Plant Circular RNA Database

Detail information of Zm00001d037346_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d037346_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009023
					
						Alias
						Zm06circ00048
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 122241022-122242279  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d037346						
					
						Parent gene annotation
						
							Chromatin structure-remodeling complex protein SYD
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d037346_circ_g.1 Zm00001d037346_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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  
						
							GT-AG							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
						Zm00001d037346_T004:3
Zm00001d037346_T011:3
Zm00001d037346_T009:3
Zm00001d037346_T014:3
Zm00001d037346_T015:3
Zm00001d037346_T007:3
Zm00001d037346_T002:3
Zm00001d037346_T006:3
Zm00001d037346_T010:3
Zm00001d037346_T012:3
Zm00001d037346_T017:1
Zm00001d037346_T003:3
Zm00001d037346_T005:3
Zm00001d037346_T013:3
Zm00001d037346_T001:3
Zm00001d037346_T008:3
Zm00001d037346_T016:2

General Information
CircRNA Name	Zm00001d037346_circ_g.2
ID in PlantcircBase	zma_circ_009023
Alias	Zm06circ00048
Organism	Zea mays
Position	chr6: 122241022-122242279 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d037346
Parent gene annotation	Chromatin structure-remodeling complex protein SYD
Parent gene strand	+
Alternative splicing	Zm00001d037346_circ_g.1 Zm00001d037346_circ_g.3
Support reads	NA
Tissues	leaf, endosperm
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	GT-AG 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	Zm00001d037346_T004:3 Zm00001d037346_T011:3 Zm00001d037346_T009:3 Zm00001d037346_T014:3 Zm00001d037346_T015:3 Zm00001d037346_T007:3 Zm00001d037346_T002:3 Zm00001d037346_T006:3 Zm00001d037346_T010:3 Zm00001d037346_T012:3 Zm00001d037346_T017:1 Zm00001d037346_T003:3 Zm00001d037346_T005:3 Zm00001d037346_T013:3 Zm00001d037346_T001:3 Zm00001d037346_T008:3 Zm00001d037346_T016:2

			
						 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  
						
							CTTAGATTACCAGAAGAGAATTTACAATGAGAAACAAAAGAGAACATTGGAGCAGCATAAGGTA
CACAGCAGAATGTCAGCAACATATGAGGAGCTAAAGggaagtcccatgcaagaaaggcaaggta
tgatcagggtgccacagagaggcgaggcatcatttcaggaacgcaggccatcttcacttccgag
tagaagta

									
								

					

						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: 1062
Transcript exons: 122241022-122241221,122241339-122241403,122241483-122242
279
GGAAGTCCCATGCAAGAAAGGCAAGGTATGATCAGGGTGCCACAGAGAGGCGAGGCATCATTTC
AGGAACGCAGGCCATCTTCACTTCCGAGTAGAAGTACTGGGCCAAGTCCAATGTCTCACATTTC
TTCCAACACACCATTTAAAGAACAGCAGCTGAAGCAGCTCAGAGCACAGTGCTTAGTATTTCTT
GCATTTAGGAATAATTTGCAGCCCAGGAAGGTACATCTTGAAATTGCTTTGGGCAGAGGGCCTC
CTGCAGAAAGTGACAGTGCAGGTCAAAGGGGCAGCGAGGGCAGAGTGTCTGATGCTCTGGGAAA
GGAAAATGGTAGCAGTCGGGAGAACTCTGGTGTCTTTTGTAGGCAAACTGATATCTCTAGACTT
CCAGCCACATCTGCAGGAAGTATTGCAGAGGATGATTCCTTATCGAAGGATCCAGAAAATGCTA
CAAAAAAAATCAAGTTAGCTGAACAGGAGAAGTCATTGATGGAAGTAGAAAATGTCCAGCAAGC
TTCTGTTATGCAAGGAACTAGTTCTGAAATGCGTTCCCAAGAAACTGCATCTCAAAATCCATAT
CGACCACAACAGTCATATTATCAAGGAGATACAAGAAGAATCGCCTCGGATATCCATAGGACTG
ATGCTGAAATTTTGAACCAGAATTTAAGTTGGGGAGGCCAGGGATCTACTGCTTTGGGTGGTAC
TAGACAGCTTCTGAATCAGGAAACTAAAGAATCACTTGCACCTTCAAAGTCACACCATATGCCT
GTTGATGGTTACAACTCCAATATACAAGGAATAGATCGGACTCCAGAGATAGCTGGAGCTGGTA
ATGATGTTGAAAATTGTAGCCACGTAGCAGATATTGTGCCTGAGCAGGCTGCTGATGAAGGAGA
TGAGGACCTCTCAGAGCATGAGGATTTATTGTCATCTCCAAAGCACACAATGACGGAAAAATGG
ATCTTAGATTACCAGAAGAGAATTTACAATGAGAAACAAAAGAGAACATTGGAGCAGCATAAGG
TACACAGCAGAATGTCAGCAACATATGAGGAGCTAAAG
						
					

						Genomic sequence
						
							GGAAGTCCCATGCAAGAAAGGCAAGGTATGATCAGGGTGCCACAGAGAGGCGAGGCATCATTTC
AGGAACGCAGGCCATCTTCACTTCCGAGTAGAAGTACTGGGCCAAGTCCAATGTCTCACATTTC
TTCCAACACACCATTTAAAGAACAGCAGCTGAAGCAGCTCAGAGCACAGTGCTTAGTATTTCTT
GCATTTAGGTCTGCTTTTCTTTTCGTATATCTTCTTCATGTAGTTTTACTGAGTATATCAACGC
TTCAGAGCATGGCATCCGAACTTCATTTTCTGGCACCCATGTAAGCTGTTTTTTCTTGTAGGAA
TAATTTGCAGCCCAGGAAGGTACATCTTGAAATTGCTTTGGGCAGAGGGCCTCCTGCAGAAAGT
AAGAACTAAAAAACACATTGTGATCTATTTGATTTTTGTTTTGTCATATCAATGATTGGTTTGT
ACATGAAAATCAGGTGACAGTGCAGGTCAAAGGGGCAGCGAGGGCAGAGTGTCTGATGCTCTGG
GAAAGGAAAATGGTAGCAGTCGGGAGAACTCTGGTGTCTTTTGTAGGCAAACTGATATCTCTAG
ACTTCCAGCCACATCTGCAGGAAGTATTGCAGAGGATGATTCCTTATCGAAGGATCCAGAAAAT
GCTACAAAAAAAATCAAGTTAGCTGAACAGGAGAAGTCATTGATGGAAGTAGAAAATGTCCAGC
AAGCTTCTGTTATGCAAGGAACTAGTTCTGAAATGCGTTCCCAAGAAACTGCATCTCAAAATCC
ATATCGACCACAACAGTCATATTATCAAGGAGATACAAGAAGAATCGCCTCGGATATCCATAGG
ACTGATGCTGAAATTTTGAACCAGAATTTAAGTTGGGGAGGCCAGGGATCTACTGCTTTGGGTG
GTACTAGACAGCTTCTGAATCAGGAAACTAAAGAATCACTTGCACCTTCAAAGTCACACCATAT
GCCTGTTGATGGTTACAACTCCAATATACAAGGAATAGATCGGACTCCAGAGATAGCTGGAGCT
GGTAATGATGTTGAAAATTGTAGCCACGTAGCAGATATTGTGCCTGAGCAGGCTGCTGATGAAG
GAGATGAGGACCTCTCAGAGCATGAGGATTTATTGTCATCTCCAAAGCACACAATGACGGAAAA
ATGGATCTTAGATTACCAGAAGAGAATTTACAATGAGAAACAAAAGAGAACATTGGAGCAGCAT
AAGGTACACAGCAGAATGTCAGCAACATATGAGGAGCTAAAG
						
					

			
		

Sequences
Splice junction sequence	CTTAGATTACCAGAAGAGAATTTACAATGAGAAACAAAAGAGAACATTGGAGCAGCATAAGGTA CACAGCAGAATGTCAGCAACATATGAGGAGCTAAAGggaagtcccatgcaagaaaggcaaggta tgatcagggtgccacagagaggcgaggcatcatttcaggaacgcaggccatcttcacttccgag tagaagta
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: 1062 Transcript exons: 122241022-122241221,122241339-122241403,122241483-122242 279 GGAAGTCCCATGCAAGAAAGGCAAGGTATGATCAGGGTGCCACAGAGAGGCGAGGCATCATTTC AGGAACGCAGGCCATCTTCACTTCCGAGTAGAAGTACTGGGCCAAGTCCAATGTCTCACATTTC TTCCAACACACCATTTAAAGAACAGCAGCTGAAGCAGCTCAGAGCACAGTGCTTAGTATTTCTT GCATTTAGGAATAATTTGCAGCCCAGGAAGGTACATCTTGAAATTGCTTTGGGCAGAGGGCCTC CTGCAGAAAGTGACAGTGCAGGTCAAAGGGGCAGCGAGGGCAGAGTGTCTGATGCTCTGGGAAA GGAAAATGGTAGCAGTCGGGAGAACTCTGGTGTCTTTTGTAGGCAAACTGATATCTCTAGACTT CCAGCCACATCTGCAGGAAGTATTGCAGAGGATGATTCCTTATCGAAGGATCCAGAAAATGCTA CAAAAAAAATCAAGTTAGCTGAACAGGAGAAGTCATTGATGGAAGTAGAAAATGTCCAGCAAGC TTCTGTTATGCAAGGAACTAGTTCTGAAATGCGTTCCCAAGAAACTGCATCTCAAAATCCATAT CGACCACAACAGTCATATTATCAAGGAGATACAAGAAGAATCGCCTCGGATATCCATAGGACTG ATGCTGAAATTTTGAACCAGAATTTAAGTTGGGGAGGCCAGGGATCTACTGCTTTGGGTGGTAC TAGACAGCTTCTGAATCAGGAAACTAAAGAATCACTTGCACCTTCAAAGTCACACCATATGCCT GTTGATGGTTACAACTCCAATATACAAGGAATAGATCGGACTCCAGAGATAGCTGGAGCTGGTA ATGATGTTGAAAATTGTAGCCACGTAGCAGATATTGTGCCTGAGCAGGCTGCTGATGAAGGAGA TGAGGACCTCTCAGAGCATGAGGATTTATTGTCATCTCCAAAGCACACAATGACGGAAAAATGG ATCTTAGATTACCAGAAGAGAATTTACAATGAGAAACAAAAGAGAACATTGGAGCAGCATAAGG TACACAGCAGAATGTCAGCAACATATGAGGAGCTAAAG
Genomic sequence	GGAAGTCCCATGCAAGAAAGGCAAGGTATGATCAGGGTGCCACAGAGAGGCGAGGCATCATTTC AGGAACGCAGGCCATCTTCACTTCCGAGTAGAAGTACTGGGCCAAGTCCAATGTCTCACATTTC TTCCAACACACCATTTAAAGAACAGCAGCTGAAGCAGCTCAGAGCACAGTGCTTAGTATTTCTT GCATTTAGGTCTGCTTTTCTTTTCGTATATCTTCTTCATGTAGTTTTACTGAGTATATCAACGC TTCAGAGCATGGCATCCGAACTTCATTTTCTGGCACCCATGTAAGCTGTTTTTTCTTGTAGGAA TAATTTGCAGCCCAGGAAGGTACATCTTGAAATTGCTTTGGGCAGAGGGCCTCCTGCAGAAAGT AAGAACTAAAAAACACATTGTGATCTATTTGATTTTTGTTTTGTCATATCAATGATTGGTTTGT ACATGAAAATCAGGTGACAGTGCAGGTCAAAGGGGCAGCGAGGGCAGAGTGTCTGATGCTCTGG GAAAGGAAAATGGTAGCAGTCGGGAGAACTCTGGTGTCTTTTGTAGGCAAACTGATATCTCTAG ACTTCCAGCCACATCTGCAGGAAGTATTGCAGAGGATGATTCCTTATCGAAGGATCCAGAAAAT GCTACAAAAAAAATCAAGTTAGCTGAACAGGAGAAGTCATTGATGGAAGTAGAAAATGTCCAGC AAGCTTCTGTTATGCAAGGAACTAGTTCTGAAATGCGTTCCCAAGAAACTGCATCTCAAAATCC ATATCGACCACAACAGTCATATTATCAAGGAGATACAAGAAGAATCGCCTCGGATATCCATAGG ACTGATGCTGAAATTTTGAACCAGAATTTAAGTTGGGGAGGCCAGGGATCTACTGCTTTGGGTG GTACTAGACAGCTTCTGAATCAGGAAACTAAAGAATCACTTGCACCTTCAAAGTCACACCATAT GCCTGTTGATGGTTACAACTCCAATATACAAGGAATAGATCGGACTCCAGAGATAGCTGGAGCT GGTAATGATGTTGAAAATTGTAGCCACGTAGCAGATATTGTGCCTGAGCAGGCTGCTGATGAAG GAGATGAGGACCTCTCAGAGCATGAGGATTTATTGTCATCTCCAAAGCACACAATGACGGAAAA ATGGATCTTAGATTACCAGAAGAGAATTTACAATGAGAAACAAAAGAGAACATTGGAGCAGCAT AAGGTACACAGCAGAATGTCAGCAACATATGAGGAGCTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.180232366

Conservation Information
Conserved circRNAs	NA
PMCS	0.180232366

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							122241032-122242276(+)
122241034-122242203(-)
						
					

						Potential amino acid sequence
						
							MQERQGMIRVPQRGEASFQERRPSSLPSRSTGPSPMSHISSNTPFKEQQLKQLRAQCLVFLAFR
NNLQPRKVHLEIALGRGPPAESDSAGQRGSEGRVSDALGKENGSSRENSGVFCRQTDISRLPAT
SAGSIAEDDSLSKDPENATKKIKLAEQEKSLMEVENVQQASVMQGTSSEMRSQETASQNPYRPQ
QSYYQGDTRRIASDIHRTDAEILNQNLSWGGQGSTALGGTRQLLNQETKESLAPSKSHHMPVDG
YNSNIQGIDRTPEIAGAGNDVENCSHVADIVPEQAADEGDEDLSEHEDLLSSPKHTMTEKWILD
YQKRIYNEKQKRTLEQHKVHSRMSATYEELKGSPMQERQGMIRVPQRGEASFQERRPSSLPSRS
TGPSPMSHISSNTPFKEQQLKQLRAQCLVFLAFRNNLQPRKVHLEIALGRGPPAESDSAGQRGS
EGRVSDALGKENGSSRENSGVFCRQTDISRLPATSAGSIAEDDSLSKDPENATKKIKLAEQEKS
LMEVENVQQASVMQGTSSEMRSQETASQNPYRPQQSYYQGDTRRIASDIHRTDAEILNQNLSWG
GQGSTALGGTRQLLNQETKESLAPSKSHHMPVDGYNSNIQGIDRTPEIAGAGNDVENCSHVADI
VPEQAADEGDEDLSEHEDLLSSPKHTMTEKWILDYQKRIYNEKQKRTLEQHKVHSRMSATYEEL
KGSPMQERQGMIRVPQRGEASFQERRPSSLPSRSTGPSPMSHISSNTPFKEQQLKQLRAQCLVF
LAFRNNLQPRKVHLEIALGRGPPAESDSAGQRGSEGRVSDALGKENGSSRENSGVFCRQTDISR
LPATSAGSIAEDDSLSKDPENATKKIKLAEQEKSLMEVENVQQASVMQGTSSEMRSQETASQNP
YRPQQSYYQGDTRRIASDIHRTDAEILNQNLSWGGQGSTALGGTRQLLNQETKESLAPSKSHHM
PVDGYNSNIQGIDRTPEIAGAGNDVENCSHVADIVPEQAADEGDEDLSEHEDLLSSPKHTMTEK
WILDYQKRIYNEKQKRTLEQHKVHSRMSATYEELKGSPMQERQGMIRVPQRGEASFQERRPSSL
PSRSTGPSPMSHISSNTPFKEQQLKQLRAQCLVFLAFRNNLQPRKVHLEIALGRGPPAESDSAG
QRGSEGRVSDALGKENGSSRENSGVFCRQTDISRLPATSAGSIAEDDSLSKDPENATKKIKLAE
QEKSLMEVENVQQASVMQGTSSEMRSQETASQNPYRPQQSYYQGDTRRIASDIHRTDAEILNQN
LSWGGQGSTALGGTRQLLNQETKESLAPSKSHHMPVDGYNSNIQGIDRTPEIAGAGNDVENCSH
VADIVPEQAADEGDEDLSEHEDLLSSPKHTMTEKWILDYQKRIYNEKQKRTLEQHKVHSRMSAT
YEELK(+)
MGLPFSSSYVADILLCTLCCSNVLFCFSL*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	122241032-122242276(+) 122241034-122242203(-)
Potential amino acid sequence	MQERQGMIRVPQRGEASFQERRPSSLPSRSTGPSPMSHISSNTPFKEQQLKQLRAQCLVFLAFR NNLQPRKVHLEIALGRGPPAESDSAGQRGSEGRVSDALGKENGSSRENSGVFCRQTDISRLPAT SAGSIAEDDSLSKDPENATKKIKLAEQEKSLMEVENVQQASVMQGTSSEMRSQETASQNPYRPQ QSYYQGDTRRIASDIHRTDAEILNQNLSWGGQGSTALGGTRQLLNQETKESLAPSKSHHMPVDG YNSNIQGIDRTPEIAGAGNDVENCSHVADIVPEQAADEGDEDLSEHEDLLSSPKHTMTEKWILD YQKRIYNEKQKRTLEQHKVHSRMSATYEELKGSPMQERQGMIRVPQRGEASFQERRPSSLPSRS TGPSPMSHISSNTPFKEQQLKQLRAQCLVFLAFRNNLQPRKVHLEIALGRGPPAESDSAGQRGS EGRVSDALGKENGSSRENSGVFCRQTDISRLPATSAGSIAEDDSLSKDPENATKKIKLAEQEKS LMEVENVQQASVMQGTSSEMRSQETASQNPYRPQQSYYQGDTRRIASDIHRTDAEILNQNLSWG GQGSTALGGTRQLLNQETKESLAPSKSHHMPVDGYNSNIQGIDRTPEIAGAGNDVENCSHVADI VPEQAADEGDEDLSEHEDLLSSPKHTMTEKWILDYQKRIYNEKQKRTLEQHKVHSRMSATYEEL KGSPMQERQGMIRVPQRGEASFQERRPSSLPSRSTGPSPMSHISSNTPFKEQQLKQLRAQCLVF LAFRNNLQPRKVHLEIALGRGPPAESDSAGQRGSEGRVSDALGKENGSSRENSGVFCRQTDISR LPATSAGSIAEDDSLSKDPENATKKIKLAEQEKSLMEVENVQQASVMQGTSSEMRSQETASQNP YRPQQSYYQGDTRRIASDIHRTDAEILNQNLSWGGQGSTALGGTRQLLNQETKESLAPSKSHHM PVDGYNSNIQGIDRTPEIAGAGNDVENCSHVADIVPEQAADEGDEDLSEHEDLLSSPKHTMTEK WILDYQKRIYNEKQKRTLEQHKVHSRMSATYEELKGSPMQERQGMIRVPQRGEASFQERRPSSL PSRSTGPSPMSHISSNTPFKEQQLKQLRAQCLVFLAFRNNLQPRKVHLEIALGRGPPAESDSAG QRGSEGRVSDALGKENGSSRENSGVFCRQTDISRLPATSAGSIAEDDSLSKDPENATKKIKLAE QEKSLMEVENVQQASVMQGTSSEMRSQETASQNPYRPQQSYYQGDTRRIASDIHRTDAEILNQN LSWGGQGSTALGGTRQLLNQETKESLAPSKSHHMPVDGYNSNIQGIDRTPEIAGAGNDVENCSH VADIVPEQAADEGDEDLSEHEDLLSSPKHTMTEKWILDYQKRIYNEKQKRTLEQHKVHSRMSAT YEELK(+) MGLPFSSSYVADILLCTLCCSNVLFCFSL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d037346_circ_g.2

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