Plant Circular RNA Database

Detail information of Zm00001d019922_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d019922_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009293
					
						Alias
						zma_circ_0002747
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 76568707-76569737  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d019922						
					
						Parent gene annotation
						
							 r-interacting factor1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d019922_circ_g.1 Zm00001d019922_circ_g.2 						
					
						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
						Zm00001d019922_T003:4
Zm00001d019922_T001:3
Zm00001d019922_T013:4
Zm00001d019922_T005:4
Zm00001d019922_T010:4
Zm00001d019922_T009:4
Zm00001d019922_T011:4
Zm00001d019922_T004:4
Zm00001d019922_T008:4
Zm00001d019922_T014:4
Zm00001d019922_T006:4
Zm00001d019922_T002:4
Zm00001d019922_T012:3

General Information
CircRNA Name	Zm00001d019922_circ_g.3
ID in PlantcircBase	zma_circ_009293
Alias	zma_circ_0002747
Organism	Zea mays
Position	chr7: 76568707-76569737 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d019922
Parent gene annotation	r-interacting factor1
Parent gene strand	-
Alternative splicing	Zm00001d019922_circ_g.1 Zm00001d019922_circ_g.2
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	Zm00001d019922_T003:4 Zm00001d019922_T001:3 Zm00001d019922_T013:4 Zm00001d019922_T005:4 Zm00001d019922_T010:4 Zm00001d019922_T009:4 Zm00001d019922_T011:4 Zm00001d019922_T004:4 Zm00001d019922_T008:4 Zm00001d019922_T014:4 Zm00001d019922_T006:4 Zm00001d019922_T002:4 Zm00001d019922_T012:3

			
						 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  
						
							GCATATGAACCGGCAGGAACAATAGTTCTCCCATTACCACTAACACGTCCGCTGCCTCTGATAC
TCCTATGTGGAAGTTGTGGAAGATCATCATCAGTTCcgtttcagcattataatcagatatgact
gcttcataaaaactattatcttcaggccaccggctcatcactttacgaccaaccaatggatcga
cattctga

									
								

					

						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: 773
Transcript exons: 76568707-76568925,76569005-76569245,76569336-76569445,76
569535-76569737
CGTTTCAGCATTATAATCAGATATGACTGCTTCATAAAAACTATTATCTTCAGGCCACCGGCTC
ATCACTTTACGACCAACCAATGGATCGACATTCTGAGCTTGAGCTTCAGGAGCAGAACCACCTG
GAAAATTCCTATTCATGTGTGGTCCTCTTCCACTAGGACCTGCTGAAGATGGCATAGGCTTGGC
TGCAGAGCCACCTGGTACCTTCTGACCTGGTTTCGTCTTTTTGCCTTTAGGGACTGGGGGTACT
GCTTTCCTAGCAGTTGAAGACGATGGCTGTGTTGGTGTAGCCAGCTGTTGTGAATGCATTGCAG
GAGGTGCAGGTAAAGCAGGAACAGATTGAGATGTCTTTTGCCTCTTACGGCCAGAGGTGGTAGG
ACTTGGAACAGGGTCATGAATCGGTTGTGGGTTATTGGACATGCTTGCTTGAAGCCCTCCTGTT
GATCTCCATTCCCTTATGCTACATATAATATTATCGTTGTTGACTTTATTTAACAGCTCCCTGT
GTGCTTTGTCAGATACTCTTAGTTCCTTCCTAAGTTCAGTCATGAGACCTTCCTTCTCCCATGT
AATGGCATCAGACTGGGCTTTGAATGCACGAAGGACTGAACAATATGCTTCTTGCTCAAGTTGT
TGAATTTGTGCTTCCATGTCAGTTGGTGCTCTAGCATATGAACCGGCAGGAACAATAGTTCTCC
CATTACCACTAACACGTCCGCTGCCTCTGATACTCCTATGTGGAAGTTGTGGAAGATCATCATC
AGTTC
						
					

						Genomic sequence
						
							CGTTTCAGCATTATAATCAGATATGACTGCTTCATAAAAACTATTATCTTCAGGCCACCGGCTC
ATCACTTTACGACCAACCAATGGATCGACATTCTGAGCTTGAGCTTCAGGAGCAGAACCACCTG
GAAAATTCCTATTCATGTGTGGTCCTCTTCCACTAGGACCTGCTGAAGATGGCATAGGCTTGGC
TGCAGAGCCACCTGGTACCTTCTGACCCTGAAAGTGCATGAACTTCAACCAAAGAACAAAAAAG
AACACTGATAGAAAAAATAACTTGTTCAAATTATCTACTTACTGGTTTCGTCTTTTTGCCTTTA
GGGACTGGGGGTACTGCTTTCCTAGCAGTTGAAGACGATGGCTGTGTTGGTGTAGCCAGCTGTT
GTGAATGCATTGCAGGAGGTGCAGGTAAAGCAGGAACAGATTGAGATGTCTTTTGCCTCTTACG
GCCAGAGGTGGTAGGACTTGGAACAGGGTCATGAATCGGTTGTGGGTTATTGGACATGCTTGCT
TGAAGCCCTCCTGTTGATCTCCATTCCCTTAAATAAAAAAGCATCACAGATTTCGAATGCTGAA
AACCAAGATAATGTGCATACTGTTACTACAAAAAAAAATGTGATTCGTGCTACCTTATGCTACA
TATAATATTATCGTTGTTGACTTTATTTAACAGCTCCCTGTGTGCTTTGTCAGATACTCTTAGT
TCCTTCCTAAGTTCAGTCATGAGACCTTCCTTCTCCTGAGAAGGTTAGAGTTAAGTCAACTTTG
AGAAATGACAACAAAATCATCAAACACCAAATAAACAGTGAACAGTTTAATGGTCTCAACCCAT
GTAATGGCATCAGACTGGGCTTTGAATGCACGAAGGACTGAACAATATGCTTCTTGCTCAAGTT
GTTGAATTTGTGCTTCCATGTCAGTTGGTGCTCTAGCATATGAACCGGCAGGAACAATAGTTCT
CCCATTACCACTAACACGTCCGCTGCCTCTGATACTCCTATGTGGAAGTTGTGGAAGATCATCA
TCAGTTC
						
					

			
		

Sequences
Splice junction sequence	GCATATGAACCGGCAGGAACAATAGTTCTCCCATTACCACTAACACGTCCGCTGCCTCTGATAC TCCTATGTGGAAGTTGTGGAAGATCATCATCAGTTCcgtttcagcattataatcagatatgact gcttcataaaaactattatcttcaggccaccggctcatcactttacgaccaaccaatggatcga cattctga
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: 773 Transcript exons: 76568707-76568925,76569005-76569245,76569336-76569445,76 569535-76569737 CGTTTCAGCATTATAATCAGATATGACTGCTTCATAAAAACTATTATCTTCAGGCCACCGGCTC ATCACTTTACGACCAACCAATGGATCGACATTCTGAGCTTGAGCTTCAGGAGCAGAACCACCTG GAAAATTCCTATTCATGTGTGGTCCTCTTCCACTAGGACCTGCTGAAGATGGCATAGGCTTGGC TGCAGAGCCACCTGGTACCTTCTGACCTGGTTTCGTCTTTTTGCCTTTAGGGACTGGGGGTACT GCTTTCCTAGCAGTTGAAGACGATGGCTGTGTTGGTGTAGCCAGCTGTTGTGAATGCATTGCAG GAGGTGCAGGTAAAGCAGGAACAGATTGAGATGTCTTTTGCCTCTTACGGCCAGAGGTGGTAGG ACTTGGAACAGGGTCATGAATCGGTTGTGGGTTATTGGACATGCTTGCTTGAAGCCCTCCTGTT GATCTCCATTCCCTTATGCTACATATAATATTATCGTTGTTGACTTTATTTAACAGCTCCCTGT GTGCTTTGTCAGATACTCTTAGTTCCTTCCTAAGTTCAGTCATGAGACCTTCCTTCTCCCATGT AATGGCATCAGACTGGGCTTTGAATGCACGAAGGACTGAACAATATGCTTCTTGCTCAAGTTGT TGAATTTGTGCTTCCATGTCAGTTGGTGCTCTAGCATATGAACCGGCAGGAACAATAGTTCTCC CATTACCACTAACACGTCCGCTGCCTCTGATACTCCTATGTGGAAGTTGTGGAAGATCATCATC AGTTC
Genomic sequence	CGTTTCAGCATTATAATCAGATATGACTGCTTCATAAAAACTATTATCTTCAGGCCACCGGCTC ATCACTTTACGACCAACCAATGGATCGACATTCTGAGCTTGAGCTTCAGGAGCAGAACCACCTG GAAAATTCCTATTCATGTGTGGTCCTCTTCCACTAGGACCTGCTGAAGATGGCATAGGCTTGGC TGCAGAGCCACCTGGTACCTTCTGACCCTGAAAGTGCATGAACTTCAACCAAAGAACAAAAAAG AACACTGATAGAAAAAATAACTTGTTCAAATTATCTACTTACTGGTTTCGTCTTTTTGCCTTTA GGGACTGGGGGTACTGCTTTCCTAGCAGTTGAAGACGATGGCTGTGTTGGTGTAGCCAGCTGTT GTGAATGCATTGCAGGAGGTGCAGGTAAAGCAGGAACAGATTGAGATGTCTTTTGCCTCTTACG GCCAGAGGTGGTAGGACTTGGAACAGGGTCATGAATCGGTTGTGGGTTATTGGACATGCTTGCT TGAAGCCCTCCTGTTGATCTCCATTCCCTTAAATAAAAAAGCATCACAGATTTCGAATGCTGAA AACCAAGATAATGTGCATACTGTTACTACAAAAAAAAATGTGATTCGTGCTACCTTATGCTACA TATAATATTATCGTTGTTGACTTTATTTAACAGCTCCCTGTGTGCTTTGTCAGATACTCTTAGT TCCTTCCTAAGTTCAGTCATGAGACCTTCCTTCTCCTGAGAAGGTTAGAGTTAAGTCAACTTTG AGAAATGACAACAAAATCATCAAACACCAAATAAACAGTGAACAGTTTAATGGTCTCAACCCAT GTAATGGCATCAGACTGGGCTTTGAATGCACGAAGGACTGAACAATATGCTTCTTGCTCAAGTT GTTGAATTTGTGCTTCCATGTCAGTTGGTGCTCTAGCATATGAACCGGCAGGAACAATAGTTCT CCCATTACCACTAACACGTCCGCTGCCTCTGATACTCCTATGTGGAAGTTGTGGAAGATCATCA TCAGTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.245648169

Conservation Information
Conserved circRNAs	NA
PMCS	0.245648169

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							76569621-76568729(+)
76569623-76569429(-)
						
						Potential amino acid sequence
						
							MSVGALAYEPAGTIVLPLPLTRPLPLILLCGSCGRSSSVPFQHYNQI*(+)
MEAQIQQLEQEAYCSVLRAFKAQSDAITWEKEGLMTELRKELRVSDKAHRELLNKVNNDNIICS
IREWRSTGGLQASMSNNPQPIHDPVPSPTTSGRKRQKTSQSVPALPAPPAMHSQQLATPTQPSS
STARKAVPPVPKGKKTKPGQKVPGGSAAKPMPSSAGPSGRGPHMNRNFPGGSAPEAQAQNVDPL
VGRKVMSRWPEDNSFYEAVISDYNAETELMMIFHNFHIGVSEAADVLVVMGELLFLPVHMLEHQ
LTWKHKFNNLSKKHIVQSFVHSKPSLMPLHGRRKVS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	76569621-76568729(+) 76569623-76569429(-)
Potential amino acid sequence	MSVGALAYEPAGTIVLPLPLTRPLPLILLCGSCGRSSSVPFQHYNQI(+) MEAQIQQLEQEAYCSVLRAFKAQSDAITWEKEGLMTELRKELRVSDKAHRELLNKVNNDNIICS IREWRSTGGLQASMSNNPQPIHDPVPSPTTSGRKRQKTSQSVPALPAPPAMHSQQLATPTQPSS STARKAVPPVPKGKKTKPGQKVPGGSAAKPMPSSAGPSGRGPHMNRNFPGGSAPEAQAQNVDPL VGRKVMSRWPEDNSFYEAVISDYNAETELMMIFHNFHIGVSEAADVLVVMGELLFLPVHMLEHQ LTWKHKFNNLSKKHIVQSFVHSKPSLMPLHGRRKVS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d019922_circ_g.3

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