Plant Circular RNA Database

Detail information of Zm00001d011512_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d011512_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009735
					
						Alias
						Zm08circ00060, GRMZM2G013625_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 152929363-152930309  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d011512						
					
						Parent gene annotation
						
							AMSH-like ubiquitin thioesterase 2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d011512_T007:2
Zm00001d011512_T001:4
Zm00001d011512_T004:5
Zm00001d011512_T003:4
Zm00001d011512_T005:4
Zm00001d011512_T002:5
Zm00001d011512_T006:4

General Information
CircRNA Name	Zm00001d011512_circ_g.1
ID in PlantcircBase	zma_circ_009735
Alias	Zm08circ00060, GRMZM2G013625_C1
Organism	Zea mays
Position	chr8: 152929363-152930309 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d011512
Parent gene annotation	AMSH-like ubiquitin thioesterase 2
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d011512_T007:2 Zm00001d011512_T001:4 Zm00001d011512_T004:5 Zm00001d011512_T003:4 Zm00001d011512_T005:4 Zm00001d011512_T002:5 Zm00001d011512_T006:4

			
						 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  
						
							AAGTCTTCCTTTCTTTTCCAAATAGTGTCAGGCTGTTAGTGAGGAGGAGATACATGCCGTGTTA
TCAGAGCAGTCACTTTATCCTGCAGGGTGGATTCATgctgaaattttggtgtccttgctcagcc
atgggtagtaggaggtatgcagtgctttaccttctgtagcggtcgacaattttgtttatgatac
atcatgac

						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
						
							GCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGGTATGCAGTGCTTTACCTTCTG
TAGCGGTCGACAATTTTGTTTATGATACATCATGACATGATCAATGCAAAATTGGCAGATATGA
CATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATCAATGTATCTGGATGCTCAA
CAAATCGTCAGCTGCCAAACTAGAGTGGGAGACCACGATGTTGGTTCCTGTGCTGTGAAGCATC
ACTTCCCGTCTCCAATCGTATCTTGGATAGAAGATCTTTCCAGCTTTGGCAATGCTTCTTTTAA
TCCTGTCTCTGAATATGTGGATGAGCAAGCCAGAGCTTCAGTGGGACAGTCTTCAGCATCAAGT
AATTTGCATGACATGCAAATAGTACGTTCTCTTTCGTTCCCCATCATTTTCTTTTAAGAATATA
CAGTGTTTCTTGGAGGATGGTAAGACTGAAGATTGAGATGAAATAACATCCTTACATGTTATTC
AGTCAGTGAGATTGACAGCCGAATTCATGGAGCTTGCAAAGGAGAATACAAGCAATAATCTAGA
GACTTGTGGAATTCTTGGTGCTTCATTTGTAAGTGAAGCGGGCAACAAGTTACCTATGTGACAA
GAATACCTAATTGTCAGATTAGATCTTGAGTATTTTATGTTTCTATGCAGAGGGATGGAACTTA
TTTTGTCACGATGTTGATTATACCAAAGCAAGAAGGAACTGCTCACTCAGTATGTCAGTAACTG
AGTGGTTTCTAACATTATTCTTAATATATTTTTGTTAGTTTATTATATGTCATGACAACTATCT
AGCTATCCCATTCTGAAGTCTTCCTTTCTTTTCCAAATAGTGTCAGGCTGTTAGTGAGGAGGAG
ATACATGCCGTGTTATCAGAGCAGTCACTTTATCCTGCAGGGTGGATTCAT

Sequences
Splice junction sequence	AAGTCTTCCTTTCTTTTCCAAATAGTGTCAGGCTGTTAGTGAGGAGGAGATACATGCCGTGTTA TCAGAGCAGTCACTTTATCCTGCAGGGTGGATTCATgctgaaattttggtgtccttgctcagcc atgggtagtaggaggtatgcagtgctttaccttctgtagcggtcgacaattttgtttatgatac atcatgac
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	GCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGGTATGCAGTGCTTTACCTTCTG TAGCGGTCGACAATTTTGTTTATGATACATCATGACATGATCAATGCAAAATTGGCAGATATGA CATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATCAATGTATCTGGATGCTCAA CAAATCGTCAGCTGCCAAACTAGAGTGGGAGACCACGATGTTGGTTCCTGTGCTGTGAAGCATC ACTTCCCGTCTCCAATCGTATCTTGGATAGAAGATCTTTCCAGCTTTGGCAATGCTTCTTTTAA TCCTGTCTCTGAATATGTGGATGAGCAAGCCAGAGCTTCAGTGGGACAGTCTTCAGCATCAAGT AATTTGCATGACATGCAAATAGTACGTTCTCTTTCGTTCCCCATCATTTTCTTTTAAGAATATA CAGTGTTTCTTGGAGGATGGTAAGACTGAAGATTGAGATGAAATAACATCCTTACATGTTATTC AGTCAGTGAGATTGACAGCCGAATTCATGGAGCTTGCAAAGGAGAATACAAGCAATAATCTAGA GACTTGTGGAATTCTTGGTGCTTCATTTGTAAGTGAAGCGGGCAACAAGTTACCTATGTGACAA GAATACCTAATTGTCAGATTAGATCTTGAGTATTTTATGTTTCTATGCAGAGGGATGGAACTTA TTTTGTCACGATGTTGATTATACCAAAGCAAGAAGGAACTGCTCACTCAGTATGTCAGTAACTG AGTGGTTTCTAACATTATTCTTAATATATTTTTGTTAGTTTATTATATGTCATGACAACTATCT AGCTATCCCATTCTGAAGTCTTCCTTTCTTTTCCAAATAGTGTCAGGCTGTTAGTGAGGAGGAG ATACATGCCGTGTTATCAGAGCAGTCACTTTATCCTGCAGGGTGGATTCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.173730729

Conservation Information
Conserved circRNAs	NA
PMCS	0.173730729

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							152929392-152929395(+)
152930264-152929395(+)
152929495-152930285(-)
						
						Potential amino acid sequence
						
							MGSRRYDIDTRRCGIHSRPTKSMYLDAQQIVSCQTRVGDHDVGSCAVKHHFPSPIVSWIEDLSS
FGNASFNPVSEYVDEQARASVGQSSASSNLHDMQISVRLTAEFMELAKENTSNNLETCGILGAS
FRDGTYFVTMLIIPKQEGTAHSCQAVSEEEIHAVLSEQSLYPAGWIHAEILVSLLSHG*(+)
MPCYQSSHFILQGGFMLKFWCPCSAMGSRRYDIDTRRCGIHSRPTKSMYLDAQQIVSCQTRVGD
HDVGSCAVKHHFPSPIVSWIEDLSSFGNASFNPVSEYVDEQARASVGQSSASSNLHDMQISVRL
TAEFMELAKENTSNNLETCGILGASFRDGTYFVTMLIIPKQEGTAHSCQAVSEEEIHAVLSEQS
LYPAGWIHAEILVSLLSHG*(+)
MSYLLLPMAEQGHQNFSMNPPCRIK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	152929392-152929395(+) 152930264-152929395(+) 152929495-152930285(-)
Potential amino acid sequence	MGSRRYDIDTRRCGIHSRPTKSMYLDAQQIVSCQTRVGDHDVGSCAVKHHFPSPIVSWIEDLSS FGNASFNPVSEYVDEQARASVGQSSASSNLHDMQISVRLTAEFMELAKENTSNNLETCGILGAS FRDGTYFVTMLIIPKQEGTAHSCQAVSEEEIHAVLSEQSLYPAGWIHAEILVSLLSHG(+) MPCYQSSHFILQGGFMLKFWCPCSAMGSRRYDIDTRRCGIHSRPTKSMYLDAQQIVSCQTRVGD HDVGSCAVKHHFPSPIVSWIEDLSSFGNASFNPVSEYVDEQARASVGQSSASSNLHDMQISVRL TAEFMELAKENTSNNLETCGILGASFRDGTYFVTMLIIPKQEGTAHSCQAVSEEEIHAVLSEQS LYPAGWIHAEILVSLLSHG(+) MSYLLLPMAEQGHQNFSMNPPCRIK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d011512_circ_g.1

Address

Any questions?

Supported by