Plant Circular RNA Database

Detail information of Zm00001d000349_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d000349_circ_g.2
					
						ID in PlantcircBase
						zma_circ_010408
					
						Alias
						Zm_ctg_circ00014, GRMZM5G809546_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chrB73V4_ctg35: 26171-26569  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d000349						
					
						Parent gene annotation
						
							Preprotein translocase subunit SCY1 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d000349_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d000349_T001:2

General Information
CircRNA Name	Zm00001d000349_circ_g.2
ID in PlantcircBase	zma_circ_010408
Alias	Zm_ctg_circ00014, GRMZM5G809546_C1
Organism	Zea mays
Position	chrB73V4_ctg35: 26171-26569 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d000349
Parent gene annotation	Preprotein translocase subunit SCY1 chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d000349_circ_g.1
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d000349_T001:2

			
						 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  
						
							CCTTCTTAAGAAAGTCTAAGCCAGAAAACCGTGCCAAAGTACCAGGCAAAGCCAGTGAAGATGT
AGAAAATATGATAGGCATGACTCCAGAACTGTTGACtgttttaatataagcagctgtacttttt
cctggtctaacaagtggtatcgaagcaccttgccgcttcaattgttcactaagatcatcaggat
ctaactgg

						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: 289
Transcript exons: ,26171-26334,26446-26569
TGTTTTAATATAAGCAGCTGTACTTTTTCCTGGTCTAACAAGTGGTATCGAAGCACCTTGCCGC
TTCAATTGTTCACTAAGATCATCAGGATCTAACTGGAGAAACGTGTAATAATAGTTGAAGAAGG
CTATAAGTAATACATTAGTTGGAAGATAGAGAGCACCTCCTGGATTAAGGGCTATGGCAGCCTT
CTTAAGAAAGTCTAAGCCAGAAAACCGTGCCAAAGTACCAGGCAAAGCCAGTGAAGATGTAGAA
AATATGATAGGCATGACTCCAGAACTGTTGAC
						
						Genomic sequence
						
							TGTTTTAATATAAGCAGCTGTACTTTTTCCTGGTCTAACAAGTGGTATCGAAGCACCTTGCCGC
TTCAATTGTTCACTAAGATCATCAGGATCTAACTGGAGAAACGTGTAATAATAGTTGAAGAAGG
CTATAAGTAATACATTAGTTGGAAGATAGAGAGCACCTACAGCAGAAAATTAAAATTCGGCTCA
GTTTGTGAAAAAATAATTCATGAGCTTGGCATTCTCCTGAAAAAAGTAGAAATTTCAATGAACT
AGAAATCAAGATAGTTTACCTCCTGGATTAAGGGCTATGGCAGCCTTCTTAAGAAAGTCTAAGC
CAGAAAACCGTGCCAAAGTACCAGGCAAAGCCAGTGAAGATGTAGAAAATATGATAGGCATGAC
TCCAGAACTGTTGAC

Sequences
Splice junction sequence	CCTTCTTAAGAAAGTCTAAGCCAGAAAACCGTGCCAAAGTACCAGGCAAAGCCAGTGAAGATGT AGAAAATATGATAGGCATGACTCCAGAACTGTTGACtgttttaatataagcagctgtacttttt cctggtctaacaagtggtatcgaagcaccttgccgcttcaattgttcactaagatcatcaggat ctaactgg
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: 289 Transcript exons: ,26171-26334,26446-26569 TGTTTTAATATAAGCAGCTGTACTTTTTCCTGGTCTAACAAGTGGTATCGAAGCACCTTGCCGC TTCAATTGTTCACTAAGATCATCAGGATCTAACTGGAGAAACGTGTAATAATAGTTGAAGAAGG CTATAAGTAATACATTAGTTGGAAGATAGAGAGCACCTCCTGGATTAAGGGCTATGGCAGCCTT CTTAAGAAAGTCTAAGCCAGAAAACCGTGCCAAAGTACCAGGCAAAGCCAGTGAAGATGTAGAA AATATGATAGGCATGACTCCAGAACTGTTGAC
Genomic sequence	TGTTTTAATATAAGCAGCTGTACTTTTTCCTGGTCTAACAAGTGGTATCGAAGCACCTTGCCGC TTCAATTGTTCACTAAGATCATCAGGATCTAACTGGAGAAACGTGTAATAATAGTTGAAGAAGG CTATAAGTAATACATTAGTTGGAAGATAGAGAGCACCTACAGCAGAAAATTAAAATTCGGCTCA GTTTGTGAAAAAATAATTCATGAGCTTGGCATTCTCCTGAAAAAAGTAGAAATTTCAATGAACT AGAAATCAAGATAGTTTACCTCCTGGATTAAGGGCTATGGCAGCCTTCTTAAGAAAGTCTAAGC CAGAAAACCGTGCCAAAGTACCAGGCAAAGCCAGTGAAGATGTAGAAAATATGATAGGCATGAC TCCAGAACTGTTGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.424489434

Conservation Information
Conserved circRNAs	NA
PMCS	0.424489434

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26464-26180(+)
26553-26173(-)
						
						Potential amino acid sequence
						
							MAAFLRKSKPENRAKVPGKASEDVENMIGMTPELLTVLI*(+)
MPIIFSTSSLALPGTLARFSGLDFLKKAAIALNPGGALYLPTNVLLIAFFNYYYTFLQLDPDDL
SEQLKRQGASIPLVRPGKSTAAYIKTVNSSGVMPIIFSTSSLALPGTLARFSGLDFLKKAAIAL
NPGGALYLPTNVLLIAFFNYYYTFLQLDPDDLSEQLKRQGASIPLVRPGKSTAAYIKTVNSSGV
MPIIFSTSSLALPGTLARFSGLDFLKKAAIALNPGGALYLPTNVLLIAFFNYYYTFLQLDPDDL
SEQLKRQGASIPLVRPGKSTAAYIKTVNSSGVMPIIFSTSSLALPGTLARFSGLDFLKKAAIAL
NPGGALYLPTNVLLIAFFNYYYTFLQLDPDDLSEQLKRQGASIPLVRPGKSTAAYIKT(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	26464-26180(+) 26553-26173(-)
Potential amino acid sequence	MAAFLRKSKPENRAKVPGKASEDVENMIGMTPELLTVLI*(+) MPIIFSTSSLALPGTLARFSGLDFLKKAAIALNPGGALYLPTNVLLIAFFNYYYTFLQLDPDDL SEQLKRQGASIPLVRPGKSTAAYIKTVNSSGVMPIIFSTSSLALPGTLARFSGLDFLKKAAIAL NPGGALYLPTNVLLIAFFNYYYTFLQLDPDDLSEQLKRQGASIPLVRPGKSTAAYIKTVNSSGV MPIIFSTSSLALPGTLARFSGLDFLKKAAIALNPGGALYLPTNVLLIAFFNYYYTFLQLDPDDL SEQLKRQGASIPLVRPGKSTAAYIKTVNSSGVMPIIFSTSSLALPGTLARFSGLDFLKKAAIAL NPGGALYLPTNVLLIAFFNYYYTFLQLDPDDLSEQLKRQGASIPLVRPGKSTAAYIKT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d000349_circ_g.2

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