Plant Circular RNA Database

Detail information of Zm00001d005100_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d005100_circ_g.3
					

						ID in PlantcircBase
						zma_circ_001128
					

						Alias
						circ478
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 158155080-158156195  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI
					

						Parent gene
						
							Zm00001d005100						
					

						Parent gene annotation
						
							RNA binding (RRM/RBD/RNP motifs) family protein
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d005100_circ_g.1 Zm00001d005100_circ_g.2 						
					

						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
						Zm00001d005100_T044:2
Zm00001d005100_T024:4
Zm00001d005100_T112:4
Zm00001d005100_T078:4
Zm00001d005100_T060:3
Zm00001d005100_T075:4
Zm00001d005100_T026:4
Zm00001d005100_T072:4
Zm00001d005100_T113:4
Zm00001d005100_T087:4
Zm00001d005100_T016:4
Zm00001d005100_T110:4
Zm00001d005100_T043:4
Zm00001d005100_T101:4
Zm00001d005100_T040:4
Zm00001d005100_T109:4
Zm00001d005100_T052:4
Zm00001d005100_T086:4
Zm00001d005100_T082:4
Zm00001d005100_T063:3
Zm00001d005100_T034:4
Zm00001d005100_T015:3
Zm00001d005100_T002:4
Zm00001d005100_T010:4
Zm00001d005100_T037:4
Zm00001d005100_T091:4
Zm00001d005100_T092:4
Zm00001d005100_T048:3
Zm00001d005100_T020:4
Zm00001d005100_T107:4
Zm00001d005100_T050:4
Zm00001d005100_T009:4
Zm00001d005100_T004:2
Zm00001d005100_T007:4
Zm00001d005100_T084:4
Zm00001d005100_T041:4
Zm00001d005100_T027:4
Zm00001d005100_T069:4
Zm00001d005100_T108:4
Zm00001d005100_T032:3
Zm00001d005100_T106:4
Zm00001d005100_T066:4
Zm00001d005100_T090:4
Zm00001d005100_T018:4
Zm00001d005100_T001:4
Zm00001d005100_T054:4
Zm00001d005100_T038:4
Zm00001d005100_T076:4
Zm00001d005100_T030:3
Zm00001d005100_T056:4
Zm00001d005100_T003:4
Zm00001d005100_T077:4
Zm00001d005100_T096:2
Zm00001d005100_T065:4
Zm00001d005100_T046:4
Zm00001d005100_T068:4
Zm00001d005100_T039:3
Zm00001d005100_T111:4

					

			
		

General Information
CircRNA Name	Zm00001d005100_circ_g.3
ID in PlantcircBase	zma_circ_001128
Alias	circ478
Organism	Zea mays
Position	chr2: 158155080-158156195 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI
Parent gene	Zm00001d005100
Parent gene annotation	RNA binding (RRM/RBD/RNP motifs) family protein
Parent gene strand	-
Alternative splicing	Zm00001d005100_circ_g.1 Zm00001d005100_circ_g.2
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	Zm00001d005100_T044:2 Zm00001d005100_T024:4 Zm00001d005100_T112:4 Zm00001d005100_T078:4 Zm00001d005100_T060:3 Zm00001d005100_T075:4 Zm00001d005100_T026:4 Zm00001d005100_T072:4 Zm00001d005100_T113:4 Zm00001d005100_T087:4 Zm00001d005100_T016:4 Zm00001d005100_T110:4 Zm00001d005100_T043:4 Zm00001d005100_T101:4 Zm00001d005100_T040:4 Zm00001d005100_T109:4 Zm00001d005100_T052:4 Zm00001d005100_T086:4 Zm00001d005100_T082:4 Zm00001d005100_T063:3 Zm00001d005100_T034:4 Zm00001d005100_T015:3 Zm00001d005100_T002:4 Zm00001d005100_T010:4 Zm00001d005100_T037:4 Zm00001d005100_T091:4 Zm00001d005100_T092:4 Zm00001d005100_T048:3 Zm00001d005100_T020:4 Zm00001d005100_T107:4 Zm00001d005100_T050:4 Zm00001d005100_T009:4 Zm00001d005100_T004:2 Zm00001d005100_T007:4 Zm00001d005100_T084:4 Zm00001d005100_T041:4 Zm00001d005100_T027:4 Zm00001d005100_T069:4 Zm00001d005100_T108:4 Zm00001d005100_T032:3 Zm00001d005100_T106:4 Zm00001d005100_T066:4 Zm00001d005100_T090:4 Zm00001d005100_T018:4 Zm00001d005100_T001:4 Zm00001d005100_T054:4 Zm00001d005100_T038:4 Zm00001d005100_T076:4 Zm00001d005100_T030:3 Zm00001d005100_T056:4 Zm00001d005100_T003:4 Zm00001d005100_T077:4 Zm00001d005100_T096:2 Zm00001d005100_T065:4 Zm00001d005100_T046:4 Zm00001d005100_T068:4 Zm00001d005100_T039:3 Zm00001d005100_T111:4

			
						 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  
						
							ATCATAGCCGCATTTGCATGGCTTGAGCTGCTGGTCAGTAGTGTCCATCTCCTCGGCACAGAGC
GGGCAGGTTCGGTCGCCATCGTCGCTCATGGTCGTCcacactaatattgctggttgctgatgcc
tgctgagagggaggcccagtcggacgggaaactgaaaccttcaaaactttcccatattgaccaa
agtactcc

						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
						
							CACACTAATATTGCTGGTTGCTGATGCCTGCTGAGAGGGAGGCCCAGTCGGACGGGAAACTGAA
ACCTTCAAAACTTTCCCATATTGACCAAAGTACTCCCTACACTCAAGCACCTAAACAAGTAATA
ACAGTAGAGTTGGTGTGAGAAGTAAAATTTAAAAACACATCCACTGTTTTCAAGTCTCCGAATA
ATCACGATTAGTCGCAATTAATCGTCCAAGTCGGTTTGGACCAATCGCGATTAGTCCCCCAAGT
TGTCTGATTAATCGTGATTAATCGCGATTAATCACCCAAGTCGGTCAGCCAGAACGACCAGCAA
GTCGCCCGACTTGAAAACAATGAACACATCACACGACTTGATCAAATCTGGATGTGAACTCACA
CTCTCGTTGCATAAATGTGCAGGTAGCCCAATTATATACACCAGATTTCTCTGGATAACCCTGA
CACTAGCCAGATGCTTCTTTGATTCTACGGTTGATGTTGCTGCTGCTGTGGGTGCTGCCTTTGG
CTTAACCTTTTGGGTCTTGTGCTTCTTCTCTACATTTTTATCTGCCACCGTCCTGCTTCCATCA
TCAGTGTAAAGTTAAATTTGAGTTACCTAGTGACAAGGCCAACTTTCGCAGATGGGTCCAGTTA
ACTGAGACAGAAATAAAGGCTGAGAAGACCTACCTGTTCCTATGATATTCCTATGATATGTAAA
AGGGTAACCAATTGCAAATGTTGTAGTATGCTGAAGTGAAACACAAATTGATTGGTAAACAGAG
AAGCATTGTGATGGACCTGTCACAAGTGGCAGCCATCTTGACGATCCTGTCCTTGTCATAGCAT
GTGCGGCATGCAGGGCAGCGGCCCACTGTTTCCTCCTTCTCAGCCATGTCTATGATGTGGTGCC
AGCACCAAACACAAATCTGCAGAGTTAAGTGACAGTTCTTGTTATATGATGAAACAAAGTGCAG
ACAAGGTGGGCTGCAATCTGATTGGTACAATAGGATAGGAGAATCAGTAGACATACATCATAGC
CGCATTTGCATGGCTTGAGCTGCTGGTCAGTAGTGTCCATCTCCTCGGCACAGAGCGGGCAGGT
TCGGTCGCCATCGTCGCTCATGGTCGTC

Sequences
Splice junction sequence	ATCATAGCCGCATTTGCATGGCTTGAGCTGCTGGTCAGTAGTGTCCATCTCCTCGGCACAGAGC GGGCAGGTTCGGTCGCCATCGTCGCTCATGGTCGTCcacactaatattgctggttgctgatgcc tgctgagagggaggcccagtcggacgggaaactgaaaccttcaaaactttcccatattgaccaa agtactcc
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	CACACTAATATTGCTGGTTGCTGATGCCTGCTGAGAGGGAGGCCCAGTCGGACGGGAAACTGAA ACCTTCAAAACTTTCCCATATTGACCAAAGTACTCCCTACACTCAAGCACCTAAACAAGTAATA ACAGTAGAGTTGGTGTGAGAAGTAAAATTTAAAAACACATCCACTGTTTTCAAGTCTCCGAATA ATCACGATTAGTCGCAATTAATCGTCCAAGTCGGTTTGGACCAATCGCGATTAGTCCCCCAAGT TGTCTGATTAATCGTGATTAATCGCGATTAATCACCCAAGTCGGTCAGCCAGAACGACCAGCAA GTCGCCCGACTTGAAAACAATGAACACATCACACGACTTGATCAAATCTGGATGTGAACTCACA CTCTCGTTGCATAAATGTGCAGGTAGCCCAATTATATACACCAGATTTCTCTGGATAACCCTGA CACTAGCCAGATGCTTCTTTGATTCTACGGTTGATGTTGCTGCTGCTGTGGGTGCTGCCTTTGG CTTAACCTTTTGGGTCTTGTGCTTCTTCTCTACATTTTTATCTGCCACCGTCCTGCTTCCATCA TCAGTGTAAAGTTAAATTTGAGTTACCTAGTGACAAGGCCAACTTTCGCAGATGGGTCCAGTTA ACTGAGACAGAAATAAAGGCTGAGAAGACCTACCTGTTCCTATGATATTCCTATGATATGTAAA AGGGTAACCAATTGCAAATGTTGTAGTATGCTGAAGTGAAACACAAATTGATTGGTAAACAGAG AAGCATTGTGATGGACCTGTCACAAGTGGCAGCCATCTTGACGATCCTGTCCTTGTCATAGCAT GTGCGGCATGCAGGGCAGCGGCCCACTGTTTCCTCCTTCTCAGCCATGTCTATGATGTGGTGCC AGCACCAAACACAAATCTGCAGAGTTAAGTGACAGTTCTTGTTATATGATGAAACAAAGTGCAG ACAAGGTGGGCTGCAATCTGATTGGTACAATAGGATAGGAGAATCAGTAGACATACATCATAGC CGCATTTGCATGGCTTGAGCTGCTGGTCAGTAGTGTCCATCTCCTCGGCACAGAGCGGGCAGGT TCGGTCGCCATCGTCGCTCATGGTCGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.033390278

Conservation Information
Conserved circRNAs	NA
PMCS	0.033390278

			
						 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 Zm00001d005100_circ_g.3

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