Plant Circular RNA Database

Detail information of Zm00001d047536_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d047536_circ_g.3
					
						ID in PlantcircBase
						zma_circ_003017
					
						Alias
						circ1900
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 134143508-134146837  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d047536						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d047536_circ_g.1 Zm00001d047536_circ_g.2 						
					
						Support reads
						3
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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-TA							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
						Zm00001d047536_T022:3
Zm00001d047536_T003:3
Zm00001d047536_T001:3
Zm00001d047536_T006:3
Zm00001d047536_T046:4
Zm00001d047536_T016:3
Zm00001d047536_T045:3
Zm00001d047536_T010:3
Zm00001d047536_T035:4
Zm00001d047536_T029:3
Zm00001d047536_T005:3
Zm00001d047536_T020:3
Zm00001d047536_T042:4
Zm00001d047536_T057:3
Zm00001d047536_T031:3
Zm00001d047536_T007:3
Zm00001d047536_T032:3
Zm00001d047536_T052:3
Zm00001d047536_T017:3
Zm00001d047536_T039:3
Zm00001d047536_T023:2
Zm00001d047536_T009:3
Zm00001d047536_T041:3
Zm00001d047536_T051:3
Zm00001d047536_T025:3
Zm00001d047536_T027:3
Zm00001d047536_T058:3
Zm00001d047536_T008:3
Zm00001d047536_T050:3
Zm00001d047536_T004:4
Zm00001d047536_T048:4
Zm00001d047536_T053:3
Zm00001d047536_T037:3

General Information
CircRNA Name	Zm00001d047536_circ_g.3
ID in PlantcircBase	zma_circ_003017
Alias	circ1900
Organism	Zea mays
Position	chr9: 134143508-134146837 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d047536
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d047536_circ_g.1 Zm00001d047536_circ_g.2
Support reads	3
Tissues	seedling leaves
Exon boundary	No-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-TA 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	Zm00001d047536_T022:3 Zm00001d047536_T003:3 Zm00001d047536_T001:3 Zm00001d047536_T006:3 Zm00001d047536_T046:4 Zm00001d047536_T016:3 Zm00001d047536_T045:3 Zm00001d047536_T010:3 Zm00001d047536_T035:4 Zm00001d047536_T029:3 Zm00001d047536_T005:3 Zm00001d047536_T020:3 Zm00001d047536_T042:4 Zm00001d047536_T057:3 Zm00001d047536_T031:3 Zm00001d047536_T007:3 Zm00001d047536_T032:3 Zm00001d047536_T052:3 Zm00001d047536_T017:3 Zm00001d047536_T039:3 Zm00001d047536_T023:2 Zm00001d047536_T009:3 Zm00001d047536_T041:3 Zm00001d047536_T051:3 Zm00001d047536_T025:3 Zm00001d047536_T027:3 Zm00001d047536_T058:3 Zm00001d047536_T008:3 Zm00001d047536_T050:3 Zm00001d047536_T004:4 Zm00001d047536_T048:4 Zm00001d047536_T053:3 Zm00001d047536_T037:3

			
						 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  
						
							TTAGCATATTCATTTTCAGCTCAATCAACTACCGGCAGCTTCAACTCTTTGAACTCGGATAAGC
TACGGGAGAGATCAGGTGCTGCCACATCAACAAGAGggaatgaattgcttcgagcactggattt
gagattaactgcactgaaggaagagatcttggtcgtattgaaccgagcagttggatccaattta
tcggcaag

									
								

					

						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
						
							GGAATGAATTGCTTCGAGCACTGGATTTGAGATTAACTGCACTGAAGGAAGAGATCTTGGTCGT
ATTGAACCGAGCAGTTGGATCCAATTTATCGGCAAGAGAAATATCTGATTTATCTGCTTTTGTT
CAGCGATTTGGAACATCAGAGTTTTGGTATGTTAAAAAGCATGGTGCTCTGCATTTTATCTCAT
TTTGTACGATCAGAGAGTACAAATAATGCTAGTTGGCTACAAGTGTGCCTTCTAGTCATTCATA
AACTTACCAACTTGGTCACTTGGAATTGTTTGCTCTTACATTTATATGATGCGTCCAATCTTTA
GAATTGTGTATTCATTATGTTGTTTAGTTGAGACAAGGAATTAACAGCTGGTCTTTCTTGTTTG
CTAGTTGGTTGATGCGGTGTACGTTGTTGATATCGGATTGTAAGCCCTCTGAGCTCCCACTACA
GCAGAATTCTACAACTGAGAAAGTTGACAAGGATGAGAATGCACATAAACCTTGCATCAGTCCT
CAGACTAATCTTCAGATGCCCATTGCCAATAATGTATCTCCAGCAAAGCTTGCACAAATTGAGC
GTGAGAGCTCAACAGAAAGTGATGATTCCTCTGAATCCAGTGATGAAGGTGAGGCCATTGTTGA
AAGGAGCCGTCCTCTTGTAAGATCTGCTTCACCTAGAAGATCTGCTTCTCCAATGCGGAGGGTT
CAAATTGGGAGATCAGGATCACGTCGTTCAACAGCAATTGCTATCAAGAGCCTCAGTTACTTCC
CTCCTAGTCAGAGGATTCCTATGGATAAAGATGATGAAAGTAGTACCTTCAATGGTGAAACTGA
TCAGCCACCAAAGAAATCTGACACTAACGTTAGAAGGATGAGTGTTCAGGATGCAATTAACCTT
TTTGAGAGCAAGCAGAAGGATCAGAATCCAGATTCACAAAATAAGAAAGCTGGCTTGTTTGCCA
CTAAGTCTGTCTTGAGAAGGTGGAGTGCAGGAATGGGTGATTCTTTGAATGAAAACTCAGAAGG
AAAAGTCTCAGATTCCACATCTGAAAGTAAATCAAACAACATAGCTTCTGAAACTGAGAAGGTT
GAAGCTGAAATGAAGGCTGAACTAGGTAACATACCAAATTTTTTTGTTACACCTGAGGCTGAAG
ATTTAACTTTCCATGCTAATTCTCATGAGATTAGAGTGTCAGAAACGGAGAGTGCTGTTTGTAG
TAATGTTTGTGCAGAACAAGCAAAGCCTGGTCTGGAGGAAAGCAGTGATCGGGCAATGGCCTCC
GCTGAGTGGAATCGCCAGAAGGAAGCCGAGCTTAATCAGATGTTATTGAAAATGATGGAAGTCA
TGCCTGGGAAATTTGCGGGTGCTAATGCCACCGCTACAGGTCTCAGTTCCACCAATCAGCAAAA
AGCTGTATCTCATGGCCAGCATACAGAGAAGCGAGACACAAAAGTCAGAACTGAGAAAGGCACA
AGGCGACCAGCAAAGGAACCAAGCACCAAGCCCTTGAAGGAAACAGCTGGGAAGAATAAACCAG
CAATGACCTCGAAATCTGGCTCTTCAACAGAGAGACGTATTTCACCAGTTCCACAAAGGGCGCG
GCGAAATTCATCACCTCCAGTCCTACCGAAAGAAGTAGCATCAAAGACACCACCAGTCAGGAAA
AGCTCACCGAAACCATCACCTGCACCTGCATCTGTGCCTACTACACGTAGTTCATGGTCAGGTG
GTTCTTTGACTAAAGCAACTACAACACAAAAAACTAAAAGGTCTCCTGGGATGGCTTCAACGTC
CACACAAACTAGCCGAAGGACTCCAACAACGCCCTCGTCGTCTCAGCCAGCTTCAAAAGCGGAA
AGGGCCATTCAATCAGTGAAGAACAAGAAGGAAACCATTACTGCTACCAAGCCAGCTATAAAGG
GACAAGAAGAGAAGAAGACCAAAACAGCAACAAAGACAAGCAGAATAACTAAAGTTTCACCTTC
AGAAGAAAAATCAGGTGTAAAAACGAAGCAAAGCTTGCAAAAGGTTTCAAATAAAAGCAGTGTT
GTACCTCTTGAGTCCAAAACCTTGAAGAAAACCACTGGAATTAGTCAGAGCATTAGGTCTGGTA
TGGTGAAGAATAAGGTACCCCAACCTAATGACTTCTCAAAAGATACCGGAAGTGTTAACCAAGC
TGAAGATAAGGAGCAATCTCCTGTGACAACCGAGCCAACTACTAAGGTACTGGAGGCTGATCTT
GCTCAACCAGCACATGATGTTGATGAAAATTTAGAAATTTCGCTCGATAATGACTTGAATATTG
AAAAAACAGAGAAACCGGCCTCGAGTTTAACTGCAACAGAAATGGGCTCCAGTATCCAAGTTGA
ACCCTCTACGGATGAGTTAGATGAGGCCATACAACCTCCTGACGATGACATGGGCATCTCATCA
TCTGCGTGGGTAGAAGTAGAGCGTCAAGAACTAGAAGTCACTGTTTCGAGTGAAAATGTAGTTG
TTGAGGATGTAACTTCTCCAGGAATTGCACCATTGCCGTCATCAAGCCCAAGAGTGCGTCATTC
GTTGTCACAAATGCTGCAAGCAGATAGCAATGAACCAGAAATTATTGAGTGGGGAAATGCTGAA
AACCCACCCGCAATAGTTTTTCATAAGGATTCTCCAAAAGGATTCAAGAGGCTTCTAAAGTTTG
CTCGAAAAAACAAGGGAGACAACAATGCTAACGGCTGGGCAAGCCCCTCGGTAGTTTCAGAAGG
AGAAGATGAACTAGAAGAACCAAGAGGCACTAGTGATGGTACAAATTCAAGCAGGAGAACTTTT
GATGGTTCAAAGACTAATAGCATCTTATCAGGTACCTTTCCGAACCATGGTTTTGAAGATGGTT
CTGCATCCAAGTCTTAACTTTTATAGGAGCAATCTCAGTACCGATATAGTTGGTGTCTGTCAAG
GCTTTTTGATAATTACATCCATGATTTAAAAATGATTATATGGTCTGACCTTGTGCTGACACCA
GGTAGTGATGATATGAGAGTTTGTATAGACAAGCACATTTCCAATTACGTTAACCTCATGGCAT
CACGCACAAATTTTACAGCTTTACCTACCCACTACTAGGCAGAACTTTTTTGTTGAAGCATTTC
ATCTTTCTATGCTTGATCAAATTAGCTCAGTAGTGTTAATGTTTGAAGGTCATGCATTTCTTGG
AGAAAAGGTTTTCATGGTCATGCATAAATCTTAGCATATTCATTTTCAGCTCAATCAACTACCG
GCAGCTTCAACTCTTTGAACTCGGATAAGCTACGGGAGAGATCAGGTGCTGCCACATCAACAAG
AG
						
					

			
		

Sequences
Splice junction sequence	TTAGCATATTCATTTTCAGCTCAATCAACTACCGGCAGCTTCAACTCTTTGAACTCGGATAAGC TACGGGAGAGATCAGGTGCTGCCACATCAACAAGAGggaatgaattgcttcgagcactggattt gagattaactgcactgaaggaagagatcttggtcgtattgaaccgagcagttggatccaattta tcggcaag
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	GGAATGAATTGCTTCGAGCACTGGATTTGAGATTAACTGCACTGAAGGAAGAGATCTTGGTCGT ATTGAACCGAGCAGTTGGATCCAATTTATCGGCAAGAGAAATATCTGATTTATCTGCTTTTGTT CAGCGATTTGGAACATCAGAGTTTTGGTATGTTAAAAAGCATGGTGCTCTGCATTTTATCTCAT TTTGTACGATCAGAGAGTACAAATAATGCTAGTTGGCTACAAGTGTGCCTTCTAGTCATTCATA AACTTACCAACTTGGTCACTTGGAATTGTTTGCTCTTACATTTATATGATGCGTCCAATCTTTA GAATTGTGTATTCATTATGTTGTTTAGTTGAGACAAGGAATTAACAGCTGGTCTTTCTTGTTTG CTAGTTGGTTGATGCGGTGTACGTTGTTGATATCGGATTGTAAGCCCTCTGAGCTCCCACTACA GCAGAATTCTACAACTGAGAAAGTTGACAAGGATGAGAATGCACATAAACCTTGCATCAGTCCT CAGACTAATCTTCAGATGCCCATTGCCAATAATGTATCTCCAGCAAAGCTTGCACAAATTGAGC GTGAGAGCTCAACAGAAAGTGATGATTCCTCTGAATCCAGTGATGAAGGTGAGGCCATTGTTGA AAGGAGCCGTCCTCTTGTAAGATCTGCTTCACCTAGAAGATCTGCTTCTCCAATGCGGAGGGTT CAAATTGGGAGATCAGGATCACGTCGTTCAACAGCAATTGCTATCAAGAGCCTCAGTTACTTCC CTCCTAGTCAGAGGATTCCTATGGATAAAGATGATGAAAGTAGTACCTTCAATGGTGAAACTGA TCAGCCACCAAAGAAATCTGACACTAACGTTAGAAGGATGAGTGTTCAGGATGCAATTAACCTT TTTGAGAGCAAGCAGAAGGATCAGAATCCAGATTCACAAAATAAGAAAGCTGGCTTGTTTGCCA CTAAGTCTGTCTTGAGAAGGTGGAGTGCAGGAATGGGTGATTCTTTGAATGAAAACTCAGAAGG AAAAGTCTCAGATTCCACATCTGAAAGTAAATCAAACAACATAGCTTCTGAAACTGAGAAGGTT GAAGCTGAAATGAAGGCTGAACTAGGTAACATACCAAATTTTTTTGTTACACCTGAGGCTGAAG ATTTAACTTTCCATGCTAATTCTCATGAGATTAGAGTGTCAGAAACGGAGAGTGCTGTTTGTAG TAATGTTTGTGCAGAACAAGCAAAGCCTGGTCTGGAGGAAAGCAGTGATCGGGCAATGGCCTCC GCTGAGTGGAATCGCCAGAAGGAAGCCGAGCTTAATCAGATGTTATTGAAAATGATGGAAGTCA TGCCTGGGAAATTTGCGGGTGCTAATGCCACCGCTACAGGTCTCAGTTCCACCAATCAGCAAAA AGCTGTATCTCATGGCCAGCATACAGAGAAGCGAGACACAAAAGTCAGAACTGAGAAAGGCACA AGGCGACCAGCAAAGGAACCAAGCACCAAGCCCTTGAAGGAAACAGCTGGGAAGAATAAACCAG CAATGACCTCGAAATCTGGCTCTTCAACAGAGAGACGTATTTCACCAGTTCCACAAAGGGCGCG GCGAAATTCATCACCTCCAGTCCTACCGAAAGAAGTAGCATCAAAGACACCACCAGTCAGGAAA AGCTCACCGAAACCATCACCTGCACCTGCATCTGTGCCTACTACACGTAGTTCATGGTCAGGTG GTTCTTTGACTAAAGCAACTACAACACAAAAAACTAAAAGGTCTCCTGGGATGGCTTCAACGTC CACACAAACTAGCCGAAGGACTCCAACAACGCCCTCGTCGTCTCAGCCAGCTTCAAAAGCGGAA AGGGCCATTCAATCAGTGAAGAACAAGAAGGAAACCATTACTGCTACCAAGCCAGCTATAAAGG GACAAGAAGAGAAGAAGACCAAAACAGCAACAAAGACAAGCAGAATAACTAAAGTTTCACCTTC AGAAGAAAAATCAGGTGTAAAAACGAAGCAAAGCTTGCAAAAGGTTTCAAATAAAAGCAGTGTT GTACCTCTTGAGTCCAAAACCTTGAAGAAAACCACTGGAATTAGTCAGAGCATTAGGTCTGGTA TGGTGAAGAATAAGGTACCCCAACCTAATGACTTCTCAAAAGATACCGGAAGTGTTAACCAAGC TGAAGATAAGGAGCAATCTCCTGTGACAACCGAGCCAACTACTAAGGTACTGGAGGCTGATCTT GCTCAACCAGCACATGATGTTGATGAAAATTTAGAAATTTCGCTCGATAATGACTTGAATATTG AAAAAACAGAGAAACCGGCCTCGAGTTTAACTGCAACAGAAATGGGCTCCAGTATCCAAGTTGA ACCCTCTACGGATGAGTTAGATGAGGCCATACAACCTCCTGACGATGACATGGGCATCTCATCA TCTGCGTGGGTAGAAGTAGAGCGTCAAGAACTAGAAGTCACTGTTTCGAGTGAAAATGTAGTTG TTGAGGATGTAACTTCTCCAGGAATTGCACCATTGCCGTCATCAAGCCCAAGAGTGCGTCATTC GTTGTCACAAATGCTGCAAGCAGATAGCAATGAACCAGAAATTATTGAGTGGGGAAATGCTGAA AACCCACCCGCAATAGTTTTTCATAAGGATTCTCCAAAAGGATTCAAGAGGCTTCTAAAGTTTG CTCGAAAAAACAAGGGAGACAACAATGCTAACGGCTGGGCAAGCCCCTCGGTAGTTTCAGAAGG AGAAGATGAACTAGAAGAACCAAGAGGCACTAGTGATGGTACAAATTCAAGCAGGAGAACTTTT GATGGTTCAAAGACTAATAGCATCTTATCAGGTACCTTTCCGAACCATGGTTTTGAAGATGGTT CTGCATCCAAGTCTTAACTTTTATAGGAGCAATCTCAGTACCGATATAGTTGGTGTCTGTCAAG GCTTTTTGATAATTACATCCATGATTTAAAAATGATTATATGGTCTGACCTTGTGCTGACACCA GGTAGTGATGATATGAGAGTTTGTATAGACAAGCACATTTCCAATTACGTTAACCTCATGGCAT CACGCACAAATTTTACAGCTTTACCTACCCACTACTAGGCAGAACTTTTTTGTTGAAGCATTTC ATCTTTCTATGCTTGATCAAATTAGCTCAGTAGTGTTAATGTTTGAAGGTCATGCATTTCTTGG AGAAAAGGTTTTCATGGTCATGCATAAATCTTAGCATATTCATTTTCAGCTCAATCAACTACCG GCAGCTTCAACTCTTTGAACTCGGATAAGCTACGGGAGAGATCAGGTGCTGCCACATCAACAAG AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.019194114

Conservation Information
Conserved circRNAs	NA
PMCS	0.019194114

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d047536_circ_g.3

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