Plant Circular RNA Database

Detail information of Zm00001d016452_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d016452_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008697
					
						Alias
						Zm05circ00092, zma_circ_0002016, GRMZM2G128865_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 162852000-162853028  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d016452						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d016452_circ_g.1 Zm00001d016452_circ_g.2 Zm00001d016452_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d016452_T030:4
Zm00001d016452_T008:4
Zm00001d016452_T022:4
Zm00001d016452_T009:3
Zm00001d016452_T049:4
Zm00001d016452_T007:3
Zm00001d016452_T032:4
Zm00001d016452_T033:4
Zm00001d016452_T028:4
Zm00001d016452_T002:4
Zm00001d016452_T035:4
Zm00001d016452_T040:4
Zm00001d016452_T001:4
Zm00001d016452_T025:4
Zm00001d016452_T043:4
Zm00001d016452_T016:4
Zm00001d016452_T029:4
Zm00001d016452_T031:4
Zm00001d016452_T047:4
Zm00001d016452_T011:4
Zm00001d016452_T038:4
Zm00001d016452_T005:4
Zm00001d016452_T019:4
Zm00001d016452_T026:4
Zm00001d016452_T012:4
Zm00001d016452_T010:4
Zm00001d016452_T045:4
Zm00001d016452_T020:4
Zm00001d016452_T042:4
Zm00001d016452_T014:4
Zm00001d016452_T034:4
Zm00001d016452_T013:4
Zm00001d016452_T018:4
Zm00001d016452_T037:4
Zm00001d016452_T050:2
Zm00001d016452_T048:4
Zm00001d016452_T003:4
Zm00001d016452_T023:4

General Information
CircRNA Name	Zm00001d016452_circ_g.4
ID in PlantcircBase	zma_circ_008697
Alias	Zm05circ00092, zma_circ_0002016, GRMZM2G128865_C2
Organism	Zea mays
Position	chr5: 162852000-162853028 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d016452
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d016452_circ_g.1 Zm00001d016452_circ_g.2 Zm00001d016452_circ_g.3
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d016452_T030:4 Zm00001d016452_T008:4 Zm00001d016452_T022:4 Zm00001d016452_T009:3 Zm00001d016452_T049:4 Zm00001d016452_T007:3 Zm00001d016452_T032:4 Zm00001d016452_T033:4 Zm00001d016452_T028:4 Zm00001d016452_T002:4 Zm00001d016452_T035:4 Zm00001d016452_T040:4 Zm00001d016452_T001:4 Zm00001d016452_T025:4 Zm00001d016452_T043:4 Zm00001d016452_T016:4 Zm00001d016452_T029:4 Zm00001d016452_T031:4 Zm00001d016452_T047:4 Zm00001d016452_T011:4 Zm00001d016452_T038:4 Zm00001d016452_T005:4 Zm00001d016452_T019:4 Zm00001d016452_T026:4 Zm00001d016452_T012:4 Zm00001d016452_T010:4 Zm00001d016452_T045:4 Zm00001d016452_T020:4 Zm00001d016452_T042:4 Zm00001d016452_T014:4 Zm00001d016452_T034:4 Zm00001d016452_T013:4 Zm00001d016452_T018:4 Zm00001d016452_T037:4 Zm00001d016452_T050:2 Zm00001d016452_T048:4 Zm00001d016452_T003:4 Zm00001d016452_T023:4

			
						 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  
						
							AGTGCAGGGCCATTTGCCTGGGGGCCTTCTGTTGGTGGTGATGGTGTCCGTACAGAACTTAGTC
TGCCAAATGTTGCAAAGACTGTCGGGGCTGTTGCAGatatcgagaagggagtcaatagaaggcc
gttatatgaaagtcatcctctatcatcattttcatggacccgaactgacagtatggatatggta
tgttttat

									
								

					

						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: 423
Transcript exons: 162852000-162852088,162852378-162852476,162852715-162852
830,162852910-162853028
ATATCGAGAAGGGAGTCAATAGAAGGCCGTTATATGAAAGTCATCCTCTATCATCATTTTCATG
GACCCGAACTGACAGTATGGATATGGGGGATTGGTCAAAGAAATGCAAGGAAGCATTAAGCAAG
TTTGAGCTGCTGAAGGAAGGGAAGAGTAAAGAGGACATTGTTTATGAAAAGGCTGTTCAGATAT
TACACGGTACAAAGGATGAGGTGCATGACATTGTTCAAAGTGCTCTTAAGTCCAGTGATTTGAA
GGGTCTCCATGCCCAATGTCTTACAGATATATGGATAGGCAGAGAGAGGTTTGCTTTTGTTGAT
CTGAGTGCAGGGCCATTTGCCTGGGGGCCTTCTGTTGGTGGTGATGGTGTCCGTACAGAACTTA
GTCTGCCAAATGTTGCAAAGACTGTCGGGGCTGTTGCAG
						
					

						Genomic sequence
						
							ATATCGAGAAGGGAGTCAATAGAAGGCCGTTATATGAAAGTCATCCTCTATCATCATTTTCATG
GACCCGAACTGACAGTATGGATATGGTATGTTTTATTTGTTATCATCTTTGGCGTTATTTGTAC
CGGGAAAACCTTTATTTCTTTGCTTGGTCCATTCAGCTCAATGATTTAACTTAGCTGATACGCT
TTTCATGATCATGAATTTTTAAGCTATTCTTAAGTTCACATTTTGATCATATGACTTGATTGTC
AGAATGATTTTGATTGAAGAGCACTTGGCTCTTTCCTCTGAAGCAGATGCATGAAGATCTTCTT
GACACTGTTTTTTAATGTATCAAAATACCTAACGGATTTCTATACACTTATCGTGCAGGGGGAT
TGGTCAAAGAAATGCAAGGAAGCATTAAGCAAGTTTGAGCTGCTGAAGGAAGGGAAGAGTAAAG
AGGACATTGTTTATGAAAAGGCTGTTCAGGTGGCACTTTTATGTTGGTACACTAAATTAAGGAA
CAATTGGATCTATACCATTAAAAGATCCAAACTTTAGATATATACCATGGACCCCACATGTCAT
TGACTCATGTGGACCCACATGTAAGTGAGATAGTAATGGTATGGATACAAAGTGGTGATCTTTT
AATGGTATGAATCCAAATTTCCCCTAAATTAAACTTCTTTTCTTTGTTTATTTAACATTGAATA
TTCTTATATAGATATTACACGGTACAAAGGATGAGGTGCATGACATTGTTCAAAGTGCTCTTAA
GTCCAGTGATTTGAAGGGTCTCCATGCCCAATGTCTTACAGATATATGGATAGGCAGAGAGAGG
TCTGATATGGTTTTTGCTTATCCCTTTCCTAAATTGAGGTTAGAGTGGTCATTCTTCTAACCTG
ATCTTTATTTTCAGGTTTGCTTTTGTTGATCTGAGTGCAGGGCCATTTGCCTGGGGGCCTTCTG
TTGGTGGTGATGGTGTCCGTACAGAACTTAGTCTGCCAAATGTTGCAAAGACTGTCGGGGCTGT
TGCAG
						
					

			
		

Sequences
Splice junction sequence	AGTGCAGGGCCATTTGCCTGGGGGCCTTCTGTTGGTGGTGATGGTGTCCGTACAGAACTTAGTC TGCCAAATGTTGCAAAGACTGTCGGGGCTGTTGCAGatatcgagaagggagtcaatagaaggcc gttatatgaaagtcatcctctatcatcattttcatggacccgaactgacagtatggatatggta tgttttat
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: 423 Transcript exons: 162852000-162852088,162852378-162852476,162852715-162852 830,162852910-162853028 ATATCGAGAAGGGAGTCAATAGAAGGCCGTTATATGAAAGTCATCCTCTATCATCATTTTCATG GACCCGAACTGACAGTATGGATATGGGGGATTGGTCAAAGAAATGCAAGGAAGCATTAAGCAAG TTTGAGCTGCTGAAGGAAGGGAAGAGTAAAGAGGACATTGTTTATGAAAAGGCTGTTCAGATAT TACACGGTACAAAGGATGAGGTGCATGACATTGTTCAAAGTGCTCTTAAGTCCAGTGATTTGAA GGGTCTCCATGCCCAATGTCTTACAGATATATGGATAGGCAGAGAGAGGTTTGCTTTTGTTGAT CTGAGTGCAGGGCCATTTGCCTGGGGGCCTTCTGTTGGTGGTGATGGTGTCCGTACAGAACTTA GTCTGCCAAATGTTGCAAAGACTGTCGGGGCTGTTGCAG
Genomic sequence	ATATCGAGAAGGGAGTCAATAGAAGGCCGTTATATGAAAGTCATCCTCTATCATCATTTTCATG GACCCGAACTGACAGTATGGATATGGTATGTTTTATTTGTTATCATCTTTGGCGTTATTTGTAC CGGGAAAACCTTTATTTCTTTGCTTGGTCCATTCAGCTCAATGATTTAACTTAGCTGATACGCT TTTCATGATCATGAATTTTTAAGCTATTCTTAAGTTCACATTTTGATCATATGACTTGATTGTC AGAATGATTTTGATTGAAGAGCACTTGGCTCTTTCCTCTGAAGCAGATGCATGAAGATCTTCTT GACACTGTTTTTTAATGTATCAAAATACCTAACGGATTTCTATACACTTATCGTGCAGGGGGAT TGGTCAAAGAAATGCAAGGAAGCATTAAGCAAGTTTGAGCTGCTGAAGGAAGGGAAGAGTAAAG AGGACATTGTTTATGAAAAGGCTGTTCAGGTGGCACTTTTATGTTGGTACACTAAATTAAGGAA CAATTGGATCTATACCATTAAAAGATCCAAACTTTAGATATATACCATGGACCCCACATGTCAT TGACTCATGTGGACCCACATGTAAGTGAGATAGTAATGGTATGGATACAAAGTGGTGATCTTTT AATGGTATGAATCCAAATTTCCCCTAAATTAAACTTCTTTTCTTTGTTTATTTAACATTGAATA TTCTTATATAGATATTACACGGTACAAAGGATGAGGTGCATGACATTGTTCAAAGTGCTCTTAA GTCCAGTGATTTGAAGGGTCTCCATGCCCAATGTCTTACAGATATATGGATAGGCAGAGAGAGG TCTGATATGGTTTTTGCTTATCCCTTTCCTAAATTGAGGTTAGAGTGGTCATTCTTCTAACCTG ATCTTTATTTTCAGGTTTGCTTTTGTTGATCTGAGTGCAGGGCCATTTGCCTGGGGGCCTTCTG TTGGTGGTGATGGTGTCCGTACAGAACTTAGTCTGCCAAATGTTGCAAAGACTGTCGGGGCTGT TGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.104375071

Conservation Information
Conserved circRNAs	NA
PMCS	0.104375071

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							162852970-162852408(+)
162852081-162853025(+)
						
						Potential amino acid sequence
						
							MVSVQNLVCQMLQRLSGLLQISRRESIEGRYMKVILYHHFHGPELTVWIWGIGQRNARKH*(+)
MDMGDWSKKCKEALSKFELLKEGKSKEDIVYEKAVQILHGTKDEVHDIVQSALKSSDLKGLHAQ
CLTDIWIGRERFAFVDLSAGPFAWGPSVGGDGVRTELSLPNVAKTVGAVADIEKGVNRRPLYES
HPLSSFSWTRTDSMDMGDWSKKCKEALSKFELLKEGKSKEDIVYEKAVQILHGTKDEVHDIVQS
ALKSSDLKGLHAQCLTDIWIGRERFAFVDLSAGPFAWGPSVGGDGVRTELSLPNVAKTVGAVAD
IEKGVNRRPLYESHPLSSFSWTRTDSMDMGDWSKKCKEALSKFELLKEGKSKEDIVYEKAVQIL
HGTKDEVHDIVQSALKSSDLKGLHAQCLTDIWIGRERFAFVDLSAGPFAWGPSVGGDGVRTELS
LPNVAKTVGAVADIEKGVNRRPLYESHPLSSFSWTRTDSMDMGDWSKKCKEALSKFELLKEGKS
KEDIVYEKAVQILHGTKDEVHDIVQSALKSSDLKGLHAQCLTDIWIGRERFAFVDLSAGPFAWG
PSVGGDGVRTELSLPNVAKTVGAVA(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	162852970-162852408(+) 162852081-162853025(+)
Potential amino acid sequence	MVSVQNLVCQMLQRLSGLLQISRRESIEGRYMKVILYHHFHGPELTVWIWGIGQRNARKH*(+) MDMGDWSKKCKEALSKFELLKEGKSKEDIVYEKAVQILHGTKDEVHDIVQSALKSSDLKGLHAQ CLTDIWIGRERFAFVDLSAGPFAWGPSVGGDGVRTELSLPNVAKTVGAVADIEKGVNRRPLYES HPLSSFSWTRTDSMDMGDWSKKCKEALSKFELLKEGKSKEDIVYEKAVQILHGTKDEVHDIVQS ALKSSDLKGLHAQCLTDIWIGRERFAFVDLSAGPFAWGPSVGGDGVRTELSLPNVAKTVGAVAD IEKGVNRRPLYESHPLSSFSWTRTDSMDMGDWSKKCKEALSKFELLKEGKSKEDIVYEKAVQIL HGTKDEVHDIVQSALKSSDLKGLHAQCLTDIWIGRERFAFVDLSAGPFAWGPSVGGDGVRTELS LPNVAKTVGAVADIEKGVNRRPLYESHPLSSFSWTRTDSMDMGDWSKKCKEALSKFELLKEGKS KEDIVYEKAVQILHGTKDEVHDIVQSALKSSDLKGLHAQCLTDIWIGRERFAFVDLSAGPFAWG PSVGGDGVRTELSLPNVAKTVGAVA(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d016452_circ_g.4

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