Plant Circular RNA Database

Detail information of Zm00001d039693_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d039693_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007496
					
						Alias
						zma_circ_0001147
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 12067000-12078170  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d039693						
					
						Parent gene annotation
						
							Protein RST1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d039693_circ_g.1 Zm00001d039693_circ_g.2 Zm00001d039693_circ_g.4 Zm00001d039693_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
						Zm00001d039693_T041:12
Zm00001d039693_T012:12
Zm00001d039693_T033:12
Zm00001d039693_T049:12
Zm00001d039693_T080:11
Zm00001d039693_T053:12
Zm00001d039693_T030:12
Zm00001d039693_T001:12
Zm00001d039693_T013:12
Zm00001d039693_T061:12
Zm00001d039693_T048:12
Zm00001d039693_T007:12
Zm00001d039693_T047:12
Zm00001d039693_T068:12
Zm00001d039693_T006:12
Zm00001d039693_T082:8
Zm00001d039693_T017:12
Zm00001d039693_T079:12
Zm00001d039693_T015:12
Zm00001d039693_T043:12
Zm00001d039693_T059:12
Zm00001d039693_T004:12
Zm00001d039693_T014:12
Zm00001d039693_T036:12
Zm00001d039693_T065:12
Zm00001d039693_T035:12
Zm00001d039693_T070:12
Zm00001d039693_T062:12
Zm00001d039693_T077:12
Zm00001d039693_T010:12
Zm00001d039693_T073:12
Zm00001d039693_T005:12
Zm00001d039693_T011:12
Zm00001d039693_T037:12
Zm00001d039693_T025:12
Zm00001d039693_T055:12
Zm00001d039693_T002:12
Zm00001d039693_T008:12
Zm00001d039693_T064:12
Zm00001d039693_T054:12
Zm00001d039693_T069:12
Zm00001d039693_T016:12
Zm00001d039693_T009:12
Zm00001d039693_T074:12

General Information
CircRNA Name	Zm00001d039693_circ_g.3
ID in PlantcircBase	zma_circ_007496
Alias	zma_circ_0001147
Organism	Zea mays
Position	chr3: 12067000-12078170 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d039693
Parent gene annotation	Protein RST1
Parent gene strand	+
Alternative splicing	Zm00001d039693_circ_g.1 Zm00001d039693_circ_g.2 Zm00001d039693_circ_g.4 Zm00001d039693_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	Zm00001d039693_T041:12 Zm00001d039693_T012:12 Zm00001d039693_T033:12 Zm00001d039693_T049:12 Zm00001d039693_T080:11 Zm00001d039693_T053:12 Zm00001d039693_T030:12 Zm00001d039693_T001:12 Zm00001d039693_T013:12 Zm00001d039693_T061:12 Zm00001d039693_T048:12 Zm00001d039693_T007:12 Zm00001d039693_T047:12 Zm00001d039693_T068:12 Zm00001d039693_T006:12 Zm00001d039693_T082:8 Zm00001d039693_T017:12 Zm00001d039693_T079:12 Zm00001d039693_T015:12 Zm00001d039693_T043:12 Zm00001d039693_T059:12 Zm00001d039693_T004:12 Zm00001d039693_T014:12 Zm00001d039693_T036:12 Zm00001d039693_T065:12 Zm00001d039693_T035:12 Zm00001d039693_T070:12 Zm00001d039693_T062:12 Zm00001d039693_T077:12 Zm00001d039693_T010:12 Zm00001d039693_T073:12 Zm00001d039693_T005:12 Zm00001d039693_T011:12 Zm00001d039693_T037:12 Zm00001d039693_T025:12 Zm00001d039693_T055:12 Zm00001d039693_T002:12 Zm00001d039693_T008:12 Zm00001d039693_T064:12 Zm00001d039693_T054:12 Zm00001d039693_T069:12 Zm00001d039693_T016:12 Zm00001d039693_T009:12 Zm00001d039693_T074:12

			
						 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  
						
							CAAGCAATGGTCAGCAGCTCTCTCTCTTGGATTAATATTCAATTGTTTTCATCCTACGGACAAA
AAGAGCAGACTTCAGGTTATTAATGGGTTTCTTGAGctcagtttgctagagtcattgccatcac
ttgctatacatggttttgttcttccactagctctgcaatggatatcgccaatgcttaaaaggga
ctcaaatt

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CAAGCAATGGTCAGCAGCTCTCTCTCTTGGATTAATATTCAATTGTTTTCATCCTACGGACAAA AAGAGCAGACTTCAGGTTATTAATGGGTTTCTTGAGctcagtttgctagagtcattgccatcac ttgctatacatggttttgttcttccactagctctgcaatggatatcgccaatgcttaaaaggga ctcaaatt
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.015523933

Conservation Information
Conserved circRNAs	NA
PMCS	0.015523933

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							12067079-12078167(+)
12070477-12078148(-)
						
					

						Potential amino acid sequence
						
							MLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCKQ
NPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVAH
SLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQDA
IPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRAV
FKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALLA
LQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKILCDQVPVSTPQVVVNIALVIGALA
LIVPPTAHLVVSSVSDFLLKWLLQYEHEHKQWSAALSLGLIFNCFHPTDKKSRLQVINGFLELS
LLESLPSLAIHGFVLPLALQWISPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPEN
FSNFISDREISASIATSIRDVCKQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVV
DFYTAWKVISKQVLDYYVEPAVAHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDP
LWDKARGTAFHSLSNYKVSLIQDAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRR
RVTTDKRTAVHKFEKLLEVFPRAVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSA
FEQAFVEIAESMYVSRNIVVALLALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKI
LCDQVPVSTPQVVVNIALVIGALALIVPPTAHLVVSSVSDFLLKWLLQYEHEHKQWSAALSLGL
IFNCFHPTDKKSRLQVINGFLELSLLESLPSLAIHGFVLPLALQWISPMLKRDSNSVLYAMAVR
LLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCKQNPDRGVDIILSVSFCI
ESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVAHSLCILLRCGAMDAEAY
SVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQDAIPDFWKLNYEFFTNEH
NLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRAVFKGMLSHHQLPGAALL
TLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALLALQSWKSFVSNWMQAVV
ALLDTKDSSKLNKAMKAANDIFKILCDQVPVSTPQVVVNIALVIGALALIVPPTAHLVVSSVSD
FLLKWLLQYEHEHKQWSAALSLGLIFNCFHPTDKKSRLQVINGFLELSLLESLPSLAIHGFVLP
LALQWISPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIAT
SIRDVCKQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDY
YVEPAVAHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNY
KVSLIQDAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKL
LEVFPRAVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSR
NIVVALLALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKILCDQVPVSTPQVVVNI
ALVIGALALIVPPTAHLVVSSVSDFLLKWLLQYEHEHKQWSAALSLGLIFNCFHPTDKKSRLQV
INGFLE(+)
MKLEKFSGSRTTCKFGNAQSVTAHILQSNRTAIAYKTEFESLLSIGDIHCRASGRTKPCIASDG
NDSSKLSSRNPLIT*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	12067079-12078167(+) 12070477-12078148(-)
Potential amino acid sequence	MLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCKQ NPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVAH SLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQDA IPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRAV FKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALLA LQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKILCDQVPVSTPQVVVNIALVIGALA LIVPPTAHLVVSSVSDFLLKWLLQYEHEHKQWSAALSLGLIFNCFHPTDKKSRLQVINGFLELS LLESLPSLAIHGFVLPLALQWISPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPEN FSNFISDREISASIATSIRDVCKQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVV DFYTAWKVISKQVLDYYVEPAVAHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDP LWDKARGTAFHSLSNYKVSLIQDAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRR RVTTDKRTAVHKFEKLLEVFPRAVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSA FEQAFVEIAESMYVSRNIVVALLALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKI LCDQVPVSTPQVVVNIALVIGALALIVPPTAHLVVSSVSDFLLKWLLQYEHEHKQWSAALSLGL IFNCFHPTDKKSRLQVINGFLELSLLESLPSLAIHGFVLPLALQWISPMLKRDSNSVLYAMAVR LLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCKQNPDRGVDIILSVSFCI ESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVAHSLCILLRCGAMDAEAY SVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQDAIPDFWKLNYEFFTNEH NLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRAVFKGMLSHHQLPGAALL TLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALLALQSWKSFVSNWMQAVV ALLDTKDSSKLNKAMKAANDIFKILCDQVPVSTPQVVVNIALVIGALALIVPPTAHLVVSSVSD FLLKWLLQYEHEHKQWSAALSLGLIFNCFHPTDKKSRLQVINGFLELSLLESLPSLAIHGFVLP LALQWISPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIAT SIRDVCKQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDY YVEPAVAHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNY KVSLIQDAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKL LEVFPRAVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSR NIVVALLALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKILCDQVPVSTPQVVVNI ALVIGALALIVPPTAHLVVSSVSDFLLKWLLQYEHEHKQWSAALSLGLIFNCFHPTDKKSRLQV INGFLE(+) MKLEKFSGSRTTCKFGNAQSVTAHILQSNRTAIAYKTEFESLLSIGDIHCRASGRTKPCIASDG NDSSKLSSRNPLIT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d039693_circ_g.3

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