Plant Circular RNA Database

Detail information of Zm00001d042720_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d042720_circ_g.6
					
						ID in PlantcircBase
						zma_circ_007728
					
						Alias
						Zm03circ00069, zma_circ_0001199, GRMZM2G149617_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 178138849-178143915  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d042720						
					
						Parent gene annotation
						
							Sterol 3-beta-glucosyltransferase  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d042720_circ_g.1 Zm00001d042720_circ_g.2 Zm00001d042720_circ_g.3 Zm00001d042720_circ_g.4 Zm00001d042720_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
						Zm00001d042720_T005:6
Zm00001d042720_T004:6
Zm00001d042720_T006:3
Zm00001d042720_T007:6
Zm00001d042720_T011:6
Zm00001d042720_T010:6
Zm00001d042720_T008:6
Zm00001d042720_T009:6
Zm00001d042720_T003:6

General Information
CircRNA Name	Zm00001d042720_circ_g.6
ID in PlantcircBase	zma_circ_007728
Alias	Zm03circ00069, zma_circ_0001199, GRMZM2G149617_C2
Organism	Zea mays
Position	chr3: 178138849-178143915 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d042720
Parent gene annotation	Sterol 3-beta-glucosyltransferase
Parent gene strand	-
Alternative splicing	Zm00001d042720_circ_g.1 Zm00001d042720_circ_g.2 Zm00001d042720_circ_g.3 Zm00001d042720_circ_g.4 Zm00001d042720_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	Zm00001d042720_T005:6 Zm00001d042720_T004:6 Zm00001d042720_T006:3 Zm00001d042720_T007:6 Zm00001d042720_T011:6 Zm00001d042720_T010:6 Zm00001d042720_T008:6 Zm00001d042720_T009:6 Zm00001d042720_T003:6

			
						 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  
						
							CCCGAGGATCACCACCCAATGGGTAAAAATCAATGCCAGCTGACTTCACAAAAGTACGAAAATT
GACATGAGTTGCCAATCTAACATAATGACCGAATTCcatgctaccaaaaccaatgtatattggc
ttgggcccctgttgaagccactgtgacagttgtggtggcggttgatactttgttccaagattta
agaagcaa

						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: 711
Transcript exons: 178138849-178138979,178139529-178139703,178139844-178139
901,178140435-178140498,178143204-178143374,178143804-17
8143915
CATGCTACCAAAACCAATGTATATTGGCTTGGGCCCCTGTTGAAGCCACTGTGACAGTTGTGGT
GGCGGTTGATACTTTGTTCCAAGATTTAAGAAGCAATATCCCACAACATCCACTAGAGGACCCC
AATCTTTTGGCTTTGGCATAAGTTGCGGGCTCCACATGTATCCAGTAGGTAAGTGTGATATAGA
TCCATGGTATGTGCTGAAGTAAGCAATAGGGGGCAAATTTAATTTCTTCCTGAAATCATTTATG
AATCCCCTGGAGCCCCACCAAACTATTAAATCCAGAATAAGATACGATAGCCTATAAGTTGCAC
TTTGAGGCATTCGTGCCAATGGATGTGGGAATTCATTAGTTGGCGTCCATGGAAAAGTGAAGAA
GATATGCAGAGGTGCTCCAAGTGCTTCTGCTATGTGTAGATGACCATAAGCAGGAGGATTCGCG
ATTATTGCCTGAGCTCTGAAAGGTGTTCCAGTATCCAAATCAGGTTCTGTGCATGCAGGTAGAA
GTGAGAAGATGATTTCCTTAAGCTGCTTTCTTTGAATGGCAATCTCTGTCGGTGCCGCCAGGAA
AAACCCTTTGTTTTTTGTCATATACTGAGCCATAACCCGAGGATCACCACCCAATGGGTAAAAA
TCAATGCCAGCTGACTTCACAAAAGTACGAAAATTGACATGAGTTGCCAATCTAACATAATGAC
CGAATTC
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CCCGAGGATCACCACCCAATGGGTAAAAATCAATGCCAGCTGACTTCACAAAAGTACGAAAATT GACATGAGTTGCCAATCTAACATAATGACCGAATTCcatgctaccaaaaccaatgtatattggc ttgggcccctgttgaagccactgtgacagttgtggtggcggttgatactttgttccaagattta agaagcaa
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: 711 Transcript exons: 178138849-178138979,178139529-178139703,178139844-178139 901,178140435-178140498,178143204-178143374,178143804-17 8143915 CATGCTACCAAAACCAATGTATATTGGCTTGGGCCCCTGTTGAAGCCACTGTGACAGTTGTGGT GGCGGTTGATACTTTGTTCCAAGATTTAAGAAGCAATATCCCACAACATCCACTAGAGGACCCC AATCTTTTGGCTTTGGCATAAGTTGCGGGCTCCACATGTATCCAGTAGGTAAGTGTGATATAGA TCCATGGTATGTGCTGAAGTAAGCAATAGGGGGCAAATTTAATTTCTTCCTGAAATCATTTATG AATCCCCTGGAGCCCCACCAAACTATTAAATCCAGAATAAGATACGATAGCCTATAAGTTGCAC TTTGAGGCATTCGTGCCAATGGATGTGGGAATTCATTAGTTGGCGTCCATGGAAAAGTGAAGAA GATATGCAGAGGTGCTCCAAGTGCTTCTGCTATGTGTAGATGACCATAAGCAGGAGGATTCGCG ATTATTGCCTGAGCTCTGAAAGGTGTTCCAGTATCCAAATCAGGTTCTGTGCATGCAGGTAGAA GTGAGAAGATGATTTCCTTAAGCTGCTTTCTTTGAATGGCAATCTCTGTCGGTGCCGCCAGGAA AAACCCTTTGTTTTTTGTCATATACTGAGCCATAACCCGAGGATCACCACCCAATGGGTAAAAA TCAATGCCAGCTGACTTCACAAAAGTACGAAAATTGACATGAGTTGCCAATCTAACATAATGAC CGAATTC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.064287548

Conservation Information
Conserved circRNAs	NA
PMCS	0.064287548

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							178143884-178138899(+)
178143815-178138851(-)
						
						Potential amino acid sequence
						
							MSCQSNIMTEFHATKTNVYWLGPLLKPL*(+)
MAQYMTKNKGFFLAAPTEIAIQRKQLKEIIFSLLPACTEPDLDTGTPFRAQAIIANPPAYGHLH
IAEALGAPLHIFFTFPWTPTNEFPHPLARMPQSATYRLSYLILDLIVWWGSRGFINDFRKKLNL
PPIAYFSTYHGSISHLPTGYMWSPQLMPKPKDWGPLVDVVGYCFLNLGTKYQPPPQLSQWLQQG
PKPIYIGFGSMEFGHYVRLATHVNFRTFVKSAGIDFYPLGGDPRVMAQYMTKNKGFFLAAPTEI
AIQRKQLKEIIFSLLPACTEPDLDTGTPFRAQAIIANPPAYGHLHIAEALGAPLHIFFTFPWTP
TNEFPHPLARMPQSATYRLSYLILDLIVWWGSRGFINDFRKKLNLPPIAYFSTYHGSISHLPTG
YMWSPQLMPKPKDWGPLVDVVGYCFLNLGTKYQPPPQLSQWLQQGPKPIYIGFGSMEFGHYVRL
ATHVNFRTFVKSAGIDFYPLGGDPRVMAQYMTKNKGFFLAAPTEIAIQRKQLKEIIFSLLPACT
EPDLDTGTPFRAQAIIANPPAYGHLHIAEALGAPLHIFFTFPWTPTNEFPHPLARMPQSATYRL
SYLILDLIVWWGSRGFINDFRKKLNLPPIAYFSTYHGSISHLPTGYMWSPQLMPKPKDWGPLVD
VVGYCFLNLGTKYQPPPQLSQWLQQGPKPIYIGFGSMEFGHYVRLATHVNFRTFVKSAGIDFYP
LGGDPRVMAQYMTKNKGFFLAAPTEIAIQRKQLKEIIFSLLPACTEPDLDTGTPFRAQAIIANP
PAYGHLHIAEALGAPLHIFFTFPWTPTNEFPHPLARMPQSATYRLSYLILDLIVWWGSRGFIND
FRKKLNLPPIAYFSTYHGSISHLPTGYMWSPQLMPKPKDWGPLVDVVGYCFLNLGTKYQPPPQL
SQWLQQGPKPIYIGFGSM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	178143884-178138899(+) 178143815-178138851(-)
Potential amino acid sequence	MSCQSNIMTEFHATKTNVYWLGPLLKPL*(+) MAQYMTKNKGFFLAAPTEIAIQRKQLKEIIFSLLPACTEPDLDTGTPFRAQAIIANPPAYGHLH IAEALGAPLHIFFTFPWTPTNEFPHPLARMPQSATYRLSYLILDLIVWWGSRGFINDFRKKLNL PPIAYFSTYHGSISHLPTGYMWSPQLMPKPKDWGPLVDVVGYCFLNLGTKYQPPPQLSQWLQQG PKPIYIGFGSMEFGHYVRLATHVNFRTFVKSAGIDFYPLGGDPRVMAQYMTKNKGFFLAAPTEI AIQRKQLKEIIFSLLPACTEPDLDTGTPFRAQAIIANPPAYGHLHIAEALGAPLHIFFTFPWTP TNEFPHPLARMPQSATYRLSYLILDLIVWWGSRGFINDFRKKLNLPPIAYFSTYHGSISHLPTG YMWSPQLMPKPKDWGPLVDVVGYCFLNLGTKYQPPPQLSQWLQQGPKPIYIGFGSMEFGHYVRL ATHVNFRTFVKSAGIDFYPLGGDPRVMAQYMTKNKGFFLAAPTEIAIQRKQLKEIIFSLLPACT EPDLDTGTPFRAQAIIANPPAYGHLHIAEALGAPLHIFFTFPWTPTNEFPHPLARMPQSATYRL SYLILDLIVWWGSRGFINDFRKKLNLPPIAYFSTYHGSISHLPTGYMWSPQLMPKPKDWGPLVD VVGYCFLNLGTKYQPPPQLSQWLQQGPKPIYIGFGSMEFGHYVRLATHVNFRTFVKSAGIDFYP LGGDPRVMAQYMTKNKGFFLAAPTEIAIQRKQLKEIIFSLLPACTEPDLDTGTPFRAQAIIANP PAYGHLHIAEALGAPLHIFFTFPWTPTNEFPHPLARMPQSATYRLSYLILDLIVWWGSRGFIND FRKKLNLPPIAYFSTYHGSISHLPTGYMWSPQLMPKPKDWGPLVDVVGYCFLNLGTKYQPPPQL SQWLQQGPKPIYIGFGSM(-)
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 Zm00001d042720_circ_g.6

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