Plant Circular RNA Database

Detail information of Zm00001d019947_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d019947_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009296
					
						Alias
						zma_circ_0002751
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 78827102-78828713  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d019947						
					
						Parent gene annotation
						
							hydrolases acting on ester bonds
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d019947_circ_g.2 Zm00001d019947_circ_g.3 Zm00001d019947_circ_g.5 Zm00001d019947_circ_g.6 Zm00001d019947_circ_g.7 Zm00001d019947_circ_g.8 Zm00001d019947_circ_g.9 						
					
						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  
						
							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
						Zm00001d019947_T032:4
Zm00001d019947_T022:4
Zm00001d019947_T014:4
Zm00001d019947_T024:4
Zm00001d019947_T023:4
Zm00001d019947_T041:4
Zm00001d019947_T001:2
Zm00001d019947_T007:4
Zm00001d019947_T037:4
Zm00001d019947_T030:4
Zm00001d019947_T004:4
Zm00001d019947_T040:4
Zm00001d019947_T012:4
Zm00001d019947_T010:4
Zm00001d019947_T019:4
Zm00001d019947_T013:4
Zm00001d019947_T002:4
Zm00001d019947_T028:4
Zm00001d019947_T035:4
Zm00001d019947_T006:4
Zm00001d019947_T025:4
Zm00001d019947_T015:4
Zm00001d019947_T033:4
Zm00001d019947_T016:4
Zm00001d019947_T017:4

General Information
CircRNA Name	Zm00001d019947_circ_g.4
ID in PlantcircBase	zma_circ_009296
Alias	zma_circ_0002751
Organism	Zea mays
Position	chr7: 78827102-78828713 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d019947
Parent gene annotation	hydrolases acting on ester bonds
Parent gene strand	+
Alternative splicing	Zm00001d019947_circ_g.2 Zm00001d019947_circ_g.3 Zm00001d019947_circ_g.5 Zm00001d019947_circ_g.6 Zm00001d019947_circ_g.7 Zm00001d019947_circ_g.8 Zm00001d019947_circ_g.9
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	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	Zm00001d019947_T032:4 Zm00001d019947_T022:4 Zm00001d019947_T014:4 Zm00001d019947_T024:4 Zm00001d019947_T023:4 Zm00001d019947_T041:4 Zm00001d019947_T001:2 Zm00001d019947_T007:4 Zm00001d019947_T037:4 Zm00001d019947_T030:4 Zm00001d019947_T004:4 Zm00001d019947_T040:4 Zm00001d019947_T012:4 Zm00001d019947_T010:4 Zm00001d019947_T019:4 Zm00001d019947_T013:4 Zm00001d019947_T002:4 Zm00001d019947_T028:4 Zm00001d019947_T035:4 Zm00001d019947_T006:4 Zm00001d019947_T025:4 Zm00001d019947_T015:4 Zm00001d019947_T033:4 Zm00001d019947_T016:4 Zm00001d019947_T017:4

			
						 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  
						
							ACATCATTCGCCTGTGCAAAATGAATTACCTGCCAGTAAAAAGATAGTGGAAGTTACATCAAAG
ATGGTCCAAATTCCTGCAGGACCTGCTCCAAAACAGattaggtcaaggttggcatcattggatg
gaattgtgccttctactcacggctttatggtaggaagctccagtatgaagaatgtttggttatc
catggaac

									
								

					

						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: 654
Transcript exons: 78827102-78827239,78827328-78827514,78828267-78828412,78
828531-78828713
ATTAGGTCAAGGTTGGCATCATTGGATGGAATTGTGCCTTCTACTCACGGCTTTATGGTAGGAA
GCTCCAGTATGAAGAATGTTTGGTTATCCATGGAACATCAATCTATCCTATGGTGTAATCAATT
AGCTGTACAGGTTGCACACACTCTTCTTAGCATAATAGATCCTGTTGACAGGCAGCCATTTTCA
AGCACACAAAAAAGAGTTTTTGTGTTCACAAAAATGCTCCAAAGTGCAGTTCCTCAGTCTCTGA
GTTCAATGACTCATGTTCCTGCTTCTCTGTCACGAAATTTACCTGCCAATGAGAATCAGGATGC
TGGCGAACTACACAAAAAAGATTCACTTTCTTGCCCATCATCCACTGAATGGACTAGTGATGGC
CTTGAAAAGGACCTGTATATTCAATCAAATTCTGTTACTGTTTTAGCCATGGATGGCAGGAGAA
GATGGTTAGATATTAAAAAGCTGGGATCAAATGGCAGAGGACACTTTGTTTTTGTAACAAATCT
TGCCCCTTGTTCTGGAGTAAGGATTCACTTGTGGCCAGAAAAACATCATTCGCCTGTGCAAAAT
GAATTACCTGCCAGTAAAAAGATAGTGGAAGTTACATCAAAGATGGTCCAAATTCCTGCAGGAC
CTGCTCCAAAACAG
						
					

						Genomic sequence
						
							ATTAGGTCAAGGTTGGCATCATTGGATGGAATTGTGCCTTCTACTCACGGCTTTATGGTAGGAA
GCTCCAGTATGAAGAATGTTTGGTTATCCATGGAACATCAATCTATCCTATGGTGTAATCAATT
AGCTGTACAGGTTCGGAACTATGTGTCAACAGCAAATTCAATGAATGCTTTGCAGTGTGCAGTA
ACATCAGTGCTTATATTGGCTTGACATTGTCCAGGTTGCACACACTCTTCTTAGCATAATAGAT
CCTGTTGACAGGCAGCCATTTTCAAGCACACAAAAAAGAGTTTTTGTGTTCACAAAAATGCTCC
AAAGTGCAGTTCCTCAGTCTCTGAGTTCAATGACTCATGTTCCTGCTTCTCTGTCACGAAATTT
ACCTGCCAATGAGAATCAGGATGCTGGCGGTATAGCTCAATCTTTACCTCCTTAAGTCCTTTGT
AGTTGGATTAATTAGAAAGTTGATTGTTTAGGAGATGAATTGTTTATGGAATGAATGAGCACAT
AAAGGTCAGTATGTGAAATCTATGTAGAAAATTTTGAAGACCATATTTATCTTTAAAAAAAACT
ATTTCTGTTTGTAAACATTCTATCGTATAAGCAGATTTTTTACCTCTTCAATTAATTTGGATTT
ATTTAATTTGTTAAGATGGCTTCTTTGCTATAGTTTATGTCGTCATTCTAAGATGTTTATTAAT
TTGTGCAACATTACTGCAACACTGCTGTAACATGAGGCTCATGGAATTGGTAACTTTGTATGCT
GTAGAGAGGATGTCAAACTGCTACTTATATCATATTTATATCACACATCAAATAGGCAGGATAC
AATTATGATAGTGTTCCAATATTTTAGTCGATATAACTTAGCATATATCTGTAAAATCAAGACT
AGCATTTATTCAATCAAATGTGATGTTTTTTTCTACAACTGTAAACCCAAAATTCATTACCAAG
GCAAGGAAATTATACAGTCATAGTTCAAGTTCATATGCAAAATCATTCATCCGCCAAGCATTCA
TACTTCTGATCTCCCAGGGGGTCTGCCAATCAAATGTGATGCCAACCCTTGTAGTTAATTATAG
GGTCTTATCCATTTACTTAGTACCAGAGTATCATATTATTTTTCTTATCTAAGCATATCTATAT
ATTTTCCTTGTAGAACTACACAAAAAAGATTCACTTTCTTGCCCATCATCCACTGAATGGACTA
GTGATGGCCTTGAAAAGGACCTGTATATTCAATCAAATTCTGTTACTGTTTTAGCCATGGATGG
CAGGAGAAGATGGTTAGATATTAAAAAGCTGGTAGGTTACTGACCTTCTAGTGTTCTCCTGCTA
TCTGTATGTGTTTTTTAGCATTAAGAAACCTTATTTGAAGTACTGCTGCATATGGTGAATAAAC
ATTGCTATTTTCTTTTGGAAGGGATCAAATGGCAGAGGACACTTTGTTTTTGTAACAAATCTTG
CCCCTTGTTCTGGAGTAAGGATTCACTTGTGGCCAGAAAAACATCATTCGCCTGTGCAAAATGA
ATTACCTGCCAGTAAAAAGATAGTGGAAGTTACATCAAAGATGGTCCAAATTCCTGCAGGACCT
GCTCCAAAACAG
						
					

			
		

Sequences
Splice junction sequence	ACATCATTCGCCTGTGCAAAATGAATTACCTGCCAGTAAAAAGATAGTGGAAGTTACATCAAAG ATGGTCCAAATTCCTGCAGGACCTGCTCCAAAACAGattaggtcaaggttggcatcattggatg gaattgtgccttctactcacggctttatggtaggaagctccagtatgaagaatgtttggttatc catggaac
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: 654 Transcript exons: 78827102-78827239,78827328-78827514,78828267-78828412,78 828531-78828713 ATTAGGTCAAGGTTGGCATCATTGGATGGAATTGTGCCTTCTACTCACGGCTTTATGGTAGGAA GCTCCAGTATGAAGAATGTTTGGTTATCCATGGAACATCAATCTATCCTATGGTGTAATCAATT AGCTGTACAGGTTGCACACACTCTTCTTAGCATAATAGATCCTGTTGACAGGCAGCCATTTTCA AGCACACAAAAAAGAGTTTTTGTGTTCACAAAAATGCTCCAAAGTGCAGTTCCTCAGTCTCTGA GTTCAATGACTCATGTTCCTGCTTCTCTGTCACGAAATTTACCTGCCAATGAGAATCAGGATGC TGGCGAACTACACAAAAAAGATTCACTTTCTTGCCCATCATCCACTGAATGGACTAGTGATGGC CTTGAAAAGGACCTGTATATTCAATCAAATTCTGTTACTGTTTTAGCCATGGATGGCAGGAGAA GATGGTTAGATATTAAAAAGCTGGGATCAAATGGCAGAGGACACTTTGTTTTTGTAACAAATCT TGCCCCTTGTTCTGGAGTAAGGATTCACTTGTGGCCAGAAAAACATCATTCGCCTGTGCAAAAT GAATTACCTGCCAGTAAAAAGATAGTGGAAGTTACATCAAAGATGGTCCAAATTCCTGCAGGAC CTGCTCCAAAACAG
Genomic sequence	ATTAGGTCAAGGTTGGCATCATTGGATGGAATTGTGCCTTCTACTCACGGCTTTATGGTAGGAA GCTCCAGTATGAAGAATGTTTGGTTATCCATGGAACATCAATCTATCCTATGGTGTAATCAATT AGCTGTACAGGTTCGGAACTATGTGTCAACAGCAAATTCAATGAATGCTTTGCAGTGTGCAGTA ACATCAGTGCTTATATTGGCTTGACATTGTCCAGGTTGCACACACTCTTCTTAGCATAATAGAT CCTGTTGACAGGCAGCCATTTTCAAGCACACAAAAAAGAGTTTTTGTGTTCACAAAAATGCTCC AAAGTGCAGTTCCTCAGTCTCTGAGTTCAATGACTCATGTTCCTGCTTCTCTGTCACGAAATTT ACCTGCCAATGAGAATCAGGATGCTGGCGGTATAGCTCAATCTTTACCTCCTTAAGTCCTTTGT AGTTGGATTAATTAGAAAGTTGATTGTTTAGGAGATGAATTGTTTATGGAATGAATGAGCACAT AAAGGTCAGTATGTGAAATCTATGTAGAAAATTTTGAAGACCATATTTATCTTTAAAAAAAACT ATTTCTGTTTGTAAACATTCTATCGTATAAGCAGATTTTTTACCTCTTCAATTAATTTGGATTT ATTTAATTTGTTAAGATGGCTTCTTTGCTATAGTTTATGTCGTCATTCTAAGATGTTTATTAAT TTGTGCAACATTACTGCAACACTGCTGTAACATGAGGCTCATGGAATTGGTAACTTTGTATGCT GTAGAGAGGATGTCAAACTGCTACTTATATCATATTTATATCACACATCAAATAGGCAGGATAC AATTATGATAGTGTTCCAATATTTTAGTCGATATAACTTAGCATATATCTGTAAAATCAAGACT AGCATTTATTCAATCAAATGTGATGTTTTTTTCTACAACTGTAAACCCAAAATTCATTACCAAG GCAAGGAAATTATACAGTCATAGTTCAAGTTCATATGCAAAATCATTCATCCGCCAAGCATTCA TACTTCTGATCTCCCAGGGGGTCTGCCAATCAAATGTGATGCCAACCCTTGTAGTTAATTATAG GGTCTTATCCATTTACTTAGTACCAGAGTATCATATTATTTTTCTTATCTAAGCATATCTATAT ATTTTCCTTGTAGAACTACACAAAAAAGATTCACTTTCTTGCCCATCATCCACTGAATGGACTA GTGATGGCCTTGAAAAGGACCTGTATATTCAATCAAATTCTGTTACTGTTTTAGCCATGGATGG CAGGAGAAGATGGTTAGATATTAAAAAGCTGGTAGGTTACTGACCTTCTAGTGTTCTCCTGCTA TCTGTATGTGTTTTTTAGCATTAAGAAACCTTATTTGAAGTACTGCTGCATATGGTGAATAAAC ATTGCTATTTTCTTTTGGAAGGGATCAAATGGCAGAGGACACTTTGTTTTTGTAACAAATCTTG CCCCTTGTTCTGGAGTAAGGATTCACTTGTGGCCAGAAAAACATCATTCGCCTGTGCAAAATGA ATTACCTGCCAGTAAAAAGATAGTGGAAGTTACATCAAAGATGGTCCAAATTCCTGCAGGACCT GCTCCAAAACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.163701217

Conservation Information
Conserved circRNAs	NA
PMCS	0.163701217

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							78827157-78828710(+)
						
						Potential amino acid sequence
						
							MVGSSSMKNVWLSMEHQSILWCNQLAVQVAHTLLSIIDPVDRQPFSSTQKRVFVFTKMLQSAVP
QSLSSMTHVPASLSRNLPANENQDAGELHKKDSLSCPSSTEWTSDGLEKDLYIQSNSVTVLAMD
GRRRWLDIKKLGSNGRGHFVFVTNLAPCSGVRIHLWPEKHHSPVQNELPASKKIVEVTSKMVQI
PAGPAPKQIRSRLASLDGIVPSTHGFMVGSSSMKNVWLSMEHQSILWCNQLAVQVAHTLLSIID
PVDRQPFSSTQKRVFVFTKMLQSAVPQSLSSMTHVPASLSRNLPANENQDAGELHKKDSLSCPS
STEWTSDGLEKDLYIQSNSVTVLAMDGRRRWLDIKKLGSNGRGHFVFVTNLAPCSGVRIHLWPE
KHHSPVQNELPASKKIVEVTSKMVQIPAGPAPKQIRSRLASLDGIVPSTHGFMVGSSSMKNVWL
SMEHQSILWCNQLAVQVAHTLLSIIDPVDRQPFSSTQKRVFVFTKMLQSAVPQSLSSMTHVPAS
LSRNLPANENQDAGELHKKDSLSCPSSTEWTSDGLEKDLYIQSNSVTVLAMDGRRRWLDIKKLG
SNGRGHFVFVTNLAPCSGVRIHLWPEKHHSPVQNELPASKKIVEVTSKMVQIPAGPAPKQIRSR
LASLDGIVPSTHGFMVGSSSMKNVWLSMEHQSILWCNQLAVQVAHTLLSIIDPVDRQPFSSTQK
RVFVFTKMLQSAVPQSLSSMTHVPASLSRNLPANENQDAGELHKKDSLSCPSSTEWTSDGLEKD
LYIQSNSVTVLAMDGRRRWLDIKKLGSNGRGHFVFVTNLAPCSGVRIHLWPEKHHSPVQNELPA
SKKIVEVTSKMVQIPAGPAPKQ(+)
						
						Sponge-miRNAs
						
							zma-miR171f-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	78827157-78828710(+)
Potential amino acid sequence	MVGSSSMKNVWLSMEHQSILWCNQLAVQVAHTLLSIIDPVDRQPFSSTQKRVFVFTKMLQSAVP QSLSSMTHVPASLSRNLPANENQDAGELHKKDSLSCPSSTEWTSDGLEKDLYIQSNSVTVLAMD GRRRWLDIKKLGSNGRGHFVFVTNLAPCSGVRIHLWPEKHHSPVQNELPASKKIVEVTSKMVQI PAGPAPKQIRSRLASLDGIVPSTHGFMVGSSSMKNVWLSMEHQSILWCNQLAVQVAHTLLSIID PVDRQPFSSTQKRVFVFTKMLQSAVPQSLSSMTHVPASLSRNLPANENQDAGELHKKDSLSCPS STEWTSDGLEKDLYIQSNSVTVLAMDGRRRWLDIKKLGSNGRGHFVFVTNLAPCSGVRIHLWPE KHHSPVQNELPASKKIVEVTSKMVQIPAGPAPKQIRSRLASLDGIVPSTHGFMVGSSSMKNVWL SMEHQSILWCNQLAVQVAHTLLSIIDPVDRQPFSSTQKRVFVFTKMLQSAVPQSLSSMTHVPAS LSRNLPANENQDAGELHKKDSLSCPSSTEWTSDGLEKDLYIQSNSVTVLAMDGRRRWLDIKKLG SNGRGHFVFVTNLAPCSGVRIHLWPEKHHSPVQNELPASKKIVEVTSKMVQIPAGPAPKQIRSR LASLDGIVPSTHGFMVGSSSMKNVWLSMEHQSILWCNQLAVQVAHTLLSIIDPVDRQPFSSTQK RVFVFTKMLQSAVPQSLSSMTHVPASLSRNLPANENQDAGELHKKDSLSCPSSTEWTSDGLEKD LYIQSNSVTVLAMDGRRRWLDIKKLGSNGRGHFVFVTNLAPCSGVRIHLWPEKHHSPVQNELPA SKKIVEVTSKMVQIPAGPAPKQ(+)
Sponge-miRNAs	zma-miR171f-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d019947_circ_g.4

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