Plant Circular RNA Database

Detail information of Zm00001d032921_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d032921_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006837
					
						Alias
						Zm01circ00153, zma_circ_0000466, GRMZM5G813143_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 243115303-243116504  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d032921						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d032921_circ_g.1 Zm00001d032921_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  
						
							GT-AG							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
						Zm00001d032921_T001:3
Zm00001d032921_T003:3
Zm00001d032921_T002:3

General Information
CircRNA Name	Zm00001d032921_circ_g.3
ID in PlantcircBase	zma_circ_006837
Alias	Zm01circ00153, zma_circ_0000466, GRMZM5G813143_C1
Organism	Zea mays
Position	chr1: 243115303-243116504 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d032921
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d032921_circ_g.1 Zm00001d032921_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	GT-AG 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	Zm00001d032921_T001:3 Zm00001d032921_T003:3 Zm00001d032921_T002:3

			
						 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  
						
							CAGGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGG
GCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgcattgaaacattttcctcgtgagaagg
tgcaaattgccaccaaatgtggcattgcaggatttgatgcaagtggcatgcgtgtgaagggcac
tccagatt

									
								

					

						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: 474
Transcript exons: 243115303-243115506,243115587-243115759,243116408-243116
504
GCATTGAAACATTTTCCTCGTGAGAAGGTGCAAATTGCCACCAAATGTGGCATTGCAGGATTTG
ATGCAAGTGGCATGCGTGTGAAGGGCACTCCAGATTATGTTCGAGCTTGTTGTGAAGCAAGCCT
TCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCT
ATAGAGGAAACTATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGCT
TATCAGAGGCTAGTGCCGATACCATTCGACGGGCACATGCTGTCCATCCAATTACTGCGGTGCA
GTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGGGAGCTT
GGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAG
AACGTGTTCCATCAGAAAGTCTATTG
						
					

						Genomic sequence
						
							GCATTGAAACATTTTCCTCGTGAGAAGGTGCAAATTGCCACCAAATGTGGCATTGCAGGATTTG
ATGCAAGTGGCATGCGTGTGAAGGGCACTCCAGATTATGTTCGAGCTTGTTGTGAAGCAAGCCT
TCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCT
ATAGAGGAAACTGTGTGTATCTGTTGACCGTGAACTATGCTTTGTAGTTTGCATTTCATCCATT
CTGTGTGACATCATCAATGGTTGTGTAGATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAA
GTGAGGTATGTTGGCTTATCAGAGGCTAGTGCCGATACCATTCGACGGGCACATGCTGTCCATC
CAATTACTGCGGTGCAGTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCC
AGTCTGCAGGTTCATCCCCTCCTTAACCTATATACTTGAACAATGTTATCTACCTTTACTTCCA
GAAACTTTGGCATGTTATATGCCTTAGCCTTCGATGCAATCTCTTTATTCCATTGGAACTTATG
TTTGCAGCCTTGATTAGCATTATTGGTTCTTAACAATTTTAGTCACAATATGTTCTTTTGGAAA
ATTCCTTATCATCGATTAAAAATAATAACCTTTGAAATGTGAGAGAAAAAATATCCTGCTTTTG
TTTATGTTACGACTGTACTACTATGCCTATCAGGTTTGTGTTGACTATTGTGAGTAAATTTTTA
AGTTTATGTACTTATATAACAATTGTATATATCTGGTGTCATGAATCTGTCTTATAAGTTTCAC
AATCATCAGAGATCAGACCCCAGCTTACATATTGTACGATGCTGACTATTGATTTTACACTGAT
GAATACACAATATGGACTGTTAGACTTTTTAAGTTATGTGTTTTAGGGACTTGCTATCAGTGTA
GACACTATGCAATGTTTACATGGAGTTTTGATTTCTCTCTTTCTATTGCAAGTTCTAATTAACT
TATGCTTCATTTTTCTTATCTTTGGTTCGTTGAACATCGATATCATGCATTTATCTGTTTGTCA
TAAATGCTTGCATTCAGGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCT
TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG
						
					

			
		

Sequences
Splice junction sequence	CAGGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGG GCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgcattgaaacattttcctcgtgagaagg tgcaaattgccaccaaatgtggcattgcaggatttgatgcaagtggcatgcgtgtgaagggcac tccagatt
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: 474 Transcript exons: 243115303-243115506,243115587-243115759,243116408-243116 504 GCATTGAAACATTTTCCTCGTGAGAAGGTGCAAATTGCCACCAAATGTGGCATTGCAGGATTTG ATGCAAGTGGCATGCGTGTGAAGGGCACTCCAGATTATGTTCGAGCTTGTTGTGAAGCAAGCCT TCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCT ATAGAGGAAACTATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGCT TATCAGAGGCTAGTGCCGATACCATTCGACGGGCACATGCTGTCCATCCAATTACTGCGGTGCA GTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGGGAGCTT GGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAG AACGTGTTCCATCAGAAAGTCTATTG
Genomic sequence	GCATTGAAACATTTTCCTCGTGAGAAGGTGCAAATTGCCACCAAATGTGGCATTGCAGGATTTG ATGCAAGTGGCATGCGTGTGAAGGGCACTCCAGATTATGTTCGAGCTTGTTGTGAAGCAAGCCT TCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCT ATAGAGGAAACTGTGTGTATCTGTTGACCGTGAACTATGCTTTGTAGTTTGCATTTCATCCATT CTGTGTGACATCATCAATGGTTGTGTAGATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAA GTGAGGTATGTTGGCTTATCAGAGGCTAGTGCCGATACCATTCGACGGGCACATGCTGTCCATC CAATTACTGCGGTGCAGTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCC AGTCTGCAGGTTCATCCCCTCCTTAACCTATATACTTGAACAATGTTATCTACCTTTACTTCCA GAAACTTTGGCATGTTATATGCCTTAGCCTTCGATGCAATCTCTTTATTCCATTGGAACTTATG TTTGCAGCCTTGATTAGCATTATTGGTTCTTAACAATTTTAGTCACAATATGTTCTTTTGGAAA ATTCCTTATCATCGATTAAAAATAATAACCTTTGAAATGTGAGAGAAAAAATATCCTGCTTTTG TTTATGTTACGACTGTACTACTATGCCTATCAGGTTTGTGTTGACTATTGTGAGTAAATTTTTA AGTTTATGTACTTATATAACAATTGTATATATCTGGTGTCATGAATCTGTCTTATAAGTTTCAC AATCATCAGAGATCAGACCCCAGCTTACATATTGTACGATGCTGACTATTGATTTTACACTGAT GAATACACAATATGGACTGTTAGACTTTTTAAGTTATGTGTTTTAGGGACTTGCTATCAGTGTA GACACTATGCAATGTTTACATGGAGTTTTGATTTCTCTCTTTCTATTGCAAGTTCTAATTAACT TATGCTTCATTTTTCTTATCTTTGGTTCGTTGAACATCGATATCATGCATTTATCTGTTTGTCA TAAATGCTTGCATTCAGGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCT TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.123999548

Conservation Information
Conserved circRNAs	NA
PMCS	0.123999548

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							243115379-243116501(+)
243115475-243116501(-)
243115381-243115484(-)
243115308-243115692(-)
						
						Potential amino acid sequence
						
							MRVKGTPDYVRACCEASLQRLATDYIDIYYQHRIDQSVPIEETMGELKKLVEEGKVRYVGLSEA
SADTIRRAHAVHPITAVQLEWSLWTRDIEEDIIPVCRELGIGIVPYSPLGRGFFAGRAAVERVP
SESLLALKHFPREKVQIATKCGIAGFDASGMRVKGTPDYVRACCEASLQRLATDYIDIYYQHRI
DQSVPIEETMGELKKLVEEGKVRYVGLSEASADTIRRAHAVHPITAVQLEWSLWTRDIEEDIIP
VCRELGIGIVPYSPLGRGFFAGRAAVERVPSESLLALKHFPREKVQIATKCGIAGFDASGMRVK
GTPDYVRACCEASLQRLATDYIDIYYQHRIDQSVPIEETMGELKKLVEEGKVRYVGLSEASADT
IRRAHAVHPITAVQLEWSLWTRDIEEDIIPVCRELGIGIVPYSPLGRGFFAGRAAVERVPSESL
LALKHFPREKVQIATKCGIAGFDASGMRVKGTPDYVRACCEASLQRLATDYIDIYYQHRIDQSV
PIEETMGELKKLVEEGKVRYVGLSEASADTIRRAHAVHPITAVQLEWSLWTRDIEEDIIPVCRE
LGIGIVPYSPLGRGFFAGRAAVERVPSESLL(+)
MLVVYINVVSSKALKACFTTSSNIIWSALHTHATCIKSCNATFGGNLHLLTRKMFQCQ*(-)
MPLASNPAMPHLVAICTFSRGKCFNANRLSDGTRSTAALPAKKPRPSGLYGTIPIPSSLQTGII
SSSISLVHSDHSNCTAVIGWTACARRMVSALASDKPTYLTFPSSTNFLSSPIVSSIGTD*(-)
MPIDFLMEHVLQLPCQQRSHGQVGYMELFQYQAPCRLELYLPLYLWSIVTTPTAPQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	243115379-243116501(+) 243115475-243116501(-) 243115381-243115484(-) 243115308-243115692(-)
Potential amino acid sequence	MRVKGTPDYVRACCEASLQRLATDYIDIYYQHRIDQSVPIEETMGELKKLVEEGKVRYVGLSEA SADTIRRAHAVHPITAVQLEWSLWTRDIEEDIIPVCRELGIGIVPYSPLGRGFFAGRAAVERVP SESLLALKHFPREKVQIATKCGIAGFDASGMRVKGTPDYVRACCEASLQRLATDYIDIYYQHRI DQSVPIEETMGELKKLVEEGKVRYVGLSEASADTIRRAHAVHPITAVQLEWSLWTRDIEEDIIP VCRELGIGIVPYSPLGRGFFAGRAAVERVPSESLLALKHFPREKVQIATKCGIAGFDASGMRVK GTPDYVRACCEASLQRLATDYIDIYYQHRIDQSVPIEETMGELKKLVEEGKVRYVGLSEASADT IRRAHAVHPITAVQLEWSLWTRDIEEDIIPVCRELGIGIVPYSPLGRGFFAGRAAVERVPSESL LALKHFPREKVQIATKCGIAGFDASGMRVKGTPDYVRACCEASLQRLATDYIDIYYQHRIDQSV PIEETMGELKKLVEEGKVRYVGLSEASADTIRRAHAVHPITAVQLEWSLWTRDIEEDIIPVCRE LGIGIVPYSPLGRGFFAGRAAVERVPSESLL(+) MLVVYINVVSSKALKACFTTSSNIIWSALHTHATCIKSCNATFGGNLHLLTRKMFQCQ(-) MPLASNPAMPHLVAICTFSRGKCFNANRLSDGTRSTAALPAKKPRPSGLYGTIPIPSSLQTGII SSSISLVHSDHSNCTAVIGWTACARRMVSALASDKPTYLTFPSSTNFLSSPIVSSIGTD(-) MPIDFLMEHVLQLPCQQRSHGQVGYMELFQYQAPCRLELYLPLYLWSIVTTPTAPQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d032921_circ_g.3

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