Plant Circular RNA Database

Detail information of Zm00001d040257_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d040257_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001352
					
						Alias
						circ597
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 34258278-34259818  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d040257						
					
						Parent gene annotation
						
							T-complex protein 1 subunit beta
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d040257_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						seedling leaves
					
						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-TA							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
						Zm00001d040257_T008:4
Zm00001d040257_T009:4
Zm00001d040257_T002:4
Zm00001d040257_T001:4
Zm00001d040257_T011:2
Zm00001d040257_T010:4
Zm00001d040257_T003:4
Zm00001d040257_T004:4
Zm00001d040257_T005:4
Zm00001d040257_T006:4
Zm00001d040257_T007:4

General Information
CircRNA Name	Zm00001d040257_circ_g.1
ID in PlantcircBase	zma_circ_001352
Alias	circ597
Organism	Zea mays
Position	chr3: 34258278-34259818 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI
Parent gene	Zm00001d040257
Parent gene annotation	T-complex protein 1 subunit beta
Parent gene strand	+
Alternative splicing	Zm00001d040257_circ_g.2
Support reads	2
Tissues	seedling leaves
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-TA 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	Zm00001d040257_T008:4 Zm00001d040257_T009:4 Zm00001d040257_T002:4 Zm00001d040257_T001:4 Zm00001d040257_T011:2 Zm00001d040257_T010:4 Zm00001d040257_T003:4 Zm00001d040257_T004:4 Zm00001d040257_T005:4 Zm00001d040257_T006:4 Zm00001d040257_T007:4

			
						 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  
						
							TCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTC
GCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGggacaagatcctgcaatcaactggcaga
ggacgtaatgttactgttacaaatgatggggctaccattttgaagtcacttcacattgacaatc
ctgctgca

									
								

					

						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
						
							GGACAAGATCCTGCAATCAACTGGCAGAGGACGTAATGTTACTGTTACAAATGATGGGGCTACC
ATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAAAGGTCCTTGTTGGTATCCTTTGCCAAT
TTGATTACTGCTTGATAATAGTATTAGTAAGGTGGTAATAGGAAAGCAAGTGGGCACCTAATGT
TGTCTGTGGAGTCAGCCATTGTAGTTTACCCCCACCCCCAAACATCAAATTAATTACGTGGCAT
GCCATTTTAGCAAGTTTTGGGTCCATCCCAATGACGATCCAAAACAACTAAAACTTGCATGCAT
AGTTTTATCTTTTATGTCATATGGTTGAGGCTTTATAACTTCTCTTGATATTTCATTGTATTGT
TCTTAATCTTCAATCTTCATATTCTACCTATGACCTCATTAAGGCCCTCTCTTGTGCAAATATT
TTTTTCCTAATGAAAGAAAGGCCAGTTGCTCCTTAATGGTTGCTAGACATCTCAAAAGTTCAAG
ATGATGAAGTTGGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGC
TGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGGTATTACTTGCTGATTG
TGTTCTGGTTAATAGTATGCTTTTCCATCCTTCACATTTTAAAGCTTGGTAACTATTTTAGCAG
GCCGTGTTACTTGGTCTTGCTTGCGTCAATCGGTCAATCCCATAGTAACAATTCAAATAGAATA
ATAGATGAGGCATACAATACAAGGTCTAAGGATGGATTCAACTGTTAAGTGTTTCAAAATTTGA
GATGTGGCTTCCTTTCTTTACATTTCATGTTTTCAGATTAATCTACCATTTTTTAGTACTAGTA
TTGTGTAGGCAGTGCACTGTTCTGGTTCTAATCTGTCATGGGTTGCCTGTTTTGTACCGAGATA
GCTAGTGTGTATTCTGAGGAACTACTAGTATGCATTCTAGATCACTGCTGCAAAGCTACAACCA
TTGTTTTTTATGATGAGATTCAACGTCTCCAGCACTTAATTCATCCTGTAAAATTTTAGGTTAC
AGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATA
CAGGTAAGTTATTTTCTCAATCTCATGGTTGGAAAGCATAGTTTTTCAGGTTCATAAGACACCA
TCTTATTTGAGCCATTCTTTTCCTTATCAATAAATTTGTATTTTGCATAGCATGTAGGATTTGA
CGTCATTAAGGATTTGTTATTTTTGAGTAATATTTAAACTCATATGGATTCAAATTCACTTCAT
CTTGCATCTCATGGATTCTCTCAGGAATATGCCACCATGCCCATCAATCTCATGACAATATTCT
TTTTCATTCTTCTGCAGATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGT
TCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGC
TTAAG
						
					

			
		

Sequences
Splice junction sequence	TCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTC GCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGggacaagatcctgcaatcaactggcaga ggacgtaatgttactgttacaaatgatggggctaccattttgaagtcacttcacattgacaatc ctgctgca
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	GGACAAGATCCTGCAATCAACTGGCAGAGGACGTAATGTTACTGTTACAAATGATGGGGCTACC ATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAAAGGTCCTTGTTGGTATCCTTTGCCAAT TTGATTACTGCTTGATAATAGTATTAGTAAGGTGGTAATAGGAAAGCAAGTGGGCACCTAATGT TGTCTGTGGAGTCAGCCATTGTAGTTTACCCCCACCCCCAAACATCAAATTAATTACGTGGCAT GCCATTTTAGCAAGTTTTGGGTCCATCCCAATGACGATCCAAAACAACTAAAACTTGCATGCAT AGTTTTATCTTTTATGTCATATGGTTGAGGCTTTATAACTTCTCTTGATATTTCATTGTATTGT TCTTAATCTTCAATCTTCATATTCTACCTATGACCTCATTAAGGCCCTCTCTTGTGCAAATATT TTTTTCCTAATGAAAGAAAGGCCAGTTGCTCCTTAATGGTTGCTAGACATCTCAAAAGTTCAAG ATGATGAAGTTGGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGC TGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGGTATTACTTGCTGATTG TGTTCTGGTTAATAGTATGCTTTTCCATCCTTCACATTTTAAAGCTTGGTAACTATTTTAGCAG GCCGTGTTACTTGGTCTTGCTTGCGTCAATCGGTCAATCCCATAGTAACAATTCAAATAGAATA ATAGATGAGGCATACAATACAAGGTCTAAGGATGGATTCAACTGTTAAGTGTTTCAAAATTTGA GATGTGGCTTCCTTTCTTTACATTTCATGTTTTCAGATTAATCTACCATTTTTTAGTACTAGTA TTGTGTAGGCAGTGCACTGTTCTGGTTCTAATCTGTCATGGGTTGCCTGTTTTGTACCGAGATA GCTAGTGTGTATTCTGAGGAACTACTAGTATGCATTCTAGATCACTGCTGCAAAGCTACAACCA TTGTTTTTTATGATGAGATTCAACGTCTCCAGCACTTAATTCATCCTGTAAAATTTTAGGTTAC AGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATA CAGGTAAGTTATTTTCTCAATCTCATGGTTGGAAAGCATAGTTTTTCAGGTTCATAAGACACCA TCTTATTTGAGCCATTCTTTTCCTTATCAATAAATTTGTATTTTGCATAGCATGTAGGATTTGA CGTCATTAAGGATTTGTTATTTTTGAGTAATATTTAAACTCATATGGATTCAAATTCACTTCAT CTTGCATCTCATGGATTCTCTCAGGAATATGCCACCATGCCCATCAATCTCATGACAATATTCT TTTTCATTCTTCTGCAGATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGT TCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGC TTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13187328

Conservation Information
Conserved circRNAs	NA
PMCS	0.13187328

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34258871-34258310(+)
34258345-34259752(-)
						
						Potential amino acid sequence
						
							MKIHPMTIIAGYRMALECARDSLLKKTMDNKENTDKFRSDLMNIAMTTLSSKILSQDKEYFAEL
AVDAVLRLKGQDPAINWQRT*(+)
MVAPSFVTVTLRPLPVDCRILSLKPQDSINRKFSEVLLVLGKYF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	34258871-34258310(+) 34258345-34259752(-)
Potential amino acid sequence	MKIHPMTIIAGYRMALECARDSLLKKTMDNKENTDKFRSDLMNIAMTTLSSKILSQDKEYFAEL AVDAVLRLKGQDPAINWQRT(+) MVAPSFVTVTLRPLPVDCRILSLKPQDSINRKFSEVLLVLGKYF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d040257_circ_g.1

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