Plant Circular RNA Database

Detail information of Zm00001d005785_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d005785_circ_g.5
					
						ID in PlantcircBase
						zma_circ_007323
					
						Alias
						zma_circ_0000861
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 188383711-188385851  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d005785						
					
						Parent gene annotation
						
							Pentatricopeptide repeat-containing protein 
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d005785_circ_g.1 Zm00001d005785_circ_g.2 Zm00001d005785_circ_g.3 Zm00001d005785_circ_g.4 						
					
						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
						Zm00001d005785_T006:3
Zm00001d005785_T012:3
Zm00001d005785_T021:4
Zm00001d005785_T005:3
Zm00001d005785_T015:2
Zm00001d005785_T011:3
Zm00001d005785_T001:3
Zm00001d005785_T020:3
Zm00001d005785_T002:2
Zm00001d005785_T008:2
Zm00001d005785_T013:1
Zm00001d005785_T014:3
Zm00001d005785_T004:3
Zm00001d005785_T003:1
Zm00001d005785_T019:3
Zm00001d005785_T018:2
Zm00001d005785_T016:2

General Information
CircRNA Name	Zm00001d005785_circ_g.5
ID in PlantcircBase	zma_circ_007323
Alias	zma_circ_0000861
Organism	Zea mays
Position	chr2: 188383711-188385851 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d005785
Parent gene annotation	Pentatricopeptide repeat-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d005785_circ_g.1 Zm00001d005785_circ_g.2 Zm00001d005785_circ_g.3 Zm00001d005785_circ_g.4
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	Zm00001d005785_T006:3 Zm00001d005785_T012:3 Zm00001d005785_T021:4 Zm00001d005785_T005:3 Zm00001d005785_T015:2 Zm00001d005785_T011:3 Zm00001d005785_T001:3 Zm00001d005785_T020:3 Zm00001d005785_T002:2 Zm00001d005785_T008:2 Zm00001d005785_T013:1 Zm00001d005785_T014:3 Zm00001d005785_T004:3 Zm00001d005785_T003:1 Zm00001d005785_T019:3 Zm00001d005785_T018:2 Zm00001d005785_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  
						
							TAACAAGCGCATGTGGCTGGATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACAT
GAGCTATTAATGGAAGCTGCCATAAATAATAATCAGgaagaagctaatacagaaagtaaccctg
aacttcttccagatgctgttacctacacaacattactcaaggtgtgcctcctgctagcgcacat
cagttagt

									
								

					

						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
						
							GAAGAAGCTAATACAGAAAGTAACCCTGAACTTCTTCCAGATGCTGTTACCTACACAACATTAC
TCAAGGTGTGCCTCCTGCTAGCGCACATCAGTTAGTGATAACAACTGCTGCCTTCTGGCTACAC
CTTTAATTTTACATTGTCAAGCAGTGATATTGTAGTGTTCTTACACTGCATAATTTATTTTTCT
TTTCACGATAGATAATGTGGAGACTACACTCTACTTCTTTTGTTGACAACTTGACATGATCATA
CAATGATATTTGAGTGTCTGTTACACAACATTCTTTTTTATGAGAATGCTTCATAATTGTTGAA
AAAGAAGATGCTGCCTACTGAAAAATGTGTTACACCTTAAAATTGATAATCATGATAGGGTTTC
TGAAGGATGCCTTTGAGACCTCTTTGAACAAGTAGTTTGATCACTGTTGTGTTCGCTATCATTT
TTGGTTACTTCTTAATTTTACAATTTGTGGAAGCATCCTGCAGGGTTTAGGAAATAGCCGTGAC
CTTTATTCAGTCGTGAAGATTGTTGTGGAGATGAAATCTTCACTAATTTCAATCGACAGGACTG
CATACACTGCTATGGTAGATGCTTTGCTAGCTTGTGGGTCCATCGACGGTAAGTTCTATACCAT
CTTTTTAGTCACTACAGTGAATTTTCCTAAAAAACAATACAATGAATTTGCAAGTTGGAAAACA
ACGTTGGTGTTTGACTAAGAACTAACAAGTGGCCTAGCACCCACTTTTCATCCTCACATTTGAT
TTATTTTCAAACTGACACTTCTCTTTTCACTTTACAGTGGTTCAGCATTTAGCGTTCCATTTGA
CGCTAACAAGTGACATATCACATTCTTATCTGTACCCTTTTATGTCCCAGTTGCCCAAGCAGCA
TATCCAGTCTAAAGTATCTAAAATGGTGAAACTGTTCTTCGTCAGTTGTGTTTGCATAATTTTT
TATAATTACATCACCGATGTGTATAACCTAGTTGTACTTCTCAAATCATCACATGCAGTGACTA
TAAGTTACACCAAAATCATTTTCTGAGGTATAGACTATAGATCACTTGTTAGTATGGTTCATTT
AACCTTACTGTTGTGCACAAGCAAATTGCTTGACAAATGACGATACTTGATGCCTCTCGCAACC
TATTAGGATCATGCCTGGTTTTAAATATTATGGTCCATGCAGGCGAATGTTTTTCATATTTTAA
GTTATCATTTCCTCACTTGCATAGTAAATGAGAATGTCAACTTTAGCACTATTTGCTTAGCATG
ACCCTCTGTTTTGTATCCTAGATATCTGCCTCTGGGTCTATTCTAATGTTTTGACAATTTATCG
CATGTCTTGATTACTCTCTAGCAATTCAGCATTATCCATAATTCTTAATCTAGTTGGTCCTGAG
ATGATAATGTTACCAGTTTACCTAAATTTAGTTTCTTCATTACATTTGTTCAAAATATCTTCAA
ATAATTTACACATATCCTTCATTGTAATGTAATATGTGTGCCCCTAGCCCCAACAAATATTTGT
GACAACAAATGTGTTCACATTTGGACTTTGTAGAAGAAATAAAAATGGATAATAACTATGCATA
TGTTAACATGAGTATTGTGTTAAATTTGAGAATCTTTCAGTGTTCATGAATATACAGAACTACA
GACTAACTTATTTTTACTTTCCATCTTAGTGTATAAACTCTTTGTCCTTGTTTAAGTGAATATA
AATGTGGATGAGGCAATCAAATTACCTTGTTGCGAGAATGGCAATGCTGTTTCATGTGTTCTTG
AGATCATGGGTTATGAGAGTGAAAGCTGTTATTCAGACAAAAAAAAACCTCTTGTTTATGATGT
GTACTAGATTTCTGTACTGATATGCTTTGAACCTTATTGGTGCTTATCGTAGGGGCCCTTTGCA
TTTTTGGTGATATAATAAAGCATGCTGGCAAGAACAATGATTTGAGACCTAAACCTCATCTTTA
TCTTTCAATCATGAGAGCTTTTGCTACCAGAGGTGATGTTGATATGGTCATGAGATTTAACAAG
CGCATGTGGCTGGATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACATGAGCTAT
TAATGGAAGCTGCCATAAATAATAATCAG
						
					

			
		

Sequences
Splice junction sequence	TAACAAGCGCATGTGGCTGGATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACAT GAGCTATTAATGGAAGCTGCCATAAATAATAATCAGgaagaagctaatacagaaagtaaccctg aacttcttccagatgctgttacctacacaacattactcaaggtgtgcctcctgctagcgcacat cagttagt
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	GAAGAAGCTAATACAGAAAGTAACCCTGAACTTCTTCCAGATGCTGTTACCTACACAACATTAC TCAAGGTGTGCCTCCTGCTAGCGCACATCAGTTAGTGATAACAACTGCTGCCTTCTGGCTACAC CTTTAATTTTACATTGTCAAGCAGTGATATTGTAGTGTTCTTACACTGCATAATTTATTTTTCT TTTCACGATAGATAATGTGGAGACTACACTCTACTTCTTTTGTTGACAACTTGACATGATCATA CAATGATATTTGAGTGTCTGTTACACAACATTCTTTTTTATGAGAATGCTTCATAATTGTTGAA AAAGAAGATGCTGCCTACTGAAAAATGTGTTACACCTTAAAATTGATAATCATGATAGGGTTTC TGAAGGATGCCTTTGAGACCTCTTTGAACAAGTAGTTTGATCACTGTTGTGTTCGCTATCATTT TTGGTTACTTCTTAATTTTACAATTTGTGGAAGCATCCTGCAGGGTTTAGGAAATAGCCGTGAC CTTTATTCAGTCGTGAAGATTGTTGTGGAGATGAAATCTTCACTAATTTCAATCGACAGGACTG CATACACTGCTATGGTAGATGCTTTGCTAGCTTGTGGGTCCATCGACGGTAAGTTCTATACCAT CTTTTTAGTCACTACAGTGAATTTTCCTAAAAAACAATACAATGAATTTGCAAGTTGGAAAACA ACGTTGGTGTTTGACTAAGAACTAACAAGTGGCCTAGCACCCACTTTTCATCCTCACATTTGAT TTATTTTCAAACTGACACTTCTCTTTTCACTTTACAGTGGTTCAGCATTTAGCGTTCCATTTGA CGCTAACAAGTGACATATCACATTCTTATCTGTACCCTTTTATGTCCCAGTTGCCCAAGCAGCA TATCCAGTCTAAAGTATCTAAAATGGTGAAACTGTTCTTCGTCAGTTGTGTTTGCATAATTTTT TATAATTACATCACCGATGTGTATAACCTAGTTGTACTTCTCAAATCATCACATGCAGTGACTA TAAGTTACACCAAAATCATTTTCTGAGGTATAGACTATAGATCACTTGTTAGTATGGTTCATTT AACCTTACTGTTGTGCACAAGCAAATTGCTTGACAAATGACGATACTTGATGCCTCTCGCAACC TATTAGGATCATGCCTGGTTTTAAATATTATGGTCCATGCAGGCGAATGTTTTTCATATTTTAA GTTATCATTTCCTCACTTGCATAGTAAATGAGAATGTCAACTTTAGCACTATTTGCTTAGCATG ACCCTCTGTTTTGTATCCTAGATATCTGCCTCTGGGTCTATTCTAATGTTTTGACAATTTATCG CATGTCTTGATTACTCTCTAGCAATTCAGCATTATCCATAATTCTTAATCTAGTTGGTCCTGAG ATGATAATGTTACCAGTTTACCTAAATTTAGTTTCTTCATTACATTTGTTCAAAATATCTTCAA ATAATTTACACATATCCTTCATTGTAATGTAATATGTGTGCCCCTAGCCCCAACAAATATTTGT GACAACAAATGTGTTCACATTTGGACTTTGTAGAAGAAATAAAAATGGATAATAACTATGCATA TGTTAACATGAGTATTGTGTTAAATTTGAGAATCTTTCAGTGTTCATGAATATACAGAACTACA GACTAACTTATTTTTACTTTCCATCTTAGTGTATAAACTCTTTGTCCTTGTTTAAGTGAATATA AATGTGGATGAGGCAATCAAATTACCTTGTTGCGAGAATGGCAATGCTGTTTCATGTGTTCTTG AGATCATGGGTTATGAGAGTGAAAGCTGTTATTCAGACAAAAAAAAACCTCTTGTTTATGATGT GTACTAGATTTCTGTACTGATATGCTTTGAACCTTATTGGTGCTTATCGTAGGGGCCCTTTGCA TTTTTGGTGATATAATAAAGCATGCTGGCAAGAACAATGATTTGAGACCTAAACCTCATCTTTA TCTTTCAATCATGAGAGCTTTTGCTACCAGAGGTGATGTTGATATGGTCATGAGATTTAACAAG CGCATGTGGCTGGATTCAGTTGGATCAATTAGCCGTGCCGCCAAAGAAGAGACACATGAGCTAT TAATGGAAGCTGCCATAAATAATAATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.032427402

Conservation Information
Conserved circRNAs	NA
PMCS	0.032427402

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							188384254-188385848(+)
						
						Potential amino acid sequence
						
							MKSSLISIDRTAYTAMVDALLACGSIDGKFYTIFLVTTVNFPKKQYNEFARALCIFGDIIKHAG
KNNDLRPKPHLYLSIMRAFATRGDVDMVMRFNKRMWLDSVGSISRAAKEETHELLMEAAINNNQ
EEANTESNPELLPDAVTYTTLLKGLGNSRDLYSVVKIVVEMKSSLISIDRTAYTAMVDALLACG
SIDGKFYTIFLVTTVNFPKKQYNEFARALCIFGDIIKHAGKNNDLRPKPHLYLSIMRAFATRGD
VDMVMRFNKRMWLDSVGSISRAAKEETHELLMEAAINNNQEEANTESNPELLPDAVTYTTLLKG
LGNSRDLYSVVKIVVEMKSSLISIDRTAYTAMVDALLACGSIDGKFYTIFLVTTVNFPKKQYNE
FARALCIFGDIIKHAGKNNDLRPKPHLYLSIMRAFATRGDVDMVMRFNKRMWLDSVGSISRAAK
EETHELLMEAAINNNQEEANTESNPELLPDAVTYTTLLKGLGNSRDLYSVVKIVVEMKSSLISI
DRTAYTAMVDALLACGSIDGKFYTIFLVTTVNFPKKQYNEFARALCIFGDIIKHAGKNNDLRPK
PHLYLSIMRAFATRGDVDMVMRFNKRMWLDSVGSISRAAKEETHELLMEAAINNNQ(+)
						
						Sponge-miRNAs
						
							zma-miR827-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	188384254-188385848(+)
Potential amino acid sequence	MKSSLISIDRTAYTAMVDALLACGSIDGKFYTIFLVTTVNFPKKQYNEFARALCIFGDIIKHAG KNNDLRPKPHLYLSIMRAFATRGDVDMVMRFNKRMWLDSVGSISRAAKEETHELLMEAAINNNQ EEANTESNPELLPDAVTYTTLLKGLGNSRDLYSVVKIVVEMKSSLISIDRTAYTAMVDALLACG SIDGKFYTIFLVTTVNFPKKQYNEFARALCIFGDIIKHAGKNNDLRPKPHLYLSIMRAFATRGD VDMVMRFNKRMWLDSVGSISRAAKEETHELLMEAAINNNQEEANTESNPELLPDAVTYTTLLKG LGNSRDLYSVVKIVVEMKSSLISIDRTAYTAMVDALLACGSIDGKFYTIFLVTTVNFPKKQYNE FARALCIFGDIIKHAGKNNDLRPKPHLYLSIMRAFATRGDVDMVMRFNKRMWLDSVGSISRAAK EETHELLMEAAINNNQEEANTESNPELLPDAVTYTTLLKGLGNSRDLYSVVKIVVEMKSSLISI DRTAYTAMVDALLACGSIDGKFYTIFLVTTVNFPKKQYNEFARALCIFGDIIKHAGKNNDLRPK PHLYLSIMRAFATRGDVDMVMRFNKRMWLDSVGSISRAAKEETHELLMEAAINNNQ(+)
Sponge-miRNAs	zma-miR827-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d005785_circ_g.5

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