Plant Circular RNA Database

Detail information of Zm00001d011713_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d011713_circ_g.6
					
						ID in PlantcircBase
						zma_circ_009758
					
						Alias
						zma_circ_0002875
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 159554904-159556558  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d011713						
					
						Parent gene annotation
						
							Myosin family protein with Dil domain
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d011713_T008:6
Zm00001d011713_T012:6
Zm00001d011713_T010:6
Zm00001d011713_T005:1
Zm00001d011713_T006:6
Zm00001d011713_T004:6
Zm00001d011713_T009:3
Zm00001d011713_T019:2
Zm00001d011713_T013:6
Zm00001d011713_T007:6
Zm00001d011713_T003:6
Zm00001d011713_T017:5
Zm00001d011713_T014:6
Zm00001d011713_T016:6
Zm00001d011713_T015:6

General Information
CircRNA Name	Zm00001d011713_circ_g.6
ID in PlantcircBase	zma_circ_009758
Alias	zma_circ_0002875
Organism	Zea mays
Position	chr8: 159554904-159556558 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d011713
Parent gene annotation	Myosin family protein with Dil domain
Parent gene strand	-
Alternative splicing	NA
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	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	Zm00001d011713_T008:6 Zm00001d011713_T012:6 Zm00001d011713_T010:6 Zm00001d011713_T005:1 Zm00001d011713_T006:6 Zm00001d011713_T004:6 Zm00001d011713_T009:3 Zm00001d011713_T019:2 Zm00001d011713_T013:6 Zm00001d011713_T007:6 Zm00001d011713_T003:6 Zm00001d011713_T017:5 Zm00001d011713_T014:6 Zm00001d011713_T016:6 Zm00001d011713_T015:6

			
						 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  
						
							GACTCTGAAGGCCTCTTGCTGCACTGTTTCGCATCTCTGTTCTTCTGCCATCCAGTTCAGCCAT
TTGACCAGCCCTCAGGAACACCTTAGTTCTTCCTATctctgtacagtatcactaaattgtttga
tcttttcatccgcatcactgattttcttatttaactcttcatttgtttctagagcattagcatg
cactttct

									
								

					

						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
						
							CTCTGTACAGTATCACTAAATTGTTTGATCTTTTCATCCGCATCACTGATTTTCTTATTTAACT
CTTCATTTGTTTCTAGAGCATTAGCATGCACTTTCTTCATTACATCATTCTCCTCTCGTTCAGC
TACTAGCAGGGCCTGTAATAATAGCATGCACCAATTGTCAAACATTCTTGGCAATGTCTAACAT
GCTAAGTTTAGAGTACAACTTAATTAAATTCTAAGAGAAATGTTATGTTAGCATACTATTGAGT
GTATGACCTTAAGATTATCCATTTGATAAAACAGAATAAGGTTAGTCCTTGTTTCAATCCTTAT
GCTTGTAGATCAGTTGCAACAAAGCAGAATATTATGGATGAAGAACGTACATTTAGGCCCTCGA
TTTCAGTAGTCAATAAACTGATCTTTTCTCTTTCTTGAGTTAGAGCTTCTTCAACAGCCTTTTT
TGCTGATTCCTGTTCCTGCATCGCTTTGACTTCTTCTACCTGCTGCTCCATCTCATAAAGAGCT
TCTTTCAATTTGGAAACTTCTTCTGCTTTGGACTTCTCAAAATCAGCCTGTAAATTGAATATAC
ACATGACTATGATCCATAGATGCTGTCTATAAGCATGAAAACTGCAGTTGCACCATGTGCCAAT
ACAGGATGCAACATAATGTACTTCTTGGTTCAAATAATAGGCACATATAACAAGTATTTAAATA
CTGTTCAAGACCAAGTATTGACCCTCAGTTTCTTCTCTCGGCCTAGGCAACTTTTTAGCTCTTC
CACATATTCCTCAAGTTTCTCTTTGGCCACCTTTAGAGCTTGTGTATCTCTTGCAGCCTAGGAA
ACGCACAAACCATAACGAGCTTAGGATAAATTTTACAGAATGAATACCATAGGTTGCAAGTACC
ATTTTGAGCTTCCTCAGCTCCTTCCTAGCAACACTTCTTCGCCAAGCACACTGATATGTTAGTG
CAGCTCTCTTCAATTTCATAAAATTTGAGTAATCTCTGTGGCATCGCCACTGGGACTGCAGGAA
AGAAGTCGCATAGTGATGGTCTAAACAGAAGCAAAAAGAAAATAGAGAAAAACGAGAACACATA
ATAGCGACATCCAACAGGAGATTAATATCCATCTGCAGTATAATAAGTAAAAATAGCTGCAAAA
TGCTATAAGTGCTATCCTACCTGGATATGGACTGAAGCTTTATTTCTCTTTCTAAAGGTGAATT
CATTACGAGCTGCCATGGCCCTTAGCCCGGCCTGCAATGTAATGGCTGACAACCGCATTTGGTA
ATAAGTTTTCCAGGCAAAATACCATCGGGCGTTTTTCTGAATTCTCAAAACTGCTGTTTGTTGT
CTCAGCAACTCATGTTGCTTACAAGCCAATCTTGCTGTAATTGAAAATAGAGATCTTAGTATAT
GTACAAGGCTCTCCACTATGGCTCCATGAGCATGCAATTTACATCAAGTGCTATACGGAAAGAG
TTTACCTCTAACGAAAGATTGTAAACAAATAGATGTGTCCCGTAGTACTAGGAATTGCTCACGA
GCAACATGAGTACGAAATTGACTCTGAAGGCCTCTTGCTGCACTGTTTCGCATCTCTGTTCTTC
TGCCATCCAGTTCAGCCATTTGACCAGCCCTCAGGAACACCTTAGTTCTTCCTAT
						
					

			
		

Sequences
Splice junction sequence	GACTCTGAAGGCCTCTTGCTGCACTGTTTCGCATCTCTGTTCTTCTGCCATCCAGTTCAGCCAT TTGACCAGCCCTCAGGAACACCTTAGTTCTTCCTATctctgtacagtatcactaaattgtttga tcttttcatccgcatcactgattttcttatttaactcttcatttgtttctagagcattagcatg cactttct
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	CTCTGTACAGTATCACTAAATTGTTTGATCTTTTCATCCGCATCACTGATTTTCTTATTTAACT CTTCATTTGTTTCTAGAGCATTAGCATGCACTTTCTTCATTACATCATTCTCCTCTCGTTCAGC TACTAGCAGGGCCTGTAATAATAGCATGCACCAATTGTCAAACATTCTTGGCAATGTCTAACAT GCTAAGTTTAGAGTACAACTTAATTAAATTCTAAGAGAAATGTTATGTTAGCATACTATTGAGT GTATGACCTTAAGATTATCCATTTGATAAAACAGAATAAGGTTAGTCCTTGTTTCAATCCTTAT GCTTGTAGATCAGTTGCAACAAAGCAGAATATTATGGATGAAGAACGTACATTTAGGCCCTCGA TTTCAGTAGTCAATAAACTGATCTTTTCTCTTTCTTGAGTTAGAGCTTCTTCAACAGCCTTTTT TGCTGATTCCTGTTCCTGCATCGCTTTGACTTCTTCTACCTGCTGCTCCATCTCATAAAGAGCT TCTTTCAATTTGGAAACTTCTTCTGCTTTGGACTTCTCAAAATCAGCCTGTAAATTGAATATAC ACATGACTATGATCCATAGATGCTGTCTATAAGCATGAAAACTGCAGTTGCACCATGTGCCAAT ACAGGATGCAACATAATGTACTTCTTGGTTCAAATAATAGGCACATATAACAAGTATTTAAATA CTGTTCAAGACCAAGTATTGACCCTCAGTTTCTTCTCTCGGCCTAGGCAACTTTTTAGCTCTTC CACATATTCCTCAAGTTTCTCTTTGGCCACCTTTAGAGCTTGTGTATCTCTTGCAGCCTAGGAA ACGCACAAACCATAACGAGCTTAGGATAAATTTTACAGAATGAATACCATAGGTTGCAAGTACC ATTTTGAGCTTCCTCAGCTCCTTCCTAGCAACACTTCTTCGCCAAGCACACTGATATGTTAGTG CAGCTCTCTTCAATTTCATAAAATTTGAGTAATCTCTGTGGCATCGCCACTGGGACTGCAGGAA AGAAGTCGCATAGTGATGGTCTAAACAGAAGCAAAAAGAAAATAGAGAAAAACGAGAACACATA ATAGCGACATCCAACAGGAGATTAATATCCATCTGCAGTATAATAAGTAAAAATAGCTGCAAAA TGCTATAAGTGCTATCCTACCTGGATATGGACTGAAGCTTTATTTCTCTTTCTAAAGGTGAATT CATTACGAGCTGCCATGGCCCTTAGCCCGGCCTGCAATGTAATGGCTGACAACCGCATTTGGTA ATAAGTTTTCCAGGCAAAATACCATCGGGCGTTTTTCTGAATTCTCAAAACTGCTGTTTGTTGT CTCAGCAACTCATGTTGCTTACAAGCCAATCTTGCTGTAATTGAAAATAGAGATCTTAGTATAT GTACAAGGCTCTCCACTATGGCTCCATGAGCATGCAATTTACATCAAGTGCTATACGGAAAGAG TTTACCTCTAACGAAAGATTGTAAACAAATAGATGTGTCCCGTAGTACTAGGAATTGCTCACGA GCAACATGAGTACGAAATTGACTCTGAAGGCCTCTTGCTGCACTGTTTCGCATCTCTGTTCTTC TGCCATCCAGTTCAGCCATTTGACCAGCCCTCAGGAACACCTTAGTTCTTCCTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.139888615

Conservation Information
Conserved circRNAs	NA
PMCS	0.139888615

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							159556446-159555322(+)
159556524-159556557(-)
						
						Potential amino acid sequence
						
							MSTKLTLKASCCTVSHLCSSAIQFSHLTSPQEHLSSSYLCTVSLNCLIFSSASLIFLFNSSFVS
RALACTFFITSFSSRSATSRAFRPSISVVNKLIFSLS*(+)
MAELDGRRTEMRNSAARGLQSQFRTHVAREQFLVLRDTSICLQSFVRARLACKQHELLRQQTAV
LRIQKNARWYFAWKTYYQMRLSAITLQAGLRAMAARNEFTFRKRNKASVHIQSQWRCHRDYSNF
MKLKRAALTYQCAWRRSVARKELRKLKMAARDTQALKVAKEKLEEYVEELKSCLGREKKLRADF
EKSKAEEVSKLKEALYEMEQQVEEVKAMQEQESAKKAVEEALTQEREKISLLTTEIEGLNALLV
AEREENDVMKKVHANALETNEELNKKISDADEKIKQFSDTVQR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	159556446-159555322(+) 159556524-159556557(-)
Potential amino acid sequence	MSTKLTLKASCCTVSHLCSSAIQFSHLTSPQEHLSSSYLCTVSLNCLIFSSASLIFLFNSSFVS RALACTFFITSFSSRSATSRAFRPSISVVNKLIFSLS(+) MAELDGRRTEMRNSAARGLQSQFRTHVAREQFLVLRDTSICLQSFVRARLACKQHELLRQQTAV LRIQKNARWYFAWKTYYQMRLSAITLQAGLRAMAARNEFTFRKRNKASVHIQSQWRCHRDYSNF MKLKRAALTYQCAWRRSVARKELRKLKMAARDTQALKVAKEKLEEYVEELKSCLGREKKLRADF EKSKAEEVSKLKEALYEMEQQVEEVKAMQEQESAKKAVEEALTQEREKISLLTTEIEGLNALLV AEREENDVMKKVHANALETNEELNKKISDADEKIKQFSDTVQR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d011713_circ_g.6

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