Plant Circular RNA Database

Detail information of Zm00001d011854_circ_g.4

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d011854_circ_g.4
					

						ID in PlantcircBase
						zma_circ_002845
					

						Alias
						circ1335
					

						Organism
						
							Zea mays						
					

						Position
						
							chr8: 162919561-162920561  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							ui-circRNA							
									
								

					

						Identification method
						CIRI
					

						Parent gene
						
							Zm00001d011854						
					

						Parent gene annotation
						
							Villin-2
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							NA						
					

						Support reads
						2
					

						Tissues
						seedling leaves
					

						Exon boundary  
						
							No-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-TA							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
						Zm00001d011854_T030:4
Zm00001d011854_T043:4
Zm00001d011854_T055:2
Zm00001d011854_T038:4
Zm00001d011854_T047:4
Zm00001d011854_T001:4
Zm00001d011854_T054:4
Zm00001d011854_T050:4
Zm00001d011854_T036:4
Zm00001d011854_T065:4
Zm00001d011854_T064:4
Zm00001d011854_T017:4
Zm00001d011854_T015:4
Zm00001d011854_T072:4
Zm00001d011854_T022:4
Zm00001d011854_T080:4
Zm00001d011854_T088:4
Zm00001d011854_T033:4
Zm00001d011854_T005:4
Zm00001d011854_T011:4
Zm00001d011854_T031:4
Zm00001d011854_T075:4
Zm00001d011854_T079:4
Zm00001d011854_T028:4
Zm00001d011854_T087:4
Zm00001d011854_T077:4
Zm00001d011854_T091:4
Zm00001d011854_T013:4
Zm00001d011854_T056:4
Zm00001d011854_T083:4
Zm00001d011854_T039:4
Zm00001d011854_T025:4
Zm00001d011854_T021:4
Zm00001d011854_T051:4
Zm00001d011854_T069:4
Zm00001d011854_T040:4
Zm00001d011854_T018:4
Zm00001d011854_T046:4
Zm00001d011854_T041:4
Zm00001d011854_T010:4
Zm00001d011854_T002:4
Zm00001d011854_T024:4
Zm00001d011854_T008:4
Zm00001d011854_T063:4
Zm00001d011854_T092:4
Zm00001d011854_T014:4
Zm00001d011854_T067:4
Zm00001d011854_T004:4
Zm00001d011854_T089:4

					

			
		

General Information
CircRNA Name	Zm00001d011854_circ_g.4
ID in PlantcircBase	zma_circ_002845
Alias	circ1335
Organism	Zea mays
Position	chr8: 162919561-162920561 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRI
Parent gene	Zm00001d011854
Parent gene annotation	Villin-2
Parent gene strand	-
Alternative splicing	NA
Support reads	2
Tissues	seedling leaves
Exon boundary	No-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-TA 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	Zm00001d011854_T030:4 Zm00001d011854_T043:4 Zm00001d011854_T055:2 Zm00001d011854_T038:4 Zm00001d011854_T047:4 Zm00001d011854_T001:4 Zm00001d011854_T054:4 Zm00001d011854_T050:4 Zm00001d011854_T036:4 Zm00001d011854_T065:4 Zm00001d011854_T064:4 Zm00001d011854_T017:4 Zm00001d011854_T015:4 Zm00001d011854_T072:4 Zm00001d011854_T022:4 Zm00001d011854_T080:4 Zm00001d011854_T088:4 Zm00001d011854_T033:4 Zm00001d011854_T005:4 Zm00001d011854_T011:4 Zm00001d011854_T031:4 Zm00001d011854_T075:4 Zm00001d011854_T079:4 Zm00001d011854_T028:4 Zm00001d011854_T087:4 Zm00001d011854_T077:4 Zm00001d011854_T091:4 Zm00001d011854_T013:4 Zm00001d011854_T056:4 Zm00001d011854_T083:4 Zm00001d011854_T039:4 Zm00001d011854_T025:4 Zm00001d011854_T021:4 Zm00001d011854_T051:4 Zm00001d011854_T069:4 Zm00001d011854_T040:4 Zm00001d011854_T018:4 Zm00001d011854_T046:4 Zm00001d011854_T041:4 Zm00001d011854_T010:4 Zm00001d011854_T002:4 Zm00001d011854_T024:4 Zm00001d011854_T008:4 Zm00001d011854_T063:4 Zm00001d011854_T092:4 Zm00001d011854_T014:4 Zm00001d011854_T067:4 Zm00001d011854_T004:4 Zm00001d011854_T089:4

			
						 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  
						
							AATGATACGTATAGAGAATGATATAACAGTCTCCACTGTAAAACTTTCCAATATCCTCTTTTGG
CAGAGCAGTCTTAGCGTTGCCATCAACACACCATACccgtatcgacttgaagagtcttgttgtt
gtggatagatgtcccagatactcgaattagagctatgccttcagtagtataagtctcacccgtc
gcaccctt

						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
						
							CCGTATCGACTTGAAGAGTCTTGTTGTTGTGGATAGATGTCCCAGATACTCGAATTAGAGCTAT
GCCTTCAGTAGTATAAGTCTCACCCGTCGCACCCTTTTCTTCTATGAGCTTCTTGTATCCAGAT
CCAATTCCACCCTACATAATTTATGTTGCCAGCAAAATATTGTGCATATATATCATTTAGCTCG
CATAGAAGGTGAGCTACAAACCCATTACTGAAAAATAAAATAAAATAAAATAATGGAAGCAAAA
AATATGTTTGGTAGCCTTGACGTGTGTACCTTCAAGATAATCATGGGCTGGAAAAGTGCAACAA
ACTGTGGTGGCTCCTTCCCTTGGTATATACGACCCTACAAAATAACTATAAATAACTAAAAGCC
ATCTCCTGTGAACAAATATTGTAGGCACATCTGAAATAAAATGCAGCACCAGAACTGGCCGTCC
TTTCAATGAATTCCACACTGTATTAGTTATTTGAGATGCCGACACTTGATCGTCCTGCAAAGCA
AACACCAAAACAGTAAATATAGATCAGGCTCAGCTGTACAAGTGCAGGAGTTGATTCTATAAAA
GGACAAGAAACAAGTGCAAAGTAACTTCAAGGGAATTTATGCCAACAGCTAAGCAGATGGGCAC
AAATTGTTTGGTTTAAGTACAAGAAATATGTTTTAACTTAAAGCAGTAAATTGTATCAGCAAAC
ACTCCACAATAAAAACAATGCCACATCGCCAACACAAAGTGGAGAAATTTTAATTAAGCACAAA
AGTAGAAAGGCAGACAGGATACTGAAACGATTTAATTAAGACAAAAAAAGAGCAAGTGCAGTAA
CATGCAATACCACCAAGCTATCCTTCCCAATCCAGTAGCTGAGATAGTATTCTTCTTTCTTGTC
GCCCGAATGATACGTATAGAGAATGATATAACAGTCTCCACTGTAAAACTTTCCAATATCCTCT
TTTGGCAGAGCAGTCTTAGCGTTGCCATCAACACACCATAC

Sequences
Splice junction sequence	AATGATACGTATAGAGAATGATATAACAGTCTCCACTGTAAAACTTTCCAATATCCTCTTTTGG CAGAGCAGTCTTAGCGTTGCCATCAACACACCATACccgtatcgacttgaagagtcttgttgtt gtggatagatgtcccagatactcgaattagagctatgccttcagtagtataagtctcacccgtc gcaccctt
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	CCGTATCGACTTGAAGAGTCTTGTTGTTGTGGATAGATGTCCCAGATACTCGAATTAGAGCTAT GCCTTCAGTAGTATAAGTCTCACCCGTCGCACCCTTTTCTTCTATGAGCTTCTTGTATCCAGAT CCAATTCCACCCTACATAATTTATGTTGCCAGCAAAATATTGTGCATATATATCATTTAGCTCG CATAGAAGGTGAGCTACAAACCCATTACTGAAAAATAAAATAAAATAAAATAATGGAAGCAAAA AATATGTTTGGTAGCCTTGACGTGTGTACCTTCAAGATAATCATGGGCTGGAAAAGTGCAACAA ACTGTGGTGGCTCCTTCCCTTGGTATATACGACCCTACAAAATAACTATAAATAACTAAAAGCC ATCTCCTGTGAACAAATATTGTAGGCACATCTGAAATAAAATGCAGCACCAGAACTGGCCGTCC TTTCAATGAATTCCACACTGTATTAGTTATTTGAGATGCCGACACTTGATCGTCCTGCAAAGCA AACACCAAAACAGTAAATATAGATCAGGCTCAGCTGTACAAGTGCAGGAGTTGATTCTATAAAA GGACAAGAAACAAGTGCAAAGTAACTTCAAGGGAATTTATGCCAACAGCTAAGCAGATGGGCAC AAATTGTTTGGTTTAAGTACAAGAAATATGTTTTAACTTAAAGCAGTAAATTGTATCAGCAAAC ACTCCACAATAAAAACAATGCCACATCGCCAACACAAAGTGGAGAAATTTTAATTAAGCACAAA AGTAGAAAGGCAGACAGGATACTGAAACGATTTAATTAAGACAAAAAAAGAGCAAGTGCAGTAA CATGCAATACCACCAAGCTATCCTTCCCAATCCAGTAGCTGAGATAGTATTCTTCTTTCTTGTC GCCCGAATGATACGTATAGAGAATGATATAACAGTCTCCACTGTAAAACTTTCCAATATCCTCT TTTGGCAGAGCAGTCTTAGCGTTGCCATCAACACACCATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.108013686

Conservation Information
Conserved circRNAs	NA
PMCS	0.108013686

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d011854_circ_g.4

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