						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  
						
							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
						Zm00001d018560_T002:5
Zm00001d018560_T006:4
Zm00001d018560_T001:5

General Information
CircRNA Name	Zm00001d018560_circ_g.1
ID in PlantcircBase	zma_circ_008854
Alias	Zm05circ00143, zma_circ_0002088
Organism	Zea mays
Position	chr5: 223233042-223234480 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d018560
Parent gene annotation	Callose synthase 3
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	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	Zm00001d018560_T002:5 Zm00001d018560_T006:4 Zm00001d018560_T001:5

			
						 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  
						
							GCTTGGAATGGTGGCACACCAAGTGATATTTTTGATAGAGGAGTATTCAAACAGGTTTTGAGCA
TATTTATAACTGCGGCTATACTGAAACTGGGTCAAGatggcctttgaactctatggtatgttgg
ctggaaatgtgagcccgacgactggtgaaaatgttaaaccagcttatggtggagaagaagaagc
cttcttga

									
								

					

						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: 544
Transcript exons: 223233042-223233179,223233251-223233327,223233423-223233
513,223234140-223234262,223234366-223234480
ATGGCCTTTGAACTCTATGGTATGTTGGCTGGAAATGTGAGCCCGACGACTGGTGAAAATGTTA
AACCAGCTTATGGTGGAGAAGAAGAAGCCTTCTTGAAAAGAGTTGTGACTCCAATCTACAAAGT
TATAGAGAAGGAAGTAGAGAGGAGCAAGACCATGAAATCAAAGCACTCACACTGGAGAAACTAC
GATGATCTTAATGAGTACTTTTGGTCAAGAGATTGCTTCCGATTGGGATGGCCTATGCGATCTG
ATGCAGATTTTTTCAAGACTCCAAATGTTCCTCTTCACCATGTGGATGGAGAGGACAGGACTGT
GGGTAATGGCAATTGGATGGGAAAAGTCAACTTTGTTGAAATACGGTCATTTTGGCACATCTTC
CGCAGCTTTGATAGGATGTGGAGCTTCTTAATTTTATCTTTACAGGCTATGGTTATAATTGCTT
GGAATGGTGGCACACCAAGTGATATTTTTGATAGAGGAGTATTCAAACAGGTTTTGAGCATATT
TATAACTGCGGCTATACTGAAACTGGGTCAAG
						
					

						Genomic sequence
						
							ATGGCCTTTGAACTCTATGGTATGTTGGCTGGAAATGTGAGCCCGACGACTGGTGAAAATGTTA
AACCAGCTTATGGTGGAGAAGAAGAAGCCTTCTTGAAAAGAGTTGTGACTCCAATCTACAAAGT
TATAGAGAAGGTACAATTTTAACTTCTTTTGCCCACTGTTATGCCTGCATCATAGTTATATCCT
TTGCACCTTTTACATAGGAAGTAGAGAGGAGCAAGACCATGAAATCAAAGCACTCACACTGGAG
AAACTACGATGATCTTAATGAGTACTTTTGGTAAGGGCTGATCTGATCACTTAGTTTTTTTTAT
ATAGTTGCATGAACCTGTATATTGAGGAATGCCATGCAACTATTTTTGCACTGCTACTCAGGTC
AAGAGATTGCTTCCGATTGGGATGGCCTATGCGATCTGATGCAGATTTTTTCAAGACTCCAAAT
GTTCCTCTTCACCATGTGGATGGAGTATGTACCTTGTGACAATGAATATACTTACGGCATTTGT
CAAATCAATTAGGTTTGAGCTAGGTAATATTTTGTTACATGAGTTATGAGTATCATAATGGGAG
CGTTGATAAAAACTAGAGTACTAGACACCTTTATAGCTTTCCATAGACCTGATACTATAGGCAT
TTGGCAAATATACGTCCGTTCTAACTATTTCTGAGAAGAAACTTCATCCGAGAATGGGAATGTA
AAACGTTCTTGAGTGTGCAGCAGTCAAACAAGATTCATCTGATACTAGTCAGTATGTTTTTGCT
ATTAATGCAAAAAGGCGTTTGCACTATGTAGCAATGTGGGTATGATACTGTACCTAAGCTACTT
CTTTTTTTTGTTTTTCATTTGGTATTTTTTGACCTTTTATTTAGCGAAGATTCTTACTAAGGGT
TTGATTCTATGCCAAAGTTCAGTTCCAATCAGATGAATTTAAGTCAAGCATAGAGGGAGAACTT
TCTACTTTCTAGGGAAGGAGACAAGTTAGCTGCGTGCTCTAGCTTTTGCAGTTTAACCTACAGG
GCACACCAGAGCTGGTGAAACGCGTGGATACACTATTTTGATAAATGGTACTGTTGTTTCTTAC
TTCGTTCCAGGAGGACAGGACTGTGGGTAATGGCAATTGGATGGGAAAAGTCAACTTTGTTGAA
ATACGGTCATTTTGGCACATCTTCCGCAGCTTTGATAGGATGTGGAGCTTCTTAATTTTATCTT
TACAGGTTTGCAATTCTCTGGTTTGTTCGAGTTCTTTTGGTTACTCTTTTTTTCGATGCGATCT
GTTTCCTTATCCTTAATTGTTACAATTCATGTATACTTACACAGGCTATGGTTATAATTGCTTG
GAATGGTGGCACACCAAGTGATATTTTTGATAGAGGAGTATTCAAACAGGTTTTGAGCATATTT
ATAACTGCGGCTATACTGAAACTGGGTCAAG
						
					

			
		

Sequences
Splice junction sequence	GCTTGGAATGGTGGCACACCAAGTGATATTTTTGATAGAGGAGTATTCAAACAGGTTTTGAGCA TATTTATAACTGCGGCTATACTGAAACTGGGTCAAGatggcctttgaactctatggtatgttgg ctggaaatgtgagcccgacgactggtgaaaatgttaaaccagcttatggtggagaagaagaagc cttcttga
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: 544 Transcript exons: 223233042-223233179,223233251-223233327,223233423-223233 513,223234140-223234262,223234366-223234480 ATGGCCTTTGAACTCTATGGTATGTTGGCTGGAAATGTGAGCCCGACGACTGGTGAAAATGTTA AACCAGCTTATGGTGGAGAAGAAGAAGCCTTCTTGAAAAGAGTTGTGACTCCAATCTACAAAGT TATAGAGAAGGAAGTAGAGAGGAGCAAGACCATGAAATCAAAGCACTCACACTGGAGAAACTAC GATGATCTTAATGAGTACTTTTGGTCAAGAGATTGCTTCCGATTGGGATGGCCTATGCGATCTG ATGCAGATTTTTTCAAGACTCCAAATGTTCCTCTTCACCATGTGGATGGAGAGGACAGGACTGT GGGTAATGGCAATTGGATGGGAAAAGTCAACTTTGTTGAAATACGGTCATTTTGGCACATCTTC CGCAGCTTTGATAGGATGTGGAGCTTCTTAATTTTATCTTTACAGGCTATGGTTATAATTGCTT GGAATGGTGGCACACCAAGTGATATTTTTGATAGAGGAGTATTCAAACAGGTTTTGAGCATATT TATAACTGCGGCTATACTGAAACTGGGTCAAG
Genomic sequence	ATGGCCTTTGAACTCTATGGTATGTTGGCTGGAAATGTGAGCCCGACGACTGGTGAAAATGTTA AACCAGCTTATGGTGGAGAAGAAGAAGCCTTCTTGAAAAGAGTTGTGACTCCAATCTACAAAGT TATAGAGAAGGTACAATTTTAACTTCTTTTGCCCACTGTTATGCCTGCATCATAGTTATATCCT TTGCACCTTTTACATAGGAAGTAGAGAGGAGCAAGACCATGAAATCAAAGCACTCACACTGGAG AAACTACGATGATCTTAATGAGTACTTTTGGTAAGGGCTGATCTGATCACTTAGTTTTTTTTAT ATAGTTGCATGAACCTGTATATTGAGGAATGCCATGCAACTATTTTTGCACTGCTACTCAGGTC AAGAGATTGCTTCCGATTGGGATGGCCTATGCGATCTGATGCAGATTTTTTCAAGACTCCAAAT GTTCCTCTTCACCATGTGGATGGAGTATGTACCTTGTGACAATGAATATACTTACGGCATTTGT CAAATCAATTAGGTTTGAGCTAGGTAATATTTTGTTACATGAGTTATGAGTATCATAATGGGAG CGTTGATAAAAACTAGAGTACTAGACACCTTTATAGCTTTCCATAGACCTGATACTATAGGCAT TTGGCAAATATACGTCCGTTCTAACTATTTCTGAGAAGAAACTTCATCCGAGAATGGGAATGTA AAACGTTCTTGAGTGTGCAGCAGTCAAACAAGATTCATCTGATACTAGTCAGTATGTTTTTGCT ATTAATGCAAAAAGGCGTTTGCACTATGTAGCAATGTGGGTATGATACTGTACCTAAGCTACTT CTTTTTTTTGTTTTTCATTTGGTATTTTTTGACCTTTTATTTAGCGAAGATTCTTACTAAGGGT TTGATTCTATGCCAAAGTTCAGTTCCAATCAGATGAATTTAAGTCAAGCATAGAGGGAGAACTT TCTACTTTCTAGGGAAGGAGACAAGTTAGCTGCGTGCTCTAGCTTTTGCAGTTTAACCTACAGG GCACACCAGAGCTGGTGAAACGCGTGGATACACTATTTTGATAAATGGTACTGTTGTTTCTTAC TTCGTTCCAGGAGGACAGGACTGTGGGTAATGGCAATTGGATGGGAAAAGTCAACTTTGTTGAA ATACGGTCATTTTGGCACATCTTCCGCAGCTTTGATAGGATGTGGAGCTTCTTAATTTTATCTT TACAGGTTTGCAATTCTCTGGTTTGTTCGAGTTCTTTTGGTTACTCTTTTTTTCGATGCGATCT GTTTCCTTATCCTTAATTGTTACAATTCATGTATACTTACACAGGCTATGGTTATAATTGCTTG GAATGGTGGCACACCAAGTGATATTTTTGATAGAGGAGTATTCAAACAGGTTTTGAGCATATTT ATAACTGCGGCTATACTGAAACTGGGTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.147533008

Conservation Information
Conserved circRNAs	NA
PMCS	0.147533008

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							223233043-223233049(+)
						
						Potential amino acid sequence
						
							MAFELYGMLAGNVSPTTGENVKPAYGGEEEAFLKRVVTPIYKVIEKEVERSKTMKSKHSHWRNY
DDLNEYFWSRDCFRLGWPMRSDADFFKTPNVPLHHVDGEDRTVGNGNWMGKVNFVEIRSFWHIF
RSFDRMWSFLILSLQAMVIIAWNGGTPSDIFDRGVFKQVLSIFITAAILKLGQDGL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	223233043-223233049(+)
Potential amino acid sequence	MAFELYGMLAGNVSPTTGENVKPAYGGEEEAFLKRVVTPIYKVIEKEVERSKTMKSKHSHWRNY DDLNEYFWSRDCFRLGWPMRSDADFFKTPNVPLHHVDGEDRTVGNGNWMGKVNFVEIRSFWHIF RSFDRMWSFLILSLQAMVIIAWNGGTPSDIFDRGVFKQVLSIFITAAILKLGQDGL*(+)
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 Zm00001d018560_circ_g.1

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