Plant Circular RNA Database

Detail information of Zm00001d011177_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d011177_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009714
					
						Alias
						Zm08circ00051, GRMZM2G003734_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 141840969-141843455  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d011177						
					
						Parent gene annotation
						
							Vacuolar protein-sorting protein 33  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d011177_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d011177_T008:3
Zm00001d011177_T006:5
Zm00001d011177_T007:5
Zm00001d011177_T001:5
Zm00001d011177_T003:5
Zm00001d011177_T002:5

General Information
CircRNA Name	Zm00001d011177_circ_g.3
ID in PlantcircBase	zma_circ_009714
Alias	Zm08circ00051, GRMZM2G003734_C2
Organism	Zea mays
Position	chr8: 141840969-141843455 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d011177
Parent gene annotation	Vacuolar protein-sorting protein 33
Parent gene strand	-
Alternative splicing	Zm00001d011177_circ_g.2
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d011177_T008:3 Zm00001d011177_T006:5 Zm00001d011177_T007:5 Zm00001d011177_T001:5 Zm00001d011177_T003:5 Zm00001d011177_T002:5

			
						 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  
						
							TTTACCTTGAATTCAGTGGAACCTTAACCTTTTTCCCATCTTGTTGAGCTCCAATGATGCTTGC
ATCAACTTCCACTGAACCATTATTAATTTGTAGCATatttcaaagttctgaacctccagtattg
tttgttctatgtctagtcgggcatgaaaggagggtttccccgtgaacgattgcaagtgttgtgc
caaatgaa

									
								

					

						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: 377
Transcript exons: 141840969-141841075,141841142-141841204,141842114-141842
173,141842354-141842405,141843361-141843455
ATTTCAAAGTTCTGAACCTCCAGTATTGTTTGTTCTATGTCTAGTCGGGCATGAAAGGAGGGTT
TCCCCGTGAACGATTGCAAGTGTTGTGCCAAATGAACATGCCTAGCTATCTCCGGTAGCGAGTG
CAACCTCCTCACAAAATCCTTGAGCTCCGAAACAGACTGAGTGTTGGTGGATTTCACTTCTGCA
TAATCTTGCTGAATAGATGTTGCTTTTTGACGTAAAACCTGAACTACAACTTCAAAATTGAGGT
CTCGAATCTCCTTGTACAACTTATCGCTTGAATTCAGTGGAACCTTAACCTTTTTCCCATCTTG
TTGAGCTCCAATGATGCTTGCATCAACTTCCACTGAACCATTATTAATTTGTAGCAT
						
					

						Genomic sequence
						
							ATTTCAAAGTTCTGAACCTCCAGTATTGTTTGTTCTATGTCTAGTCGGGCATGAAAGGAGGGTT
TCCCCGTGAACGATTGCAAGTGTTGTGCCAAATGAACATGCCTCTAAACAACATGCTATAAGTT
AGTAAAATAATATAGGATAAAAATGAAGGCATGCAATCAACTCACAGCTATCTCCGGTAGCGAG
TGCAACCTCCTCACAAAATCCTTGAGCTCCGAAACAGACTGAGTCTGTTAAAAATTACAATATC
AAATAATCAATTCCCTTTTCTACATTGTACTAGCCAAAGGTAATTTACTGTAGAAACAAACAGG
CATAACATTTTAAAAAATGTAGATATAAAGTCACATAACACTGGAAGCAAGAAACATACTAACA
AAGTAACAAGTAGCAAATTCTTCAACTAAGAGTTCCATCAAAGCGCCCACATTTAGACTAATTT
TGGTATTGTTATCCAAGCAATGACACCTAGATCACTCAGTATTGTAGAGATGCCCCTCAATCTT
CAAATAAGACAAATTTATTTAGGTCAAGCAGAGCTGTTGATTATACAATGTCGATGACATTACT
CGATACTTTAATATTTTTTGATCTTGTGTAAATATTAAACTAGCTGCATCAGTCCAAATCCATA
TCCATGTCACTTCTCAACAGCAAGCAAATGCCATATGTCCAGGTTATCAACTTATCATAATCAC
AGGCAGAAATCTAAGACTGAGAAGTGGGTATTGTCTAATATTTTTTTAGACGTTAATCCACCTG
CCATTAATTCAATCCTCTGGCATGGTTAAAGAACAAAACCAGATTATACACTTTTGTTTATCAA
CTGTCCTGATTGAAGCAATTACAATCCATTATAGAGGCTTCCTCCAAAAAGAAAAAAATGATAA
CTTGATTAACATACAAATACTTGATTTGTTGGGGAACAATAATTCAATATTAATATAACATGGG
GACTCGTTCTAATTCCAACAGTAAATGGTATAAAAATAAATTTATATCAGTAAATCATCTGAAA
AAGGTGGCATGTACTTAAAACACGCAATAACTCAGCATTTGCATCCTTGCTTTTGAACAATGCT
GCAAGTGACAACAGACATAGAGGACACAGGGCATAACACAACACACTTAATTCTTACGTTGGTG
GATTTCACTTCTGCATAATCTTGCTGAATAGATGTTGCTTTTTGACGTAAAACCTGCAGTCAAT
ACAATTTGCAATAATTTAATATGGGTAAAAATGATGATAGTTGGTAGATATAACTAAACAAACT
GGAATTAGAAATGGCTATGACAATAGCAGGTATAACAAAAACCACAAAAGTTACCACAAAGCCC
CTTCACATGAATAAACAAAAGTTGAAGGCAGTGGAGTGAACCTGAACTACAACTTCAAAATTGA
GGTCTCGAATCTCCTTGTACAACTTATCGCTGAAAAAAAAACACCAATATAAATGCATAGGTCC
AAATACAGCAAAAAAACCTGTAAAAATACAAGCCTATGTACAATAAGACGATTACACATATATT
TGCACTATCTACAGTCACAAATAAGTAGCAGTCTCTATCCAATAAATTTGTACGGGAGTAATTT
TCATGAAAAGCCAACTGGTACATTTCCACAGCCAATCTAGGTACTCATGAAGGTAAGTTGATCA
GACATCGGAAGTTTGATTTAGGCATTTGCACCATCACTTACACTTGATAGGAAGGAGCAACAGA
TATTAACTTCAAAAACTAAGAAATCAATTAAATCATTAATAACAATTTTCTCAACTTTCTAGAT
CCAAAAGTTTCAATGTGCAAAACAAATCATAAGTATCTTGATAATGACAAGGATGCAAATAGAG
TAAGAATAATAAATAAATAAAAAACATCAATGTTGGGTTACGAAGTATTCATTGGCACAAAGCA
AATTTACAATTTAGTAGTGCGTACTCTTTCAATAGCAAATATATGTCATTTAGGATAGCTAAAA
AGCGAAAGGGCCTCTAGTTGAGTTGGTTAGGTGGTCTGAGTAGTGAGTAGCACTCCTCAGGTAC
TGAGTTCAACTCCCCGTGGGAACGAATTTCAGACTGTGGTTAAAAAATTCCCCTCGTTTGTTCC
ACGCCAAAGCACAGGTCTAAGACCTGGTCCCAGTCGTTTCTCAGATGGGTTGTGTATGGGTGGG
GGTAGGGCAGGGGTTCGAGGGTTTTCTCGACCTGCGTGAGAAGGTCTTCTTAATATAATGCTCG
AGGGTTGTCTTACCCCCACAGGTCGAATTTTTTTAGGACAACTAAAAAGGTTTGACTTACTGCA
GATCTAAAACGATTCATATTTGTAACCAGGAGTATTTCAAAATTTAAAGATCAGGTTAAAAGCC
GCTAACTGAGGCAGGGAAATTTACCTTGAATTCAGTGGAACCTTAACCTTTTTCCCATCTTGTT
GAGCTCCAATGATGCTTGCATCAACTTCCACTGAACCATTATTAATTTGTAGCAT
						
					

			
		

Sequences
Splice junction sequence	TTTACCTTGAATTCAGTGGAACCTTAACCTTTTTCCCATCTTGTTGAGCTCCAATGATGCTTGC ATCAACTTCCACTGAACCATTATTAATTTGTAGCATatttcaaagttctgaacctccagtattg tttgttctatgtctagtcgggcatgaaaggagggtttccccgtgaacgattgcaagtgttgtgc caaatgaa
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: 377 Transcript exons: 141840969-141841075,141841142-141841204,141842114-141842 173,141842354-141842405,141843361-141843455 ATTTCAAAGTTCTGAACCTCCAGTATTGTTTGTTCTATGTCTAGTCGGGCATGAAAGGAGGGTT TCCCCGTGAACGATTGCAAGTGTTGTGCCAAATGAACATGCCTAGCTATCTCCGGTAGCGAGTG CAACCTCCTCACAAAATCCTTGAGCTCCGAAACAGACTGAGTGTTGGTGGATTTCACTTCTGCA TAATCTTGCTGAATAGATGTTGCTTTTTGACGTAAAACCTGAACTACAACTTCAAAATTGAGGT CTCGAATCTCCTTGTACAACTTATCGCTTGAATTCAGTGGAACCTTAACCTTTTTCCCATCTTG TTGAGCTCCAATGATGCTTGCATCAACTTCCACTGAACCATTATTAATTTGTAGCAT
Genomic sequence	ATTTCAAAGTTCTGAACCTCCAGTATTGTTTGTTCTATGTCTAGTCGGGCATGAAAGGAGGGTT TCCCCGTGAACGATTGCAAGTGTTGTGCCAAATGAACATGCCTCTAAACAACATGCTATAAGTT AGTAAAATAATATAGGATAAAAATGAAGGCATGCAATCAACTCACAGCTATCTCCGGTAGCGAG TGCAACCTCCTCACAAAATCCTTGAGCTCCGAAACAGACTGAGTCTGTTAAAAATTACAATATC AAATAATCAATTCCCTTTTCTACATTGTACTAGCCAAAGGTAATTTACTGTAGAAACAAACAGG CATAACATTTTAAAAAATGTAGATATAAAGTCACATAACACTGGAAGCAAGAAACATACTAACA AAGTAACAAGTAGCAAATTCTTCAACTAAGAGTTCCATCAAAGCGCCCACATTTAGACTAATTT TGGTATTGTTATCCAAGCAATGACACCTAGATCACTCAGTATTGTAGAGATGCCCCTCAATCTT CAAATAAGACAAATTTATTTAGGTCAAGCAGAGCTGTTGATTATACAATGTCGATGACATTACT CGATACTTTAATATTTTTTGATCTTGTGTAAATATTAAACTAGCTGCATCAGTCCAAATCCATA TCCATGTCACTTCTCAACAGCAAGCAAATGCCATATGTCCAGGTTATCAACTTATCATAATCAC AGGCAGAAATCTAAGACTGAGAAGTGGGTATTGTCTAATATTTTTTTAGACGTTAATCCACCTG CCATTAATTCAATCCTCTGGCATGGTTAAAGAACAAAACCAGATTATACACTTTTGTTTATCAA CTGTCCTGATTGAAGCAATTACAATCCATTATAGAGGCTTCCTCCAAAAAGAAAAAAATGATAA CTTGATTAACATACAAATACTTGATTTGTTGGGGAACAATAATTCAATATTAATATAACATGGG GACTCGTTCTAATTCCAACAGTAAATGGTATAAAAATAAATTTATATCAGTAAATCATCTGAAA AAGGTGGCATGTACTTAAAACACGCAATAACTCAGCATTTGCATCCTTGCTTTTGAACAATGCT GCAAGTGACAACAGACATAGAGGACACAGGGCATAACACAACACACTTAATTCTTACGTTGGTG GATTTCACTTCTGCATAATCTTGCTGAATAGATGTTGCTTTTTGACGTAAAACCTGCAGTCAAT ACAATTTGCAATAATTTAATATGGGTAAAAATGATGATAGTTGGTAGATATAACTAAACAAACT GGAATTAGAAATGGCTATGACAATAGCAGGTATAACAAAAACCACAAAAGTTACCACAAAGCCC CTTCACATGAATAAACAAAAGTTGAAGGCAGTGGAGTGAACCTGAACTACAACTTCAAAATTGA GGTCTCGAATCTCCTTGTACAACTTATCGCTGAAAAAAAAACACCAATATAAATGCATAGGTCC AAATACAGCAAAAAAACCTGTAAAAATACAAGCCTATGTACAATAAGACGATTACACATATATT TGCACTATCTACAGTCACAAATAAGTAGCAGTCTCTATCCAATAAATTTGTACGGGAGTAATTT TCATGAAAAGCCAACTGGTACATTTCCACAGCCAATCTAGGTACTCATGAAGGTAAGTTGATCA GACATCGGAAGTTTGATTTAGGCATTTGCACCATCACTTACACTTGATAGGAAGGAGCAACAGA TATTAACTTCAAAAACTAAGAAATCAATTAAATCATTAATAACAATTTTCTCAACTTTCTAGAT CCAAAAGTTTCAATGTGCAAAACAAATCATAAGTATCTTGATAATGACAAGGATGCAAATAGAG TAAGAATAATAAATAAATAAAAAACATCAATGTTGGGTTACGAAGTATTCATTGGCACAAAGCA AATTTACAATTTAGTAGTGCGTACTCTTTCAATAGCAAATATATGTCATTTAGGATAGCTAAAA AGCGAAAGGGCCTCTAGTTGAGTTGGTTAGGTGGTCTGAGTAGTGAGTAGCACTCCTCAGGTAC TGAGTTCAACTCCCCGTGGGAACGAATTTCAGACTGTGGTTAAAAAATTCCCCTCGTTTGTTCC ACGCCAAAGCACAGGTCTAAGACCTGGTCCCAGTCGTTTCTCAGATGGGTTGTGTATGGGTGGG GGTAGGGCAGGGGTTCGAGGGTTTTCTCGACCTGCGTGAGAAGGTCTTCTTAATATAATGCTCG AGGGTTGTCTTACCCCCACAGGTCGAATTTTTTTAGGACAACTAAAAAGGTTTGACTTACTGCA GATCTAAAACGATTCATATTTGTAACCAGGAGTATTTCAAAATTTAAAGATCAGGTTAAAAGCC GCTAACTGAGGCAGGGAAATTTACCTTGAATTCAGTGGAACCTTAACCTTTTTCCCATCTTGTT GAGCTCCAATGATGCTTGCATCAACTTCCACTGAACCATTATTAATTTGTAGCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.145466779

Conservation Information
Conserved circRNAs	NA
PMCS	0.145466779

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							141843410-141841038(+)
141843457-141843370(-)
						
						Potential amino acid sequence
						
							MMLASTSTEPLLICSIFQSSEPPVLFVLCLVGHERRVSP*(+)
MLQINNGSVEVDASIIGAQQDGKKVKVPLNSSDKLYKEIRDLNFEVVVQVLRQKATSIQQDYAE
VKSTNTQSVSELKDFVRRLHSLPEIARHVHLAQHLQSFTGKPSFHARLDIEQTILEVQNFEICY
KLIMVQWKLMQASLELNKMGKRLRFH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	141843410-141841038(+) 141843457-141843370(-)
Potential amino acid sequence	MMLASTSTEPLLICSIFQSSEPPVLFVLCLVGHERRVSP(+) MLQINNGSVEVDASIIGAQQDGKKVKVPLNSSDKLYKEIRDLNFEVVVQVLRQKATSIQQDYAE VKSTNTQSVSELKDFVRRLHSLPEIARHVHLAQHLQSFTGKPSFHARLDIEQTILEVQNFEICY KLIMVQWKLMQASLELNKMGKRLRFH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d011177_circ_g.3

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