Plant Circular RNA Database

Detail information of Zm00001d047536_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d047536_circ_g.1
					
						ID in PlantcircBase
						zma_circ_003015
					
						Alias
						circ1899
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 134141759-134143661  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d047536						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d047536_circ_g.2 Zm00001d047536_circ_g.3 						
					
						Support reads
						5
					
						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
						Zm00001d047536_T032:7
Zm00001d047536_T048:6
Zm00001d047536_T022:6
Zm00001d047536_T004:6
Zm00001d047536_T010:6
Zm00001d047536_T006:6
Zm00001d047536_T008:7
Zm00001d047536_T025:6
Zm00001d047536_T039:6
Zm00001d047536_T037:6
Zm00001d047536_T057:3
Zm00001d047536_T052:7
Zm00001d047536_T001:6
Zm00001d047536_T042:6
Zm00001d047536_T035:6
Zm00001d047536_T051:6
Zm00001d047536_T045:7
Zm00001d047536_T041:6
Zm00001d047536_T017:6
Zm00001d047536_T005:6
Zm00001d047536_T029:7
Zm00001d047536_T046:6
Zm00001d047536_T027:7
Zm00001d047536_T020:6
Zm00001d047536_T016:4
Zm00001d047536_T053:6
Zm00001d047536_T023:6
Zm00001d047536_T007:6
Zm00001d047536_T058:2
Zm00001d047536_T031:6
Zm00001d047536_T050:6
Zm00001d047536_T009:7
Zm00001d047536_T003:6

General Information
CircRNA Name	Zm00001d047536_circ_g.1
ID in PlantcircBase	zma_circ_003015
Alias	circ1899
Organism	Zea mays
Position	chr9: 134141759-134143661 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d047536
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d047536_circ_g.2 Zm00001d047536_circ_g.3
Support reads	5
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	Zm00001d047536_T032:7 Zm00001d047536_T048:6 Zm00001d047536_T022:6 Zm00001d047536_T004:6 Zm00001d047536_T010:6 Zm00001d047536_T006:6 Zm00001d047536_T008:7 Zm00001d047536_T025:6 Zm00001d047536_T039:6 Zm00001d047536_T037:6 Zm00001d047536_T057:3 Zm00001d047536_T052:7 Zm00001d047536_T001:6 Zm00001d047536_T042:6 Zm00001d047536_T035:6 Zm00001d047536_T051:6 Zm00001d047536_T045:7 Zm00001d047536_T041:6 Zm00001d047536_T017:6 Zm00001d047536_T005:6 Zm00001d047536_T029:7 Zm00001d047536_T046:6 Zm00001d047536_T027:7 Zm00001d047536_T020:6 Zm00001d047536_T016:4 Zm00001d047536_T053:6 Zm00001d047536_T023:6 Zm00001d047536_T007:6 Zm00001d047536_T058:2 Zm00001d047536_T031:6 Zm00001d047536_T050:6 Zm00001d047536_T009:7 Zm00001d047536_T003:6

			
						 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  
						
							TCTTGGTCGTATTGAACCGAGCAGTTGGATCCAATTTATCGGCAAGAGAAATATCTGATTTATC
TGCTTTTGTTCAGCGATTTGGAACATCAGAGTTTTGggtatgaagcaattgcttgcagtaaggg
aaaaacagaactgatagcttctggtccttttgaccagttagttctgcacctggaagatgccaaa
acattcca

									
								

					

						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
						
							GGTATGAAGCAATTGCTTGCAGTAAGGGAAAAACAGAACTGATAGCTTCTGGTCCTTTTGACCA
GTTAGTTCTGCACCTGGAAGATGCCAAAACATTCCAATCTTGTTCATCAAGTGGTACTTTTAAA
CTGTTATTGGCTGGGGATGGAAAAGACTCTTCCTGGTTTACCAAATCCACCTTGCAGAGGTACT
TGCAGCCATCCTATTTGCTTATGGTTATGTCAGCTGTAATGACTAAATTGAACTACTACACCAG
ATTTTTGCATATCATAAGTTCATTTGATACATCAAAATCGGTCAATGGAGTTTTAGACGAGATG
TCACAGCTGGAGGAAACAAGAAAGTTTCATCAATCACTTTATGTTAAGGTATCACTTGTTTGCG
TAAATAAAAGTTTCAGCTAAGTTCACTTTTAACACTTCACCGCACATGCCATTAATAATAGAGA
CACATTTGTTTCGCAGGAGCAACAGAATGTTATTAGTGGCGCTTTAACAGGTACTTTCATATAA
GCATCTGGTTCTTCCATTGTTGTTTGTTATTTGAAGACCTTCAAAGTTGTATATAATGGATATG
CATGCATTATATACTTTCCTGCCTGGCTGCCTTGTTATTGTAGTCCCTGTGATCCACTTCAGCT
GCTTTAGGGTTATTTTACCATCTGTGTGTAATGTAGGTTGTGGGATCCAACTTTCATCTGTAAT
GTAATCATGCTCTTAGTTGACCTTTCGGTGAATCACATCGCTTTCTGGTTGATAATCTATTATA
GACAATCAGTCCCACAAATATTGTACCCTTGATTTACTTGCTTATTATTATTGAAGAAATAGTT
GTCAGCTGTATCTTCTGAGAATAACCCTTCCTTCCAACAGATGCTTGGACTTTAGTTGATAACC
TGTAATTTCAATGTACTCATCTACGTTTCCATGGGTCTAACTCGTGCTTTTCTCATGTATTTTT
TACTGGCAAAACTCATTATGCTCTAAAGGTAGCACTGTTGAAGTTTAACTACATTTTCTTTGAG
AACATATCTGGTGCATATGATGCATATATTAAATCATCATCATACATCTCAGATCTAACGTCTC
TAGTTGCCTGTTATATTTTACAAATAACACCTTCCACCACTCCACTCCACCACTTCAGATGGTG
TTCTTTGCAAAATATACTGAGCAACTAGAAATGTTAGATTTAAGATGGATGCTGATGATTTAGT
ATATGCACCATGTGCACCAAGCTCTCATGTGCATCACGTATGTTCTCATTTTCTTTTCACCAAA
CATTGTATCAAGGCTCCGCTTGAACTTCCATACTTCACAAATTTGTGTATATATGCAAATGCAC
ATAAAAACCATGAAATATGTAGACACAACTGCTAGTGCTTATGTGGTAGTTATTCCTGTTAATA
TCCAAACATGAAAGTCTGTTCATATTCCATGTGATATTAACATTCCTGAAACTCTTTCGACCTT
ATAATGGTAGACATTAGTTTAATATGACGTTCTGTTTCTTCAGGAGGTTTATTTGGTACTGGTG
CCATAGCACAGCAGGTAATTTCTAGTGCTGCAAGGATTTAATATTACATGGTTTTACTCTTTCA
TGATTCACCTACTTAATTTTTAAACACCACTTTTAGGGAAATGATGGGCCAAATTCATCGGATA
CGACAAAGTAAAATTCCTTTCCTTTTCTCTGCTACTTTACTTTGCTACCTCATTTGGTTGACAT
TTGCGATGGTTAAATATGCTAGGAATGAATTGCTTCGAGCACTGGATTTGAGATTAACTGCACT
GAAGGAAGAGATCTTGGTCGTATTGAACCGAGCAGTTGGATCCAATTTATCGGCAAGAGAAATA
TCTGATTTATCTGCTTTTGTTCAGCGATTTGGAACATCAGAGTTTTG
						
					

			
		

Sequences
Splice junction sequence	TCTTGGTCGTATTGAACCGAGCAGTTGGATCCAATTTATCGGCAAGAGAAATATCTGATTTATC TGCTTTTGTTCAGCGATTTGGAACATCAGAGTTTTGggtatgaagcaattgcttgcagtaaggg aaaaacagaactgatagcttctggtccttttgaccagttagttctgcacctggaagatgccaaa acattcca
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	GGTATGAAGCAATTGCTTGCAGTAAGGGAAAAACAGAACTGATAGCTTCTGGTCCTTTTGACCA GTTAGTTCTGCACCTGGAAGATGCCAAAACATTCCAATCTTGTTCATCAAGTGGTACTTTTAAA CTGTTATTGGCTGGGGATGGAAAAGACTCTTCCTGGTTTACCAAATCCACCTTGCAGAGGTACT TGCAGCCATCCTATTTGCTTATGGTTATGTCAGCTGTAATGACTAAATTGAACTACTACACCAG ATTTTTGCATATCATAAGTTCATTTGATACATCAAAATCGGTCAATGGAGTTTTAGACGAGATG TCACAGCTGGAGGAAACAAGAAAGTTTCATCAATCACTTTATGTTAAGGTATCACTTGTTTGCG TAAATAAAAGTTTCAGCTAAGTTCACTTTTAACACTTCACCGCACATGCCATTAATAATAGAGA CACATTTGTTTCGCAGGAGCAACAGAATGTTATTAGTGGCGCTTTAACAGGTACTTTCATATAA GCATCTGGTTCTTCCATTGTTGTTTGTTATTTGAAGACCTTCAAAGTTGTATATAATGGATATG CATGCATTATATACTTTCCTGCCTGGCTGCCTTGTTATTGTAGTCCCTGTGATCCACTTCAGCT GCTTTAGGGTTATTTTACCATCTGTGTGTAATGTAGGTTGTGGGATCCAACTTTCATCTGTAAT GTAATCATGCTCTTAGTTGACCTTTCGGTGAATCACATCGCTTTCTGGTTGATAATCTATTATA GACAATCAGTCCCACAAATATTGTACCCTTGATTTACTTGCTTATTATTATTGAAGAAATAGTT GTCAGCTGTATCTTCTGAGAATAACCCTTCCTTCCAACAGATGCTTGGACTTTAGTTGATAACC TGTAATTTCAATGTACTCATCTACGTTTCCATGGGTCTAACTCGTGCTTTTCTCATGTATTTTT TACTGGCAAAACTCATTATGCTCTAAAGGTAGCACTGTTGAAGTTTAACTACATTTTCTTTGAG AACATATCTGGTGCATATGATGCATATATTAAATCATCATCATACATCTCAGATCTAACGTCTC TAGTTGCCTGTTATATTTTACAAATAACACCTTCCACCACTCCACTCCACCACTTCAGATGGTG TTCTTTGCAAAATATACTGAGCAACTAGAAATGTTAGATTTAAGATGGATGCTGATGATTTAGT ATATGCACCATGTGCACCAAGCTCTCATGTGCATCACGTATGTTCTCATTTTCTTTTCACCAAA CATTGTATCAAGGCTCCGCTTGAACTTCCATACTTCACAAATTTGTGTATATATGCAAATGCAC ATAAAAACCATGAAATATGTAGACACAACTGCTAGTGCTTATGTGGTAGTTATTCCTGTTAATA TCCAAACATGAAAGTCTGTTCATATTCCATGTGATATTAACATTCCTGAAACTCTTTCGACCTT ATAATGGTAGACATTAGTTTAATATGACGTTCTGTTTCTTCAGGAGGTTTATTTGGTACTGGTG CCATAGCACAGCAGGTAATTTCTAGTGCTGCAAGGATTTAATATTACATGGTTTTACTCTTTCA TGATTCACCTACTTAATTTTTAAACACCACTTTTAGGGAAATGATGGGCCAAATTCATCGGATA CGACAAAGTAAAATTCCTTTCCTTTTCTCTGCTACTTTACTTTGCTACCTCATTTGGTTGACAT TTGCGATGGTTAAATATGCTAGGAATGAATTGCTTCGAGCACTGGATTTGAGATTAACTGCACT GAAGGAAGAGATCTTGGTCGTATTGAACCGAGCAGTTGGATCCAATTTATCGGCAAGAGAAATA TCTGATTTATCTGCTTTTGTTCAGCGATTTGGAACATCAGAGTTTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.168628065

Conservation Information
Conserved circRNAs	NA
PMCS	0.168628065

			
						 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 Zm00001d047536_circ_g.1

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