Plant Circular RNA Database

Detail information of Zm00001d039693_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d039693_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007495
					
						Alias
						zma_circ_0001146, GRMZM2G319169_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 12067000-12072351  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d039693						
					
						Parent gene annotation
						
							Protein RST1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d039693_circ_g.1 Zm00001d039693_circ_g.3 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_T036:10
Zm00001d039693_T043:10
Zm00001d039693_T061:10
Zm00001d039693_T059:10
Zm00001d039693_T064:10
Zm00001d039693_T012:10
Zm00001d039693_T062:10
Zm00001d039693_T074:10
Zm00001d039693_T079:10
Zm00001d039693_T007:10
Zm00001d039693_T014:10
Zm00001d039693_T077:10
Zm00001d039693_T017:10
Zm00001d039693_T069:10
Zm00001d039693_T013:10
Zm00001d039693_T068:10
Zm00001d039693_T002:10
Zm00001d039693_T080:9
Zm00001d039693_T006:10
Zm00001d039693_T001:10
Zm00001d039693_T009:10
Zm00001d039693_T011:10
Zm00001d039693_T049:10
Zm00001d039693_T035:10
Zm00001d039693_T047:10
Zm00001d039693_T055:10
Zm00001d039693_T048:10
Zm00001d039693_T004:10
Zm00001d039693_T015:10
Zm00001d039693_T037:10
Zm00001d039693_T030:10
Zm00001d039693_T033:10
Zm00001d039693_T073:10
Zm00001d039693_T082:6
Zm00001d039693_T005:10
Zm00001d039693_T025:10
Zm00001d039693_T065:10
Zm00001d039693_T016:10
Zm00001d039693_T041:10
Zm00001d039693_T053:10
Zm00001d039693_T008:10
Zm00001d039693_T054:10
Zm00001d039693_T010:10
Zm00001d039693_T070:10

General Information
CircRNA Name	Zm00001d039693_circ_g.2
ID in PlantcircBase	zma_circ_007495
Alias	zma_circ_0001146, GRMZM2G319169_C1
Organism	Zea mays
Position	chr3: 12067000-12072351 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d039693
Parent gene annotation	Protein RST1
Parent gene strand	+
Alternative splicing	Zm00001d039693_circ_g.1 Zm00001d039693_circ_g.3 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_T036:10 Zm00001d039693_T043:10 Zm00001d039693_T061:10 Zm00001d039693_T059:10 Zm00001d039693_T064:10 Zm00001d039693_T012:10 Zm00001d039693_T062:10 Zm00001d039693_T074:10 Zm00001d039693_T079:10 Zm00001d039693_T007:10 Zm00001d039693_T014:10 Zm00001d039693_T077:10 Zm00001d039693_T017:10 Zm00001d039693_T069:10 Zm00001d039693_T013:10 Zm00001d039693_T068:10 Zm00001d039693_T002:10 Zm00001d039693_T080:9 Zm00001d039693_T006:10 Zm00001d039693_T001:10 Zm00001d039693_T009:10 Zm00001d039693_T011:10 Zm00001d039693_T049:10 Zm00001d039693_T035:10 Zm00001d039693_T047:10 Zm00001d039693_T055:10 Zm00001d039693_T048:10 Zm00001d039693_T004:10 Zm00001d039693_T015:10 Zm00001d039693_T037:10 Zm00001d039693_T030:10 Zm00001d039693_T033:10 Zm00001d039693_T073:10 Zm00001d039693_T082:6 Zm00001d039693_T005:10 Zm00001d039693_T025:10 Zm00001d039693_T065:10 Zm00001d039693_T016:10 Zm00001d039693_T041:10 Zm00001d039693_T053:10 Zm00001d039693_T008:10 Zm00001d039693_T054:10 Zm00001d039693_T010:10 Zm00001d039693_T070:10

			
						 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  
						
							ATTTGTTTCCAACTGGATGCAAGCAGTTGTGGCATTGCTTGACACTAAAGACTCGTCAAAGTTG
AACAAAGCAATGAAAGCTGCTAATGATATATTTAAGctcagtttgctagagtcattgccatcac
ttgctatacatggttttgttcttccactagctctgcaatggatatcgccaatgcttaaaaggga
ctcaaatt

									
								

					

						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: 1155
Transcript exons: 12067000-12067100,12068020-12068095,12070441-12070572,12
070651-12070732,12070937-12071009,12071134-12071302,1207
1406-12071536,12071615-12071703,12071931-12072019,120721
39-12072351
CTCAGTTTGCTAGAGTCATTGCCATCACTTGCTATACATGGTTTTGTTCTTCCACTAGCTCTGC
AATGGATATCGCCAATGCTTAAAAGGGACTCAAATTCGGTTTTGTATGCTATGGCTGTTCGATT
ACTCTGCAAGATATGGGCTGTAACCGACTGGGCATTTCCAAACTTACAAGTGGTTCTGGATCCT
GAGAATTTTTCCAATTTCATCTCTGACAGAGAGATCTCTGCAAGTATTGCCACATCAATACGCG
ATGTTTGCAAGCAAAATCCAGATAGAGGCGTTGATATAATATTATCTGTCTCTTTTTGTATTGA
GAGTCGTGATTCTGTGGTTCAAGCTCTTGGCCTCGAGAGCCTCTCGTACCTTTGTGAAGCAGAT
GTGGTCGATTTCTACACGGCGTGGAAAGTTATATCAAAGCAGGTGCTTGATTATTACGTTGAGC
CTGCTGTTGCTCACAGTTTGTGTATTCTGTTGAGGTGCGGAGCGATGGATGCTGAGGCATATTC
TGTAATATCTGGTAACCTTGTAAGAACATTGTGGAGAATTGGAACATCCAAGAAAAATAATCCC
GATCCACTCTGGGATAAAGCAAGAGGAACTGCTTTTCACTCCTTGTCCAACTACAAGGTATCAC
TTATTCAAGATGCTATTCCTGATTTCTGGAAACTAAACTATGAGTTCTTTACGAACGAACATAA
TCTGGCAGTTCTCAAGGCCATGGAGCACCTTCAAGATGAGATCATCAGATATGAGCACATAAAT
CGTCGTCGAGTGACTACTGACAAAAGAACTGCAGTGCATAAATTTGAGAAGCTACTGGAGGTTT
TTCCTCGGGCGGTATTTAAAGGGATGTTATCTCATCATCAGTTGCCTGGTGCTGCTCTTTTAAC
TCTCAATTTTACTCCAAAGGACATACTTAATGAAGGGAAACCTAAGGATTTGCCTAGAGTTCAT
TCCGCTTTTGAGCAAGCTTTTGTGGAAATTGCTGAATCTATGTATGTGTCAAGAAACATAGTGG
TAGCTCTTCTTGCCTTGCAGTCATGGAAGTCATTTGTTTCCAACTGGATGCAAGCAGTTGTGGC
ATTGCTTGACACTAAAGACTCGTCAAAGTTGAACAAAGCAATGAAAGCTGCTAATGATATATTT
AAG
						
					

						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	ATTTGTTTCCAACTGGATGCAAGCAGTTGTGGCATTGCTTGACACTAAAGACTCGTCAAAGTTG AACAAAGCAATGAAAGCTGCTAATGATATATTTAAGctcagtttgctagagtcattgccatcac ttgctatacatggttttgttcttccactagctctgcaatggatatcgccaatgcttaaaaggga ctcaaatt
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: 1155 Transcript exons: 12067000-12067100,12068020-12068095,12070441-12070572,12 070651-12070732,12070937-12071009,12071134-12071302,1207 1406-12071536,12071615-12071703,12071931-12072019,120721 39-12072351 CTCAGTTTGCTAGAGTCATTGCCATCACTTGCTATACATGGTTTTGTTCTTCCACTAGCTCTGC AATGGATATCGCCAATGCTTAAAAGGGACTCAAATTCGGTTTTGTATGCTATGGCTGTTCGATT ACTCTGCAAGATATGGGCTGTAACCGACTGGGCATTTCCAAACTTACAAGTGGTTCTGGATCCT GAGAATTTTTCCAATTTCATCTCTGACAGAGAGATCTCTGCAAGTATTGCCACATCAATACGCG ATGTTTGCAAGCAAAATCCAGATAGAGGCGTTGATATAATATTATCTGTCTCTTTTTGTATTGA GAGTCGTGATTCTGTGGTTCAAGCTCTTGGCCTCGAGAGCCTCTCGTACCTTTGTGAAGCAGAT GTGGTCGATTTCTACACGGCGTGGAAAGTTATATCAAAGCAGGTGCTTGATTATTACGTTGAGC CTGCTGTTGCTCACAGTTTGTGTATTCTGTTGAGGTGCGGAGCGATGGATGCTGAGGCATATTC TGTAATATCTGGTAACCTTGTAAGAACATTGTGGAGAATTGGAACATCCAAGAAAAATAATCCC GATCCACTCTGGGATAAAGCAAGAGGAACTGCTTTTCACTCCTTGTCCAACTACAAGGTATCAC TTATTCAAGATGCTATTCCTGATTTCTGGAAACTAAACTATGAGTTCTTTACGAACGAACATAA TCTGGCAGTTCTCAAGGCCATGGAGCACCTTCAAGATGAGATCATCAGATATGAGCACATAAAT CGTCGTCGAGTGACTACTGACAAAAGAACTGCAGTGCATAAATTTGAGAAGCTACTGGAGGTTT TTCCTCGGGCGGTATTTAAAGGGATGTTATCTCATCATCAGTTGCCTGGTGCTGCTCTTTTAAC TCTCAATTTTACTCCAAAGGACATACTTAATGAAGGGAAACCTAAGGATTTGCCTAGAGTTCAT TCCGCTTTTGAGCAAGCTTTTGTGGAAATTGCTGAATCTATGTATGTGTCAAGAAACATAGTGG TAGCTCTTCTTGCCTTGCAGTCATGGAAGTCATTTGTTTCCAACTGGATGCAAGCAGTTGTGGC ATTGCTTGACACTAAAGACTCGTCAAAGTTGAACAAAGCAATGAAAGCTGCTAATGATATATTT AAG
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
						0.063875403

Conservation Information
Conserved circRNAs	NA
PMCS	0.063875403

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							12067079-12072348(+)
12070477-12072155(-)
						
					

						Potential amino acid sequence
						
							MLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCKQ
NPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVAH
SLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQDA
IPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRAV
FKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALLA
LQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKLSLLESLPSLAIHGFVLPLALQWIS
PMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCK
QNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVA
HSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQD
AIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRA
VFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALL
ALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKLSLLESLPSLAIHGFVLPLALQWI
SPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVC
KQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAV
AHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQ
DAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPR
AVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVAL
LALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKLSLLESLPSLAIHGFVLPLALQW
ISPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDV
CKQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPA
VAHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLI
QDAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFP
RAVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVA
LLALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFK(+)
MKLEKFSGSRTTCKFGNAQSVTAHILQSNRTAIAYKTEFESLLSIGDIHCRASGRTKPCIASDG
NDSSKLSLNISLAAFIALFNFDESLVSSNATTACIQLETNDFHDCKARRATTMFLDTYIDSAIS
TKACSKAE*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						responsive to drought stress
					

			
		

Functional Information
Coding potential	Y
Potential coding position	12067079-12072348(+) 12070477-12072155(-)
Potential amino acid sequence	MLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCKQ NPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVAH SLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQDA IPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRAV FKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALLA LQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKLSLLESLPSLAIHGFVLPLALQWIS PMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVCK QNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAVA HSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQD AIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPRA VFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVALL ALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKLSLLESLPSLAIHGFVLPLALQWI SPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDVC KQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPAV AHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLIQ DAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFPR AVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVAL LALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFKLSLLESLPSLAIHGFVLPLALQW ISPMLKRDSNSVLYAMAVRLLCKIWAVTDWAFPNLQVVLDPENFSNFISDREISASIATSIRDV CKQNPDRGVDIILSVSFCIESRDSVVQALGLESLSYLCEADVVDFYTAWKVISKQVLDYYVEPA VAHSLCILLRCGAMDAEAYSVISGNLVRTLWRIGTSKKNNPDPLWDKARGTAFHSLSNYKVSLI QDAIPDFWKLNYEFFTNEHNLAVLKAMEHLQDEIIRYEHINRRRVTTDKRTAVHKFEKLLEVFP RAVFKGMLSHHQLPGAALLTLNFTPKDILNEGKPKDLPRVHSAFEQAFVEIAESMYVSRNIVVA LLALQSWKSFVSNWMQAVVALLDTKDSSKLNKAMKAANDIFK(+) MKLEKFSGSRTTCKFGNAQSVTAHILQSNRTAIAYKTEFESLLSIGDIHCRASGRTKPCIASDG NDSSKLSLNISLAAFIALFNFDESLVSSNATTACIQLETNDFHDCKARRATTMFLDTYIDSAIS TKACSKAE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d039693_circ_g.2

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