Plant Circular RNA Database

Detail information of Zm00001d013863_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d013863_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008422
					
						Alias
						Zm05circ00022, zma_circ_0001694
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 23258657-23262207  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d013863						
					
						Parent gene annotation
						
							Zinc finger CCCH domain-containing protein 19
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d013863_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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  
						
							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
						Zm00001d013863_T008:5
Zm00001d013863_T010:5
Zm00001d013863_T011:5
Zm00001d013863_T007:6

General Information
CircRNA Name	Zm00001d013863_circ_g.3
ID in PlantcircBase	zma_circ_008422
Alias	Zm05circ00022, zma_circ_0001694
Organism	Zea mays
Position	chr5: 23258657-23262207 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d013863
Parent gene annotation	Zinc finger CCCH domain-containing protein 19
Parent gene strand	-
Alternative splicing	Zm00001d013863_circ_g.2
Support reads	NA
Tissues	leaf, endosperm, 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	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	Zm00001d013863_T008:5 Zm00001d013863_T010:5 Zm00001d013863_T011:5 Zm00001d013863_T007:6

			
						 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  
						
							AAGAATTTGCCTTGTTTGATGCATCCTTTGCAGACAGAGTACGTACAAGTATAACACATGTACT
GTACTGCCTTTTCGCAGCTGCTGCATATGTGCCAACatctttaaatcgcagagattggaagatt
ttagctttctcatagacatctacctgattgattaaaaaggaaaaaggagatatcagactgtaaa
ttctatag

									
								

					

						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
						
							ATCTTTAAATCGCAGAGATTGGAAGATTTTAGCTTTCTCATAGACATCTACCTGATTGATTAAA
AAGGAAAAAGGAGATATCAGACTGTAAATTCTATAGAGATGTGAATCAGATGTGTCGTCATATA
TTAAATCACAGCAGTACCACTTTTAACCGGGCAGTTAGACCAAACTTCATACTCTGACGTAATC
GTTTGCATTCCTCCTACATAAGTACATGCAAATAAACAGTGTAAATAGCTAGTTAAACTAAAAT
GACAAAAAAACAGTCCAGCTCCAACATGTATTAATGATTCATTATGGGCAATAATGAGATGTAA
GCATTTTAAGTAGCTAGTTAAATTAAAATAACGAAAAAAAAATGTCCAACATGTATTCAATACA
TTTAGCGAAAGGGTCTCTAGCCTAGTGGTTAAGGACTTCCGAGTAGCACCTCCAAGTCCTGGGT
TCGATTCCTCTCGGGAGCGAATTTTTAGGCTTGTTTAAAAAAATCCCCTCGTTGTGCCCCATCC
GCTCTCGGGTTACGATGTCCTGTGCGCCACCCTCCGGTTGGGCCGTTGCAGAGTGGACAGTTGA
CGTCGGCCCGTTAGTGATGGGGGGCCAGGGTTCGGGGATTTTCTCGGCCGGGACCATTGTTTCG
GTCTCTTCTTAATATAATACCGGGAGGGCGGTCTTTCCCTCCCCGGCCGAGTTTTTTTTTTATT
CAATACATTTATTATGGGGCAATTTCTAATTATTAGCAACTTCTAAGAATGTAAACAAAATTTC
TAATTATTAGCAACTTCTAAGAATATAAACAAAATATCGTATCATAGAGGTAGTTAGCTAAAAA
CAAGAACAAGGCTGAGGAAACAGGCAATATACTGCATTTTATCAGATCGAATGAAATAGCAGAG
ATCAGATTTTGTACAACAGTGTTTGAAAAACATATAAACTTAGTATACAATAATATTCAACAAC
AAACTCTGAACCAATATATAATATACTCCCTCCGTCCCAAAATAAAATCCGTTTTAAGAAATTA
AGAGATTCATATAATACTTGATGTATGTGTTTTATATTTATGTCTAGATTCATCATCATCTATT
TGAATATAGACATAAAAATCAAGAGCTAAAACGACTACTATTTTAGAACGGAGGGAGTATATCA
CAATCAGGAAGGATCATTCTACAGTACTAGCTTACTAGGTCTCGAAAATTAAATGTTTGCACTG
CATATCCTTGGACATATCATCATTAAATCGTTGTCTTATATTTAGTTACCTCTGTGAAATCCTG
ATTTGAAATCGTATCCATTGTGATAATCTCTTTCTTTTCTAAATTAGATATCTCAAGAGCATAA
TCTGTTGTCTTCTTACTGACAGTGTATCGCTCTGCAACTTTATGCGTACCTACATATAGAATCA
TACCCAGGTAGTATAAGTATTTAGCATCTCAGATTTATACTCTGTAGTATTAGTTAATCTTACC
AAGAACTTTCACCAGTCGGTACATATCTTCCTTGTTGCCAAGACCAGAAATTCTTATCCTCACA
AAAGCACCAGCAATTTTGTTAGAAAATGCAGCAACCTGATCAATAAGATCCTCCATCACACTGC
GCCGCAAGTAAATTAGATTGATATTGTGCATGTCAATGGCTGCATAATCTTCTGGATTAATTGT
CAATTCTCTTTCAATCTTCTTATGAGCCTTCCTCCTATCAAAACCTAATGTATCGGCCAACTCA
TTATGTCCTCCATTATTTACTTGAGCTGAATCTGAATAAATTGCTCTTTGACTGTCTGCATTCG
GTGTTGAAGCCTGTTTCACAAGATAATGCATCTCCAAAAGCTTTAACATCTCAAAATGATCGAC
ACGTGGTTTTTTAAACAAATTGCTAAGCCTTGCATCACATATAATCTGACTTTTTCTGCGAGGA
TCATGGAGGTTATTTTGCTTTATATATTCAAGCAAAAGAACCTGGACATCAAACTGGGAAATAT
AAGAATTATCACCATTTCTCATGTGTCCAATGAATTCCAATAACTCAGATGATGCCCAGTTTTT
GTCACCAGCCAAGGCCATCCCTTCACCTGTTGATCCATTTGGTAAGCCTCCAGCACTGTTAATT
GAGATTCCACATTTCCTTGAAGTAATGTTGCCGTCTTTTTTGCGTTTTTGTCCTCTTTTTCCTG
AAGAGTTATTCTGTATTCGTTTCTTTGACGAAATGTCAAAAGTAGCATCTTGGCCATTGCTTGC
ATCATATAATTCATCAGATGACTCCTCTTTCTCTCTTCTACCAGCAGTAGTAGGAACAATCCAA
TGGCTCTTGGCACTTTTTAGCTCTTCAATCGTTAGTAAATGCTTCCCTTTCAGATCCAACCAAT
ATAACTTGAAAAGGTACTCCCAGCTATATATATCATCAAAATCAACACCAACCTGAAAGGGCGA
AATAGGATGATCAATAGACCTAGGATGGAACTATTATTTGCTCAAGGTAATTGTATGCCAACAA
AGTAGTACTGCTTGTTTCAGGCAGGTGTCTGCCAAAAGCAAAAGCCCAGCCAATACAGTTGTGT
GATGTATCAGGATCAGTGTCTATTTAGTTAAAGGGTGACTTATAAAAAAATCACAGTATCCAGT
TCGTCCAAGTGAATGAAGTCAAAATTGAATTTTGAGTTTAAAGGCATACCAGTTTTTTACTCCA
CGTACATTATCCAACATTCCTGCAATCTAAAACTATTTTTTTGCGCAGTAAATTGAAGCCAAGG
CTACCCATACCAAAAACTTAAAGCTAATACACTGGATAAACCAACTAAAAAAGGTACCAACAGC
ATACGCACAATACCCTGTAGCAAAATTTTAAGCACTAATGTAAAAACCTCAGGAAAGGCATGGC
ATTTGATATGACAATTGAAAATAGCGTAAAAGATGCAGAATAACAAGGGATCTTGACACAAAAA
CATGGCTCAGTAGCAAGATAAGAAAATCGTTGTGGAAAAATATCAATAAGAAAATAAATCATAA
TCTATGCCAAATTATCCCTTATCAACTATCAAGACTTGTCTTCCAACATTAGCACAACTTACGG
ACTGGCTGTTGCCTTTGCCAATTTACGACTTCTTGATGCCATTTCAGCCTGCTGGCTGAAAGTA
TCTATTTAACCATATACTGAAGGATGAAGGCTCAATCGAAAATTTTGAAAGTATAGGGATCGAA
ATGAAGCTTAAGTAAAGCTTGGGGCCAGACGGCCAGTAGCAATATTTATTCAACTATTTTTACT
TCTTCAATAAGAGTGGGACCTAACATTCTCTATAAATATCTGTGTAAAAGGCGCTTCTCTAGCT
GAAGAAGTGGAAAGCACAAACATGAGTTAAAAGTTGGGTACCTTTGCACCATCTTCTTTGGATT
CTATCAATAATATAGTACCATAACATGTGTCACAGAAGCCCTTGTTCCCTCTAACGCCAAAGAA
TTTGCCTTGTTTGATGCATCCTTTGCAGACAGAGTACGTACAAGTATAACACATGTACTGTACT
GCCTTTTCGCAGCTGCTGCATATGTGCCAAC
						
					

			
		

Sequences
Splice junction sequence	AAGAATTTGCCTTGTTTGATGCATCCTTTGCAGACAGAGTACGTACAAGTATAACACATGTACT GTACTGCCTTTTCGCAGCTGCTGCATATGTGCCAACatctttaaatcgcagagattggaagatt ttagctttctcatagacatctacctgattgattaaaaaggaaaaaggagatatcagactgtaaa ttctatag
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	ATCTTTAAATCGCAGAGATTGGAAGATTTTAGCTTTCTCATAGACATCTACCTGATTGATTAAA AAGGAAAAAGGAGATATCAGACTGTAAATTCTATAGAGATGTGAATCAGATGTGTCGTCATATA TTAAATCACAGCAGTACCACTTTTAACCGGGCAGTTAGACCAAACTTCATACTCTGACGTAATC GTTTGCATTCCTCCTACATAAGTACATGCAAATAAACAGTGTAAATAGCTAGTTAAACTAAAAT GACAAAAAAACAGTCCAGCTCCAACATGTATTAATGATTCATTATGGGCAATAATGAGATGTAA GCATTTTAAGTAGCTAGTTAAATTAAAATAACGAAAAAAAAATGTCCAACATGTATTCAATACA TTTAGCGAAAGGGTCTCTAGCCTAGTGGTTAAGGACTTCCGAGTAGCACCTCCAAGTCCTGGGT TCGATTCCTCTCGGGAGCGAATTTTTAGGCTTGTTTAAAAAAATCCCCTCGTTGTGCCCCATCC GCTCTCGGGTTACGATGTCCTGTGCGCCACCCTCCGGTTGGGCCGTTGCAGAGTGGACAGTTGA CGTCGGCCCGTTAGTGATGGGGGGCCAGGGTTCGGGGATTTTCTCGGCCGGGACCATTGTTTCG GTCTCTTCTTAATATAATACCGGGAGGGCGGTCTTTCCCTCCCCGGCCGAGTTTTTTTTTTATT CAATACATTTATTATGGGGCAATTTCTAATTATTAGCAACTTCTAAGAATGTAAACAAAATTTC TAATTATTAGCAACTTCTAAGAATATAAACAAAATATCGTATCATAGAGGTAGTTAGCTAAAAA CAAGAACAAGGCTGAGGAAACAGGCAATATACTGCATTTTATCAGATCGAATGAAATAGCAGAG ATCAGATTTTGTACAACAGTGTTTGAAAAACATATAAACTTAGTATACAATAATATTCAACAAC AAACTCTGAACCAATATATAATATACTCCCTCCGTCCCAAAATAAAATCCGTTTTAAGAAATTA AGAGATTCATATAATACTTGATGTATGTGTTTTATATTTATGTCTAGATTCATCATCATCTATT TGAATATAGACATAAAAATCAAGAGCTAAAACGACTACTATTTTAGAACGGAGGGAGTATATCA CAATCAGGAAGGATCATTCTACAGTACTAGCTTACTAGGTCTCGAAAATTAAATGTTTGCACTG CATATCCTTGGACATATCATCATTAAATCGTTGTCTTATATTTAGTTACCTCTGTGAAATCCTG ATTTGAAATCGTATCCATTGTGATAATCTCTTTCTTTTCTAAATTAGATATCTCAAGAGCATAA TCTGTTGTCTTCTTACTGACAGTGTATCGCTCTGCAACTTTATGCGTACCTACATATAGAATCA TACCCAGGTAGTATAAGTATTTAGCATCTCAGATTTATACTCTGTAGTATTAGTTAATCTTACC AAGAACTTTCACCAGTCGGTACATATCTTCCTTGTTGCCAAGACCAGAAATTCTTATCCTCACA AAAGCACCAGCAATTTTGTTAGAAAATGCAGCAACCTGATCAATAAGATCCTCCATCACACTGC GCCGCAAGTAAATTAGATTGATATTGTGCATGTCAATGGCTGCATAATCTTCTGGATTAATTGT CAATTCTCTTTCAATCTTCTTATGAGCCTTCCTCCTATCAAAACCTAATGTATCGGCCAACTCA TTATGTCCTCCATTATTTACTTGAGCTGAATCTGAATAAATTGCTCTTTGACTGTCTGCATTCG GTGTTGAAGCCTGTTTCACAAGATAATGCATCTCCAAAAGCTTTAACATCTCAAAATGATCGAC ACGTGGTTTTTTAAACAAATTGCTAAGCCTTGCATCACATATAATCTGACTTTTTCTGCGAGGA TCATGGAGGTTATTTTGCTTTATATATTCAAGCAAAAGAACCTGGACATCAAACTGGGAAATAT AAGAATTATCACCATTTCTCATGTGTCCAATGAATTCCAATAACTCAGATGATGCCCAGTTTTT GTCACCAGCCAAGGCCATCCCTTCACCTGTTGATCCATTTGGTAAGCCTCCAGCACTGTTAATT GAGATTCCACATTTCCTTGAAGTAATGTTGCCGTCTTTTTTGCGTTTTTGTCCTCTTTTTCCTG AAGAGTTATTCTGTATTCGTTTCTTTGACGAAATGTCAAAAGTAGCATCTTGGCCATTGCTTGC ATCATATAATTCATCAGATGACTCCTCTTTCTCTCTTCTACCAGCAGTAGTAGGAACAATCCAA TGGCTCTTGGCACTTTTTAGCTCTTCAATCGTTAGTAAATGCTTCCCTTTCAGATCCAACCAAT ATAACTTGAAAAGGTACTCCCAGCTATATATATCATCAAAATCAACACCAACCTGAAAGGGCGA AATAGGATGATCAATAGACCTAGGATGGAACTATTATTTGCTCAAGGTAATTGTATGCCAACAA AGTAGTACTGCTTGTTTCAGGCAGGTGTCTGCCAAAAGCAAAAGCCCAGCCAATACAGTTGTGT GATGTATCAGGATCAGTGTCTATTTAGTTAAAGGGTGACTTATAAAAAAATCACAGTATCCAGT TCGTCCAAGTGAATGAAGTCAAAATTGAATTTTGAGTTTAAAGGCATACCAGTTTTTTACTCCA CGTACATTATCCAACATTCCTGCAATCTAAAACTATTTTTTTGCGCAGTAAATTGAAGCCAAGG CTACCCATACCAAAAACTTAAAGCTAATACACTGGATAAACCAACTAAAAAAGGTACCAACAGC ATACGCACAATACCCTGTAGCAAAATTTTAAGCACTAATGTAAAAACCTCAGGAAAGGCATGGC ATTTGATATGACAATTGAAAATAGCGTAAAAGATGCAGAATAACAAGGGATCTTGACACAAAAA CATGGCTCAGTAGCAAGATAAGAAAATCGTTGTGGAAAAATATCAATAAGAAAATAAATCATAA TCTATGCCAAATTATCCCTTATCAACTATCAAGACTTGTCTTCCAACATTAGCACAACTTACGG ACTGGCTGTTGCCTTTGCCAATTTACGACTTCTTGATGCCATTTCAGCCTGCTGGCTGAAAGTA TCTATTTAACCATATACTGAAGGATGAAGGCTCAATCGAAAATTTTGAAAGTATAGGGATCGAA ATGAAGCTTAAGTAAAGCTTGGGGCCAGACGGCCAGTAGCAATATTTATTCAACTATTTTTACT TCTTCAATAAGAGTGGGACCTAACATTCTCTATAAATATCTGTGTAAAAGGCGCTTCTCTAGCT GAAGAAGTGGAAAGCACAAACATGAGTTAAAAGTTGGGTACCTTTGCACCATCTTCTTTGGATT CTATCAATAATATAGTACCATAACATGTGTCACAGAAGCCCTTGTTCCCTCTAACGCCAAAGAA TTTGCCTTGTTTGATGCATCCTTTGCAGACAGAGTACGTACAAGTATAACACATGTACTGTACT GCCTTTTCGCAGCTGCTGCATATGTGCCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.083415712

Conservation Information
Conserved circRNAs	NA
PMCS	0.083415712

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23258705-23262101(-)
23262168-23262054(-)
						
						Potential amino acid sequence
						
							MSMRKLKSSNLCDLKMLAHMQQLRKGSTVHVLYLYVLCLQRMHQTRQILWR*(-)
MCYTCTYSVCKGCIKQGKFFGVRGNKGFCDTCYGTILLIESKEDGAKGIVRMLLVPFLVGLSSV
LALSFWSIDHPISPFQVGVDFDDIYSWEYLFKLYWLDLKGKHLLTIEELKSAKSHWIVPTTAGR
REKEESSDELYDASNGQDATFDISSKKRIQNNSSGKRGQKRKKDGNITSRKCGISINSAGGLPN
GSTGEGMALAGDKNWASSELLEFIGHMRNGDNSYISQFDVQVLLLEYIKQNNLHDPRRKSQIIC
DARLSNLFKKPRVDHFEMLKLLEMHYLVKQASTPNADSQRAIYSDSAQVNNGGHNELADTLGFD
RRKAHKKIERELTINPEDYAAIDMHNINLIYLRRSVMEDLIDQVAAFSNKIAGAFVRIRISGLG
NKEDMYRLVKVLGTHKVAERYTVSKKTTDYALEISNLEKKEIITMDTISNQDFTEEECKRLRQS
MKFGLTARLKVVDVYEKAKIFQSLRFKDVGTYAAAAKRQYSTCVILVRTLSAKDASNKANSLAL
EGTRASVTHVMVLYY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23258705-23262101(-) 23262168-23262054(-)
Potential amino acid sequence	MSMRKLKSSNLCDLKMLAHMQQLRKGSTVHVLYLYVLCLQRMHQTRQILWR(-) MCYTCTYSVCKGCIKQGKFFGVRGNKGFCDTCYGTILLIESKEDGAKGIVRMLLVPFLVGLSSV LALSFWSIDHPISPFQVGVDFDDIYSWEYLFKLYWLDLKGKHLLTIEELKSAKSHWIVPTTAGR REKEESSDELYDASNGQDATFDISSKKRIQNNSSGKRGQKRKKDGNITSRKCGISINSAGGLPN GSTGEGMALAGDKNWASSELLEFIGHMRNGDNSYISQFDVQVLLLEYIKQNNLHDPRRKSQIIC DARLSNLFKKPRVDHFEMLKLLEMHYLVKQASTPNADSQRAIYSDSAQVNNGGHNELADTLGFD RRKAHKKIERELTINPEDYAAIDMHNINLIYLRRSVMEDLIDQVAAFSNKIAGAFVRIRISGLG NKEDMYRLVKVLGTHKVAERYTVSKKTTDYALEISNLEKKEIITMDTISNQDFTEEECKRLRQS MKFGLTARLKVVDVYEKAKIFQSLRFKDVGTYAAAAKRQYSTCVILVRTLSAKDASNKANSLAL EGTRASVTHVMVLYY(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d013863_circ_g.3

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