Plant Circular RNA Database

Detail information of Zm00001d049379_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d049379_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007998
					
						Alias
						zma_circ_0001768
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 28378456-28385222  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d049379						
					
						Parent gene annotation
						
							tetratricopeptide repeat (TPR)-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d049379_circ_g.3 						
					
						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  
						
							GT-AG							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
						Zm00001d049379_T010:3
Zm00001d049379_T019:3
Zm00001d049379_T015:3
Zm00001d049379_T009:3
Zm00001d049379_T011:3
Zm00001d049379_T007:3
Zm00001d049379_T012:3
Zm00001d049379_T008:3
Zm00001d049379_T006:3
Zm00001d049379_T014:3
Zm00001d049379_T016:3
Zm00001d049379_T020:3
Zm00001d049379_T003:3
Zm00001d049379_T005:3
Zm00001d049379_T017:3
Zm00001d049379_T013:3

General Information
CircRNA Name	Zm00001d049379_circ_g.2
ID in PlantcircBase	zma_circ_007998
Alias	zma_circ_0001768
Organism	Zea mays
Position	chr4: 28378456-28385222 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d049379
Parent gene annotation	tetratricopeptide repeat (TPR)-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d049379_circ_g.3
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	GT-AG 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	Zm00001d049379_T010:3 Zm00001d049379_T019:3 Zm00001d049379_T015:3 Zm00001d049379_T009:3 Zm00001d049379_T011:3 Zm00001d049379_T007:3 Zm00001d049379_T012:3 Zm00001d049379_T008:3 Zm00001d049379_T006:3 Zm00001d049379_T014:3 Zm00001d049379_T016:3 Zm00001d049379_T020:3 Zm00001d049379_T003:3 Zm00001d049379_T005:3 Zm00001d049379_T017:3 Zm00001d049379_T013:3

			
						 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  
						
							TGCAAAACTTTATTACAATAAAGGAAATTTGGAAGATTTTGTGGACACAATTTTTCATCCTATT
CTAGAAACTTTGAATGTTGAATATGCTAATCGAAAGggtggtttatgctttgatcacaaagaaa
tgggtagttggtatgtcaaagctgctcagtgctacatgatcttaggggacaaaaaaaatgctat
tccttatt

						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: 393
Transcript exons: 28378456-28378564,28384797-28384910,28385053-28385222
GGTGGTTTATGCTTTGATCACAAAGAAATGGGTAGTTGGTATGTCAAAGCTGCTCAGTGCTACA
TGATCTTAGGGGACAAAAAAAATGCTATTCCTTATTTTTATAAAGCGTTACAAAGCATGAAGGA
CAATATTGGTATACGATTGACCTTATCCTCCCTTCTTATTGATGACGACAAGACAGATGAAGCT
GCCACTTTGCTTTCTCCTCCCAAAATTCCAGAGTTGCAGTCTGCTAATACTCCAGACCAACAGA
AACCTTGGTGGTGTGATGGGAAAGTTAAGATGGCGCTTGCAAAACTTTATTACAATAAAGGAAA
TTTGGAAGATTTTGTGGACACAATTTTTCATCCTATTCTAGAAACTTTGAATGTTGAATATGCT
AATCGAAAG
						
						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	TGCAAAACTTTATTACAATAAAGGAAATTTGGAAGATTTTGTGGACACAATTTTTCATCCTATT CTAGAAACTTTGAATGTTGAATATGCTAATCGAAAGggtggtttatgctttgatcacaaagaaa tgggtagttggtatgtcaaagctgctcagtgctacatgatcttaggggacaaaaaaaatgctat tccttatt
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: 393 Transcript exons: 28378456-28378564,28384797-28384910,28385053-28385222 GGTGGTTTATGCTTTGATCACAAAGAAATGGGTAGTTGGTATGTCAAAGCTGCTCAGTGCTACA TGATCTTAGGGGACAAAAAAAATGCTATTCCTTATTTTTATAAAGCGTTACAAAGCATGAAGGA CAATATTGGTATACGATTGACCTTATCCTCCCTTCTTATTGATGACGACAAGACAGATGAAGCT GCCACTTTGCTTTCTCCTCCCAAAATTCCAGAGTTGCAGTCTGCTAATACTCCAGACCAACAGA AACCTTGGTGGTGTGATGGGAAAGTTAAGATGGCGCTTGCAAAACTTTATTACAATAAAGGAAA TTTGGAAGATTTTGTGGACACAATTTTTCATCCTATTCTAGAAACTTTGAATGTTGAATATGCT AATCGAAAG
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
						0.139313612

Conservation Information
Conserved circRNAs	NA
PMCS	0.139313612

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28378484-28385219(+)
28385201-28378519(+)
						
						Potential amino acid sequence
						
							MGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEAATLLSPPKI
PELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYANRKGGLCFD
HKEMGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEAATLLSP
PKIPELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYANRKGGL
CFDHKEMGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEAATL
LSPPKIPELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYANRK
GGLCFDHKEMGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEA
ATLLSPPKIPELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYA
NRK(+)
MLNMLIERVVYALITKKWVVGMSKLLSAT*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28378484-28385219(+) 28385201-28378519(+)
Potential amino acid sequence	MGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEAATLLSPPKI PELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYANRKGGLCFD HKEMGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEAATLLSP PKIPELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYANRKGGL CFDHKEMGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEAATL LSPPKIPELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYANRK GGLCFDHKEMGSWYVKAAQCYMILGDKKNAIPYFYKALQSMKDNIGIRLTLSSLLIDDDKTDEA ATLLSPPKIPELQSANTPDQQKPWWCDGKVKMALAKLYYNKGNLEDFVDTIFHPILETLNVEYA NRK(+) MLNMLIERVVYALITKKWVVGMSKLLSAT*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d049379_circ_g.2

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