Plant Circular RNA Database

Detail information of Zm00001d005127_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d005127_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007289
					
						Alias
						zma_circ_0000819
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 159755495-159759177  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d005127						
					
						Parent gene annotation
						
							E3 ubiquitin-protein ligase UPL1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d005127_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
						Zm00001d005127_T009:9
Zm00001d005127_T002:9
Zm00001d005127_T001:9
Zm00001d005127_T006:9
Zm00001d005127_T023:9
Zm00001d005127_T011:9
Zm00001d005127_T012:9
Zm00001d005127_T021:9
Zm00001d005127_T003:9
Zm00001d005127_T014:9
Zm00001d005127_T018:9
Zm00001d005127_T004:9
Zm00001d005127_T008:9
Zm00001d005127_T019:9
Zm00001d005127_T016:9
Zm00001d005127_T024:9
Zm00001d005127_T026:4

General Information
CircRNA Name	Zm00001d005127_circ_g.4
ID in PlantcircBase	zma_circ_007289
Alias	zma_circ_0000819
Organism	Zea mays
Position	chr2: 159755495-159759177 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d005127
Parent gene annotation	E3 ubiquitin-protein ligase UPL1
Parent gene strand	+
Alternative splicing	Zm00001d005127_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	Zm00001d005127_T009:9 Zm00001d005127_T002:9 Zm00001d005127_T001:9 Zm00001d005127_T006:9 Zm00001d005127_T023:9 Zm00001d005127_T011:9 Zm00001d005127_T012:9 Zm00001d005127_T021:9 Zm00001d005127_T003:9 Zm00001d005127_T014:9 Zm00001d005127_T018:9 Zm00001d005127_T004:9 Zm00001d005127_T008:9 Zm00001d005127_T019:9 Zm00001d005127_T016:9 Zm00001d005127_T024:9 Zm00001d005127_T026:4

			
						 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  
						
							CATTCATGAAGCTAGTGAAGGTTTTGGCTTTGGTTGATTGGTTCCTCGGGAGGTTGTAAAGCGT
GCACTGGGTCATTGGTTTTCTGCTTGACATGTACAGgtgtaccaccacttgtaacacgccgact
tcttgaaatattgacatatcttgcttcagctagtccttctgttgtggatcttttgatctatttc
aatccttc

									
								

					

						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
						
							GTGTACCACCACTTGTAACACGCCGACTTCTTGAAATATTGACATATCTTGCTTCAGCTAGTCC
TTCTGTTGTGGATCTTTTGATCTATTTCAATCCTTCAGCTAGTCCAAACTGTTTGACATTACAG
CACAATAAAGAGACATCTCAAGAAAGTTCAATGCAGAATATGATGCCACCATATTCAAAGGCTT
ATACACCTATTATATTGCTTCTTAAGCTTCTAAATAAACCCTTATTTCTGCGGAGTCGAGTATA
CCTTGAGAAGGTATTTATCAGCACTTGTTTTAGTGTATGGTAGCTTTTGGTTCTCTTCAAATAT
TTCTCATACCTTTTCATTTTGTACTCCAGGTGTTGTATTTGCTTGAAGTAGTTATTAACAATGC
TGCATCCCAAGTTGATTGTCCACCTCACTCTGTACAGATAACTAACAATTCAGATATTGAATTC
GTTGATGGGACACCATATCAAACACAGGTGGAACCATCTACTTTGGAACAAGGTCATATCCCGG
ATAATAACCAAAGTAGAGATGTTGAGGTCCCACCATCTTGTGCTAAACTGGATGTTAATGTGCA
TGCAATCCTTACCCAACTTCCTGATGCTGAATTGCATAATCTGTGCAATATTCTTGCACTTGAG
GGGTTAGTGTTTGCCTTACCCTTCTATTTTATTTACTTAATTTTGGATAGCTTCTACAAATGAT
GATTGACTACAAAGGTTGAGTGTTCATGTACCTATTGTATATTTGTTTCTTAGCTTTGATGATC
TAATTAGAATGTTACTCCAGGGGCACATTGTTTTCCTTCCATCTCTTGTGGAATTTGTTTCTTG
TATCCATAACAGTGGCCACCATTTGTTTTCTAGATTAATGTATGCAGCAAAACTTGTCCATGTG
CAGTAATTTGAAACTAATTGATATGCTTTATATAAATGGTACCTTTTGCTGCTCGAATACTCGA
AAAAGTTATTGTTTGAGTGTAAATCTGATGTGTGATATGTGGAATGTTCATTCTTAATTCATAG
TTTAGATATTTGAAAATTTTGAAAAATGCCCTTTTCTCAGAGCTATAGACAAATATGCTTATGT
TTTGTTGTTGAAATATTCAGTCTTCCAGATAAAGTGTACTCACTTGCGGCAGAGGTGGTGAAAA
AATTGGCTAGTGTTGCAGCATCGCATCGGAAATTCTTTTCCATTGAGTTAGCTGGTGTTGCTCA
GAGTTTAAGTTCTTCTGCCGTTGAGGAGCTTGTAACCCTGAAGAACACTCAAATGCTTGGGCTC
AGTACTTGCTCTATGGCTGGAGCTGCGATTTTGCGGATACTGCAAGTCCTATCTACACTAACTT
CGTGTGTGATGGATAGTAGACATGAGCAAGATTTAGGACAGGAAGAGCAGTCTTTTTTGTGGGA
TCTGAATGCTGGTCTTCAACCTTTGTGGCAAGAGTTAAGTGATTGTATAAGTGCCACAGAGGCA
AAACTTGTACACAATTCATCATTCGCTTCCCATGCCCCATCGGTGGATGCTTTAGCAGTTAGTG
CTTCATCATCTGTTTCTTCACCGCTTCCTCCAGGCACTCAGCGCTTGTTGCCGTTCATAGAATC
ATTCTTTGTCCTATGTGAGAAGCTTCAAACAAATCAACCAGTTGCACAATCAGATTACACTGTT
ATTGCCCCTGAAGTAAAAGAATCTGCTGGAAGTTCATCTTCACCTTCACTGAAGACTGGTGGAA
CTTGCAATGTTACTTTTATAAGGATTGCTGAAAAGCATCGACGGCTGCTCAACGTTTTCATTAG
ACAAAACCCAAGCATACTGGAGAAGTCACTTTCTATGATGTTGAAAGTGCCAAGGCTGATAGAT
TTTGACAACAAACGTGCTTACTTTCGGTCACGTATCAGACAGCAGCATGATCAGCACCTTCCAG
CTCCTCTACACATTAGTGTTCGCAGGGCTTATGTTTTGGATGACTCATATAATCAGTTGAGATT
ACGTCGTACCCAGGATCTCAAAGGTCGTTTGACTGTGCAATTTCAAGGGGAAGAGGGCATAGAT
GCAGGAGGACTAACTAGGGAGTGGTATCAACTGCTCTCTAGAGTTATTTTTGACAAAGGAACTC
TTCTTTTCACTACAGTTGGAAACAATGCGACTTTCCAGCCTAATCCAAACTCAGATTTTCAAAC
GGAGCACCTTTCTTACTTCAAGTTTGTTGGTCGAGTGGTAATTTCTTGACAATATCCACGATAG
TTCAATACTGCATCATTTGTTTTCCCTTCTTCTGAGGCTTAGTTATTTTCACAGGTTGCTAAAG
CGTTATTTGATGGCCAATTGTTGGACGTCCACTTCACCCGTTCATTTTACAAACATATCTTAGG
TGCTAAAGTAACATATCATGATATAGAGGCTATTGATCCTGATTACTACAGAAATTTGAAGTGG
ATGCTGGAGGTCTGGATTCAATTTCTGCAGTTTCATATTTATTAATTTATTTATGTGGATCTAT
GCAGATCCTTAATCATGTGTTTTTTGAACAGAATGATGTAAGTGACCTTCCCTATTTAACATTT
AGCATGGATCCTGATGAGGAAAAACATATTCTCTATGAGAAGACCGAGGTATTGAAAAGCCATC
ACGGGTTTTAGCCGAAACCTTTTCTGCTTGCGTCAGCTATTATCTTAGCTGTGCAGTTTAACAA
ATTTTCAATTCAGGTTACCGATTATGAGCTAAAACCGGGTGGAAGAAACATCAGGGTTACTGAG
GAAACAAAACAAGAATATGTTGACCTTGTAGCTGAACATATACTGACCACAGCAATTCGTCCTC
AAATCAATGGTTTCCTTGAAGGCTTCACAGAGTTAGTTCCAAGGGATCTAATATCGCTATTCAA
TGATAAAGAACTTGAACTGCTGATCAGTGGTCTTCCTGAAATTGACTGTAAGTGGGTTTTATCT
GTCAGGAATAATTCATCGTCTTTATTGCCTAAGTTATTTATTTCCTTCCATCTTGTTGTGTTGT
TTTCCCTGCAGTGGATGATCTGAAGGCCAACACGGAATATATAGGATATTCAGCTGCATCTCCT
GTTATCCAGTGGTTCTGGGAAGTTGTTAGAGCATTCAGCAAGGAGGACATGGCGAGACTACTAC
AGTTCGTTACCGGAACATCTAAGGTCAAAAGCCGCTTCACTCTTAATTTTGATGCATTTTAAAA
TAAAACTTCAGTGCAACTATAGTTTCACCTTAGAAGTGTCGCAAATCTTGAACAATATATTTTG
CTCTATAACTTCAATCAATAACACACACAGAATTTATTTCTATAGGTACCATTGGAGGGTTTCA
AAGCGCTACAAGGTATCTCTGGCCCCCAGAGATTTCAGATTTACAAGGCGTATGGATCTCCTGG
TCGACTTCCATCTGCTCATACCTGGTAACATATCAACACTTAATTTACTGCCTTCGACTTGTGT
ACCTCTTTATGCTATTGTCTGCTCGTTTGGTAATTGGGTTAAGTGCACGTTAAATACACAGCTT
TAACCAGTTGGATTTACCGGAATATACCTCAAAGGAGCAATTAGAAGAACGACTGCTTCTTGCC
ATTCATGAAGCTAGTGAAGGTTTTGGCTTTGGTTGATTGGTTCCTCGGGAGGTTGTAAAGCGTG
CACTGGGTCATTGGTTTTCTGCTTGACATGTACAG
						
					

			
		

Sequences
Splice junction sequence	CATTCATGAAGCTAGTGAAGGTTTTGGCTTTGGTTGATTGGTTCCTCGGGAGGTTGTAAAGCGT GCACTGGGTCATTGGTTTTCTGCTTGACATGTACAGgtgtaccaccacttgtaacacgccgact tcttgaaatattgacatatcttgcttcagctagtccttctgttgtggatcttttgatctatttc aatccttc
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	GTGTACCACCACTTGTAACACGCCGACTTCTTGAAATATTGACATATCTTGCTTCAGCTAGTCC TTCTGTTGTGGATCTTTTGATCTATTTCAATCCTTCAGCTAGTCCAAACTGTTTGACATTACAG CACAATAAAGAGACATCTCAAGAAAGTTCAATGCAGAATATGATGCCACCATATTCAAAGGCTT ATACACCTATTATATTGCTTCTTAAGCTTCTAAATAAACCCTTATTTCTGCGGAGTCGAGTATA CCTTGAGAAGGTATTTATCAGCACTTGTTTTAGTGTATGGTAGCTTTTGGTTCTCTTCAAATAT TTCTCATACCTTTTCATTTTGTACTCCAGGTGTTGTATTTGCTTGAAGTAGTTATTAACAATGC TGCATCCCAAGTTGATTGTCCACCTCACTCTGTACAGATAACTAACAATTCAGATATTGAATTC GTTGATGGGACACCATATCAAACACAGGTGGAACCATCTACTTTGGAACAAGGTCATATCCCGG ATAATAACCAAAGTAGAGATGTTGAGGTCCCACCATCTTGTGCTAAACTGGATGTTAATGTGCA TGCAATCCTTACCCAACTTCCTGATGCTGAATTGCATAATCTGTGCAATATTCTTGCACTTGAG GGGTTAGTGTTTGCCTTACCCTTCTATTTTATTTACTTAATTTTGGATAGCTTCTACAAATGAT GATTGACTACAAAGGTTGAGTGTTCATGTACCTATTGTATATTTGTTTCTTAGCTTTGATGATC TAATTAGAATGTTACTCCAGGGGCACATTGTTTTCCTTCCATCTCTTGTGGAATTTGTTTCTTG TATCCATAACAGTGGCCACCATTTGTTTTCTAGATTAATGTATGCAGCAAAACTTGTCCATGTG CAGTAATTTGAAACTAATTGATATGCTTTATATAAATGGTACCTTTTGCTGCTCGAATACTCGA AAAAGTTATTGTTTGAGTGTAAATCTGATGTGTGATATGTGGAATGTTCATTCTTAATTCATAG TTTAGATATTTGAAAATTTTGAAAAATGCCCTTTTCTCAGAGCTATAGACAAATATGCTTATGT TTTGTTGTTGAAATATTCAGTCTTCCAGATAAAGTGTACTCACTTGCGGCAGAGGTGGTGAAAA AATTGGCTAGTGTTGCAGCATCGCATCGGAAATTCTTTTCCATTGAGTTAGCTGGTGTTGCTCA GAGTTTAAGTTCTTCTGCCGTTGAGGAGCTTGTAACCCTGAAGAACACTCAAATGCTTGGGCTC AGTACTTGCTCTATGGCTGGAGCTGCGATTTTGCGGATACTGCAAGTCCTATCTACACTAACTT CGTGTGTGATGGATAGTAGACATGAGCAAGATTTAGGACAGGAAGAGCAGTCTTTTTTGTGGGA TCTGAATGCTGGTCTTCAACCTTTGTGGCAAGAGTTAAGTGATTGTATAAGTGCCACAGAGGCA AAACTTGTACACAATTCATCATTCGCTTCCCATGCCCCATCGGTGGATGCTTTAGCAGTTAGTG CTTCATCATCTGTTTCTTCACCGCTTCCTCCAGGCACTCAGCGCTTGTTGCCGTTCATAGAATC ATTCTTTGTCCTATGTGAGAAGCTTCAAACAAATCAACCAGTTGCACAATCAGATTACACTGTT ATTGCCCCTGAAGTAAAAGAATCTGCTGGAAGTTCATCTTCACCTTCACTGAAGACTGGTGGAA CTTGCAATGTTACTTTTATAAGGATTGCTGAAAAGCATCGACGGCTGCTCAACGTTTTCATTAG ACAAAACCCAAGCATACTGGAGAAGTCACTTTCTATGATGTTGAAAGTGCCAAGGCTGATAGAT TTTGACAACAAACGTGCTTACTTTCGGTCACGTATCAGACAGCAGCATGATCAGCACCTTCCAG CTCCTCTACACATTAGTGTTCGCAGGGCTTATGTTTTGGATGACTCATATAATCAGTTGAGATT ACGTCGTACCCAGGATCTCAAAGGTCGTTTGACTGTGCAATTTCAAGGGGAAGAGGGCATAGAT GCAGGAGGACTAACTAGGGAGTGGTATCAACTGCTCTCTAGAGTTATTTTTGACAAAGGAACTC TTCTTTTCACTACAGTTGGAAACAATGCGACTTTCCAGCCTAATCCAAACTCAGATTTTCAAAC GGAGCACCTTTCTTACTTCAAGTTTGTTGGTCGAGTGGTAATTTCTTGACAATATCCACGATAG TTCAATACTGCATCATTTGTTTTCCCTTCTTCTGAGGCTTAGTTATTTTCACAGGTTGCTAAAG CGTTATTTGATGGCCAATTGTTGGACGTCCACTTCACCCGTTCATTTTACAAACATATCTTAGG TGCTAAAGTAACATATCATGATATAGAGGCTATTGATCCTGATTACTACAGAAATTTGAAGTGG ATGCTGGAGGTCTGGATTCAATTTCTGCAGTTTCATATTTATTAATTTATTTATGTGGATCTAT GCAGATCCTTAATCATGTGTTTTTTGAACAGAATGATGTAAGTGACCTTCCCTATTTAACATTT AGCATGGATCCTGATGAGGAAAAACATATTCTCTATGAGAAGACCGAGGTATTGAAAAGCCATC ACGGGTTTTAGCCGAAACCTTTTCTGCTTGCGTCAGCTATTATCTTAGCTGTGCAGTTTAACAA ATTTTCAATTCAGGTTACCGATTATGAGCTAAAACCGGGTGGAAGAAACATCAGGGTTACTGAG GAAACAAAACAAGAATATGTTGACCTTGTAGCTGAACATATACTGACCACAGCAATTCGTCCTC AAATCAATGGTTTCCTTGAAGGCTTCACAGAGTTAGTTCCAAGGGATCTAATATCGCTATTCAA TGATAAAGAACTTGAACTGCTGATCAGTGGTCTTCCTGAAATTGACTGTAAGTGGGTTTTATCT GTCAGGAATAATTCATCGTCTTTATTGCCTAAGTTATTTATTTCCTTCCATCTTGTTGTGTTGT TTTCCCTGCAGTGGATGATCTGAAGGCCAACACGGAATATATAGGATATTCAGCTGCATCTCCT GTTATCCAGTGGTTCTGGGAAGTTGTTAGAGCATTCAGCAAGGAGGACATGGCGAGACTACTAC AGTTCGTTACCGGAACATCTAAGGTCAAAAGCCGCTTCACTCTTAATTTTGATGCATTTTAAAA TAAAACTTCAGTGCAACTATAGTTTCACCTTAGAAGTGTCGCAAATCTTGAACAATATATTTTG CTCTATAACTTCAATCAATAACACACACAGAATTTATTTCTATAGGTACCATTGGAGGGTTTCA AAGCGCTACAAGGTATCTCTGGCCCCCAGAGATTTCAGATTTACAAGGCGTATGGATCTCCTGG TCGACTTCCATCTGCTCATACCTGGTAACATATCAACACTTAATTTACTGCCTTCGACTTGTGT ACCTCTTTATGCTATTGTCTGCTCGTTTGGTAATTGGGTTAAGTGCACGTTAAATACACAGCTT TAACCAGTTGGATTTACCGGAATATACCTCAAAGGAGCAATTAGAAGAACGACTGCTTCTTGCC ATTCATGAAGCTAGTGAAGGTTTTGGCTTTGGTTGATTGGTTCCTCGGGAGGTTGTAAAGCGTG CACTGGGTCATTGGTTTTCTGCTTGACATGTACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.060883103

Conservation Information
Conserved circRNAs	NA
PMCS	0.060883103

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							159755541-159759057(-)
						
						Potential amino acid sequence
						
							MSIFQEVGVLQVVVHLYMSSRKPMTQCTLYNLPRNQSTKAKTFTSFMNGKKQSFF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	159755541-159759057(-)
Potential amino acid sequence	MSIFQEVGVLQVVVHLYMSSRKPMTQCTLYNLPRNQSTKAKTFTSFMNGKKQSFF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d005127_circ_g.4

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