Plant Circular RNA Database

Detail information of Zm00001d051308_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d051308_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008121
					
						Alias
						Zm04circ00059, zma_circ_0001480
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 152678434-152678761  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d051308						
					
						Parent gene annotation
						
							 kinesin-related protein1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d051308_circ_g.2 						
					
						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  
						
							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
						Zm00001d051308_T003:2
Zm00001d051308_T004:2
Zm00001d051308_T014:1
Zm00001d051308_T009:1
Zm00001d051308_T010:1
Zm00001d051308_T016:1
Zm00001d051308_T022:2
Zm00001d051308_T008:1
Zm00001d051308_T011:2
Zm00001d051308_T002:1
Zm00001d051308_T007:2
Zm00001d051308_T005:1
Zm00001d051308_T019:1
Zm00001d051308_T020:1
Zm00001d051308_T018:1
Zm00001d051308_T021:1

General Information
CircRNA Name	Zm00001d051308_circ_g.3
ID in PlantcircBase	zma_circ_008121
Alias	Zm04circ00059, zma_circ_0001480
Organism	Zea mays
Position	chr4: 152678434-152678761 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d051308
Parent gene annotation	kinesin-related protein1
Parent gene strand	-
Alternative splicing	Zm00001d051308_circ_g.2
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	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	Zm00001d051308_T003:2 Zm00001d051308_T004:2 Zm00001d051308_T014:1 Zm00001d051308_T009:1 Zm00001d051308_T010:1 Zm00001d051308_T016:1 Zm00001d051308_T022:2 Zm00001d051308_T008:1 Zm00001d051308_T011:2 Zm00001d051308_T002:1 Zm00001d051308_T007:2 Zm00001d051308_T005:1 Zm00001d051308_T019:1 Zm00001d051308_T020:1 Zm00001d051308_T018:1 Zm00001d051308_T021:1

			
						 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  
						
							TGTACAGATAATAGCCGTTCTTGCATTACCTCCTAAAGATGGTTGTAATATGCGTGTGAGCTTT
GAATCTCTGTATGGTATGTGTGCATTACTCCCCATGctttctaatttggttatccttttccttt
actaatgcttcaagactggaatttgaagctggttgccgcaactcactctccaacctagcaactt
ccttttgc

						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: 328
Transcript exons: 152678434-152678761
CTTTCTAATTTGGTTATCCTTTTCCTTTACTAATGCTTCAAGACTGGAATTTGAAGCTGGTTGC
CGCAACTCACTCTCCAACCTAGCAACTTCCTTTTGCAAATGCTTTACTAGTGCTTTATCAGACA
TGACCACATTTACCTGAGCATTTGTAACTACTTCCTTTGCACAACTTCCAAATAACAAAGTATT
TCTTGAATGCTCAATATGGCTAGTGGCAGGGCTCAGTGTACAGATAATAGCCGTTCTTGCATTA
CCTCCTAAAGAAGGTTGTAATATGCATGTGAGCTTTGAATCTCTGTATGGTATGTGTGCATTAC
TCCCCATG
Transcript length: 328
Transcript exons: 152678434-152678761
CTTTCTAATTTGGTTATCCTTTTCCTTTACTAATGCTTCAAGACTGGAATTTGAAGCTGGTTGC
CGCAACTCACTCTCCAACCTAGCAACTTCCTTTTGCAAATGCTTTACTAGTGCTTTATCAGACA
TGACCACATTTACCTGAGCATTTGTAACTACTTCCTTTGCACAACTTCCAAATAATAAAGTATT
TCTTGAATGCTCAATATGGCTAGTGGCAGGGCTCAGTGTACAGATAATAGCCGTTCTTGCATTA
CCTCCTAAAGATGGTTGTAATATGCGTGTGAGCTTTGAATCTCTGTATGGTATGTGTGCATTAC
TCCCCATG
						
						Genomic sequence
						
							CTTTCTAATTTGGTTATCCTTTTCCTTTACTAATGCTTCAAGACTGGAATTTGAAGCTGGTTGC
CGCAACTCACTCTCCAACCTAGCAACTTCCTTTTGCAAATGCTTTACTAGTGCTTTATCAGACA
TGACCACATTTACCTGAGCATTTGTAACTACTTCCTTTGCACAACTTCCAAATAATAAAGTATT
TCTTGAATGCTCAATATGGCTAGTGGCAGGGCTCAGTGTACAGATAATAGCCGTTCTTGCATTA
CCTCCTAAAGATGGTTGTAATATGCGTGTGAGCTTTGAATCTCTGTATGGTATGTGTGCATTAC
TCCCCATG

Sequences
Splice junction sequence	TGTACAGATAATAGCCGTTCTTGCATTACCTCCTAAAGATGGTTGTAATATGCGTGTGAGCTTT GAATCTCTGTATGGTATGTGTGCATTACTCCCCATGctttctaatttggttatccttttccttt actaatgcttcaagactggaatttgaagctggttgccgcaactcactctccaacctagcaactt ccttttgc
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: 328 Transcript exons: 152678434-152678761 CTTTCTAATTTGGTTATCCTTTTCCTTTACTAATGCTTCAAGACTGGAATTTGAAGCTGGTTGC CGCAACTCACTCTCCAACCTAGCAACTTCCTTTTGCAAATGCTTTACTAGTGCTTTATCAGACA TGACCACATTTACCTGAGCATTTGTAACTACTTCCTTTGCACAACTTCCAAATAACAAAGTATT TCTTGAATGCTCAATATGGCTAGTGGCAGGGCTCAGTGTACAGATAATAGCCGTTCTTGCATTA CCTCCTAAAGAAGGTTGTAATATGCATGTGAGCTTTGAATCTCTGTATGGTATGTGTGCATTAC TCCCCATG Transcript length: 328 Transcript exons: 152678434-152678761 CTTTCTAATTTGGTTATCCTTTTCCTTTACTAATGCTTCAAGACTGGAATTTGAAGCTGGTTGC CGCAACTCACTCTCCAACCTAGCAACTTCCTTTTGCAAATGCTTTACTAGTGCTTTATCAGACA TGACCACATTTACCTGAGCATTTGTAACTACTTCCTTTGCACAACTTCCAAATAATAAAGTATT TCTTGAATGCTCAATATGGCTAGTGGCAGGGCTCAGTGTACAGATAATAGCCGTTCTTGCATTA CCTCCTAAAGATGGTTGTAATATGCGTGTGAGCTTTGAATCTCTGTATGGTATGTGTGCATTAC TCCCCATG
Genomic sequence	CTTTCTAATTTGGTTATCCTTTTCCTTTACTAATGCTTCAAGACTGGAATTTGAAGCTGGTTGC CGCAACTCACTCTCCAACCTAGCAACTTCCTTTTGCAAATGCTTTACTAGTGCTTTATCAGACA TGACCACATTTACCTGAGCATTTGTAACTACTTCCTTTGCACAACTTCCAAATAATAAAGTATT TCTTGAATGCTCAATATGGCTAGTGGCAGGGCTCAGTGTACAGATAATAGCCGTTCTTGCATTA CCTCCTAAAGATGGTTGTAATATGCGTGTGAGCTTTGAATCTCTGTATGGTATGTGTGCATTAC TCCCCATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.641063239

Conservation Information
Conserved circRNAs	NA
PMCS	0.641063239

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							152678712-152678463(+)
152678737-152678575(+)
152678762-152678752(-)
						
						Potential amino acid sequence
						
							MRVSFESLYGMCALLPMLSNLVILFLY*(+)
MVCVHYSPCFLIWLSFSFTNASRLEFEAGCRNSLSNLATSFCKCFTSALSDMTTFT*(+)
MGSNAHIPYRDSKLTRILQPSLGGNARTAIICTLSPATSHIEHSRNTLLFGSCAKEVVTNAQVN
VVMSDKALVKHLQKEVARLESELRQPASNSSLEALVKEKDNQIRKHGE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	152678712-152678463(+) 152678737-152678575(+) 152678762-152678752(-)
Potential amino acid sequence	MRVSFESLYGMCALLPMLSNLVILFLY(+) MVCVHYSPCFLIWLSFSFTNASRLEFEAGCRNSLSNLATSFCKCFTSALSDMTTFT(+) MGSNAHIPYRDSKLTRILQPSLGGNARTAIICTLSPATSHIEHSRNTLLFGSCAKEVVTNAQVN VVMSDKALVKHLQKEVARLESELRQPASNSSLEALVKEKDNQIRKHGE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d051308_circ_g.3

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