Plant Circular RNA Database

Detail information of Zm00001d013083_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d013083_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008357
					
						Alias
						Zm05circ00006, zma_circ_0001663, GRMZM2G099630_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 4467553-4468774  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d013083						
					
						Parent gene annotation
						
							5'-3' exoribonuclease 4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d013083_circ_g.1 Zm00001d013083_circ_g.2 Zm00001d013083_circ_g.4 Zm00001d013083_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
						Zm00001d013083_T004:7
Zm00001d013083_T005:7
Zm00001d013083_T019:7
Zm00001d013083_T001:7
Zm00001d013083_T006:7
Zm00001d013083_T011:7
Zm00001d013083_T003:7
Zm00001d013083_T014:7
Zm00001d013083_T009:7
Zm00001d013083_T008:7
Zm00001d013083_T015:7
Zm00001d013083_T007:7
Zm00001d013083_T010:7
Zm00001d013083_T017:7
Zm00001d013083_T002:7

General Information
CircRNA Name	Zm00001d013083_circ_g.3
ID in PlantcircBase	zma_circ_008357
Alias	Zm05circ00006, zma_circ_0001663, GRMZM2G099630_C1
Organism	Zea mays
Position	chr5: 4467553-4468774 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d013083
Parent gene annotation	5'-3' exoribonuclease 4
Parent gene strand	-
Alternative splicing	Zm00001d013083_circ_g.1 Zm00001d013083_circ_g.2 Zm00001d013083_circ_g.4 Zm00001d013083_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	Zm00001d013083_T004:7 Zm00001d013083_T005:7 Zm00001d013083_T019:7 Zm00001d013083_T001:7 Zm00001d013083_T006:7 Zm00001d013083_T011:7 Zm00001d013083_T003:7 Zm00001d013083_T014:7 Zm00001d013083_T009:7 Zm00001d013083_T008:7 Zm00001d013083_T015:7 Zm00001d013083_T007:7 Zm00001d013083_T010:7 Zm00001d013083_T017:7 Zm00001d013083_T002:7

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F:GTCCAGAAATACGTGGAAGGTCT
 R:TCTCCGAACTTGAACAATGGGT
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	Yes 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	F:GTCCAGAAATACGTGGAAGGTCT R:TCTCCGAACTTGAACAATGGGT 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  
						
							ATCAAATGGCTTGAAAGGTTGACCCAAAAAAAAGGTTATTTCCAATTCAGCCAAGCCTTTTAGA
TCAGATGCGAAAGGCGCATAATGATAGGGATAAAACcttcgcaggtatgatgacccccgctgga
ggctctgggatgtgtttgtgatactgaggattgagataggcagcattcctgaaaaaatgtagaa
aaaattat

									
								

					

						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: 655
Transcript exons: 4467553-4467628,4467724-4467828,4467910-4468061,4468150-
4468224,4468305-4468345,4468473-4468549,4468646-4468774
CTTCGCAGGTATGATGACCCCCGCTGGAGGCTCTGGGATGTGTTTGTGATACTGAGGATTGAGA
TAGGCAGCATTCAAAACTCTGTTCTGAGCAATGCCATTGAACCCCTTAACTGGAGAAGTGACAG
TGACACTATACCAGTTCCTTTCAGATAAACATAGGAATCCATTCATTCCACCACTAGCAGCAGG
CTCAATGGGAATAACATAAGGGTCTGTTCTTGATAGATGGTAATAGTTCTGATACAGGAAGATA
ATCTGAGTGATCAATGGATGAGTATCTCTAACGTAAATTATGTCAAGCATAGTCCTATTCCTGA
ATTTCTCTTCTTCTGTCAAAGTATCTTCAAGTTTTCTTGTTTCCGCAAGCAGACGCCTTTCATC
AATAAAAGGCAATTTTGCAACACCCTGCCATGCAAAACGTTTCCCATTCATGTCTATCTCAAAA
TCTTTTGGGTAGAAAGACTTCAACGGTGAATCTGGATCACTCATCAAATCCCCATAGTATTTTG
GCAGTGCATTGGAGCTTGCAGCTGGTAGGGTTCCCATTAGTTGATCAAATGGCTTGAAAGGTTG
ACCCAAAAAAAAGGTTATTTCCAATTCAGCCAAGCCTTTTAGATCAGATGCGAAAGGCGCATAA
TGATAGGGATAAAAC
						
					

						Genomic sequence
						
							CTTCGCAGGTATGATGACCCCCGCTGGAGGCTCTGGGATGTGTTTGTGATACTGAGGATTGAGA
TAGGCAGCATTCCTGAAAAAATGTAGAAAAAATTATAAATATAGTTCTAGTAGATTTAAAGGGT
AGCTTTTAGTTTACAATATGCCTTTACACGATAAGATGCTTACAAAACTCTGTTCTGAGCAATG
CCATTGAACCCCTTAACTGGAGAAGTGACAGTGACACTATACCAGTTCCTTTCAGATAAACATA
GGAATCCATTCATTCCACCACTGCATATAGTCGACATATCCAAAACAGTAAATAAATGAGGGCA
AAATAATCCAAAACAATGTATCTAACATTCTACCAACCTAGCAGCAGGCTCAATGGGAATAACA
TAAGGGTCTGTTCTTGATAGATGGTAATAGTTCTGATACAGGAAGATAATCTGAGTGATCAATG
GATGAGTATCTCTAACGTAAATTATGTCAAGCATAGTCCTATTCCTGAATTTCTCTTCTTCCTG
CGAAAGCCAGCAAAAATAAAGCTCAGCCAAAATGGAAGTCACAAGCCCAGATGGTTAAAAAATA
AGGATTGTAACATATACATACTGTCAAAGTATCTTCAAGTTTTCTTGTTTCCGCAAGCAGACGC
CTTTCATCAATAAAAGGCAATTTTGCAACACCCTGAGTAAAAGAGAACATAAACATTTCTACAT
AACACAATTAGTAGCCTGAAAGAAGAATGATTTACTCATTTGCATTACCTGCCATGCAAAACGT
TTCCCATTCATGTCTATCTCAAAATCTGCAGGTACAATATAAGGCTTTAGAAGCAATGGATAAA
TATGATTTTATGGATACACAATATCACCCTATGCATGGGGCAGTTTTCAGGTAATTTCGTTTTT
GCTTTACAAAATAGATGGTGATACCTTTTGGGTAGAAAGACTTCAACGGTGAATCTGGATCACT
CATCAAATCCCCATAGTATTTTGGCAGTGCATTGGAGCTACAGAAAAAAAAAATAGCGGACATC
TCAGAATCATTGCTTTGACATTCTTTCCATCTGAACGTGGAACAGATTCATTTGCATAAGGGGG
CAGACCTTGCAGCTGGTAGGGTTCCCATTAGTTGATCAAATGGCTTGAAAGGTTGACCCAAAAA
AAAGGTTATTTCCAATTCAGCCAAGCCTTTTAGATCAGATGCGAAAGGCGCATAATGATAGGGA
TAAAAC
						
					

			
		

Sequences
Splice junction sequence	ATCAAATGGCTTGAAAGGTTGACCCAAAAAAAAGGTTATTTCCAATTCAGCCAAGCCTTTTAGA TCAGATGCGAAAGGCGCATAATGATAGGGATAAAACcttcgcaggtatgatgacccccgctgga ggctctgggatgtgtttgtgatactgaggattgagataggcagcattcctgaaaaaatgtagaa aaaattat
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: 655 Transcript exons: 4467553-4467628,4467724-4467828,4467910-4468061,4468150- 4468224,4468305-4468345,4468473-4468549,4468646-4468774 CTTCGCAGGTATGATGACCCCCGCTGGAGGCTCTGGGATGTGTTTGTGATACTGAGGATTGAGA TAGGCAGCATTCAAAACTCTGTTCTGAGCAATGCCATTGAACCCCTTAACTGGAGAAGTGACAG TGACACTATACCAGTTCCTTTCAGATAAACATAGGAATCCATTCATTCCACCACTAGCAGCAGG CTCAATGGGAATAACATAAGGGTCTGTTCTTGATAGATGGTAATAGTTCTGATACAGGAAGATA ATCTGAGTGATCAATGGATGAGTATCTCTAACGTAAATTATGTCAAGCATAGTCCTATTCCTGA ATTTCTCTTCTTCTGTCAAAGTATCTTCAAGTTTTCTTGTTTCCGCAAGCAGACGCCTTTCATC AATAAAAGGCAATTTTGCAACACCCTGCCATGCAAAACGTTTCCCATTCATGTCTATCTCAAAA TCTTTTGGGTAGAAAGACTTCAACGGTGAATCTGGATCACTCATCAAATCCCCATAGTATTTTG GCAGTGCATTGGAGCTTGCAGCTGGTAGGGTTCCCATTAGTTGATCAAATGGCTTGAAAGGTTG ACCCAAAAAAAAGGTTATTTCCAATTCAGCCAAGCCTTTTAGATCAGATGCGAAAGGCGCATAA TGATAGGGATAAAAC
Genomic sequence	CTTCGCAGGTATGATGACCCCCGCTGGAGGCTCTGGGATGTGTTTGTGATACTGAGGATTGAGA TAGGCAGCATTCCTGAAAAAATGTAGAAAAAATTATAAATATAGTTCTAGTAGATTTAAAGGGT AGCTTTTAGTTTACAATATGCCTTTACACGATAAGATGCTTACAAAACTCTGTTCTGAGCAATG CCATTGAACCCCTTAACTGGAGAAGTGACAGTGACACTATACCAGTTCCTTTCAGATAAACATA GGAATCCATTCATTCCACCACTGCATATAGTCGACATATCCAAAACAGTAAATAAATGAGGGCA AAATAATCCAAAACAATGTATCTAACATTCTACCAACCTAGCAGCAGGCTCAATGGGAATAACA TAAGGGTCTGTTCTTGATAGATGGTAATAGTTCTGATACAGGAAGATAATCTGAGTGATCAATG GATGAGTATCTCTAACGTAAATTATGTCAAGCATAGTCCTATTCCTGAATTTCTCTTCTTCCTG CGAAAGCCAGCAAAAATAAAGCTCAGCCAAAATGGAAGTCACAAGCCCAGATGGTTAAAAAATA AGGATTGTAACATATACATACTGTCAAAGTATCTTCAAGTTTTCTTGTTTCCGCAAGCAGACGC CTTTCATCAATAAAAGGCAATTTTGCAACACCCTGAGTAAAAGAGAACATAAACATTTCTACAT AACACAATTAGTAGCCTGAAAGAAGAATGATTTACTCATTTGCATTACCTGCCATGCAAAACGT TTCCCATTCATGTCTATCTCAAAATCTGCAGGTACAATATAAGGCTTTAGAAGCAATGGATAAA TATGATTTTATGGATACACAATATCACCCTATGCATGGGGCAGTTTTCAGGTAATTTCGTTTTT GCTTTACAAAATAGATGGTGATACCTTTTGGGTAGAAAGACTTCAACGGTGAATCTGGATCACT CATCAAATCCCCATAGTATTTTGGCAGTGCATTGGAGCTACAGAAAAAAAAAATAGCGGACATC TCAGAATCATTGCTTTGACATTCTTTCCATCTGAACGTGGAACAGATTCATTTGCATAAGGGGG CAGACCTTGCAGCTGGTAGGGTTCCCATTAGTTGATCAAATGGCTTGAAAGGTTGACCCAAAAA AAAGGTTATTTCCAATTCAGCCAAGCCTTTTAGATCAGATGCGAAAGGCGCATAATGATAGGGA TAAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.100697512

Conservation Information
Conserved circRNAs	NA
PMCS	0.100697512

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4468744-4467598(+)
4468670-4468741(-)
4467628-4468741(-)
						
						Potential amino acid sequence
						
							MRKAHNDRDKTFAGMMTPAGGSGMCL*(+)
MGTLPAASSNALPKYYGDLMSDPDSPLKSFYPKDFEIDMNGKRFAWQGVAKLPFIDERRLLAET
RKLEDTLTEEEKFRNRTMLDIIYVRDTHPLITQIIFLYQNYYHLSRTDPYVIPIEPAASGGMNG
FLCLSERNWYSVTVTSPVKGFNGIAQNRVLNAAYLNPQYHKHIPEPPAGVIIPAKVLSLSLCAF
RI*(-)
MLPISILSITNTSQSLQRGSSYLRRFYPYHYAPFASDLKGLAELEITFFLGQPFKPFDQLMGTL
PAASSNALPKYYGDLMSDPDSPLKSFYPKDFEIDMNGKRFAWQGVAKLPFIDERRLLAETRKLE
DTLTEEEKFRNRTMLDIIYVRDTHPLITQIIFLYQNYYHLSRTDPYVIPIEPAASGGMNGFLCL
SERNWYSVTVTSPVKGFNGIAQNRVLNAAYLNPQYHKHIPEPPAGVIIPAKVLSLSLCAFRI*(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4468744-4467598(+) 4468670-4468741(-) 4467628-4468741(-)
Potential amino acid sequence	MRKAHNDRDKTFAGMMTPAGGSGMCL(+) MGTLPAASSNALPKYYGDLMSDPDSPLKSFYPKDFEIDMNGKRFAWQGVAKLPFIDERRLLAET RKLEDTLTEEEKFRNRTMLDIIYVRDTHPLITQIIFLYQNYYHLSRTDPYVIPIEPAASGGMNG FLCLSERNWYSVTVTSPVKGFNGIAQNRVLNAAYLNPQYHKHIPEPPAGVIIPAKVLSLSLCAF RI(-) MLPISILSITNTSQSLQRGSSYLRRFYPYHYAPFASDLKGLAELEITFFLGQPFKPFDQLMGTL PAASSNALPKYYGDLMSDPDSPLKSFYPKDFEIDMNGKRFAWQGVAKLPFIDERRLLAETRKLE DTLTEEEKFRNRTMLDIIYVRDTHPLITQIIFLYQNYYHLSRTDPYVIPIEPAASGGMNGFLCL SERNWYSVTVTSPVKGFNGIAQNRVLNAAYLNPQYHKHIPEPPAGVIIPAKVLSLSLCAFRI*( -)
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 Zm00001d013083_circ_g.3

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