Plant Circular RNA Database

Detail information of Zm00001d040123_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d040123_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007529
					
						Alias
						zma_circ_0001424
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 28451251-28451519  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d040123						
					
						Parent gene annotation
						
							Paired amphipathic helix protein Sin3-like 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d040123_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						Exon boundary  
						
							Yes-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-AC							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
						Zm00001d040123_T008:1
Zm00001d040123_T001:1
Zm00001d040123_T037:1
Zm00001d040123_T011:1
Zm00001d040123_T004:1
Zm00001d040123_T044:1
Zm00001d040123_T020:1
Zm00001d040123_T002:1
Zm00001d040123_T016:1
Zm00001d040123_T029:1
Zm00001d040123_T050:1
Zm00001d040123_T048:1
Zm00001d040123_T034:1
Zm00001d040123_T019:1
Zm00001d040123_T039:1
Zm00001d040123_T022:1
Zm00001d040123_T046:1
Zm00001d040123_T042:1
Zm00001d040123_T015:1
Zm00001d040123_T010:1
Zm00001d040123_T027:1
Zm00001d040123_T028:1
Zm00001d040123_T031:1
Zm00001d040123_T007:1
Zm00001d040123_T041:1
Zm00001d040123_T030:1
Zm00001d040123_T017:1
Zm00001d040123_T021:1
Zm00001d040123_T032:1
Zm00001d040123_T038:1
Zm00001d040123_T005:1
Zm00001d040123_T036:1
Zm00001d040123_T014:1
Zm00001d040123_T023:1
Zm00001d040123_T045:1
Zm00001d040123_T047:1
Zm00001d040123_T013:1
Zm00001d040123_T025:1

General Information
CircRNA Name	Zm00001d040123_circ_g.3
ID in PlantcircBase	zma_circ_007529
Alias	zma_circ_0001424
Organism	Zea mays
Position	chr3: 28451251-28451519 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d040123
Parent gene annotation	Paired amphipathic helix protein Sin3-like 3
Parent gene strand	-
Alternative splicing	Zm00001d040123_circ_g.2
Support reads	NA
Tissues	leaf, root
Exon boundary	Yes-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-AC 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	Zm00001d040123_T008:1 Zm00001d040123_T001:1 Zm00001d040123_T037:1 Zm00001d040123_T011:1 Zm00001d040123_T004:1 Zm00001d040123_T044:1 Zm00001d040123_T020:1 Zm00001d040123_T002:1 Zm00001d040123_T016:1 Zm00001d040123_T029:1 Zm00001d040123_T050:1 Zm00001d040123_T048:1 Zm00001d040123_T034:1 Zm00001d040123_T019:1 Zm00001d040123_T039:1 Zm00001d040123_T022:1 Zm00001d040123_T046:1 Zm00001d040123_T042:1 Zm00001d040123_T015:1 Zm00001d040123_T010:1 Zm00001d040123_T027:1 Zm00001d040123_T028:1 Zm00001d040123_T031:1 Zm00001d040123_T007:1 Zm00001d040123_T041:1 Zm00001d040123_T030:1 Zm00001d040123_T017:1 Zm00001d040123_T021:1 Zm00001d040123_T032:1 Zm00001d040123_T038:1 Zm00001d040123_T005:1 Zm00001d040123_T036:1 Zm00001d040123_T014:1 Zm00001d040123_T023:1 Zm00001d040123_T045:1 Zm00001d040123_T047:1 Zm00001d040123_T013:1 Zm00001d040123_T025:1

			
						 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  
						
							TCCTTTTCTCTTTCCTTTTCCCGATCTCTATCCTTGTCCTCCCTGTCCCGATCTCTATCCTTTT
CTTTATCCTCAGTTTTAACAGCCCTCGTGCTTGGCCatttttaggtagaagccggtaactcgga
gtgcagcgttgacagtttgagagatcaagctctgatattggtttggataggttgtacttctctt
tgccagag

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 269
Transcript exons: 28451251-28451519
ATTTTTAGGTAGAAGCCGGTAACTCGGAGTGCAGCGTTGACAGTTTGAGAGATCAAGCTCTGAT
ATTGGTTTGGATAGGTTGTACTTCTCTTTGCCAGAGAACATAGAAGGTTTGTGACTAGAACCTT
CCTTTGAATTGAATGTTGATCCTTTATCGAGCCTTTCTCGTTCCTTTTCTCTTTCCTTTTCCCG
ATCTCTATCCTTGTCCTCCCTGTCCCGATCTCTATCCTTTTCTTTATCCTCAGTTTTAACAGCC
CTCGTGCTTGGCC
						
						Genomic sequence
						
							ATTTTTAGGTAGAAGCCGGTAACTCGGAGTGCAGCGTTGACAGTTTGAGAGATCAAGCTCTGAT
ATTGGTTTGGATAGGTTGTACTTCTCTTTGCCAGAGAACATAGAAGGTTTGTGACTAGAACCTT
CCTTTGAATTGAATGTTGATCCTTTATCGAGCCTTTCTCGTTCCTTTTCTCTTTCCTTTTCCCG
ATCTCTATCCTTGTCCTCCCTGTCCCGATCTCTATCCTTTTCTTTATCCTCAGTTTTAACAGCC
CTCGTGCTTGGCC

Sequences
Splice junction sequence	TCCTTTTCTCTTTCCTTTTCCCGATCTCTATCCTTGTCCTCCCTGTCCCGATCTCTATCCTTTT CTTTATCCTCAGTTTTAACAGCCCTCGTGCTTGGCCatttttaggtagaagccggtaactcgga gtgcagcgttgacagtttgagagatcaagctctgatattggtttggataggttgtacttctctt tgccagag
Assembled circRNA sequence	Yes 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	Transcript length: 269 Transcript exons: 28451251-28451519 ATTTTTAGGTAGAAGCCGGTAACTCGGAGTGCAGCGTTGACAGTTTGAGAGATCAAGCTCTGAT ATTGGTTTGGATAGGTTGTACTTCTCTTTGCCAGAGAACATAGAAGGTTTGTGACTAGAACCTT CCTTTGAATTGAATGTTGATCCTTTATCGAGCCTTTCTCGTTCCTTTTCTCTTTCCTTTTCCCG ATCTCTATCCTTGTCCTCCCTGTCCCGATCTCTATCCTTTTCTTTATCCTCAGTTTTAACAGCC CTCGTGCTTGGCC
Genomic sequence	ATTTTTAGGTAGAAGCCGGTAACTCGGAGTGCAGCGTTGACAGTTTGAGAGATCAAGCTCTGAT ATTGGTTTGGATAGGTTGTACTTCTCTTTGCCAGAGAACATAGAAGGTTTGTGACTAGAACCTT CCTTTGAATTGAATGTTGATCCTTTATCGAGCCTTTCTCGTTCCTTTTCTCTTTCCTTTTCCCG ATCTCTATCCTTGTCCTCCCTGTCCCGATCTCTATCCTTTTCTTTATCCTCAGTTTTAACAGCC CTCGTGCTTGGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.272136467

Conservation Information
Conserved circRNAs	NA
PMCS	0.272136467

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28451357-28451500(-)
						
						Potential amino acid sequence
						
							MFSGKEKYNLSKPISELDLSNCQRCTPSYRLLPKNGQARGLLKLRIKKRIEIGTGRTRIEIGKR
KEKRNEKGSIKDQHSIQRKVLVTNLLCSLAKRSTTYPNQYQSLISQTVNAALRVTGFYLKMAKH
EGC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28451357-28451500(-)
Potential amino acid sequence	MFSGKEKYNLSKPISELDLSNCQRCTPSYRLLPKNGQARGLLKLRIKKRIEIGTGRTRIEIGKR KEKRNEKGSIKDQHSIQRKVLVTNLLCSLAKRSTTYPNQYQSLISQTVNAALRVTGFYLKMAKH EGC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d040123_circ_g.3

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