Plant Circular RNA Database

Detail information of Zm00001d051965_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d051965_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001762
					
						Alias
						circ2280
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 175520001-175522017  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d051965						
					
						Parent gene annotation
						
							Putative lysine-specific demethylase JMJ16
							
						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  
						
							GT-CA							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
						Zm00001d051965_T035:6
Zm00001d051965_T015:1
Zm00001d051965_T026:6
Zm00001d051965_T041:3
Zm00001d051965_T002:6
Zm00001d051965_T030:6
Zm00001d051965_T021:6
Zm00001d051965_T029:6
Zm00001d051965_T017:6
Zm00001d051965_T033:6
Zm00001d051965_T019:6
Zm00001d051965_T009:6
Zm00001d051965_T025:6
Zm00001d051965_T001:6
Zm00001d051965_T005:6
Zm00001d051965_T014:6
Zm00001d051965_T004:6
Zm00001d051965_T010:6
Zm00001d051965_T022:6
Zm00001d051965_T008:6
Zm00001d051965_T027:6

General Information
CircRNA Name	Zm00001d051965_circ_g.1
ID in PlantcircBase	zma_circ_001762
Alias	circ2280
Organism	Zea mays
Position	chr4: 175520001-175522017 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d051965
Parent gene annotation	Putative lysine-specific demethylase JMJ16
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	GT-CA 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	Zm00001d051965_T035:6 Zm00001d051965_T015:1 Zm00001d051965_T026:6 Zm00001d051965_T041:3 Zm00001d051965_T002:6 Zm00001d051965_T030:6 Zm00001d051965_T021:6 Zm00001d051965_T029:6 Zm00001d051965_T017:6 Zm00001d051965_T033:6 Zm00001d051965_T019:6 Zm00001d051965_T009:6 Zm00001d051965_T025:6 Zm00001d051965_T001:6 Zm00001d051965_T005:6 Zm00001d051965_T014:6 Zm00001d051965_T004:6 Zm00001d051965_T010:6 Zm00001d051965_T022:6 Zm00001d051965_T008:6 Zm00001d051965_T027:6

			
						 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  
						
							GTATGGAGTTCCAGGAAAGGATGCCGTAAATTTGGAGGCAGCAATGAGGAAACATCTACCTGAC
TTGTTTGAGGAACAACCTGATTTGCTTCACAACCTGgcaatgatgggaacagagtgcatcatgg
ccacactcggcggggatcctgaaccctcaattccacctggattcggaccttttgttgccctcgc
gctacagg

									
								

					

						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
						
							GCAATGATGGGAACAGAGTGCATCATGGCCACACTCGGCGGGGATCCTGAACCCTCAATTCCAC
CTGGATTCGGACCTTTTGTTGCCCTCGCGCTACAGGGCATCCAAAACAATGCCAAATCAGCTGA
TGCTCATTCTAGTTCTGCTCAAGCAGCACACTGCATGGAGAAAGATGTTGAAGTTCTGGAACAC
GGTTCGGCGCATGGTTGGAGTGACACTCCTGCTAGTACTTCAGGGACCCATAGTTGCAGGAGGT
CACTTCGTAACAGGCCTCCAATAGACTATAGCCAGTTCGACCTTATCTCGGACGAAGAATCTGA
TGTTGAATCAGCAGAAAAGGTTTCATTCGTGTATTGATCCTTATGTGATTACCTGAATTCGTCA
TGATTTTAATGCATTGCCATGACATGGCTCTGTTTTCTTGACAGGGAGTGGGATTAGTGAGACG
CAGACGACAATTACCGAAAGGAGTACTTCGGGGATGCGCACAATGTGCTGATTGTCAAAAGGTT
TGTGTAACTGTGCTAAATTGCTGAGTCACTTCCAGGAAGATGTTTTTTGTCAGCTTATGCACAT
CACATCGACATCGTGCAGGTTGTTGCAAGGTGGAATCCATCTGGTGCAAGGAGGCCTGTTCTTG
AGGAAGCTCCTGTTTTCTATCCATCCGAAGAGGTATCTTATGTTTATCGCACTGCCTTGTAGTA
TGGCAGTACTTGGTTTATTTTTGCATACACTAATCTCATGATACCTTCTTGTGGATCAGGAATT
CAAGGACACCTTAAAATACATTGAGAGTATACGGTCTACAGCAGAACCATATGGAATTTGTCGT
ATTGTCCCGCCGCCTTCATGGAAACCTCCATGCCTTCTTAAAGAGAAGAACATATGGGAATGCT
CAAAATTTTGTACTCGGGTACAGAAGGTTGACAAGCTCCAAAACCGTAAATCATCCAAGAAGGG
CAGAAGAGGTGGGATGATGAAGAAGCGGAGGAAGCTTTTAGAGCTGGAAGATAACAATAATATT
AATCACAATCAAACTGGGGTGCAGCAAAACCAAGAGAGGTTTGGATTTGAACCTGGACCTGAGT
TCACACTTCAGACATTTAAGAAGTATGCAGATGATTTCCGTGAACAATATTTTAAGAAAGAAGT
GTCCGCGGACTCACCACCATCAGTAGAAGACATTGAAGGCGAGTATTGGCGTATAGTCGAAAAG
CCTACTGAAGAGATAGAGGTACCAGACTTCTGCTATCATAGAGTAACTATGTCATTTGCAATTC
ATAGCTTTGTCCAAACTTTAGAAAGTACAGTATATGTCATTTTAGATCTGGATTTGTTAGATAG
TTTCTGGTTTAGCTTCCCAGTGCAGTTCTGTTCTTTTGTATATGATTCCTGATTGCCTGAACAT
AGTCCTTGCAGATGTTTCTTGGCCTAATTATAGTATATTCGAAGTTCTGATTTCTGTTTTTGAC
ATATAGTTCTGCTATCGACTAACTTATCAGAGAATACATTCTCGTACAGGTAGTATATGGTGCT
GATTTGGAGACTGGAACTTTTGGTAGCGGCTTCCCAAAGTCTTCTCCCGAAGTAAAATCTGATG
TTGAGCATAAGTACTTAGAGTCTGGTTGGAACCTAAACAACTTGCCTAGACTACAAGGTTCAGT
ACTATCTTTTGAAGGTGGGGACATCTCTGGTGTTTTGGTCCCTTGGCTGTATGTTGGAATGTGC
TTTTCATCATTCTGCTGGGTAAGATGCTTGTTGGCATGTCTACTTCTCTTACCATTAATATTGT
TGTCATTATCCAAATTTAACATTCATGTTCTGAGATTTTACACTGGCATGTCTCTGCTGACAGC
ATGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTA
TGGAGTTCCAGGAAAGGATGCCGTAAATTTGGAGGCAGCAATGAGGAAACATCTACCTGACTTG
TTTGAGGAACAACCTGATTTGCTTCACAACCTG
						
					

			
		

Sequences
Splice junction sequence	GTATGGAGTTCCAGGAAAGGATGCCGTAAATTTGGAGGCAGCAATGAGGAAACATCTACCTGAC TTGTTTGAGGAACAACCTGATTTGCTTCACAACCTGgcaatgatgggaacagagtgcatcatgg ccacactcggcggggatcctgaaccctcaattccacctggattcggaccttttgttgccctcgc gctacagg
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	GCAATGATGGGAACAGAGTGCATCATGGCCACACTCGGCGGGGATCCTGAACCCTCAATTCCAC CTGGATTCGGACCTTTTGTTGCCCTCGCGCTACAGGGCATCCAAAACAATGCCAAATCAGCTGA TGCTCATTCTAGTTCTGCTCAAGCAGCACACTGCATGGAGAAAGATGTTGAAGTTCTGGAACAC GGTTCGGCGCATGGTTGGAGTGACACTCCTGCTAGTACTTCAGGGACCCATAGTTGCAGGAGGT CACTTCGTAACAGGCCTCCAATAGACTATAGCCAGTTCGACCTTATCTCGGACGAAGAATCTGA TGTTGAATCAGCAGAAAAGGTTTCATTCGTGTATTGATCCTTATGTGATTACCTGAATTCGTCA TGATTTTAATGCATTGCCATGACATGGCTCTGTTTTCTTGACAGGGAGTGGGATTAGTGAGACG CAGACGACAATTACCGAAAGGAGTACTTCGGGGATGCGCACAATGTGCTGATTGTCAAAAGGTT TGTGTAACTGTGCTAAATTGCTGAGTCACTTCCAGGAAGATGTTTTTTGTCAGCTTATGCACAT CACATCGACATCGTGCAGGTTGTTGCAAGGTGGAATCCATCTGGTGCAAGGAGGCCTGTTCTTG AGGAAGCTCCTGTTTTCTATCCATCCGAAGAGGTATCTTATGTTTATCGCACTGCCTTGTAGTA TGGCAGTACTTGGTTTATTTTTGCATACACTAATCTCATGATACCTTCTTGTGGATCAGGAATT CAAGGACACCTTAAAATACATTGAGAGTATACGGTCTACAGCAGAACCATATGGAATTTGTCGT ATTGTCCCGCCGCCTTCATGGAAACCTCCATGCCTTCTTAAAGAGAAGAACATATGGGAATGCT CAAAATTTTGTACTCGGGTACAGAAGGTTGACAAGCTCCAAAACCGTAAATCATCCAAGAAGGG CAGAAGAGGTGGGATGATGAAGAAGCGGAGGAAGCTTTTAGAGCTGGAAGATAACAATAATATT AATCACAATCAAACTGGGGTGCAGCAAAACCAAGAGAGGTTTGGATTTGAACCTGGACCTGAGT TCACACTTCAGACATTTAAGAAGTATGCAGATGATTTCCGTGAACAATATTTTAAGAAAGAAGT GTCCGCGGACTCACCACCATCAGTAGAAGACATTGAAGGCGAGTATTGGCGTATAGTCGAAAAG CCTACTGAAGAGATAGAGGTACCAGACTTCTGCTATCATAGAGTAACTATGTCATTTGCAATTC ATAGCTTTGTCCAAACTTTAGAAAGTACAGTATATGTCATTTTAGATCTGGATTTGTTAGATAG TTTCTGGTTTAGCTTCCCAGTGCAGTTCTGTTCTTTTGTATATGATTCCTGATTGCCTGAACAT AGTCCTTGCAGATGTTTCTTGGCCTAATTATAGTATATTCGAAGTTCTGATTTCTGTTTTTGAC ATATAGTTCTGCTATCGACTAACTTATCAGAGAATACATTCTCGTACAGGTAGTATATGGTGCT GATTTGGAGACTGGAACTTTTGGTAGCGGCTTCCCAAAGTCTTCTCCCGAAGTAAAATCTGATG TTGAGCATAAGTACTTAGAGTCTGGTTGGAACCTAAACAACTTGCCTAGACTACAAGGTTCAGT ACTATCTTTTGAAGGTGGGGACATCTCTGGTGTTTTGGTCCCTTGGCTGTATGTTGGAATGTGC TTTTCATCATTCTGCTGGGTAAGATGCTTGTTGGCATGTCTACTTCTCTTACCATTAATATTGT TGTCATTATCCAAATTTAACATTCATGTTCTGAGATTTTACACTGGCATGTCTCTGCTGACAGC ATGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTA TGGAGTTCCAGGAAAGGATGCCGTAAATTTGGAGGCAGCAATGAGGAAACATCTACCTGACTTG TTTGAGGAACAACCTGATTTGCTTCACAACCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13191565

Conservation Information
Conserved circRNAs	NA
PMCS	0.13191565

			
						 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 Zm00001d051965_circ_g.1

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