Plant Circular RNA Database

Detail information of Zm00001d028546_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d028546_circ_g.1
					
						ID in PlantcircBase
						zma_circ_000590
					
						Alias
						circ2516
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 38905150-38907986  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d028546						
					
						Parent gene annotation
						
							SH3 domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d028546_circ_g.2 						
					
						Support reads
						4
					
						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-AA							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
						Zm00001d028546_T028:8
Zm00001d028546_T035:7
Zm00001d028546_T021:7
Zm00001d028546_T037:5
Zm00001d028546_T018:7
Zm00001d028546_T001:7
Zm00001d028546_T031:7
Zm00001d028546_T038:4
Zm00001d028546_T025:7
Zm00001d028546_T034:7
Zm00001d028546_T013:6
Zm00001d028546_T040:3
Zm00001d028546_T022:7
Zm00001d028546_T015:7
Zm00001d028546_T016:7
Zm00001d028546_T006:7
Zm00001d028546_T027:7
Zm00001d028546_T032:7
Zm00001d028546_T008:7
Zm00001d028546_T009:7
Zm00001d028546_T003:7
Zm00001d028546_T011:7

General Information
CircRNA Name	Zm00001d028546_circ_g.1
ID in PlantcircBase	zma_circ_000590
Alias	circ2516
Organism	Zea mays
Position	chr1: 38905150-38907986 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d028546
Parent gene annotation	SH3 domain-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d028546_circ_g.2
Support reads	4
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-AA 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	Zm00001d028546_T028:8 Zm00001d028546_T035:7 Zm00001d028546_T021:7 Zm00001d028546_T037:5 Zm00001d028546_T018:7 Zm00001d028546_T001:7 Zm00001d028546_T031:7 Zm00001d028546_T038:4 Zm00001d028546_T025:7 Zm00001d028546_T034:7 Zm00001d028546_T013:6 Zm00001d028546_T040:3 Zm00001d028546_T022:7 Zm00001d028546_T015:7 Zm00001d028546_T016:7 Zm00001d028546_T006:7 Zm00001d028546_T027:7 Zm00001d028546_T032:7 Zm00001d028546_T008:7 Zm00001d028546_T009:7 Zm00001d028546_T003:7 Zm00001d028546_T011:7

			
						 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  
						
							AGTACAGTTCCCTCCTTTATCAACTTCTTCTGGATCCCAGTGACAGGGTCTGCTTTGAGGCCAT
AAATTGTGTGTTGGGAAAAGTCGACAACACAGAAAGgttcatgcacggagacttgctgctctga
aggcccttacctcctgttccactagcagttctgagatgatggaaaagctaaatgaaattgtgtt
tggcatct

									
								

					

						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
						
							GTTCATGCACGGAGACTTGCTGCTCTGAAGGCCCTTACCTCCTGTTCCACTAGCAGTTCTGAGA
TGATGGAAAAGCTAAATGAAATTGTGTTTGGCATCTTGGAAAAGGTTGGCCATCCATAATTTCA
GTTGTTCTTTGTACAGTTACATTAGTCTTTAAACTACTTTTCTTAGCTCCTTTTCTGTTTCCCT
GGTCTGTGGCACTAAAGTTGACAGTGTTCTCTACATGATATATCTGGATACTTTCAGGTAGCAG
ATACTAAACAAAAACGGAAAAAGGGTATTTTTACTAAGCAAGGTGGTGATAAGGAGGTGCTGTT
TCGTTTCAAGAATGTGCATTTATTTTTGGTGCTGCTAAGGACTCCTGTTTGTATACCATTATTG
ACCTTGCTAATTATAAGCATGAAAAGGCAGTAAGGCACCAATTACTACAGTGCGCTTAAACTTG
CAGCTCATTATTATCTGGCTAAGATGATGGGCCAACTTAGTTTATTTGATCTGAAAATTGCGAG
TCTTATGTTCTGAACTCAATCTTGTGACACTTTTATTTTATTTTCGTAGTCTATCATACGTGGT
AATTTGCAATATGCTTCTCTAAGTGCACTGAGAAGGTTTCCACTTGATCCCGGTAACCAAGCAT
TCCTCCACCGAGCTGTGCAAGGGTGAGTCTGGACTTTGTAAAACTAGTTTTACCACCTTGTATT
CTGGACCTTATTTATTTTACAAGTTCTCAACTATTCAATACAAGGGCAGAAGCATTATTTATGG
TTTCTTGTCTTTGGTTGTCTTTATAAATGTGAAGAATCAAGAAACCAATATTGACGTGACTTCT
GAACCAGTTACTGATTTATTAATTTATTATTATGTCATGTTTCTGTATTCAACTATCTATCAAG
ATGAACAGCATTATAAAAACATCTACCTGTTCTATGAAAGATCAATCCATGTCTGCAAATGTAT
GAACATGCTGTTTCATATTCATTTTCTTCTCATTGGACTTGATATGACTGCAGGATTGAATTTT
CCGACCCAGTTGCAGTCAGACATGCATTGTCAATAATATCTGAAATTGCTGCGAAAGATCCATA
CTCTGTCGCAATGGCATTGGGTCAGTTTACTGTTTACTCACATACTGCTAACAATTGCTCACGT
TGTCTATTTTATTTTGACATGCATAAAGAACATATGCCATTATGGTTTAGAATATTGTTGATCT
TCCATGCACTGAAAATAGTAAATACTAACAAGCCAAATGTAACATTAGACTTCAGTTGCGATCC
TGATTTTTTTTCATATTTAGTCAATTTGCGATGAGTCTTGTTTCATGCCATTTATGTGGTTTAT
AATCTCATGTATGGCTTCGTTTTATGCAGGCAAAAGTGCACAACCCGGTGGTATGCTTCCTTTT
TCTTCAGCATCTTTTGTTAGTCTTCTTTAATCATTTGAATACAAACATGTTCCAAAGTGATTTC
AGCTAATAGTTTATAACTTTCTATTGCCCATGATAAATGTTTCAAACAATACAGTTATCAGTAA
AAAGCAAGTAAAGCGAGGTTATTAAATAGCTAGCTTTAGATTGGCTATTTTTAGCTATATTTTG
ACGCCTCGACACTATGCCACTTGTTTGCTACAAACTCTATTTAAAATGCTGGGCAAAACAATTC
TAGTTTTCATTTGATTTGAGTTACAAGAATCAAGATTTTTGTGCAAAATACAGATATACCAATG
AATTTGGTATTGTGGAGAAGTGAATATCTTAATTGCTCTTTGTAAAGAAAAAGCTAGACCAACC
TAGGAGGAACTAGGCGGCTGTATATTGTAAGGCCAGTCTCAGTGGGGGTTTCATGTCCCTGTTT
TTAAGACTCACAAGTCACAAGTGTTGGAAACAGTGCAAACAATGAAACTTTTATCATCTTTCTC
TCTTCATTTATGCTATGCCACCATTGCCATGTCATCTTATTCAATGCCCATGAAATTCTCACGA
AAGTCCCATTGAGCCTGGCCTAAGAAGAAAACAAACAGCCAGATGAGGACTCGGACTTATGTGG
TTTAGGCATATATCTACATCCTCAATCAATGGAGCTAGGCTCAGTTCATACTGCCCTTCATAAC
TATCCCTTTAAATATGTTTACTCATTGTCATTGGCCTACCCGATTATAAGTAACATGCAGGGGA
CAATATATCTTCTTGTCAGTGTCTCAAGTATTACATCATCATTAACAACAACAACAAAACCTTT
TAGTCCCAAGCAAGTCAGGGTAGTCTAGTGTTTCAAGTATTACATGCTCTAAATAATATCAGGA
AAATATCGTATAACTTTGTGTAATATCTGGTTACAGTGGCCAATTCTACTACCAATTTCTCCCA
GCTCTATCTAAAAGCCATTACTTCTTAGATTGTATATAATTGATTCCTTCCTCTTTTGTCAAAT
CCAGTTATGTTAAAATTTCTTATTTTCACTTCGATGTACTTATTTGTGTACAATATCATATATC
ATTGTTCCAAACTGAAACAGGAGCTCTTCAGGACATTCTTCATTTGCATGATGTCCTTGCCAGG
GTTTACCTTGCAAAGTTGTGTCATTCGATATCTAGAGCACGTGTATTGGACCGTAAGTGAATTG
TTTTGTGCATAACCTGAATTTATGTGTGATTTGTGATGCAAATCAGGGTGCATGCATCAAATCG
CGGTTCTAATCATATACAATTTATGCAGAGAGGCCTGACATAAAGTCACAGTACAGTTCCCTCC
TTTATCAACTTCTTCTGGATCCCAGTGACAGGGTCTGCTTTGAGGCCATAAATTGTGTGTTGGG
AAAAGTCGACAACACAGAAAG
						
					

			
		

Sequences
Splice junction sequence	AGTACAGTTCCCTCCTTTATCAACTTCTTCTGGATCCCAGTGACAGGGTCTGCTTTGAGGCCAT AAATTGTGTGTTGGGAAAAGTCGACAACACAGAAAGgttcatgcacggagacttgctgctctga aggcccttacctcctgttccactagcagttctgagatgatggaaaagctaaatgaaattgtgtt tggcatct
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	GTTCATGCACGGAGACTTGCTGCTCTGAAGGCCCTTACCTCCTGTTCCACTAGCAGTTCTGAGA TGATGGAAAAGCTAAATGAAATTGTGTTTGGCATCTTGGAAAAGGTTGGCCATCCATAATTTCA GTTGTTCTTTGTACAGTTACATTAGTCTTTAAACTACTTTTCTTAGCTCCTTTTCTGTTTCCCT GGTCTGTGGCACTAAAGTTGACAGTGTTCTCTACATGATATATCTGGATACTTTCAGGTAGCAG ATACTAAACAAAAACGGAAAAAGGGTATTTTTACTAAGCAAGGTGGTGATAAGGAGGTGCTGTT TCGTTTCAAGAATGTGCATTTATTTTTGGTGCTGCTAAGGACTCCTGTTTGTATACCATTATTG ACCTTGCTAATTATAAGCATGAAAAGGCAGTAAGGCACCAATTACTACAGTGCGCTTAAACTTG CAGCTCATTATTATCTGGCTAAGATGATGGGCCAACTTAGTTTATTTGATCTGAAAATTGCGAG TCTTATGTTCTGAACTCAATCTTGTGACACTTTTATTTTATTTTCGTAGTCTATCATACGTGGT AATTTGCAATATGCTTCTCTAAGTGCACTGAGAAGGTTTCCACTTGATCCCGGTAACCAAGCAT TCCTCCACCGAGCTGTGCAAGGGTGAGTCTGGACTTTGTAAAACTAGTTTTACCACCTTGTATT CTGGACCTTATTTATTTTACAAGTTCTCAACTATTCAATACAAGGGCAGAAGCATTATTTATGG TTTCTTGTCTTTGGTTGTCTTTATAAATGTGAAGAATCAAGAAACCAATATTGACGTGACTTCT GAACCAGTTACTGATTTATTAATTTATTATTATGTCATGTTTCTGTATTCAACTATCTATCAAG ATGAACAGCATTATAAAAACATCTACCTGTTCTATGAAAGATCAATCCATGTCTGCAAATGTAT GAACATGCTGTTTCATATTCATTTTCTTCTCATTGGACTTGATATGACTGCAGGATTGAATTTT CCGACCCAGTTGCAGTCAGACATGCATTGTCAATAATATCTGAAATTGCTGCGAAAGATCCATA CTCTGTCGCAATGGCATTGGGTCAGTTTACTGTTTACTCACATACTGCTAACAATTGCTCACGT TGTCTATTTTATTTTGACATGCATAAAGAACATATGCCATTATGGTTTAGAATATTGTTGATCT TCCATGCACTGAAAATAGTAAATACTAACAAGCCAAATGTAACATTAGACTTCAGTTGCGATCC TGATTTTTTTTCATATTTAGTCAATTTGCGATGAGTCTTGTTTCATGCCATTTATGTGGTTTAT AATCTCATGTATGGCTTCGTTTTATGCAGGCAAAAGTGCACAACCCGGTGGTATGCTTCCTTTT TCTTCAGCATCTTTTGTTAGTCTTCTTTAATCATTTGAATACAAACATGTTCCAAAGTGATTTC AGCTAATAGTTTATAACTTTCTATTGCCCATGATAAATGTTTCAAACAATACAGTTATCAGTAA AAAGCAAGTAAAGCGAGGTTATTAAATAGCTAGCTTTAGATTGGCTATTTTTAGCTATATTTTG ACGCCTCGACACTATGCCACTTGTTTGCTACAAACTCTATTTAAAATGCTGGGCAAAACAATTC TAGTTTTCATTTGATTTGAGTTACAAGAATCAAGATTTTTGTGCAAAATACAGATATACCAATG AATTTGGTATTGTGGAGAAGTGAATATCTTAATTGCTCTTTGTAAAGAAAAAGCTAGACCAACC TAGGAGGAACTAGGCGGCTGTATATTGTAAGGCCAGTCTCAGTGGGGGTTTCATGTCCCTGTTT TTAAGACTCACAAGTCACAAGTGTTGGAAACAGTGCAAACAATGAAACTTTTATCATCTTTCTC TCTTCATTTATGCTATGCCACCATTGCCATGTCATCTTATTCAATGCCCATGAAATTCTCACGA AAGTCCCATTGAGCCTGGCCTAAGAAGAAAACAAACAGCCAGATGAGGACTCGGACTTATGTGG TTTAGGCATATATCTACATCCTCAATCAATGGAGCTAGGCTCAGTTCATACTGCCCTTCATAAC TATCCCTTTAAATATGTTTACTCATTGTCATTGGCCTACCCGATTATAAGTAACATGCAGGGGA CAATATATCTTCTTGTCAGTGTCTCAAGTATTACATCATCATTAACAACAACAACAAAACCTTT TAGTCCCAAGCAAGTCAGGGTAGTCTAGTGTTTCAAGTATTACATGCTCTAAATAATATCAGGA AAATATCGTATAACTTTGTGTAATATCTGGTTACAGTGGCCAATTCTACTACCAATTTCTCCCA GCTCTATCTAAAAGCCATTACTTCTTAGATTGTATATAATTGATTCCTTCCTCTTTTGTCAAAT CCAGTTATGTTAAAATTTCTTATTTTCACTTCGATGTACTTATTTGTGTACAATATCATATATC ATTGTTCCAAACTGAAACAGGAGCTCTTCAGGACATTCTTCATTTGCATGATGTCCTTGCCAGG GTTTACCTTGCAAAGTTGTGTCATTCGATATCTAGAGCACGTGTATTGGACCGTAAGTGAATTG TTTTGTGCATAACCTGAATTTATGTGTGATTTGTGATGCAAATCAGGGTGCATGCATCAAATCG CGGTTCTAATCATATACAATTTATGCAGAGAGGCCTGACATAAAGTCACAGTACAGTTCCCTCC TTTATCAACTTCTTCTGGATCCCAGTGACAGGGTCTGCTTTGAGGCCATAAATTGTGTGTTGGG AAAAGTCGACAACACAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.11755289

Conservation Information
Conserved circRNAs	NA
PMCS	0.11755289

			
						 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 Zm00001d028546_circ_g.1

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