Plant Circular RNA Database

Detail information of Zm00001d046579_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d046579_circ_g.3
					
						ID in PlantcircBase
						zma_circ_002979
					
						Alias
						circ1879
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 96781625-96787549  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d046579						
					
						Parent gene annotation
						
							Transcription initiation factor TFIID subunit 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d046579_circ_g.1 Zm00001d046579_circ_g.2 Zm00001d046579_circ_g.4 Zm00001d046579_circ_g.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.7 Zm00001d046579_circ_g.8 Zm00001d046579_circ_g.9 Zm00001d046579_circ_g.10 Zm00001d046579_circ_g.11 Zm00001d046579_circ_g.12 Zm00001d046579_circ_g.13 Zm00001d046579_circ_g.14 						
					
						Support reads
						8
					
						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
						Zm00001d046579_T011:7
Zm00001d046579_T006:7
Zm00001d046579_T008:6
Zm00001d046579_T001:7
Zm00001d046579_T029:1
Zm00001d046579_T015:7
Zm00001d046579_T007:7
Zm00001d046579_T023:7
Zm00001d046579_T016:7
Zm00001d046579_T020:7
Zm00001d046579_T004:7
Zm00001d046579_T005:7
Zm00001d046579_T024:7
Zm00001d046579_T019:7
Zm00001d046579_T003:7
Zm00001d046579_T009:7
Zm00001d046579_T026:3
Zm00001d046579_T018:7
Zm00001d046579_T027:1
Zm00001d046579_T025:6
Zm00001d046579_T002:6

General Information
CircRNA Name	Zm00001d046579_circ_g.3
ID in PlantcircBase	zma_circ_002979
Alias	circ1879
Organism	Zea mays
Position	chr9: 96781625-96787549 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d046579
Parent gene annotation	Transcription initiation factor TFIID subunit 1
Parent gene strand	+
Alternative splicing	Zm00001d046579_circ_g.1 Zm00001d046579_circ_g.2 Zm00001d046579_circ_g.4 Zm00001d046579_circ_g.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.7 Zm00001d046579_circ_g.8 Zm00001d046579_circ_g.9 Zm00001d046579_circ_g.10 Zm00001d046579_circ_g.11 Zm00001d046579_circ_g.12 Zm00001d046579_circ_g.13 Zm00001d046579_circ_g.14
Support reads	8
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	Zm00001d046579_T011:7 Zm00001d046579_T006:7 Zm00001d046579_T008:6 Zm00001d046579_T001:7 Zm00001d046579_T029:1 Zm00001d046579_T015:7 Zm00001d046579_T007:7 Zm00001d046579_T023:7 Zm00001d046579_T016:7 Zm00001d046579_T020:7 Zm00001d046579_T004:7 Zm00001d046579_T005:7 Zm00001d046579_T024:7 Zm00001d046579_T019:7 Zm00001d046579_T003:7 Zm00001d046579_T009:7 Zm00001d046579_T026:3 Zm00001d046579_T018:7 Zm00001d046579_T027:1 Zm00001d046579_T025:6 Zm00001d046579_T002:6

			
						 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: GGTTCAACATCTCCAATGACAAGT
 R: TCAGCATCTAAATCACCAGAATCAT
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: GGTTCAACATCTCCAATGACAAGT R: TCAGCATCTAAATCACCAGAATCAT 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  
						
							AAGCTAAATCTCATACTAAAAAACGCGCTTTAATGGGCATAAAGGTGGTGCATTCTGCTCCAGC
TCATAAGCTGCAAACCATGAAGCCAGTGTTGAGCAAgatgacgatgacgacgaggattatgagg
agcctggtggaggaaatcacttattggggtttatgttcggcaatgtagatgattctggtgattt
agatgctg

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAGCTAAATCTCATACTAAAAAACGCGCTTTAATGGGCATAAAGGTGGTGCATTCTGCTCCAGC TCATAAGCTGCAAACCATGAAGCCAGTGTTGAGCAAgatgacgatgacgacgaggattatgagg agcctggtggaggaaatcacttattggggtttatgttcggcaatgtagatgattctggtgattt agatgctg
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.006427567

Conservation Information
Conserved circRNAs	NA
PMCS	0.006427567

			
						 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 Zm00001d046579_circ_g.3

Address

Any questions?

Supported by