Plant Circular RNA Database

Detail information of Zm00001d002654_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d002654_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007084
					
						Alias
						Zm02circ00020, GRMZM2G129261_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 18316922-18319133  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d002654						
					
						Parent gene annotation
						
							 naked endosperm1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d002654_circ_g.1 Zm00001d002654_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  
						
							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
						Zm00001d002654_T002:2
Zm00001d002654_T005:2
Zm00001d002654_T022:3
Zm00001d002654_T018:3
Zm00001d002654_T001:2
Zm00001d002654_T024:2
Zm00001d002654_T012:3
Zm00001d002654_T020:3
Zm00001d002654_T009:1
Zm00001d002654_T015:2
Zm00001d002654_T017:1
Zm00001d002654_T016:2
Zm00001d002654_T003:2
Zm00001d002654_T013:2
Zm00001d002654_T026:3
Zm00001d002654_T023:2
Zm00001d002654_T021:3
Zm00001d002654_T014:2
Zm00001d002654_T008:1
Zm00001d002654_T004:2
Zm00001d002654_T019:3
Zm00001d002654_T011:4
Zm00001d002654_T010:3
Zm00001d002654_T006:2
Zm00001d002654_T007:2
Zm00001d002654_T025:3

General Information
CircRNA Name	Zm00001d002654_circ_g.2
ID in PlantcircBase	zma_circ_007084
Alias	Zm02circ00020, GRMZM2G129261_C1
Organism	Zea mays
Position	chr2: 18316922-18319133 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d002654
Parent gene annotation	naked endosperm1
Parent gene strand	-
Alternative splicing	Zm00001d002654_circ_g.1 Zm00001d002654_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	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	Zm00001d002654_T002:2 Zm00001d002654_T005:2 Zm00001d002654_T022:3 Zm00001d002654_T018:3 Zm00001d002654_T001:2 Zm00001d002654_T024:2 Zm00001d002654_T012:3 Zm00001d002654_T020:3 Zm00001d002654_T009:1 Zm00001d002654_T015:2 Zm00001d002654_T017:1 Zm00001d002654_T016:2 Zm00001d002654_T003:2 Zm00001d002654_T013:2 Zm00001d002654_T026:3 Zm00001d002654_T023:2 Zm00001d002654_T021:3 Zm00001d002654_T014:2 Zm00001d002654_T008:1 Zm00001d002654_T004:2 Zm00001d002654_T019:3 Zm00001d002654_T011:4 Zm00001d002654_T010:3 Zm00001d002654_T006:2 Zm00001d002654_T007:2 Zm00001d002654_T025:3

			
						 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  
						
							GCTCGAACGCGCCAACACTGCTTCTCCTTCCTGCAGCTGGTCGCTTTGGCCCGTTGCTAGGAAT
AGGGTCGGCAGTGTTCTTCGTCCTTCCCCTTCTTCGctggagaagagtgtgccgcagtcgcatc
ggtactcacgggtgccgcagatcttggagtgcgccttccagtccgactgcacggcgtagcgctt
ggagcact

									
								

					

						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: 724
Transcript exons: 18316922-18317321,18318810-18319133
CTGGAGAAGAGTGTGCCGCAGTCGCATCGGTACTCACGGGTGCCGCAGATCTTGGAGTGCGCCT
TCCAGTCCGACTGCACGGCGTAGCGCTTGGAGCACTTGTCGCACTTCCACTTCTTCTCGCCGTG
CTTGCGGCAGAAGTGCTTCTTGATCCCCGTCAGGTCGCCGAGGGCGCGGGCCGGGTCGTGGTGC
ACGCACGTCGGCTCCGGGCACAGGTACACGCGCCGCCGCTGCGCCTGTAGCGGGTTCTTCTGCT
TCAGCTTCCACGGCAGGTTGTGCCCGCGCCGGTGCAGCTGCAGGTTCTGCTCGCGCTGGAACCC
CTTGTTGCACACCTCGCACACGAACCTGTTGGTCGCCATAAGCGTCTTGGGCGACAGCGCGATC
ACCTCAGCGTCGGGGTCAGGCATAGTCCTCTTCTTCTTGGGCGGTGGCTGCGCCGGCGGCGCGC
CTTGGCCGGACGCCGCAGGAACACCGCCTGCCACACCGGGCAGCGCCGCTGCCAGCTGTTGCTG
CGGTGATATCAGCGGCTTAATCTGGTCTTGCTGGTCCCCATCCCTAACACCAAAGAACGCCGCC
GATGAATTCGATGCCATCACTTCCTCCCGATTTATCCTGGCACCACCAGCTCGAACGCGCCAAC
ACTGCTTCTCCTTCCTGCAGCTGGTCGCTTTGGCCCGTTGCTAGGAATAGGGTCGGCAGTGTTC
TTCGTCCTTCCCCTTCTTCG
						
					

						Genomic sequence
						
							CTGGAGAAGAGTGTGCCGCAGTCGCATCGGTACTCACGGGTGCCGCAGATCTTGGAGTGCGCCT
TCCAGTCCGACTGCACGGCGTAGCGCTTGGAGCACTTGTCGCACTTCCACTTCTTCTCGCCGTG
CTTGCGGCAGAAGTGCTTCTTGATCCCCGTCAGGTCGCCGAGGGCGCGGGCCGGGTCGTGGTGC
ACGCACGTCGGCTCCGGGCACAGGTACACGCGCCGCCGCTGCGCCTGTAGCGGGTTCTTCTGCT
TCAGCTTCCACGGCAGGTTGTGCCCGCGCCGGTGCAGCTGCAGGTTCTGCTCGCGCTGGAACCC
CTTGTTGCACACCTCGCACACGAACCTGTTGGTCGCCATAAGCGTCTTGGGCGACAGCGCGATC
ACCTCAGCGTCGGGGTCTGCTTCGTCATCGCACCGGTCGATATGAAATCAAAACACAAAGTCTG
CTGGTTAGCTAATAGTATATAACCCTAGTATATATAGCTTTTATTATTTGCAAAAGAAGAGGAA
GAAGAAATGCTATACATGATCGGTCGAACTGACGCATGCATGATATGATGGACAGCAGGGAAAT
TAAAACTAACTTTGATTTCAGTGAATAAACAGTAAAAGCATGCATGGGTCACTAATGAGGATAT
AGATGATCGTCAGTCAGCACTTGTCGTGGATTAGGATGGACGACAATAGCACATGGTTTTTGTA
TATTGATGACTGATGCGTTTTATTAATTATTTCGAGGGAATTATTGTTCTATGTGGGAGTAATT
AATACTAGTATTTTTCTTATAAGTTAGTCCTGCATACATGATTAAGAAACGATGGTGGGAGCTA
GTAGTGATGGCGGTATAGTAATCTGGGCAAGATATTTGTTTTTGTTTCAGCTTTCTCTCGGTGG
GTGTGAGCGGTAGTAGAGACAAGCTACGAGAGATGGAGAGAGAGGGGAATATTTTGCAAGAGAT
TGTTTTTTTTTGGGGGGACGGAGGAGTTTGCAGGAAGAGATATAGAGAACAAAGGAATCGATCG
ACATGGATTGTGTCATGGCTCCTATTTACTTCTCTCATAGCTGGGGAAGGAAGAACTGAGTAAC
AGCTCATGCATGCACATGGAATCTTGGGAGGTGAACAGATTTTGTTTTCTTCTTGAAAAAAATA
CAAACTTTGTTATTTTTATTAACCAAATAAACAAAAGTTGATAGGATAGTTCGAATTCTTCAAC
CGGTTGAAACAAAAACGTGAGCATTGCTCAGAAAGAAGAGGCCAGGGGGTGAAAACTAGTAGTA
GCGCCATGAATTGAATGAAGTCTCTACTCCAACCTTCCATATTCACCTGAATTAATTCTCACTC
TCAGGTGTGACTGTGAGGACAGAGCTTTAAATGAAGTATATTGATTGAAAGATGCAAACTGGAG
GCTCTCGTCTCGTCAAGTCTACTTGCTTTGCAGCGAAGGTAGGGAGGGGATCCACCTCGAACTA
GGGAGGGAGGGAAGAGAGAGAACCAAGAGGAACTTGGGTACTATTTTCATAAAATCCAGTTCCC
AGTGAAAAAAACAGGCTGTAGTTTGCACACATCGATCTGCGTTGAAAAACCAGGCAACAACTCT
CGGAACTATATTAATTACGCAGTGTAGAGAGCAGCGATCACGAATCAAGAGAAACACACACAGA
CAAGAAGTGAAGAAACCAAGAAGACATGGAAAGAGAAACCGAGTGCATATGAGAGAAGAAGATG
CTCCTGGTGTCAGCATCCAACTCATAAAACTCCAATAGATCCAGACGAGCGAGATCTCTCGCGC
GCAGGCAGCATAGGCCTGACCTGTATGCAGTGTGCATGCACGACCGGAATCAAAAGGGGGAGGG
GAGGGGGGTACTTGCGTTGCGTAATAAATTACCAGGCATAGTCCTCTTCTTCTTGGGCGGTGGC
TGCGCCGGCGGCGCGCCTTGGCCGGACGCCGCAGGAACACCGCCTGCCACACCGGGCAGCGCCG
CTGCCAGCTGTTGCTGCGGTGATATCAGCGGCTTAATCTGGTCTTGCTGGTCCCCATCCCTAAC
ACCAAAGAACGCCGCCGATGAATTCGATGCCATCACTTCCTCCCGATTTATCCTGGCACCACCA
GCTCGAACGCGCCAACACTGCTTCTCCTTCCTGCAGCTGGTCGCTTTGGCCCGTTGCTAGGAAT
AGGGTCGGCAGTGTTCTTCGTCCTTCCCCTTCTTCG
						
					

			
		

Sequences
Splice junction sequence	GCTCGAACGCGCCAACACTGCTTCTCCTTCCTGCAGCTGGTCGCTTTGGCCCGTTGCTAGGAAT AGGGTCGGCAGTGTTCTTCGTCCTTCCCCTTCTTCGctggagaagagtgtgccgcagtcgcatc ggtactcacgggtgccgcagatcttggagtgcgccttccagtccgactgcacggcgtagcgctt ggagcact
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: 724 Transcript exons: 18316922-18317321,18318810-18319133 CTGGAGAAGAGTGTGCCGCAGTCGCATCGGTACTCACGGGTGCCGCAGATCTTGGAGTGCGCCT TCCAGTCCGACTGCACGGCGTAGCGCTTGGAGCACTTGTCGCACTTCCACTTCTTCTCGCCGTG CTTGCGGCAGAAGTGCTTCTTGATCCCCGTCAGGTCGCCGAGGGCGCGGGCCGGGTCGTGGTGC ACGCACGTCGGCTCCGGGCACAGGTACACGCGCCGCCGCTGCGCCTGTAGCGGGTTCTTCTGCT TCAGCTTCCACGGCAGGTTGTGCCCGCGCCGGTGCAGCTGCAGGTTCTGCTCGCGCTGGAACCC CTTGTTGCACACCTCGCACACGAACCTGTTGGTCGCCATAAGCGTCTTGGGCGACAGCGCGATC ACCTCAGCGTCGGGGTCAGGCATAGTCCTCTTCTTCTTGGGCGGTGGCTGCGCCGGCGGCGCGC CTTGGCCGGACGCCGCAGGAACACCGCCTGCCACACCGGGCAGCGCCGCTGCCAGCTGTTGCTG CGGTGATATCAGCGGCTTAATCTGGTCTTGCTGGTCCCCATCCCTAACACCAAAGAACGCCGCC GATGAATTCGATGCCATCACTTCCTCCCGATTTATCCTGGCACCACCAGCTCGAACGCGCCAAC ACTGCTTCTCCTTCCTGCAGCTGGTCGCTTTGGCCCGTTGCTAGGAATAGGGTCGGCAGTGTTC TTCGTCCTTCCCCTTCTTCG
Genomic sequence	CTGGAGAAGAGTGTGCCGCAGTCGCATCGGTACTCACGGGTGCCGCAGATCTTGGAGTGCGCCT TCCAGTCCGACTGCACGGCGTAGCGCTTGGAGCACTTGTCGCACTTCCACTTCTTCTCGCCGTG CTTGCGGCAGAAGTGCTTCTTGATCCCCGTCAGGTCGCCGAGGGCGCGGGCCGGGTCGTGGTGC ACGCACGTCGGCTCCGGGCACAGGTACACGCGCCGCCGCTGCGCCTGTAGCGGGTTCTTCTGCT TCAGCTTCCACGGCAGGTTGTGCCCGCGCCGGTGCAGCTGCAGGTTCTGCTCGCGCTGGAACCC CTTGTTGCACACCTCGCACACGAACCTGTTGGTCGCCATAAGCGTCTTGGGCGACAGCGCGATC ACCTCAGCGTCGGGGTCTGCTTCGTCATCGCACCGGTCGATATGAAATCAAAACACAAAGTCTG CTGGTTAGCTAATAGTATATAACCCTAGTATATATAGCTTTTATTATTTGCAAAAGAAGAGGAA GAAGAAATGCTATACATGATCGGTCGAACTGACGCATGCATGATATGATGGACAGCAGGGAAAT TAAAACTAACTTTGATTTCAGTGAATAAACAGTAAAAGCATGCATGGGTCACTAATGAGGATAT AGATGATCGTCAGTCAGCACTTGTCGTGGATTAGGATGGACGACAATAGCACATGGTTTTTGTA TATTGATGACTGATGCGTTTTATTAATTATTTCGAGGGAATTATTGTTCTATGTGGGAGTAATT AATACTAGTATTTTTCTTATAAGTTAGTCCTGCATACATGATTAAGAAACGATGGTGGGAGCTA GTAGTGATGGCGGTATAGTAATCTGGGCAAGATATTTGTTTTTGTTTCAGCTTTCTCTCGGTGG GTGTGAGCGGTAGTAGAGACAAGCTACGAGAGATGGAGAGAGAGGGGAATATTTTGCAAGAGAT TGTTTTTTTTTGGGGGGACGGAGGAGTTTGCAGGAAGAGATATAGAGAACAAAGGAATCGATCG ACATGGATTGTGTCATGGCTCCTATTTACTTCTCTCATAGCTGGGGAAGGAAGAACTGAGTAAC AGCTCATGCATGCACATGGAATCTTGGGAGGTGAACAGATTTTGTTTTCTTCTTGAAAAAAATA CAAACTTTGTTATTTTTATTAACCAAATAAACAAAAGTTGATAGGATAGTTCGAATTCTTCAAC CGGTTGAAACAAAAACGTGAGCATTGCTCAGAAAGAAGAGGCCAGGGGGTGAAAACTAGTAGTA GCGCCATGAATTGAATGAAGTCTCTACTCCAACCTTCCATATTCACCTGAATTAATTCTCACTC TCAGGTGTGACTGTGAGGACAGAGCTTTAAATGAAGTATATTGATTGAAAGATGCAAACTGGAG GCTCTCGTCTCGTCAAGTCTACTTGCTTTGCAGCGAAGGTAGGGAGGGGATCCACCTCGAACTA GGGAGGGAGGGAAGAGAGAGAACCAAGAGGAACTTGGGTACTATTTTCATAAAATCCAGTTCCC AGTGAAAAAAACAGGCTGTAGTTTGCACACATCGATCTGCGTTGAAAAACCAGGCAACAACTCT CGGAACTATATTAATTACGCAGTGTAGAGAGCAGCGATCACGAATCAAGAGAAACACACACAGA CAAGAAGTGAAGAAACCAAGAAGACATGGAAAGAGAAACCGAGTGCATATGAGAGAAGAAGATG CTCCTGGTGTCAGCATCCAACTCATAAAACTCCAATAGATCCAGACGAGCGAGATCTCTCGCGC GCAGGCAGCATAGGCCTGACCTGTATGCAGTGTGCATGCACGACCGGAATCAAAAGGGGGAGGG GAGGGGGGTACTTGCGTTGCGTAATAAATTACCAGGCATAGTCCTCTTCTTCTTGGGCGGTGGC TGCGCCGGCGGCGCGCCTTGGCCGGACGCCGCAGGAACACCGCCTGCCACACCGGGCAGCGCCG CTGCCAGCTGTTGCTGCGGTGATATCAGCGGCTTAATCTGGTCTTGCTGGTCCCCATCCCTAAC ACCAAAGAACGCCGCCGATGAATTCGATGCCATCACTTCCTCCCGATTTATCCTGGCACCACCA GCTCGAACGCGCCAACACTGCTTCTCCTTCCTGCAGCTGGTCGCTTTGGCCCGTTGCTAGGAAT AGGGTCGGCAGTGTTCTTCGTCCTTCCCCTTCTTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.137970943

Conservation Information
Conserved circRNAs	NA
PMCS	0.137970943

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18318988-18317005(+)
18316950-18319019(-)
18319004-18318967(-)
						
						Potential amino acid sequence
						
							MNSMPSLPPDLSWHHQLERANTASPSCSWSLWPVARNRVGSVLRPSPSSLEKSVPQSHRYSRVP
QILECAFQSDCTA*(+)
MRLRHTLLQRRRGRTKNTADPIPSNGPKRPAAGRRSSVGAFELVVPG*(-)
MASNSSAAFFGVRDGDQQDQIKPLISPQQQLAAALPGVAGGVPAASGQGAPPAQPPPKKKRTMP
DPDAEVIALSPKTLMATNRFVCEVCNKGFQREQNLQLHRRGHNLPWKLKQKNPLQAQRRRVYLC
PEPTCVHHDPARALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKICGTREYRCDC
GTLFSSEEGEGRRTLPTLFLATGQSDQLQEGEAVLARSSWWCQDKSGGSDGIEFIGGVLWC*(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18318988-18317005(+) 18316950-18319019(-) 18319004-18318967(-)
Potential amino acid sequence	MNSMPSLPPDLSWHHQLERANTASPSCSWSLWPVARNRVGSVLRPSPSSLEKSVPQSHRYSRVP QILECAFQSDCTA(+) MRLRHTLLQRRRGRTKNTADPIPSNGPKRPAAGRRSSVGAFELVVPG(-) MASNSSAAFFGVRDGDQQDQIKPLISPQQQLAAALPGVAGGVPAASGQGAPPAQPPPKKKRTMP DPDAEVIALSPKTLMATNRFVCEVCNKGFQREQNLQLHRRGHNLPWKLKQKNPLQAQRRRVYLC PEPTCVHHDPARALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKICGTREYRCDC GTLFSSEEGEGRRTLPTLFLATGQSDQLQEGEAVLARSSWWCQDKSGGSDGIEFIGGVLWC*(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d002654_circ_g.2

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