Plant Circular RNA Database

Detail information of Zm00001d004702_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d004702_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007264
					
						Alias
						zma_circ_0000787, GRMZM2G082330_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 132221634-132222290  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d004702						
					
						Parent gene annotation
						
							Signal peptide peptidase-like 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d004702_circ_g.2 Zm00001d004702_circ_g.3 Zm00001d004702_circ_g.5 Zm00001d004702_circ_g.6 Zm00001d004702_circ_g.7 Zm00001d004702_circ_g.8 Zm00001d004702_circ_g.9 Zm00001d004702_circ_g.10 Zm00001d004702_circ_g.11 Zm00001d004702_circ_g.12 						
					
						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
						Zm00001d004702_T007:2
Zm00001d004702_T008:2
Zm00001d004702_T006:2
Zm00001d004702_T005:2
Zm00001d004702_T004:2
Zm00001d004702_T003:2
Zm00001d004702_T002:2
Zm00001d004702_T001:2

General Information
CircRNA Name	Zm00001d004702_circ_g.4
ID in PlantcircBase	zma_circ_007264
Alias	zma_circ_0000787, GRMZM2G082330_C1
Organism	Zea mays
Position	chr2: 132221634-132222290 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d004702
Parent gene annotation	Signal peptide peptidase-like 3
Parent gene strand	-
Alternative splicing	Zm00001d004702_circ_g.2 Zm00001d004702_circ_g.3 Zm00001d004702_circ_g.5 Zm00001d004702_circ_g.6 Zm00001d004702_circ_g.7 Zm00001d004702_circ_g.8 Zm00001d004702_circ_g.9 Zm00001d004702_circ_g.10 Zm00001d004702_circ_g.11 Zm00001d004702_circ_g.12
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	Zm00001d004702_T007:2 Zm00001d004702_T008:2 Zm00001d004702_T006:2 Zm00001d004702_T005:2 Zm00001d004702_T004:2 Zm00001d004702_T003:2 Zm00001d004702_T002:2 Zm00001d004702_T001:2

			
						 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  
						
							CACCAAAGCCTATCATATCATAACCACCCCATGGATCAAAGAAGCGGGGTATCCTTAGGAGCAT
AGGAATTGATTCCCCAGTGTTATCACCACGAGCAACcaactgcatatcccacaattagccagag
aaaatatccactcaagacaccctttctgtttgctctgtcaaatctgttcagcgtaatatcaaag
aaatgtga

						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: 211
Transcript exons: 132221634-132221704,132222151-132222290
CAACTGCATATCCCACAATTAGCCAGAGAAAATATCCACTCAAGACACCCTTTCTGTTTGCTCT
GTCAAATCTATAGCTGAATCCAACAAGCAATCCAGGGAAGATAATGTCACCAAAGCCTATCATA
TCATAACCACCCCATGGATCAAAGAAGCGGGGTATCCTTAGGAGCATAGGAATTGATTCCCCAG
TGTTATCACCACGAGCAAC
						
						Genomic sequence
						
							CAACTGCATATCCCACAATTAGCCAGAGAAAATATCCACTCAAGACACCCTTTCTGTTTGCTCT
GTCAAATCTGTTCAGCGTAATATCAAAGAAATGTGAAACAACAACAAATGCCAAAAAGATATTG
GAAAAAGTAGACATTACAAGGTTGGTGAATAATTACTACACTGAAGGCAAAACTCACTAACCCC
AAGTTACAAGCATAATGATTGTTAATTAGAGCAGTAGTCCCCACATTTACTAAAACTGGAAAAG
ACAAATCCAGATAAGGAAAGAAAATAAAGAATAGTCATCTAATAATCCTGGATGTAGTCGCTCT
ACTTCCCTTAAAATCCTAGGTGGTTTAACCGATAAACTAATTTGCTTCTTAACACCACCATTGC
ATTTAGCAGGACACGAATCAGGGTCTGGTTGTGATAGACAACCAGCGCACAACTATATTGTTCT
ATACGTGAAGCCTTAGTGGAACTAATGGATCACAAGGAAGTAAATAATGTATATGGCAAAATCA
CATACCTATAGCTGAATCCAACAAGCAATCCAGGGAAGATAATGTCACCAAAGCCTATCATATC
ATAACCACCCCATGGATCAAAGAAGCGGGGTATCCTTAGGAGCATAGGAATTGATTCCCCAGTG
TTATCACCACGAGCAAC

Sequences
Splice junction sequence	CACCAAAGCCTATCATATCATAACCACCCCATGGATCAAAGAAGCGGGGTATCCTTAGGAGCAT AGGAATTGATTCCCCAGTGTTATCACCACGAGCAACcaactgcatatcccacaattagccagag aaaatatccactcaagacaccctttctgtttgctctgtcaaatctgttcagcgtaatatcaaag aaatgtga
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: 211 Transcript exons: 132221634-132221704,132222151-132222290 CAACTGCATATCCCACAATTAGCCAGAGAAAATATCCACTCAAGACACCCTTTCTGTTTGCTCT GTCAAATCTATAGCTGAATCCAACAAGCAATCCAGGGAAGATAATGTCACCAAAGCCTATCATA TCATAACCACCCCATGGATCAAAGAAGCGGGGTATCCTTAGGAGCATAGGAATTGATTCCCCAG TGTTATCACCACGAGCAAC
Genomic sequence	CAACTGCATATCCCACAATTAGCCAGAGAAAATATCCACTCAAGACACCCTTTCTGTTTGCTCT GTCAAATCTGTTCAGCGTAATATCAAAGAAATGTGAAACAACAACAAATGCCAAAAAGATATTG GAAAAAGTAGACATTACAAGGTTGGTGAATAATTACTACACTGAAGGCAAAACTCACTAACCCC AAGTTACAAGCATAATGATTGTTAATTAGAGCAGTAGTCCCCACATTTACTAAAACTGGAAAAG ACAAATCCAGATAAGGAAAGAAAATAAAGAATAGTCATCTAATAATCCTGGATGTAGTCGCTCT ACTTCCCTTAAAATCCTAGGTGGTTTAACCGATAAACTAATTTGCTTCTTAACACCACCATTGC ATTTAGCAGGACACGAATCAGGGTCTGGTTGTGATAGACAACCAGCGCACAACTATATTGTTCT ATACGTGAAGCCTTAGTGGAACTAATGGATCACAAGGAAGTAAATAATGTATATGGCAAAATCA CATACCTATAGCTGAATCCAACAAGCAATCCAGGGAAGATAATGTCACCAAAGCCTATCATATC ATAACCACCCCATGGATCAAAGAAGCGGGGTATCCTTAGGAGCATAGGAATTGATTCCCCAGTG TTATCACCACGAGCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.138957161

Conservation Information
Conserved circRNAs	NA
PMCS	0.138957161

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							132222256-132222279(-)
132221644-132222279(-)
						
						Potential amino acid sequence
						
							MLLRIPRFFDPWGGYDMIGFGDIIFPGLLVGFSYRFDRANRKGVLSGYFLWLIVGYAVGCSW*(
-)
MQLVARGDNTGESIPMLLRIPRFFDPWGGYDMIGFGDIIFPGLLVGFSYRFDRANRKGVLSGYF
LWLIVGYAVGCSW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	132222256-132222279(-) 132221644-132222279(-)
Potential amino acid sequence	MLLRIPRFFDPWGGYDMIGFGDIIFPGLLVGFSYRFDRANRKGVLSGYFLWLIVGYAVGCSW( -) MQLVARGDNTGESIPMLLRIPRFFDPWGGYDMIGFGDIIFPGLLVGFSYRFDRANRKGVLSGYF LWLIVGYAVGCSW(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d004702_circ_g.4

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