Plant Circular RNA Database

Detail information of Zm00001d051961_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d051961_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001761
					
						Alias
						circ2279
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 175388964-175390979  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d051961						
					
						Parent gene annotation
						
							Putative lysine-specific demethylase JMJ16
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d051959_circ_g.1 Zm00001d051959_circ_ag.1 						
					
						Support reads
						3
					
						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
						Zm00001d051961_T001:6
Zm00001d051961_T009:6
Zm00001d051961_T027:6
Zm00001d051961_T033:6
Zm00001d051961_T025:6
Zm00001d051961_T015:1
Zm00001d051961_T022:6
Zm00001d051961_T044:3
Zm00001d051961_T018:7
Zm00001d051961_T014:6
Zm00001d051961_T028:6
Zm00001d051961_T004:6
Zm00001d051961_T040:3
Zm00001d051961_T006:6
Zm00001d051961_T016:6
Zm00001d051961_T007:6
Zm00001d051961_T031:6
Zm00001d051961_T002:7
Zm00001d051961_T024:6
Zm00001d051961_T037:6
Zm00001d051961_T020:6
Zm00001d051961_T045:3
Zm00001d051961_T010:6
Zm00001d051961_T029:6

General Information
CircRNA Name	Zm00001d051961_circ_g.1
ID in PlantcircBase	zma_circ_001761
Alias	circ2279
Organism	Zea mays
Position	chr4: 175388964-175390979 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d051961
Parent gene annotation	Putative lysine-specific demethylase JMJ16
Parent gene strand	+
Alternative splicing	Zm00001d051959_circ_g.1 Zm00001d051959_circ_ag.1
Support reads	3
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	Zm00001d051961_T001:6 Zm00001d051961_T009:6 Zm00001d051961_T027:6 Zm00001d051961_T033:6 Zm00001d051961_T025:6 Zm00001d051961_T015:1 Zm00001d051961_T022:6 Zm00001d051961_T044:3 Zm00001d051961_T018:7 Zm00001d051961_T014:6 Zm00001d051961_T028:6 Zm00001d051961_T004:6 Zm00001d051961_T040:3 Zm00001d051961_T006:6 Zm00001d051961_T016:6 Zm00001d051961_T007:6 Zm00001d051961_T031:6 Zm00001d051961_T002:7 Zm00001d051961_T024:6 Zm00001d051961_T037:6 Zm00001d051961_T020:6 Zm00001d051961_T045:3 Zm00001d051961_T010:6 Zm00001d051961_T029:6

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: ACTACATGCATTGGGGTGCT
 R: CCGAGATAAGGTCGAACTGG
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	Yes 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	F: ACTACATGCATTGGGGTGCT R: CCGAGATAAGGTCGAACTGG 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  
						
							GTATGGAGTTCCAGGAAAGGATGCTGTAAATTTGGAGGCAGCAATGAGGAAACACCTACCTGAC
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
TGATTTTAATGCATTGCCATGACATGGCTCTGTTTTCTTGACAGGGAGTGGGATTAGTGAGACA
CAGACGACAATTACCGAAAGGAGTACTTCGGGGATGCGCACAATGTGCTGATTGTCAAAAGGTT
TGTGTAACTGTGCTAAATTGCTGAGTCACTTCCAGGAAGATGTTTTTTGTCAGCTTATGCACAT
CACATCGACATCGTGCAGGTTGTTGCAAGGTGGAATCCATCTGGTGCAAGGAGGCCTGTTCTTG
AGGAAGCTCCTGTTTTCTATCCATCCGAAGAGGTATCTTATGTTTATCGCACTGCCTTGTAGTA
TGGCAGTACTTGGTTTATTTTTGCATACACTAATCTCATGATACCTTCTTGTGGATCAGGAATT
CAAGGACACCTTAAAATACATTGAGAGTATACGGTCTACAGCAGAACCATATGGAATTTGTCGT
ATTGTCCCGCCGCCTTCATGGAAACCTCCATGCCTTCTTAAAGAGAAGAACATATGGGAATGCT
CAAAATTTTGTACTCGGGTACAGAAGGTTGACAAGCTCCAAAACCGTAAATCATCCAAGAAGGG
CAGAAGAGGTGGGGTGATGAAGAAGCGGAGAAGCTTTTAGAGCTGGAAGATAACAATAATATTA
ATCACAATCAAACTGGGGTGCAGCAAAACCAAGAGAGGTTTGGATTTGAACCTGGACCTGAGTT
CACACTTCAGACATTTAAGAAGTATGCAGATGATTTCCGTGAACAATATTTTAAGAAAGAAGTG
CCCGCGGACTCACCACCATCAGTAGAAGACATTGAAGGCGAGTATTGGCGTATAGTCGAAAAGC
CTACTGAAGAGATAGAGGTACCGGTCTTCTGCTATCATAGAGTAACTATGTCATTTGCAATTCA
TAGCTCTGTCCAAACTTTAGAAAGTACAGTATATGTCATTTTAGATCTGGATTTGTTAGATAGT
TTCTGATTTAGCTTCCCAGTGCAGTTCTGTTCTTTTGTATATGATTCCTGATTGCCTGAACATA
GTCCTTGCAGATGTTTCTTGGCCTAATTATAATATTTTCGAAGTTCTTATTTCTGTTTTTGACA
TATAGTTCTGCTATCGACTAACTTATCAGAGAATACGTTCTCGTACAGGTAGTATATGGTGCTG
ATTTGGAGACTGGAACTTTTGGTAGCGGCTTCCCAAAGTCTTCTCCCGAAGTAAAATCTGATGT
TGAGCATAAGTACTTAGAGTCTGGTTGGAACCTAAACAACTTGCCTAGACTACAAGGTTCAGTA
CTATCTTTTGAGGGCGGTGACATCTCTGGTGTTTTGGTCCCTTGGATGTATGTCGGAATGTGCT
TTTCATCATTCTGCTGGGTAAGATGCTTGTTGGCATGTCTACTTCTCTTACAATTAAGATTGTT
GTCATTATCCAAATTTAACATTCATGTTCTGAGATTTTACACTGGCATGTCTCTGCTGACAGCA
TGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTAT
GGAGTTCCAGGAAAGGATGCTGTAAATTTGGAGGCAGCAATGAGGAAACACCTACCTGACTTGT
TTGAGGAACAACCTGATTTGCTTCACAACCTG
						
					

			
		

Sequences
Splice junction sequence	GTATGGAGTTCCAGGAAAGGATGCTGTAAATTTGGAGGCAGCAATGAGGAAACACCTACCTGAC 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 TGATTTTAATGCATTGCCATGACATGGCTCTGTTTTCTTGACAGGGAGTGGGATTAGTGAGACA CAGACGACAATTACCGAAAGGAGTACTTCGGGGATGCGCACAATGTGCTGATTGTCAAAAGGTT TGTGTAACTGTGCTAAATTGCTGAGTCACTTCCAGGAAGATGTTTTTTGTCAGCTTATGCACAT CACATCGACATCGTGCAGGTTGTTGCAAGGTGGAATCCATCTGGTGCAAGGAGGCCTGTTCTTG AGGAAGCTCCTGTTTTCTATCCATCCGAAGAGGTATCTTATGTTTATCGCACTGCCTTGTAGTA TGGCAGTACTTGGTTTATTTTTGCATACACTAATCTCATGATACCTTCTTGTGGATCAGGAATT CAAGGACACCTTAAAATACATTGAGAGTATACGGTCTACAGCAGAACCATATGGAATTTGTCGT ATTGTCCCGCCGCCTTCATGGAAACCTCCATGCCTTCTTAAAGAGAAGAACATATGGGAATGCT CAAAATTTTGTACTCGGGTACAGAAGGTTGACAAGCTCCAAAACCGTAAATCATCCAAGAAGGG CAGAAGAGGTGGGGTGATGAAGAAGCGGAGAAGCTTTTAGAGCTGGAAGATAACAATAATATTA ATCACAATCAAACTGGGGTGCAGCAAAACCAAGAGAGGTTTGGATTTGAACCTGGACCTGAGTT CACACTTCAGACATTTAAGAAGTATGCAGATGATTTCCGTGAACAATATTTTAAGAAAGAAGTG CCCGCGGACTCACCACCATCAGTAGAAGACATTGAAGGCGAGTATTGGCGTATAGTCGAAAAGC CTACTGAAGAGATAGAGGTACCGGTCTTCTGCTATCATAGAGTAACTATGTCATTTGCAATTCA TAGCTCTGTCCAAACTTTAGAAAGTACAGTATATGTCATTTTAGATCTGGATTTGTTAGATAGT TTCTGATTTAGCTTCCCAGTGCAGTTCTGTTCTTTTGTATATGATTCCTGATTGCCTGAACATA GTCCTTGCAGATGTTTCTTGGCCTAATTATAATATTTTCGAAGTTCTTATTTCTGTTTTTGACA TATAGTTCTGCTATCGACTAACTTATCAGAGAATACGTTCTCGTACAGGTAGTATATGGTGCTG ATTTGGAGACTGGAACTTTTGGTAGCGGCTTCCCAAAGTCTTCTCCCGAAGTAAAATCTGATGT TGAGCATAAGTACTTAGAGTCTGGTTGGAACCTAAACAACTTGCCTAGACTACAAGGTTCAGTA CTATCTTTTGAGGGCGGTGACATCTCTGGTGTTTTGGTCCCTTGGATGTATGTCGGAATGTGCT TTTCATCATTCTGCTGGGTAAGATGCTTGTTGGCATGTCTACTTCTCTTACAATTAAGATTGTT GTCATTATCCAAATTTAACATTCATGTTCTGAGATTTTACACTGGCATGTCTCTGCTGACAGCA TGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTAT GGAGTTCCAGGAAAGGATGCTGTAAATTTGGAGGCAGCAATGAGGAAACACCTACCTGACTTGT TTGAGGAACAACCTGATTTGCTTCACAACCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.091778435

Conservation Information
Conserved circRNAs	NA
PMCS	0.091778435

			
						 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 Zm00001d051961_circ_g.1

Address

Any questions?

Supported by