Plant Circular RNA Database

Detail information of Zm00001d013358_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d013358_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008385
					
						Alias
						zma_circ_0002261
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 9529236-9532517  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d013358						
					
						Parent gene annotation
						
							DEAD-box ATP-dependent RNA helicase 16
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d013358_circ_g.2 						
					
						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  
						
							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
						Zm00001d013358_T019:4
Zm00001d013358_T020:1
Zm00001d013358_T017:4
Zm00001d013358_T002:5
Zm00001d013358_T004:3
Zm00001d013358_T005:6
Zm00001d013358_T015:5
Zm00001d013358_T014:5
Zm00001d013358_T016:3
Zm00001d013358_T013:3
Zm00001d013358_T009:5
Zm00001d013358_T003:6
Zm00001d013358_T008:2
Zm00001d013358_T006:3
Zm00001d013358_T018:3
Zm00001d013358_T001:3
Zm00001d013358_T012:4
Zm00001d013358_T010:5

General Information
CircRNA Name	Zm00001d013358_circ_g.3
ID in PlantcircBase	zma_circ_008385
Alias	zma_circ_0002261
Organism	Zea mays
Position	chr5: 9529236-9532517 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d013358
Parent gene annotation	DEAD-box ATP-dependent RNA helicase 16
Parent gene strand	-
Alternative splicing	Zm00001d013358_circ_g.2
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	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	Zm00001d013358_T019:4 Zm00001d013358_T020:1 Zm00001d013358_T017:4 Zm00001d013358_T002:5 Zm00001d013358_T004:3 Zm00001d013358_T005:6 Zm00001d013358_T015:5 Zm00001d013358_T014:5 Zm00001d013358_T016:3 Zm00001d013358_T013:3 Zm00001d013358_T009:5 Zm00001d013358_T003:6 Zm00001d013358_T008:2 Zm00001d013358_T006:3 Zm00001d013358_T018:3 Zm00001d013358_T001:3 Zm00001d013358_T012:4 Zm00001d013358_T010:5

			
						 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  
						
							CTTTAACTGCAGGTCCACGAATAATTCCCTTTGATATGCATGTTGCAACACAAGCTGGAGTTGA
TACGAGAATGTTAGGGGGGCCAGACAATGCAACAGTctctataatatgtagtcgggaattttgt
ggcaactcagcattcaaaactgcagatcttatcccaaactgcaaaaagcagagcatattcatca
taagtatg

									
								

					

						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
						
							CTCTATAATATGTAGTCGGGAATTTTGTGGCAACTCAGCATTCAAAACTGCAGATCTTATCCCA
AACTGCAAAAAGCAGAGCATATTCATCATAAGTATGTTAATACTACAAATGAAGCATACATTAA
AAATAGAATCGAAATAGAAGCAACATAGTATGTGAACAAAAGCAGTTAAGTGAATAGTGTACAC
ATAGAAACAATCATAGCATAGGCAAAGTTTGTATAGCATTATCCAAAAATGGCAGTACAAGATG
TCGCATTATCCAAGGTGAGTGTGGTGTTGTATGGGAGGTTCTTGCCCCCTTTGGTCTTCTTAAC
ATAATAATACACAACTCTCCAGCATGTTCGAGAAAAAAGATGTAGCGCCAATCCTTCAGTTAAT
TTTTTACAAGACTTGCCTAACCTGGTATTATGGTTATCTGAAGAGACAAATGAACTTAATGACA
TAGCAAGAGAGTCAACTGTGACATGATTGTATGCTCAACTTTATAACATCAAATACAGAAGGAA
CAAAGTAGGTCACAAGGTCAATAATTGCAGCATATAAAGTCCAGGTTATCTCAAACCAGAATTC
TAAGAATCAAACAATTCAGGATATGTACAAGTTTTTTAAGGTGTCGAGTAAAATAAAATACCTT
TTTATAGATCCAGATGATCAATCACGTTGTAAGGGTAATAACACAAAGCAGTGGTTTGATTTAC
CTTTTCCAAGATCAGTCGTAATCTGAAAGCCATATCAATTGAGTTTACAAATATAAGAACTTTC
TTCTGAATGAGCTCAAACTTTAGAAGTGCAAGGATATGAAGTATTTTATCCTTGGCATCACAGG
AGATCTGTGGGCAAAAAATGAATGATATGCGATGAGCAGGAATGAAGAAATAGCAGTGTAAAAA
GCCAAGTAACTTCAGCAAAATGAATACGATTTTTTAAAATACGCCCATAGCTTAAGGATGACCT
CAGATAAGGGACGGTCAGGAAAATGTAACCCTGTCAAGCATGAGAACTTTTGGTTTTCCAGTTT
TTTTTTTTGGAACCTTCAAGTTGCAATGGTAATATGAAAAGGAGCACAAGTACAGGAAGGAGGA
AGCAGAAGATACTTGCCCAAAACTGCTGAACATTTTTGGGGATCACATCATCCTTTGCTTGACC
AACCTCCGAAAGAGTTAGAACAAATGGGTTATGCAGAAGTAGTTTTGTCAACTTGTCAACATCA
GAGCTGCCATATAGTCAAATTTCAGTATCACCAAAAATAACACAAATGCAAGCAAGGGCCCAAG
TTACTAATGATATTTCTTAGCAAGGGCCTAAGTGGGAAACAGTAGCATGAATTCAATCCCCAAC
ACTTACATGTCAGATGCATTCAAACAATTATTAAACTATCAGCATAGACACATAAAGAGAAGCA
ACAGCACAAACAGGTCTAACAGCAACCACCCACTTAACCAGCATGATAAAAATTTGGAAATAGA
AAAAAAACAGAATTTCAAGAGCAAACCATCTGAGGCAAGTAATTATAAAATAATGAAATGCTTA
GATAAATCATAAATGTAGGGTGCAGAATCGAGATTTAATGGGTAGCTGCAGAAAAAGGACGAAC
ATTGACCAGATTTAACCTTGAAGTTGCAGACATCAGAATAGACTGACAGCTTCTCGGGATATGT
GGGATGAGAGCTTTCAAGTCAACTTCGCAGCGGTAGGATAGAAGTAGGTCAGCCTGGCAACTAA
AGATTGGTATATTAGTAACTTCTTCAAAAAGGAACTTGCGTGATGAACATTGTAATTAATACAC
AATAGGTGTGGATTCTGGTGTACATCACTTCAAAAAATGTTGTACTCCCTCCCTCAACCTTCTA
AGGCATATTTTGATGCAAAAAAGTTGTAATTTTGACCAACTGTTGTCAAATTAAATGTATGTTT
TGAAGTCATATTAATACATTCATATTTTTGAAGTGTTTTGTAGTAATTGAAAATATACTGTGAA
AAGAATTCAAAGGTTCAAATATGATTTTGAAAACTTTACATACCAAAGTATACCCTACAATAAT
AAACAGAAGGCTCATATGGCAATGCAGCTTTAAATAAAGTGTCACCAGATATGTAAAGTATGAT
CTCCAAGTCTTTAAAATGGTACAAATCAAATTGTTTTCGAGTCAAGAGTCAAGTCGTGCAACTA
CTGACTAGACGACCAGTCGTGACTAGTCGAATATAAGTCGATGATTATATTTTTTATATTTTTC
TATATATGCTAATACTAAAAACATGCTGAAACACTAAAAACACTTTGTTTAGTATATCTTCATC
CATCTCTATTTCCTACAATATATCATTAAATATTGAACAGTTTTGTAGCGAGTCTCCTATTGTT
CTCTCTGATTTCAAAGAACTTGCTTGGATTCAAAAACAGTGCATGCCCCATAAAGATTGGTAGT
CATCTGACTGTCCCACCTCTTACCAACAATAGAAATTACTTCATCAATTAGTCGCTCTTTGTGT
TCCGAAGCTTCCTTGATGCTCTTTTTTTATAGTCCATGGCGGCCCACATTTCAGCCATTGCTGG
TCTCTACCATTTCAGCCTAACAAGATCTCTACCATTTGTCTTGGTCCTCATCAAGTCTTAAATC
CTTCCTTGTCCATTGATCAACCTGGTCATCTTCTTTGCTTTAGCAATGCAGCCACTAAACTCTT
TTATCTTCCCAATAACCTCCAGCATGAGATCCAAGTAGTAGGTAGCACAAGGTGTCCAAAATAA
GGTAGGAAACTTACTAGGGTTTGAGATGGTTGGGTGGGTTCACATTTTTATACCTAGGCCCAAA
TAAGTCGCCCGACTCAAATGCTATGACTAGTCGACGAGTCGAGCGACTAGCAGAGAAAGTCGAG
TCGTCCGACTAGCAGAGAAAGTCGAGTCGCTCGACTTTAAAACCTTGAATCAAAATCACCATAT
GCAAATACATGGGGAAAAATTAAACTATAGCTCAATTAAGAAAAATGGAATAACAGAAATTTCT
TTTTATTATTTTATTAGACTGTGACAGAAAATATAGCATCACAAATTCAACGCTAGCATTCTTC
TTTACATTGCAGGGCCAATGAAATATGTAAACAAAATGAAAGTAAACAAAAATATATATATGAA
CGACAACTGGAGAGCACCTCATCAAGAATCATCATTGAAAGTGACTCTTTAACTGCAGGTCCAC
GAATAATTCCCTTTGATATGCATGTTGCAACACAAGCTGGAGTTGATACGAGAATGTTAGGGGG
GCCAGACAATGCAACAGT
						
					

			
		

Sequences
Splice junction sequence	CTTTAACTGCAGGTCCACGAATAATTCCCTTTGATATGCATGTTGCAACACAAGCTGGAGTTGA TACGAGAATGTTAGGGGGGCCAGACAATGCAACAGTctctataatatgtagtcgggaattttgt ggcaactcagcattcaaaactgcagatcttatcccaaactgcaaaaagcagagcatattcatca taagtatg
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	CTCTATAATATGTAGTCGGGAATTTTGTGGCAACTCAGCATTCAAAACTGCAGATCTTATCCCA AACTGCAAAAAGCAGAGCATATTCATCATAAGTATGTTAATACTACAAATGAAGCATACATTAA AAATAGAATCGAAATAGAAGCAACATAGTATGTGAACAAAAGCAGTTAAGTGAATAGTGTACAC ATAGAAACAATCATAGCATAGGCAAAGTTTGTATAGCATTATCCAAAAATGGCAGTACAAGATG TCGCATTATCCAAGGTGAGTGTGGTGTTGTATGGGAGGTTCTTGCCCCCTTTGGTCTTCTTAAC ATAATAATACACAACTCTCCAGCATGTTCGAGAAAAAAGATGTAGCGCCAATCCTTCAGTTAAT TTTTTACAAGACTTGCCTAACCTGGTATTATGGTTATCTGAAGAGACAAATGAACTTAATGACA TAGCAAGAGAGTCAACTGTGACATGATTGTATGCTCAACTTTATAACATCAAATACAGAAGGAA CAAAGTAGGTCACAAGGTCAATAATTGCAGCATATAAAGTCCAGGTTATCTCAAACCAGAATTC TAAGAATCAAACAATTCAGGATATGTACAAGTTTTTTAAGGTGTCGAGTAAAATAAAATACCTT TTTATAGATCCAGATGATCAATCACGTTGTAAGGGTAATAACACAAAGCAGTGGTTTGATTTAC CTTTTCCAAGATCAGTCGTAATCTGAAAGCCATATCAATTGAGTTTACAAATATAAGAACTTTC TTCTGAATGAGCTCAAACTTTAGAAGTGCAAGGATATGAAGTATTTTATCCTTGGCATCACAGG AGATCTGTGGGCAAAAAATGAATGATATGCGATGAGCAGGAATGAAGAAATAGCAGTGTAAAAA GCCAAGTAACTTCAGCAAAATGAATACGATTTTTTAAAATACGCCCATAGCTTAAGGATGACCT CAGATAAGGGACGGTCAGGAAAATGTAACCCTGTCAAGCATGAGAACTTTTGGTTTTCCAGTTT TTTTTTTTGGAACCTTCAAGTTGCAATGGTAATATGAAAAGGAGCACAAGTACAGGAAGGAGGA AGCAGAAGATACTTGCCCAAAACTGCTGAACATTTTTGGGGATCACATCATCCTTTGCTTGACC AACCTCCGAAAGAGTTAGAACAAATGGGTTATGCAGAAGTAGTTTTGTCAACTTGTCAACATCA GAGCTGCCATATAGTCAAATTTCAGTATCACCAAAAATAACACAAATGCAAGCAAGGGCCCAAG TTACTAATGATATTTCTTAGCAAGGGCCTAAGTGGGAAACAGTAGCATGAATTCAATCCCCAAC ACTTACATGTCAGATGCATTCAAACAATTATTAAACTATCAGCATAGACACATAAAGAGAAGCA ACAGCACAAACAGGTCTAACAGCAACCACCCACTTAACCAGCATGATAAAAATTTGGAAATAGA AAAAAAACAGAATTTCAAGAGCAAACCATCTGAGGCAAGTAATTATAAAATAATGAAATGCTTA GATAAATCATAAATGTAGGGTGCAGAATCGAGATTTAATGGGTAGCTGCAGAAAAAGGACGAAC ATTGACCAGATTTAACCTTGAAGTTGCAGACATCAGAATAGACTGACAGCTTCTCGGGATATGT GGGATGAGAGCTTTCAAGTCAACTTCGCAGCGGTAGGATAGAAGTAGGTCAGCCTGGCAACTAA AGATTGGTATATTAGTAACTTCTTCAAAAAGGAACTTGCGTGATGAACATTGTAATTAATACAC AATAGGTGTGGATTCTGGTGTACATCACTTCAAAAAATGTTGTACTCCCTCCCTCAACCTTCTA AGGCATATTTTGATGCAAAAAAGTTGTAATTTTGACCAACTGTTGTCAAATTAAATGTATGTTT TGAAGTCATATTAATACATTCATATTTTTGAAGTGTTTTGTAGTAATTGAAAATATACTGTGAA AAGAATTCAAAGGTTCAAATATGATTTTGAAAACTTTACATACCAAAGTATACCCTACAATAAT AAACAGAAGGCTCATATGGCAATGCAGCTTTAAATAAAGTGTCACCAGATATGTAAAGTATGAT CTCCAAGTCTTTAAAATGGTACAAATCAAATTGTTTTCGAGTCAAGAGTCAAGTCGTGCAACTA CTGACTAGACGACCAGTCGTGACTAGTCGAATATAAGTCGATGATTATATTTTTTATATTTTTC TATATATGCTAATACTAAAAACATGCTGAAACACTAAAAACACTTTGTTTAGTATATCTTCATC CATCTCTATTTCCTACAATATATCATTAAATATTGAACAGTTTTGTAGCGAGTCTCCTATTGTT CTCTCTGATTTCAAAGAACTTGCTTGGATTCAAAAACAGTGCATGCCCCATAAAGATTGGTAGT CATCTGACTGTCCCACCTCTTACCAACAATAGAAATTACTTCATCAATTAGTCGCTCTTTGTGT TCCGAAGCTTCCTTGATGCTCTTTTTTTATAGTCCATGGCGGCCCACATTTCAGCCATTGCTGG TCTCTACCATTTCAGCCTAACAAGATCTCTACCATTTGTCTTGGTCCTCATCAAGTCTTAAATC CTTCCTTGTCCATTGATCAACCTGGTCATCTTCTTTGCTTTAGCAATGCAGCCACTAAACTCTT TTATCTTCCCAATAACCTCCAGCATGAGATCCAAGTAGTAGGTAGCACAAGGTGTCCAAAATAA GGTAGGAAACTTACTAGGGTTTGAGATGGTTGGGTGGGTTCACATTTTTATACCTAGGCCCAAA TAAGTCGCCCGACTCAAATGCTATGACTAGTCGACGAGTCGAGCGACTAGCAGAGAAAGTCGAG TCGTCCGACTAGCAGAGAAAGTCGAGTCGCTCGACTTTAAAACCTTGAATCAAAATCACCATAT GCAAATACATGGGGAAAAATTAAACTATAGCTCAATTAAGAAAAATGGAATAACAGAAATTTCT TTTTATTATTTTATTAGACTGTGACAGAAAATATAGCATCACAAATTCAACGCTAGCATTCTTC TTTACATTGCAGGGCCAATGAAATATGTAAACAAAATGAAAGTAAACAAAAATATATATATGAA CGACAACTGGAGAGCACCTCATCAAGAATCATCATTGAAAGTGACTCTTTAACTGCAGGTCCAC GAATAATTCCCTTTGATATGCATGTTGCAACACAAGCTGGAGTTGATACGAGAATGTTAGGGGG GCCAGACAATGCAACAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.027465996

Conservation Information
Conserved circRNAs	NA
PMCS	0.027465996

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9532454-9529904(+)
9532408-9529238(-)
						
						Potential amino acid sequence
						
							MHVATQAGVDTRMLGGPDNATVSIICSREFCGNSAFKTADLIPKL*(+)
MMILDEISCDAKDKILHILALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNF
GIRSAVLNAELPQNSRLHIIETVALSGPPNILVSTPACVATCISKGIIRGPAVKESLSMMILDE
ISCDAKDKILHILALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNFGIRSAV
LNAELPQNSRLHIIETVALSGPPNILVSTPACVATCISKGIIRGPAVKESLSMMILDEISCDAK
DKILHILALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNFGIRSAVLNAELP
QNSRLHIIETVALSGPPNILVSTPACVATCISKGIIRGPAVKESLSMMILDEISCDAKDKILHI
LALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNFGIRSAVLNAELPQNSRLH
IIE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9532454-9529904(+) 9532408-9529238(-)
Potential amino acid sequence	MHVATQAGVDTRMLGGPDNATVSIICSREFCGNSAFKTADLIPKL*(+) MMILDEISCDAKDKILHILALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNF GIRSAVLNAELPQNSRLHIIETVALSGPPNILVSTPACVATCISKGIIRGPAVKESLSMMILDE ISCDAKDKILHILALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNFGIRSAV LNAELPQNSRLHIIETVALSGPPNILVSTPACVATCISKGIIRGPAVKESLSMMILDEISCDAK DKILHILALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNFGIRSAVLNAELP QNSRLHIIETVALSGPPNILVSTPACVATCISKGIIRGPAVKESLSMMILDEISCDAKDKILHI LALLKFELIQKKVLIFVNSIDMAFRLRLILEKVNQTTALCYYPYNFGIRSAVLNAELPQNSRLH IIE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d013358_circ_g.3

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