Plant Circular RNA Database

Detail information of Zm00001d040154_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d040154_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007532
					
						Alias
						zma_circ_0001427, GRMZM2G036206_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 29452542-29453502  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d040154						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d040154_circ_g.3 						
					
						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
						Zm00001d040154_T001:5

General Information
CircRNA Name	Zm00001d040154_circ_g.4
ID in PlantcircBase	zma_circ_007532
Alias	zma_circ_0001427, GRMZM2G036206_C2
Organism	Zea mays
Position	chr3: 29452542-29453502 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d040154
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Zm00001d040154_circ_g.3
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	Zm00001d040154_T001:5

			
						 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  
						
							GAGGATTTACTGAAGAGCTAGAGCCATCCATTTTATTAGAAACAGAATTGCGCTCTTGACCTAG
TCCACTGAAAGAACTTTGGGATGTAGCATCTTCCCTctgcaacgcatacgtgagacgaatgttt
tcctcaataatatcttgcctgtatgacaaagcttttgaagctgcatcaattaaatcatgctgct
gctggtca

									
								

					

						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: 618
Transcript exons: 29452542-29452646,29452723-29452782,29452862-29452939,29
453022-29453097,29453204-29453502
CTGCAACGCATACGTGAGACGAATGTTTTCCTCAATAATATCTTGCCTGTATGACAAAGCTTTT
GAAGCTGCATCAATTAAATCATGCTGCTGCTGGTCAAATGCCATACGCATATAAGCAATCCGTT
TTTCTAACTTGTATTTATCATCGAGTATTTGAGCTTCCTTCACAGAGTAATCAGCAAGATGTTT
TCTTAATTGTGCAATCTCTTCTTCCCCTTCTTTGACCTTAACAGTAAGGTCCTGCTTCCAGGAT
ATGTTCGAGTTCATCTCTGAAACTGGTAATAATCTAGAATCATAATCTCCATCTTTTCTATGTC
TATTTGGAGAATGGGACCGAGATGAGGGAGTAGAGAATTGTGATGGGCCACCACTATCAACAGC
AGTTTGTTCGCCTAATGATCTTTTAAATGCTCCATTTGCCTGGGGACTGTCAAGGTATTTTTGT
TTTGAGCTTTCATCAATCAGATGCTCTCTACTCTCACAACATCCATTCTGAGGATGGATCAAGG
TACTTTGAGGATTTACTGAAGAGCTAGAGCCATCCATTTTATTAGAAACAGAATTGCGCTCTTG
ACCTAGTCCACTGAAAGAACTTTGGGATGTAGCATCTTCCCT
						
					

						Genomic sequence
						
							CTGCAACGCATACGTGAGACGAATGTTTTCCTCAATAATATCTTGCCTGTATGACAAAGCTTTT
GAAGCTGCATCAATTAAATCATGCTGCTGCTGGTCAAATGCCTGAAAACAACTATTAAGATGAG
ATGATAGACACACTCCAAGGAATTATTCTCTTTCGATAAAATGAACATCTTACCATACGCATAT
AAGCAATCCGTTTTTCTAACTTGTATTTATCATCGAGTATTTGAGCTTCCTGTCAGGAGTTGTT
TGTGGTCAACAGAAGCTCAAAAAGGAAAATACAGTAAGGTGACCTTTACATGTAAATGGTTTAC
CTTCACAGAGTAATCAGCAAGATGTTTTCTTAATTGTGCAATCTCTTCTTCCCCTTCTTTGACC
TTAACAGTAAGGTCCTGTGTAGGACCTATCATTATTAGGAACGGTGTACCATAGGTATGCAGAA
TTGCAGATGACGCTGAACAAGAACTAGTTTACCTGCTTCCAGGATATGTTCGAGTTCATCTCTG
AAACTGGTAATAATCTAGAATCATAATCTCCATCTTTTCTATGTCTGCAACAGATCTATATCAA
TATAAGGCAACCAAAATACCATCCCAAGACACAAACATAGACATATATATAGACATATATATAT
ATATATATATCTGCTACTTTACCTATTTGGAGAATGGGACCGAGATGAGGGAGTAGAGAATTGT
GATGGGCCACCACTATCAACAGCAGTTTGTTCGCCTAATGATCTTTTAAATGCTCCATTTGCCT
GGGGACTGTCAAGGTATTTTTGTTTTGAGCTTTCATCAATCAGATGCTCTCTACTCTCACAACA
TCCATTCTGAGGATGGATCAAGGTACTTTGAGGATTTACTGAAGAGCTAGAGCCATCCATTTTA
TTAGAAACAGAATTGCGCTCTTGACCTAGTCCACTGAAAGAACTTTGGGATGTAGCATCTTCCC
T
						
					

			
		

Sequences
Splice junction sequence	GAGGATTTACTGAAGAGCTAGAGCCATCCATTTTATTAGAAACAGAATTGCGCTCTTGACCTAG TCCACTGAAAGAACTTTGGGATGTAGCATCTTCCCTctgcaacgcatacgtgagacgaatgttt tcctcaataatatcttgcctgtatgacaaagcttttgaagctgcatcaattaaatcatgctgct gctggtca
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: 618 Transcript exons: 29452542-29452646,29452723-29452782,29452862-29452939,29 453022-29453097,29453204-29453502 CTGCAACGCATACGTGAGACGAATGTTTTCCTCAATAATATCTTGCCTGTATGACAAAGCTTTT GAAGCTGCATCAATTAAATCATGCTGCTGCTGGTCAAATGCCATACGCATATAAGCAATCCGTT TTTCTAACTTGTATTTATCATCGAGTATTTGAGCTTCCTTCACAGAGTAATCAGCAAGATGTTT TCTTAATTGTGCAATCTCTTCTTCCCCTTCTTTGACCTTAACAGTAAGGTCCTGCTTCCAGGAT ATGTTCGAGTTCATCTCTGAAACTGGTAATAATCTAGAATCATAATCTCCATCTTTTCTATGTC TATTTGGAGAATGGGACCGAGATGAGGGAGTAGAGAATTGTGATGGGCCACCACTATCAACAGC AGTTTGTTCGCCTAATGATCTTTTAAATGCTCCATTTGCCTGGGGACTGTCAAGGTATTTTTGT TTTGAGCTTTCATCAATCAGATGCTCTCTACTCTCACAACATCCATTCTGAGGATGGATCAAGG TACTTTGAGGATTTACTGAAGAGCTAGAGCCATCCATTTTATTAGAAACAGAATTGCGCTCTTG ACCTAGTCCACTGAAAGAACTTTGGGATGTAGCATCTTCCCT
Genomic sequence	CTGCAACGCATACGTGAGACGAATGTTTTCCTCAATAATATCTTGCCTGTATGACAAAGCTTTT GAAGCTGCATCAATTAAATCATGCTGCTGCTGGTCAAATGCCTGAAAACAACTATTAAGATGAG ATGATAGACACACTCCAAGGAATTATTCTCTTTCGATAAAATGAACATCTTACCATACGCATAT AAGCAATCCGTTTTTCTAACTTGTATTTATCATCGAGTATTTGAGCTTCCTGTCAGGAGTTGTT TGTGGTCAACAGAAGCTCAAAAAGGAAAATACAGTAAGGTGACCTTTACATGTAAATGGTTTAC CTTCACAGAGTAATCAGCAAGATGTTTTCTTAATTGTGCAATCTCTTCTTCCCCTTCTTTGACC TTAACAGTAAGGTCCTGTGTAGGACCTATCATTATTAGGAACGGTGTACCATAGGTATGCAGAA TTGCAGATGACGCTGAACAAGAACTAGTTTACCTGCTTCCAGGATATGTTCGAGTTCATCTCTG AAACTGGTAATAATCTAGAATCATAATCTCCATCTTTTCTATGTCTGCAACAGATCTATATCAA TATAAGGCAACCAAAATACCATCCCAAGACACAAACATAGACATATATATAGACATATATATAT ATATATATATCTGCTACTTTACCTATTTGGAGAATGGGACCGAGATGAGGGAGTAGAGAATTGT GATGGGCCACCACTATCAACAGCAGTTTGTTCGCCTAATGATCTTTTAAATGCTCCATTTGCCT GGGGACTGTCAAGGTATTTTTGTTTTGAGCTTTCATCAATCAGATGCTCTCTACTCTCACAACA TCCATTCTGAGGATGGATCAAGGTACTTTGAGGATTTACTGAAGAGCTAGAGCCATCCATTTTA TTAGAAACAGAATTGCGCTCTTGACCTAGTCCACTGAAAGAACTTTGGGATGTAGCATCTTCCC T

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211037068

Conservation Information
Conserved circRNAs	NA
PMCS	0.211037068

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29453435-29452544(-)
29452617-29453465(-)
						
						Potential amino acid sequence
						
							MDGSSSSVNPQSTLIHPQNGCCESREHLIDESSKQKYLDSPQANGAFKRSLGEQTAVDSGGPSQ
FSTPSSRSHSPNRHRKDGDYDSRLLPVSEMNSNISWKQDLTVKVKEGEEEIAQLRKHLADYSVK
EAQILDDKYKLEKRIAYMRMAFDQQQHDLIDAASKALSYRQDIIEENIRLTYALQREDATSQSS
FSGLGQERNSVSNKMDGSSSSVNPQSTLIHPQNGCCESREHLIDESSKQKYLDSPQANGAFKRS
LGEQTAVDSGGPSQFSTPSSRSHSPNRHRKDGDYDSRLLPVSEMNSNISWKQDLTVKVKEGEEE
IAQLRKHLADYSVKEAQILDDKYKLEKRIAYMRMAFDQQQHDLIDAASKALSYRQDIIEENIRL
TYALQREDATSQSSFSGLGQERNSVSNKMDGSSSSVNPQSTLIHPQNGCCESREHLIDESSKQK
YLDSPQANGAFKRSLGEQTAVDSGGPSQFSTPSSRSHSPNRHRKDGDYDSRLLPVSEMNSNISW
KQDLTVKVKEGEEEIAQLRKHLADYSVKEAQILDDKYKLEKRIAYMRMAFDQQQHDLIDAASKA
LSYRQDIIEENIRLTYALQREDATSQSSFSGLGQERNSVSNKMDGSSSSVNPQSTLIHPQNGCC
ESREHLIDESSKQKYLDSPQANGAFKRSLGEQTAVDSGGPSQFSTPSSRSHSPNRHRKDGDYDS
RLLPVSEMNSNISWKQDLTVKVKEGEEEIAQLRKHLADYSVKEAQILDDKYKLEKRIAYMRMAF
DQQQHDLIDAASKALSYRQDIIEENIRLTYALQ(-)
MQLQKLCHTGKILLRKTFVSRMRCRGKMLHPKVLSVD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29453435-29452544(-) 29452617-29453465(-)
Potential amino acid sequence	MDGSSSSVNPQSTLIHPQNGCCESREHLIDESSKQKYLDSPQANGAFKRSLGEQTAVDSGGPSQ FSTPSSRSHSPNRHRKDGDYDSRLLPVSEMNSNISWKQDLTVKVKEGEEEIAQLRKHLADYSVK EAQILDDKYKLEKRIAYMRMAFDQQQHDLIDAASKALSYRQDIIEENIRLTYALQREDATSQSS FSGLGQERNSVSNKMDGSSSSVNPQSTLIHPQNGCCESREHLIDESSKQKYLDSPQANGAFKRS LGEQTAVDSGGPSQFSTPSSRSHSPNRHRKDGDYDSRLLPVSEMNSNISWKQDLTVKVKEGEEE IAQLRKHLADYSVKEAQILDDKYKLEKRIAYMRMAFDQQQHDLIDAASKALSYRQDIIEENIRL TYALQREDATSQSSFSGLGQERNSVSNKMDGSSSSVNPQSTLIHPQNGCCESREHLIDESSKQK YLDSPQANGAFKRSLGEQTAVDSGGPSQFSTPSSRSHSPNRHRKDGDYDSRLLPVSEMNSNISW KQDLTVKVKEGEEEIAQLRKHLADYSVKEAQILDDKYKLEKRIAYMRMAFDQQQHDLIDAASKA LSYRQDIIEENIRLTYALQREDATSQSSFSGLGQERNSVSNKMDGSSSSVNPQSTLIHPQNGCC ESREHLIDESSKQKYLDSPQANGAFKRSLGEQTAVDSGGPSQFSTPSSRSHSPNRHRKDGDYDS RLLPVSEMNSNISWKQDLTVKVKEGEEEIAQLRKHLADYSVKEAQILDDKYKLEKRIAYMRMAF DQQQHDLIDAASKALSYRQDIIEENIRLTYALQ(-) MQLQKLCHTGKILLRKTFVSRMRCRGKMLHPKVLSVD*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d040154_circ_g.4

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