Plant Circular RNA Database

Detail information of Zm00001d045109_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d045109_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009851
					
						Alias
						zma_circ_0003076
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 13093388-13095342  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d045109						
					
						Parent gene annotation
						
							Putative homeodomain-like transcription factor superfamily prote
in  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d045109_circ_g.1 Zm00001d045109_circ_g.2 Zm00001d045109_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
						Zm00001d045109_T031:5
Zm00001d045109_T025:5
Zm00001d045109_T005:5
Zm00001d045109_T002:5
Zm00001d045109_T022:5
Zm00001d045109_T028:5
Zm00001d045109_T001:5
Zm00001d045109_T015:5
Zm00001d045109_T024:5
Zm00001d045109_T004:5
Zm00001d045109_T032:5
Zm00001d045109_T008:5
Zm00001d045109_T011:1
Zm00001d045109_T007:5
Zm00001d045109_T026:5
Zm00001d045109_T009:5
Zm00001d045109_T016:5
Zm00001d045109_T010:5
Zm00001d045109_T018:5
Zm00001d045109_T012:5
Zm00001d045109_T023:5
Zm00001d045109_T017:5
Zm00001d045109_T034:5
Zm00001d045109_T033:5
Zm00001d045109_T003:5

General Information
CircRNA Name	Zm00001d045109_circ_g.4
ID in PlantcircBase	zma_circ_009851
Alias	zma_circ_0003076
Organism	Zea mays
Position	chr9: 13093388-13095342 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d045109
Parent gene annotation	Putative homeodomain-like transcription factor superfamily prote in
Parent gene strand	+
Alternative splicing	Zm00001d045109_circ_g.1 Zm00001d045109_circ_g.2 Zm00001d045109_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	Zm00001d045109_T031:5 Zm00001d045109_T025:5 Zm00001d045109_T005:5 Zm00001d045109_T002:5 Zm00001d045109_T022:5 Zm00001d045109_T028:5 Zm00001d045109_T001:5 Zm00001d045109_T015:5 Zm00001d045109_T024:5 Zm00001d045109_T004:5 Zm00001d045109_T032:5 Zm00001d045109_T008:5 Zm00001d045109_T011:1 Zm00001d045109_T007:5 Zm00001d045109_T026:5 Zm00001d045109_T009:5 Zm00001d045109_T016:5 Zm00001d045109_T010:5 Zm00001d045109_T018:5 Zm00001d045109_T012:5 Zm00001d045109_T023:5 Zm00001d045109_T017:5 Zm00001d045109_T034:5 Zm00001d045109_T033:5 Zm00001d045109_T003:5

			
						 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  
						
							AGGAGTTGGATGATATTATACGCTATGGATCAAAGGAGCTTTTTGAAGACGAGAATGATGAATC
TCGCCAAATTCATTATGACGAAGCTGCAATTGAGAGgaggcttctagattcatcaggtaagatg
cagctgctggacaagatgatggtgaaactgaaagagcagggtcatagagttctaatttattcac
agttccag

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GAGGCTTCTAGATTCATCAGGTAAGATGCAGCTGCTGGACAAGATGATGGTGAAACTGAAAGAG
CAGGGTCATAGAGTTCTAATTTATTCACAGTTCCAGCACATGTTGGACTTGCTGGAGGACTATT
TAAGTTACAGGGTACTTAGTTATCTTCCCATCGTGACTATGCTAGCTTTACAGGCTAATGTATC
TCATCCACTGTTCTATGAATTATACATGTTTCAGAAATGGACTTATGAACGCATCGATGGCAAG
ATAAGTGGCGCTGATAGGCAGATACGGATAGATCGCTTCAACGCTAAGAATTCAACTAGGTTTT
GCTTTCTTCTTTCTACTAGAGCTGGTGGTCTGGGAATAAACTTGGCAACTGCAGATACTGTAAT
CATCTATGACAGGTGAAAAATCTCTCTGTTTAGACAAAACAGTTAACATAATGGATTCGCTTCA
ATTTCTCACCTATGTATGTACAGTGATTGGAACCCACATGCGGATTTGCAAGCTATGGCAAGAG
CTCATCGCTTAGGACAGACTAGTAAGGTATTTTACCTTACACTTTATATTGTATAAAAAAACAG
ATTTTCAATAAGTTTTGTGGTGATTTTATAATTTTCATCTGTTTTTCTTTTAGGTGATGATATA
CAGGCTTGTTAGCCGAGGTACAATTGAGGAGCGAATGATGCAGCTTACAAAAAAGAAGATTTTA
TTGGAGCACTTAGTTGTTGGTCGACTCACCAAAGCTAATAATGTCAATCAGGTATGTTGACTAC
TTTTTAATGGTGAATTTTGTAAACCATCAACTTAGGTTGATCTTTTATGGCCTAAGCTATTTAT
GAATTCATTTATGGATTGAGGGTTGAGTAGTTACATGTTACTCCCTCCATTTTTTATATTTGTG
GTGTTTTAGTTCAAAAATAAACTAACGGGTGACAAATATTCGAGAACGGAGGTAGTACTAGTAC
CTTCTGTCTGGGATGACATGAAATGAATGTAGCATCTGTTAGTATCATGTCCATTTCTTTGTGT
TACATTTTACAAGGCTTAAAACCTTACACATATTGCCGGAGTTGGTGACTATTTAGTCTTATCT
GTAAATTTAGTTGTTTCTCTTGATGTCAATAGCAATTTATGGTTGTATGAGATTTCGTGGGTTT
GTTAGCATGTGTGCCATATAGGTTTAGCTCCGCTGATGTGTTATGCACTTATAATTCAGACCCA
TTTTGGAGCTGTGATGTGATACACAATGCTAGTTGTTAAGGCCCCATTTGTTTGTTTCATATTC
ATAATCTATGTGCATGCATTAGTCCAGATCAGGCTGGGTGATCTGGTGGGCATTGGTACATGCA
TGGCTGAATAAGAGTTTGATGACCAAGGGTAAGGCACCCCACATCTACTCTTGGCTGGCCAACT
GGGTAGTATCTGCTAGTTATCATGGAAATAAGGTTGGCAACCTCTTTAAGGTTGTCTTCAAGAA
CTAAACATAAAAAGAATGCCATGAAGATGGAACCCAGGATCTCAGGACCTATTTGTCGTAAGAT
TTCTGAATCTTTGCTGGAGCTGGCAACGGGCTGGTTGCTGGTCTCATCCCTACATTATAGTTTT
GTGTATGTTTCTTCCAGACTTTCAACACTTCTCAACTTCTAGAACATGTAACCGGCATGTACAA
ACAGAACAATTTAGAACAGTTCAAAGTGCATGTCCTTACTGCGATGGGACCACACACTTCTGGT
CTCTTTAGGACTTGATTGATTTAATGCAGATTAATAATTAACCCAATTTGCTCTTCTGACCTGC
TAGTGAGCCCTTCATTGGTTTTTAAGTACTAAATAATAAATATGTGTCTTTGCCTATTTTAGGA
GGAGTTGGATGATATTATACGCTATGGATCAAAGGAGCTTTTTGAAGACGAGAATGATGAATCT
CGCCAAATTCATTATGACGAAGCTGCAATTGAGAG
						
					

			
		

Sequences
Splice junction sequence	AGGAGTTGGATGATATTATACGCTATGGATCAAAGGAGCTTTTTGAAGACGAGAATGATGAATC TCGCCAAATTCATTATGACGAAGCTGCAATTGAGAGgaggcttctagattcatcaggtaagatg cagctgctggacaagatgatggtgaaactgaaagagcagggtcatagagttctaatttattcac agttccag
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GAGGCTTCTAGATTCATCAGGTAAGATGCAGCTGCTGGACAAGATGATGGTGAAACTGAAAGAG CAGGGTCATAGAGTTCTAATTTATTCACAGTTCCAGCACATGTTGGACTTGCTGGAGGACTATT TAAGTTACAGGGTACTTAGTTATCTTCCCATCGTGACTATGCTAGCTTTACAGGCTAATGTATC TCATCCACTGTTCTATGAATTATACATGTTTCAGAAATGGACTTATGAACGCATCGATGGCAAG ATAAGTGGCGCTGATAGGCAGATACGGATAGATCGCTTCAACGCTAAGAATTCAACTAGGTTTT GCTTTCTTCTTTCTACTAGAGCTGGTGGTCTGGGAATAAACTTGGCAACTGCAGATACTGTAAT CATCTATGACAGGTGAAAAATCTCTCTGTTTAGACAAAACAGTTAACATAATGGATTCGCTTCA ATTTCTCACCTATGTATGTACAGTGATTGGAACCCACATGCGGATTTGCAAGCTATGGCAAGAG CTCATCGCTTAGGACAGACTAGTAAGGTATTTTACCTTACACTTTATATTGTATAAAAAAACAG ATTTTCAATAAGTTTTGTGGTGATTTTATAATTTTCATCTGTTTTTCTTTTAGGTGATGATATA CAGGCTTGTTAGCCGAGGTACAATTGAGGAGCGAATGATGCAGCTTACAAAAAAGAAGATTTTA TTGGAGCACTTAGTTGTTGGTCGACTCACCAAAGCTAATAATGTCAATCAGGTATGTTGACTAC TTTTTAATGGTGAATTTTGTAAACCATCAACTTAGGTTGATCTTTTATGGCCTAAGCTATTTAT GAATTCATTTATGGATTGAGGGTTGAGTAGTTACATGTTACTCCCTCCATTTTTTATATTTGTG GTGTTTTAGTTCAAAAATAAACTAACGGGTGACAAATATTCGAGAACGGAGGTAGTACTAGTAC CTTCTGTCTGGGATGACATGAAATGAATGTAGCATCTGTTAGTATCATGTCCATTTCTTTGTGT TACATTTTACAAGGCTTAAAACCTTACACATATTGCCGGAGTTGGTGACTATTTAGTCTTATCT GTAAATTTAGTTGTTTCTCTTGATGTCAATAGCAATTTATGGTTGTATGAGATTTCGTGGGTTT GTTAGCATGTGTGCCATATAGGTTTAGCTCCGCTGATGTGTTATGCACTTATAATTCAGACCCA TTTTGGAGCTGTGATGTGATACACAATGCTAGTTGTTAAGGCCCCATTTGTTTGTTTCATATTC ATAATCTATGTGCATGCATTAGTCCAGATCAGGCTGGGTGATCTGGTGGGCATTGGTACATGCA TGGCTGAATAAGAGTTTGATGACCAAGGGTAAGGCACCCCACATCTACTCTTGGCTGGCCAACT GGGTAGTATCTGCTAGTTATCATGGAAATAAGGTTGGCAACCTCTTTAAGGTTGTCTTCAAGAA CTAAACATAAAAAGAATGCCATGAAGATGGAACCCAGGATCTCAGGACCTATTTGTCGTAAGAT TTCTGAATCTTTGCTGGAGCTGGCAACGGGCTGGTTGCTGGTCTCATCCCTACATTATAGTTTT GTGTATGTTTCTTCCAGACTTTCAACACTTCTCAACTTCTAGAACATGTAACCGGCATGTACAA ACAGAACAATTTAGAACAGTTCAAAGTGCATGTCCTTACTGCGATGGGACCACACACTTCTGGT CTCTTTAGGACTTGATTGATTTAATGCAGATTAATAATTAACCCAATTTGCTCTTCTGACCTGC TAGTGAGCCCTTCATTGGTTTTTAAGTACTAAATAATAAATATGTGTCTTTGCCTATTTTAGGA GGAGTTGGATGATATTATACGCTATGGATCAAAGGAGCTTTTTGAAGACGAGAATGATGAATCT CGCCAAATTCATTATGACGAAGCTGCAATTGAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.17206824

Conservation Information
Conserved circRNAs	NA
PMCS	0.17206824

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13093414-13095339(+)
13094133-13093395(+)
13093406-13095260(-)
						
						Potential amino acid sequence
						
							MQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSYRKWTYERIDGKISGADRQIRIDRFNAK
NSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHADLQAMARAHRLGQTSKVMIYRLVSRGT
IEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDIIRYGSKELFEDENDESRQIHYDEAAIE
RRLLDSSGKMQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSYRKWTYERIDGKISGADRQ
IRIDRFNAKNSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHADLQAMARAHRLGQTSKVM
IYRLVSRGTIEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDIIRYGSKELFEDENDESRQ
IHYDEAAIERRLLDSSGKMQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSYRKWTYERID
GKISGADRQIRIDRFNAKNSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHADLQAMARAH
RLGQTSKVMIYRLVSRGTIEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDIIRYGSKELF
EDENDESRQIHYDEAAIERRLLDSSGKMQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSY
RKWTYERIDGKISGADRQIRIDRFNAKNSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHA
DLQAMARAHRLGQTSKVMIYRLVSRGTIEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDI
IRYGSKELFEDENDESRQIHYDEAAIE(+)
MSIRRSWMILYAMDQRSFLKTRMMNLAKFIMTKLQLRGGF*(+)
MNLEASSQLQLRHNEFGEIHHSRLQKAPLIHSV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13093414-13095339(+) 13094133-13093395(+) 13093406-13095260(-)
Potential amino acid sequence	MQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSYRKWTYERIDGKISGADRQIRIDRFNAK NSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHADLQAMARAHRLGQTSKVMIYRLVSRGT IEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDIIRYGSKELFEDENDESRQIHYDEAAIE RRLLDSSGKMQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSYRKWTYERIDGKISGADRQ IRIDRFNAKNSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHADLQAMARAHRLGQTSKVM IYRLVSRGTIEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDIIRYGSKELFEDENDESRQ IHYDEAAIERRLLDSSGKMQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSYRKWTYERID GKISGADRQIRIDRFNAKNSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHADLQAMARAH RLGQTSKVMIYRLVSRGTIEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDIIRYGSKELF EDENDESRQIHYDEAAIERRLLDSSGKMQLLDKMMVKLKEQGHRVLIYSQFQHMLDLLEDYLSY RKWTYERIDGKISGADRQIRIDRFNAKNSTRFCFLLSTRAGGLGINLATADTVIIYDSDWNPHA DLQAMARAHRLGQTSKVMIYRLVSRGTIEERMMQLTKKKILLEHLVVGRLTKANNVNQEELDDI IRYGSKELFEDENDESRQIHYDEAAIE(+) MSIRRSWMILYAMDQRSFLKTRMMNLAKFIMTKLQLRGGF(+) MNLEASSQLQLRHNEFGEIHHSRLQKAPLIHSV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d045109_circ_g.4

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