Plant Circular RNA Database

Detail information of Zm00001d003203_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d003203_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007149
					
						Alias
						zma_circ_0001034, GRMZM2G080176_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 35523736-35526323  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d003203						
					
						Parent gene annotation
						
							DNA-directed RNA polymerase III subunit 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d003203_circ_g.1 Zm00001d003203_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
						Zm00001d003203_T007:3
Zm00001d003203_T001:3
Zm00001d003203_T015:3
Zm00001d003203_T012:3
Zm00001d003203_T004:3
Zm00001d003203_T003:3
Zm00001d003203_T014:3
Zm00001d003203_T009:3
Zm00001d003203_T002:3
Zm00001d003203_T013:3
Zm00001d003203_T011:3
Zm00001d003203_T005:3
Zm00001d003203_T006:3

General Information
CircRNA Name	Zm00001d003203_circ_g.3
ID in PlantcircBase	zma_circ_007149
Alias	zma_circ_0001034, GRMZM2G080176_C1
Organism	Zea mays
Position	chr2: 35523736-35526323 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d003203
Parent gene annotation	DNA-directed RNA polymerase III subunit 1
Parent gene strand	-
Alternative splicing	Zm00001d003203_circ_g.1 Zm00001d003203_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	Zm00001d003203_T007:3 Zm00001d003203_T001:3 Zm00001d003203_T015:3 Zm00001d003203_T012:3 Zm00001d003203_T004:3 Zm00001d003203_T003:3 Zm00001d003203_T014:3 Zm00001d003203_T009:3 Zm00001d003203_T002:3 Zm00001d003203_T013:3 Zm00001d003203_T011:3 Zm00001d003203_T005:3 Zm00001d003203_T006:3

			
						 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  
						
							CCGCCGTGTCAACAAGACCTTCTCGTCCACCCATTGTGTGGAAGAAAAACTCAGTAGCAGTCAA
ACCAGTATAGAATGAATTAGCAACAAAACCTTTAGCctgaagttgttttgcagatataccagat
ataatagcagcaatagattcttctaggcaagaatctttcttttctacatgatcctcatgtagat
ggagtgcc

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTGAAGTTGTTTTGCAGATATACCAGATATAATAGCAGCAATAGATTCTTCTAGGCAAGAATCT
TTCTTTTCTACATGATCCTCATGTAGATGGAGTGCCCTTCTTGTGCATTTCATTAATTCTATAC
GTTTATCAAGGAATTCAGTTAAGTTTTTCTTGAACTCTGCACTACAGCCACCATCAGATGAGGT
GTCATGCTGCAAGAACTTATCCTCTAACATCTGTTTGATGCCCACTGGAGATAATGTATCTGAT
CCCCTTTGAGGACATGTGGCCTATAATAGAAGTTAAATGATCAGAGCACATTTTCATGGCTATC
TAACAAAGTATTATGTACATTAAACTAACCATGACTTTCATAAACAATTGATCCAAATTTAAGG
GCATGCCATCTTTTCCTTCCATCTTTGCAGGATCCATGCCATCATCTCCATACAAAAATTGAAC
TATACCACCGCTAGCATTTCGAACTGTCTGATCATAGAAAACTGAGAGATCTTCCAAGCCTTTC
ATCAATCTGCGGGACATATATCCAGTTTCTGCTGTTTTGACCTAATATTAAGAAAAGATCAAAA
CGAAGGAAACAACAGGTAGGGGCCGACTAAAAATTTTGAATGGGAAAAAATGCACTGGAAATAG
ATGTTGGCACTGTTCTGAGGATACGAGGTCTAGTGCAGATGATTATGTAGTAACAGTATAACAC
TGGTGAGATCAATGGGATTCTCTTTAAATTCTACTTGAAGATATAATACTGCTCTGTAATAGCC
ACTTTGTAGTTATTGACTTGATCTATTGCTGTTCCGAAGTAACTAATACATGGTTGTCAGTCTC
TTAGGTTGAATGTTGCATTATCTTGCAGCAAGTCTTAGAAAACAAGTGGTGTTGTATGCCAGGT
GTCAGGGGAGTAATGATTTATCTAATTACATCTCGGCTTCAGAGAAAACTGGGTTACTCTTTTC
CTTCAATGTGAGTCTGTAACAGTTGTTAGGATCAAGTTATTAGATTGGGCCATTAGGATTGAAT
AGTAGAACTACTAAAATATACCGAATTGTGGTATTTAATAATGCTCAGAATTAGATCATTAGGG
AGTTTGTACATATACCAGGACCATAATCAGATTGGGGAGGAAGGTTGTAATTAGCAGTCGATAA
AAAAAAAGGTATTGGCTCATGTGAGAAAACAAAAGAAATATTTCCTCCATTCCAAAAAAATGTC
GGCCATTTTAGCATTGTTATAAGTCAAACTTCCCTAACTTTGACAAAGTTTGCAGAAAAAAAGA
TATATTAACATCATAGTACCAAATAAATACACTGTTTAATGTGATGTGTAGATGTTGATGCACT
TTTCTATAAACTTGGTCAAGAAGTTTGGCTTAAGACAAAACTAAAAAAATTACACTTCGGAGCA
GAGGAGTACCATCCATAGTGGCAAACATTTTGGCCAGGAAAACAAAATGACACCATTGTCTGTT
TCAACTGAGTAACAAATGCAAGTCATATTTAAGCCTATATGAACAATTGTGACATCATTTATGA
TGTAATCCCTAGAGAATGCAAAAACTTAATAAATACAAAACAAGGTTTTAAAGTCGAGAGACTA
GTCGAGAATGACTAGTCGAGAAGTCGGTGTAGAGGTGATAGTCGACCAGAACGACTCGACTTAC
TCTGCTAGTCGCTCGACTTGTCGACTAGTCACGACTAGTCGTAGCATTTGAATCGTGCGACTTA
TTTGGACCTAGGTATAAAAATGTAAGCCCGCCCAACCATTTCAACCCTAGTAGGTAGGATGCTA
ATGGACAAGTTTCCTACCTTATTTTGGACATCTTGTGCTAACCACTACTTGGATCTCATGCTGG
AGGTTATTGGGAAGATAAATGAGTTTAGTGGCTGCATTGCTAAAGCAAAGAAGATAACCAGATT
TATCTATGGGCATGGAAGGATTTAAGACTTGGTGAGGACCAAGACAAATGGTAGAGATCTTGTT
AGGCTGAAATGGTAGGACCAGCAATGGCTGAAATGCAGGTTGCCATGGACAATGCAAAAAAGAG
CATCAAGGAAGCTTTGGAACACAGCGATTAATGGATGAAGTAATTTCTATTGTTGATAAGATAA
GAGGTGGGACAATCAGATGAATACCAATCTGTATGAGGCATGCACTGTTTTTGAATGCAAACAA
GTTCTTTGAAATCAGAGAGCACAATAGGAGACTTGCTACAAGACTGTTCAATATTTAATGATGT
ATTGTAGAAGATGGAGATTGATGAAGATACACTAAACGAGGTGTTTTTTAGTGTTTCAGTGTGT
TTTTAGTATTAGCATATATAGAAAATTATAAAAATGTAATCATCGACTTATATTCAACTAGTCA
CGAGTAGTCTATCCTAGTCATCACTAGTCTACTAGTCAGTAGCTACACGACTCGACTCGACTCG
ACTTCACGACTCAAAAACATTGATGCAAGAAAGAAACATGTTTAAATTTAGGCATACCGCCGTG
TCAACAAGACCTTCTCGTCCACCCATTGTGTGGAAGAAAAACTCAGTAGCAGTCAAACCAGTAT
AGAATGAATTAGCAACAAAACCTTTAGC
						
					

			
		

Sequences
Splice junction sequence	CCGCCGTGTCAACAAGACCTTCTCGTCCACCCATTGTGTGGAAGAAAAACTCAGTAGCAGTCAA ACCAGTATAGAATGAATTAGCAACAAAACCTTTAGCctgaagttgttttgcagatataccagat ataatagcagcaatagattcttctaggcaagaatctttcttttctacatgatcctcatgtagat ggagtgcc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTGAAGTTGTTTTGCAGATATACCAGATATAATAGCAGCAATAGATTCTTCTAGGCAAGAATCT TTCTTTTCTACATGATCCTCATGTAGATGGAGTGCCCTTCTTGTGCATTTCATTAATTCTATAC GTTTATCAAGGAATTCAGTTAAGTTTTTCTTGAACTCTGCACTACAGCCACCATCAGATGAGGT GTCATGCTGCAAGAACTTATCCTCTAACATCTGTTTGATGCCCACTGGAGATAATGTATCTGAT CCCCTTTGAGGACATGTGGCCTATAATAGAAGTTAAATGATCAGAGCACATTTTCATGGCTATC TAACAAAGTATTATGTACATTAAACTAACCATGACTTTCATAAACAATTGATCCAAATTTAAGG GCATGCCATCTTTTCCTTCCATCTTTGCAGGATCCATGCCATCATCTCCATACAAAAATTGAAC TATACCACCGCTAGCATTTCGAACTGTCTGATCATAGAAAACTGAGAGATCTTCCAAGCCTTTC ATCAATCTGCGGGACATATATCCAGTTTCTGCTGTTTTGACCTAATATTAAGAAAAGATCAAAA CGAAGGAAACAACAGGTAGGGGCCGACTAAAAATTTTGAATGGGAAAAAATGCACTGGAAATAG ATGTTGGCACTGTTCTGAGGATACGAGGTCTAGTGCAGATGATTATGTAGTAACAGTATAACAC TGGTGAGATCAATGGGATTCTCTTTAAATTCTACTTGAAGATATAATACTGCTCTGTAATAGCC ACTTTGTAGTTATTGACTTGATCTATTGCTGTTCCGAAGTAACTAATACATGGTTGTCAGTCTC TTAGGTTGAATGTTGCATTATCTTGCAGCAAGTCTTAGAAAACAAGTGGTGTTGTATGCCAGGT GTCAGGGGAGTAATGATTTATCTAATTACATCTCGGCTTCAGAGAAAACTGGGTTACTCTTTTC CTTCAATGTGAGTCTGTAACAGTTGTTAGGATCAAGTTATTAGATTGGGCCATTAGGATTGAAT AGTAGAACTACTAAAATATACCGAATTGTGGTATTTAATAATGCTCAGAATTAGATCATTAGGG AGTTTGTACATATACCAGGACCATAATCAGATTGGGGAGGAAGGTTGTAATTAGCAGTCGATAA AAAAAAAGGTATTGGCTCATGTGAGAAAACAAAAGAAATATTTCCTCCATTCCAAAAAAATGTC GGCCATTTTAGCATTGTTATAAGTCAAACTTCCCTAACTTTGACAAAGTTTGCAGAAAAAAAGA TATATTAACATCATAGTACCAAATAAATACACTGTTTAATGTGATGTGTAGATGTTGATGCACT TTTCTATAAACTTGGTCAAGAAGTTTGGCTTAAGACAAAACTAAAAAAATTACACTTCGGAGCA GAGGAGTACCATCCATAGTGGCAAACATTTTGGCCAGGAAAACAAAATGACACCATTGTCTGTT TCAACTGAGTAACAAATGCAAGTCATATTTAAGCCTATATGAACAATTGTGACATCATTTATGA TGTAATCCCTAGAGAATGCAAAAACTTAATAAATACAAAACAAGGTTTTAAAGTCGAGAGACTA GTCGAGAATGACTAGTCGAGAAGTCGGTGTAGAGGTGATAGTCGACCAGAACGACTCGACTTAC TCTGCTAGTCGCTCGACTTGTCGACTAGTCACGACTAGTCGTAGCATTTGAATCGTGCGACTTA TTTGGACCTAGGTATAAAAATGTAAGCCCGCCCAACCATTTCAACCCTAGTAGGTAGGATGCTA ATGGACAAGTTTCCTACCTTATTTTGGACATCTTGTGCTAACCACTACTTGGATCTCATGCTGG AGGTTATTGGGAAGATAAATGAGTTTAGTGGCTGCATTGCTAAAGCAAAGAAGATAACCAGATT TATCTATGGGCATGGAAGGATTTAAGACTTGGTGAGGACCAAGACAAATGGTAGAGATCTTGTT AGGCTGAAATGGTAGGACCAGCAATGGCTGAAATGCAGGTTGCCATGGACAATGCAAAAAAGAG CATCAAGGAAGCTTTGGAACACAGCGATTAATGGATGAAGTAATTTCTATTGTTGATAAGATAA GAGGTGGGACAATCAGATGAATACCAATCTGTATGAGGCATGCACTGTTTTTGAATGCAAACAA GTTCTTTGAAATCAGAGAGCACAATAGGAGACTTGCTACAAGACTGTTCAATATTTAATGATGT ATTGTAGAAGATGGAGATTGATGAAGATACACTAAACGAGGTGTTTTTTAGTGTTTCAGTGTGT TTTTAGTATTAGCATATATAGAAAATTATAAAAATGTAATCATCGACTTATATTCAACTAGTCA CGAGTAGTCTATCCTAGTCATCACTAGTCTACTAGTCAGTAGCTACACGACTCGACTCGACTCG ACTTCACGACTCAAAAACATTGATGCAAGAAAGAAACATGTTTAAATTTAGGCATACCGCCGTG TCAACAAGACCTTCTCGTCCACCCATTGTGTGGAAGAAAAACTCAGTAGCAGTCAAACCAGTAT AGAATGAATTAGCAACAAAACCTTTAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.058199018

Conservation Information
Conserved circRNAs	NA
PMCS	0.058199018

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35526259-35523738(-)
						
						Potential amino acid sequence
						
							MGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKMEGK
DGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEFLDK
RIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQAKGFVANSFYTGLTATEFFFH
TMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKMEG
KDGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEFLD
KRIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQAKGFVANSFYTGLTATEFFF
HTMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKME
GKDGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEFL
DKRIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQAKGFVANSFYTGLTATEFF
FHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKM
EGKDGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEF
LDKRIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	35526259-35523738(-)
Potential amino acid sequence	MGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKMEGK DGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEFLDK RIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQAKGFVANSFYTGLTATEFFFH TMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKMEG KDGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEFLD KRIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQAKGFVANSFYTGLTATEFFF HTMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKME GKDGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEFL DKRIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQAKGFVANSFYTGLTATEFF FHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFYDQTVRNASGGIVQFLYGDDGMDPAKM EGKDGMPLNLDQLFMKVMATCPQRGSDTLSPVGIKQMLEDKFLQHDTSSDGGCSAEFKKNLTEF LDKRIELMKCTRRALHLHEDHVEKKDSCLEESIAAIISGISAKQLQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d003203_circ_g.3

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