Plant Circular RNA Database

Detail information of Zm00001d042809_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d042809_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007737
					
						Alias
						zma_circ_0001248, GRMZM2G127949_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 180801836-180802301  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d042809						
					
						Parent gene annotation
						
							Auxin transporter-like protein 1  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d042809_circ_g.1 Zm00001d042809_circ_g.2 Zm00001d042809_circ_g.4 Zm00001d042809_circ_g.5 						
					
						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
						Zm00001d042809_T006:1
Zm00001d042809_T003:1
Zm00001d042809_T008:1
Zm00001d042809_T005:1
Zm00001d042809_T002:1
Zm00001d042809_T001:1

General Information
CircRNA Name	Zm00001d042809_circ_g.3
ID in PlantcircBase	zma_circ_007737
Alias	zma_circ_0001248, GRMZM2G127949_C1
Organism	Zea mays
Position	chr3: 180801836-180802301 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d042809
Parent gene annotation	Auxin transporter-like protein 1
Parent gene strand	-
Alternative splicing	Zm00001d042809_circ_g.1 Zm00001d042809_circ_g.2 Zm00001d042809_circ_g.4 Zm00001d042809_circ_g.5
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	Zm00001d042809_T006:1 Zm00001d042809_T003:1 Zm00001d042809_T008:1 Zm00001d042809_T005:1 Zm00001d042809_T002:1 Zm00001d042809_T001:1

			
						 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  
						
							GGCCGCCGACGACGGCAGCGTCAGCGTGAACACGTACAGCGTCGCCAGCAGGTAGATGTATTTG
AACTTGGCGGGCTTCCACATCGCGTGCATGATCTCGcatgcgcgcggacgccgtgcggtaggtg
aggacgtgcgccagggccgggatgatgtagacggtgaagctgacgagcagcgcgccgacggcgg
agttgatg

						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: 466
Transcript exons: 180801836-180802301
CATGCGCGCGGACGCCGTGCGGTAGGTGAGGACGTGCGCCAGGGCCGGGATGATGTAGACGGTG
AAGCTGACGAGCAGCGCGCCGACGGCGGAGTTGATGGGCCCGAAGAAGGGGAAGATGATGGCGA
GGAACCAGATGGGCACGACGATGGGCAGCCTCGCCAGCGCGCGCTTGAAGATGCTCTTGGCGTC
GTGCATCCCGATCACCTTCTCCCACACGAAGTAGAGCGGCGTGCACGCGAAGCCGAAGGTGATG
AACTGGTGGATCAGCATCAGGATCACCGCCGCGTCGCGCCACCGGGTCTTGGGCAGCAGCGAGA
AGGCGTTCGAGTGGGTCAGCAGCTCGTCGCCGAACGCCCAGTACATGGCCGCCGACGACGGCAG
CGTCAGCGTGAACACGTACAGCGTCGCCAGCAGGTAGATGTATTTGAACTTGGCGGGCTTCCAC
ATCGCGTGCATGATCTCG
						
						Genomic sequence
						
							CATGCGCGCGGACGCCGTGCGGTAGGTGAGGACGTGCGCCAGGGCCGGGATGATGTAGACGGTG
AAGCTGACGAGCAGCGCGCCGACGGCGGAGTTGATGGGCCCGAAGAAGGGGAAGATGATGGCGA
GGAACCAGATGGGCACGACGATGGGCAGCCTCGCCAGCGCGCGCTTGAAGATGCTCTTGGCGTC
GTGCATCCCGATCACCTTCTCCCACACGAAGTAGAGCGGCGTGCACGCGAAGCCGAAGGTGATG
AACTGGTGGATCAGCATCAGGATCACCGCCGCGTCGCGCCACCGGGTCTTGGGCAGCAGCGAGA
AGGCGTTCGAGTGGGTCAGCAGCTCGTCGCCGAACGCCCAGTACATGGCCGCCGACGACGGCAG
CGTCAGCGTGAACACGTACAGCGTCGCCAGCAGGTAGATGTATTTGAACTTGGCGGGCTTCCAC
ATCGCGTGCATGATCTCG

Sequences
Splice junction sequence	GGCCGCCGACGACGGCAGCGTCAGCGTGAACACGTACAGCGTCGCCAGCAGGTAGATGTATTTG AACTTGGCGGGCTTCCACATCGCGTGCATGATCTCGcatgcgcgcggacgccgtgcggtaggtg aggacgtgcgccagggccgggatgatgtagacggtgaagctgacgagcagcgcgccgacggcgg agttgatg
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: 466 Transcript exons: 180801836-180802301 CATGCGCGCGGACGCCGTGCGGTAGGTGAGGACGTGCGCCAGGGCCGGGATGATGTAGACGGTG AAGCTGACGAGCAGCGCGCCGACGGCGGAGTTGATGGGCCCGAAGAAGGGGAAGATGATGGCGA GGAACCAGATGGGCACGACGATGGGCAGCCTCGCCAGCGCGCGCTTGAAGATGCTCTTGGCGTC GTGCATCCCGATCACCTTCTCCCACACGAAGTAGAGCGGCGTGCACGCGAAGCCGAAGGTGATG AACTGGTGGATCAGCATCAGGATCACCGCCGCGTCGCGCCACCGGGTCTTGGGCAGCAGCGAGA AGGCGTTCGAGTGGGTCAGCAGCTCGTCGCCGAACGCCCAGTACATGGCCGCCGACGACGGCAG CGTCAGCGTGAACACGTACAGCGTCGCCAGCAGGTAGATGTATTTGAACTTGGCGGGCTTCCAC ATCGCGTGCATGATCTCG
Genomic sequence	CATGCGCGCGGACGCCGTGCGGTAGGTGAGGACGTGCGCCAGGGCCGGGATGATGTAGACGGTG AAGCTGACGAGCAGCGCGCCGACGGCGGAGTTGATGGGCCCGAAGAAGGGGAAGATGATGGCGA GGAACCAGATGGGCACGACGATGGGCAGCCTCGCCAGCGCGCGCTTGAAGATGCTCTTGGCGTC GTGCATCCCGATCACCTTCTCCCACACGAAGTAGAGCGGCGTGCACGCGAAGCCGAAGGTGATG AACTGGTGGATCAGCATCAGGATCACCGCCGCGTCGCGCCACCGGGTCTTGGGCAGCAGCGAGA AGGCGTTCGAGTGGGTCAGCAGCTCGTCGCCGAACGCCCAGTACATGGCCGCCGACGACGGCAG CGTCAGCGTGAACACGTACAGCGTCGCCAGCAGGTAGATGTATTTGAACTTGGCGGGCTTCCAC ATCGCGTGCATGATCTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_004870 osa_circ_004869 osi_circ_010944 hvu_circ_000018* 
osa_circ_028081* osi_circ_015536 osa_circ_006214* osa_circ_006213 
osi_circ_008779 						
					
						PMCS
						0.450046823

Conservation Information
Conserved circRNAs	osa_circ_004870 osa_circ_004869 osi_circ_010944 hvu_circ_000018* osa_circ_028081* osi_circ_015536 osa_circ_006214* osa_circ_006213 osi_circ_008779
PMCS	0.450046823

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							180802258-180801861(+)
180802296-180802224(-)
						
						Potential amino acid sequence
						
							MYLNLAGFHIACMISHARGRRAVGEDVRQGRDDVDGEADEQRADGGVDGPEEGEDDGEEPDGHD
DGQPRQRALEDALGVVHPDHLLPHEVERRAREAEGDELVDQHQDHRRVAPPGLGQQREGVRVGQ
QLVAERPVHGRRRRQRQREHVQRRQQVDVFELGGLPHRVHDLACARTPCGR*(+)
MHAMWKPAKFKYIYLLATLYVFTLTLPSSAAMYWAFGDELLTHSNAFSLLPKTRWRDAAVILML
IHQFITFGFACTPLYFVWEKVIGMHDAKSIFKRALARLPIVVPIWFLAIIFPFFGPINSAVGAL
LVSFTVYIIPALAHVLTYRTASARMRDHARDVEARQVQIHLPAGDAVRVHADAAVVGGHVLGVR
RRAADPLERLLAAAQDPVARRGGDPDADPPVHHLRLRVHAALLRVGEGDRDARRQEHLQARAGE
AAHRRAHLVPRHHLPLLRAHQLRRRRAARQLHRLHHPGPGARPHLPHGVRAHARSCTRCGSPPS
SNTSTCWRRCTCSR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	180802258-180801861(+) 180802296-180802224(-)
Potential amino acid sequence	MYLNLAGFHIACMISHARGRRAVGEDVRQGRDDVDGEADEQRADGGVDGPEEGEDDGEEPDGHD DGQPRQRALEDALGVVHPDHLLPHEVERRAREAEGDELVDQHQDHRRVAPPGLGQQREGVRVGQ QLVAERPVHGRRRRQRQREHVQRRQQVDVFELGGLPHRVHDLACARTPCGR(+) MHAMWKPAKFKYIYLLATLYVFTLTLPSSAAMYWAFGDELLTHSNAFSLLPKTRWRDAAVILML IHQFITFGFACTPLYFVWEKVIGMHDAKSIFKRALARLPIVVPIWFLAIIFPFFGPINSAVGAL LVSFTVYIIPALAHVLTYRTASARMRDHARDVEARQVQIHLPAGDAVRVHADAAVVGGHVLGVR RRAADPLERLLAAAQDPVARRGGDPDADPPVHHLRLRVHAALLRVGEGDRDARRQEHLQARAGE AAHRRAHLVPRHHLPLLRAHQLRRRRAARQLHRLHHPGPGARPHLPHGVRAHARSCTRCGSPPS SNTSTCWRRCTCSR(-)
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 Zm00001d042809_circ_g.3

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