Plant Circular RNA Database

Detail information of Zm00001d039453_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d039453_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007468
					
						Alias
						Zm03circ00004, zma_circ_0000948, GRMZM2G143235_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 4748141-4749265  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d039453						
					
						Parent gene annotation
						
							3-epi-6-deoxocathasterone 23-monooxygenase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d039453_circ_g.1 Zm00001d039453_circ_g.3 Zm00001d039453_circ_g.4 Zm00001d039453_circ_g.5 						
					
						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  
						
							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
						Zm00001d039453_T002:3
Zm00001d039453_T001:3

General Information
CircRNA Name	Zm00001d039453_circ_g.2
ID in PlantcircBase	zma_circ_007468
Alias	Zm03circ00004, zma_circ_0000948, GRMZM2G143235_C1
Organism	Zea mays
Position	chr3: 4748141-4749265 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d039453
Parent gene annotation	3-epi-6-deoxocathasterone 23-monooxygenase
Parent gene strand	-
Alternative splicing	Zm00001d039453_circ_g.1 Zm00001d039453_circ_g.3 Zm00001d039453_circ_g.4 Zm00001d039453_circ_g.5
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	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	Zm00001d039453_T002:3 Zm00001d039453_T001:3

			
						 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  
						
							GTCTACTTACATGTTGTGTGAACGACAGTGACATGTAGTCCGTCCACTGCAAGGTCTCTCCCAC
GTCGGTTTTCCGCCTCTTCAGCTGCATGTTCTCCTCctgaagctggtcaccaggtgatggagaa
agatggaagcttccagcctggccagatccaggcctgggcacagcctctgcccaccgccaaaagg
ggtgaagc

									
								

					

						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: 398
Transcript exons: 4748141-4748262,4748843-4749028,4749176-4749265
CTGAAGCTGGTCACCAGGTGATGGAGAAAGATGGAAGCTTCCAGCCTGGCCAGATCCAGGCCTG
GGCACAGCCTCTGCCCACCGCCAAAAGGGGTGAAGCCCATGGTGCTCGTGTCCTTCTCCTTCCA
CCTCCACGGGTTGAACCTGTAGGGCTCGTCGTAGCGCTTGTCGTCGAGGTGGACCGACCGGAAG
TACACGAACACGCACCAGCCCTTGGGGATGAGGTGCCCCTTCACCTCCACGTCCCGCACCGCTT
TGCGCATGATCCCGTTGATGATATTCCCCATCCGCAGTGTCTCCGTTATCACATGTTGTGTGAA
CGACAGTGACATGTAGTCCGTCCACTGCAAGGTCTCTCCCACGTCGGTTTTCCGCCTCTTCAGC
TGCATGTTCTCCTC
						
					

						Genomic sequence
						
							CTGAAGCTGGTCACCAGGTGATGGAGAAAGATGGAAGCTTCCAGCCTGGCCAGATCCAGGCCTG
GGCACAGCCTCTGCCCACCGCCAAAAGGGGTGAAGCCCATGGTGCTCGTGTCCTTCTCCTGTTC
ATCATTACGTTGTTGACCAAGTGAAGGCGTTAGTAGGCTTCCAAGAACCAAATCACGGTCACTG
TAAGCTTCACAAAGGCAGCTACCCAAAGCTCTGACCCACGACACCAATCATGGGTTTGGAATTC
TCCATCTATGTAATAATAACTACATAATGGCGCGGTAACATCCGACACTCTAAACAACCGTGAC
CAAGAAAAAAATAGAGAGTAATAGGCAGTCTATCAATGCATAATTAGGGACTAAGTTCTTTCCG
ATAAATGCTAAACATGCAGCGCAGTCGTTTCCAAGAACTAATTAAGCAAAAGTTGAGCGTGATA
AGAACAGCAACACGCATGCAGAGGTTTGACAGTGGACGGTCTCTGTTATTTTCCTGGCATACTT
ACTAGGTGCTGGTTCAGGGCAACTCCTCCATGATGAGCCTCCATATAATACAGGAGTAAATTAA
CCCACATGTTAGGGGACCCATGTGCAAGCAAGCCCCACTCATCAAATCTCTATTATGCCGGTGT
TGCCTAAAGGAGTAGCAACTGGATGAACATCTCTACCAAATGTGGGGGCTCAAAAACCTCACCT
TCCACCTCCACGGGTTGAACCTGTAGGGCTCGTCGTAGCGCTTGTCGTCGAGGTGGACCGACCG
GAAGTACACGAACACGCACCAGCCCTTGGGGATGAGGTGCCCCTTCACCTCCACGTCCCGCACC
GCTTTGCGCATGATCCCGTTGATGATATTCCCCATCCGCAGTGTCTCCGTTATCACCTATATAT
TGTATCACCCATATTTATATAAATAAATATGTTAATCCATGCAAGATTTGATTGGAAAACCGGA
TCAAAATGCACATAAACACTGGTCACTGGTGACAAGAGAAATTTTGGAGCCTTGACCACAACTG
GGTCTACTTACATGTTGTGTGAACGACAGTGACATGTAGTCCGTCCACTGCAAGGTCTCTCCCA
CGTCGGTTTTCCGCCTCTTCAGCTGCATGTTCTCCTC
						
					

			
		

Sequences
Splice junction sequence	GTCTACTTACATGTTGTGTGAACGACAGTGACATGTAGTCCGTCCACTGCAAGGTCTCTCCCAC GTCGGTTTTCCGCCTCTTCAGCTGCATGTTCTCCTCctgaagctggtcaccaggtgatggagaa agatggaagcttccagcctggccagatccaggcctgggcacagcctctgcccaccgccaaaagg ggtgaagc
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: 398 Transcript exons: 4748141-4748262,4748843-4749028,4749176-4749265 CTGAAGCTGGTCACCAGGTGATGGAGAAAGATGGAAGCTTCCAGCCTGGCCAGATCCAGGCCTG GGCACAGCCTCTGCCCACCGCCAAAAGGGGTGAAGCCCATGGTGCTCGTGTCCTTCTCCTTCCA CCTCCACGGGTTGAACCTGTAGGGCTCGTCGTAGCGCTTGTCGTCGAGGTGGACCGACCGGAAG TACACGAACACGCACCAGCCCTTGGGGATGAGGTGCCCCTTCACCTCCACGTCCCGCACCGCTT TGCGCATGATCCCGTTGATGATATTCCCCATCCGCAGTGTCTCCGTTATCACATGTTGTGTGAA CGACAGTGACATGTAGTCCGTCCACTGCAAGGTCTCTCCCACGTCGGTTTTCCGCCTCTTCAGC TGCATGTTCTCCTC
Genomic sequence	CTGAAGCTGGTCACCAGGTGATGGAGAAAGATGGAAGCTTCCAGCCTGGCCAGATCCAGGCCTG GGCACAGCCTCTGCCCACCGCCAAAAGGGGTGAAGCCCATGGTGCTCGTGTCCTTCTCCTGTTC ATCATTACGTTGTTGACCAAGTGAAGGCGTTAGTAGGCTTCCAAGAACCAAATCACGGTCACTG TAAGCTTCACAAAGGCAGCTACCCAAAGCTCTGACCCACGACACCAATCATGGGTTTGGAATTC TCCATCTATGTAATAATAACTACATAATGGCGCGGTAACATCCGACACTCTAAACAACCGTGAC CAAGAAAAAAATAGAGAGTAATAGGCAGTCTATCAATGCATAATTAGGGACTAAGTTCTTTCCG ATAAATGCTAAACATGCAGCGCAGTCGTTTCCAAGAACTAATTAAGCAAAAGTTGAGCGTGATA AGAACAGCAACACGCATGCAGAGGTTTGACAGTGGACGGTCTCTGTTATTTTCCTGGCATACTT ACTAGGTGCTGGTTCAGGGCAACTCCTCCATGATGAGCCTCCATATAATACAGGAGTAAATTAA CCCACATGTTAGGGGACCCATGTGCAAGCAAGCCCCACTCATCAAATCTCTATTATGCCGGTGT TGCCTAAAGGAGTAGCAACTGGATGAACATCTCTACCAAATGTGGGGGCTCAAAAACCTCACCT TCCACCTCCACGGGTTGAACCTGTAGGGCTCGTCGTAGCGCTTGTCGTCGAGGTGGACCGACCG GAAGTACACGAACACGCACCAGCCCTTGGGGATGAGGTGCCCCTTCACCTCCACGTCCCGCACC GCTTTGCGCATGATCCCGTTGATGATATTCCCCATCCGCAGTGTCTCCGTTATCACCTATATAT TGTATCACCCATATTTATATAAATAAATATGTTAATCCATGCAAGATTTGATTGGAAAACCGGA TCAAAATGCACATAAACACTGGTCACTGGTGACAAGAGAAATTTTGGAGCCTTGACCACAACTG GGTCTACTTACATGTTGTGTGAACGACAGTGACATGTAGTCCGTCCACTGCAAGGTCTCTCCCA CGTCGGTTTTCCGCCTCTTCAGCTGCATGTTCTCCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_000724 						
					
						PMCS
						0.115362966

Conservation Information
Conserved circRNAs	osa_circ_000724
PMCS	0.115362966

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4749258-4749249(-)
						
						Potential amino acid sequence
						
							MQLKRRKTDVGETLQWTDYMSLSFTQHVITETLRMGNIINGIMRKAVRDVEVKGHLIPKGWCVF
VYFRSVHLDDKRYDEPYRFNPWRWKEKDTSTMGFTPFGGGQRLCPGLDLARLEASIFLHHLVTS
FRRRTCS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4749258-4749249(-)
Potential amino acid sequence	MQLKRRKTDVGETLQWTDYMSLSFTQHVITETLRMGNIINGIMRKAVRDVEVKGHLIPKGWCVF VYFRSVHLDDKRYDEPYRFNPWRWKEKDTSTMGFTPFGGGQRLCPGLDLARLEASIFLHHLVTS FRRRTCS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d039453_circ_g.2

Address

Any questions?

Supported by