Plant Circular RNA Database

Detail information of Zm00001d048292_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d048292_circ_g.4
					
						ID in PlantcircBase
						zma_circ_010098
					
						Alias
						Zm09circ00076, GRMZM2G169365_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 154004620-154005372  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d048292						
					
						Parent gene annotation
						
							Omega-amidase chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d048292_circ_g.1 Zm00001d048292_circ_g.2 Zm00001d048292_circ_g.3 						
					
						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  
						
							CT-AC							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
						Zm00001d048292_T004:2
Zm00001d048292_T003:2
Zm00001d048292_T001:2
Zm00001d048292_T002:2

General Information
CircRNA Name	Zm00001d048292_circ_g.4
ID in PlantcircBase	zma_circ_010098
Alias	Zm09circ00076, GRMZM2G169365_C1
Organism	Zea mays
Position	chr9: 154004620-154005372 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d048292
Parent gene annotation	Omega-amidase chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d048292_circ_g.1 Zm00001d048292_circ_g.2 Zm00001d048292_circ_g.3
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	CT-AC 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	Zm00001d048292_T004:2 Zm00001d048292_T003:2 Zm00001d048292_T001:2 Zm00001d048292_T002:2

			
						 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  
						
							CTGACAGCATTGAAAATGAAGGGGCTGCATCTCCGCCAGCTTCAATGTCCTCGGCGTACTCTGG
AAAGCTGTCATTTGAGTAAGGGCCATTCCATATCTCctgtgtctacaacagtagggctctgccc
agcagtaagagtctttgattccttgaaagtgatctttcctggaatgtcaatgtcgaaaagatgg
atctgcag

						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: 319
Transcript exons: 154004620-154004713,154005148-154005372
CTGTGTCTACAACAGTAGGGCTCTGCCCAGCAGTAAGAGTCTTTGATTCCTTGAAAGTGATCTT
TCCTGGAATGTCAATGTCGAAAAGATGGATCTTTCTATGTTTACCCTTCAGCTGGCCATCTGAA
CCAAAGACACAGCATGTATTGTATAAGTTGTTGCCAGAACGTTCAGCTATGGACCCACCAACAA
GAGTGATTTGTAAACTGCGAGCAACCTCTGACAGCATTGAAAATGAAGGGGCTGCATCTCCGCC
AGCTTCAATGTCCTCGGCGTACTCTGGAAAGCTGTCATTTGAGTAAGGGCCATTCCATATCTC
						
						Genomic sequence
						
							CTGTGTCTACAACAGTAGGGCTCTGCCCAGCAGTAAGAGTCTTTGATTCCTTGAAAGTGATCTT
TCCTGGAATGTCAATGTCGAAAAGATGGATCTGCAGGTGCACAAATTTTTATTGCCAGAAAGCA
CTAGGAATGAACCAAACTTACTACACATATTCAGGACAATGAAAGGAAAAGAGAGCATAAATAA
GATGGGAGCAAGCAAATCAGAACCGGAATTTCAGCGTCGACCACAATTTGATCGAACTTACTAC
TCTATTGATCACACTCAAAAGTAAAAGAAGGCATAAGACATGATCTAATATGCATCTGTCAGCA
CTATGGCATGTTCAGTGCTCATGTTGGAGCTGGACTCATCGAGGTACTGTTGGGAGCTGGTATG
ATGGGAGATAGGATTCAACATTAATTCGGTATATACAGATTTCTCATTATAATGTCTACACATA
AATCATAGCTTCTCATCAAATCTAATATTCGCAAATAGCAATAGAAAACTTTACTCCAGCTACT
AGAAGTTTGAACATACCTTTCTATGTTTACCCTTCAGCTGGCCATCTGAACCAAAGACACAGCA
TGTATTGTATAAGTTGTTGCCAGAACGTTCAGCTATGGACCCACCAACAAGAGTGATTTGTAAA
CTGCGAGCAACCTCTGACAGCATTGAAAATGAAGGGGCTGCATCTCCGCCAGCTTCAATGTCCT
CGGCGTACTCTGGAAAGCTGTCATTTGAGTAAGGGCCATTCCATATCTC

Sequences
Splice junction sequence	CTGACAGCATTGAAAATGAAGGGGCTGCATCTCCGCCAGCTTCAATGTCCTCGGCGTACTCTGG AAAGCTGTCATTTGAGTAAGGGCCATTCCATATCTCctgtgtctacaacagtagggctctgccc agcagtaagagtctttgattccttgaaagtgatctttcctggaatgtcaatgtcgaaaagatgg atctgcag
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: 319 Transcript exons: 154004620-154004713,154005148-154005372 CTGTGTCTACAACAGTAGGGCTCTGCCCAGCAGTAAGAGTCTTTGATTCCTTGAAAGTGATCTT TCCTGGAATGTCAATGTCGAAAAGATGGATCTTTCTATGTTTACCCTTCAGCTGGCCATCTGAA CCAAAGACACAGCATGTATTGTATAAGTTGTTGCCAGAACGTTCAGCTATGGACCCACCAACAA GAGTGATTTGTAAACTGCGAGCAACCTCTGACAGCATTGAAAATGAAGGGGCTGCATCTCCGCC AGCTTCAATGTCCTCGGCGTACTCTGGAAAGCTGTCATTTGAGTAAGGGCCATTCCATATCTC
Genomic sequence	CTGTGTCTACAACAGTAGGGCTCTGCCCAGCAGTAAGAGTCTTTGATTCCTTGAAAGTGATCTT TCCTGGAATGTCAATGTCGAAAAGATGGATCTGCAGGTGCACAAATTTTTATTGCCAGAAAGCA CTAGGAATGAACCAAACTTACTACACATATTCAGGACAATGAAAGGAAAAGAGAGCATAAATAA GATGGGAGCAAGCAAATCAGAACCGGAATTTCAGCGTCGACCACAATTTGATCGAACTTACTAC TCTATTGATCACACTCAAAAGTAAAAGAAGGCATAAGACATGATCTAATATGCATCTGTCAGCA CTATGGCATGTTCAGTGCTCATGTTGGAGCTGGACTCATCGAGGTACTGTTGGGAGCTGGTATG ATGGGAGATAGGATTCAACATTAATTCGGTATATACAGATTTCTCATTATAATGTCTACACATA AATCATAGCTTCTCATCAAATCTAATATTCGCAAATAGCAATAGAAAACTTTACTCCAGCTACT AGAAGTTTGAACATACCTTTCTATGTTTACCCTTCAGCTGGCCATCTGAACCAAAGACACAGCA TGTATTGTATAAGTTGTTGCCAGAACGTTCAGCTATGGACCCACCAACAAGAGTGATTTGTAAA CTGCGAGCAACCTCTGACAGCATTGAAAATGAAGGGGCTGCATCTCCGCCAGCTTCAATGTCCT CGGCGTACTCTGGAAAGCTGTCATTTGAGTAAGGGCCATTCCATATCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.214182475

Conservation Information
Conserved circRNAs	NA
PMCS	0.214182475

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							154005289-154005352(+)
154005284-154005346(-)
						
						Potential amino acid sequence
						
							MKGLHLRQLQCPRRTLESCHLSKGHSISPVSTTVGLCPAVRVFDSLKVIFPGMSMSKRWIFLCL
PFSWPSEPKTQHVLYKLLPERSAMDPPTRVICKLRATSDSIENEGAASPPASMSSAYSGKLSFE
*(+)
MLSEVARSLQITLVGGSIAERSGNNLYNTCCVFGSDGQLKGKHRKIHLFDIDIPGKITFKESKT
LTAGQSPTVVDTGDMEWPLLK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	154005289-154005352(+) 154005284-154005346(-)
Potential amino acid sequence	MKGLHLRQLQCPRRTLESCHLSKGHSISPVSTTVGLCPAVRVFDSLKVIFPGMSMSKRWIFLCL PFSWPSEPKTQHVLYKLLPERSAMDPPTRVICKLRATSDSIENEGAASPPASMSSAYSGKLSFE (+) MLSEVARSLQITLVGGSIAERSGNNLYNTCCVFGSDGQLKGKHRKIHLFDIDIPGKITFKESKT LTAGQSPTVVDTGDMEWPLLK(-)
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 Zm00001d048292_circ_g.4

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