Plant Circular RNA Database

Detail information of Zm00001d027259_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d027259_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006333
					
						Alias
						zma_circ_0000698
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 700404-701105  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d027259						
					
						Parent gene annotation
						
							tRNA/rRNA methyltransferase (SpoU) family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d027259_circ_g.1 						
					
						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
						Zm00001d027259_T048:3
Zm00001d027259_T055:3
Zm00001d027259_T043:3
Zm00001d027259_T019:3
Zm00001d027259_T040:3
Zm00001d027259_T002:3
Zm00001d027259_T008:3
Zm00001d027259_T009:3
Zm00001d027259_T053:3
Zm00001d027259_T021:3
Zm00001d027259_T051:2
Zm00001d027259_T010:3
Zm00001d027259_T013:3
Zm00001d027259_T006:3
Zm00001d027259_T067:3
Zm00001d027259_T046:3
Zm00001d027259_T024:3
Zm00001d027259_T045:3
Zm00001d027259_T015:3
Zm00001d027259_T056:3
Zm00001d027259_T016:3
Zm00001d027259_T032:3
Zm00001d027259_T042:3
Zm00001d027259_T025:3
Zm00001d027259_T038:3
Zm00001d027259_T011:3
Zm00001d027259_T007:3
Zm00001d027259_T029:3
Zm00001d027259_T049:1
Zm00001d027259_T004:3
Zm00001d027259_T064:3
Zm00001d027259_T060:3
Zm00001d027259_T058:3
Zm00001d027259_T035:3
Zm00001d027259_T062:3
Zm00001d027259_T027:3
Zm00001d027259_T034:3
Zm00001d027259_T018:3
Zm00001d027259_T003:3

General Information
CircRNA Name	Zm00001d027259_circ_g.2
ID in PlantcircBase	zma_circ_006333
Alias	zma_circ_0000698
Organism	Zea mays
Position	chr1: 700404-701105 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d027259
Parent gene annotation	tRNA/rRNA methyltransferase (SpoU) family protein
Parent gene strand	-
Alternative splicing	Zm00001d027259_circ_g.1
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	Zm00001d027259_T048:3 Zm00001d027259_T055:3 Zm00001d027259_T043:3 Zm00001d027259_T019:3 Zm00001d027259_T040:3 Zm00001d027259_T002:3 Zm00001d027259_T008:3 Zm00001d027259_T009:3 Zm00001d027259_T053:3 Zm00001d027259_T021:3 Zm00001d027259_T051:2 Zm00001d027259_T010:3 Zm00001d027259_T013:3 Zm00001d027259_T006:3 Zm00001d027259_T067:3 Zm00001d027259_T046:3 Zm00001d027259_T024:3 Zm00001d027259_T045:3 Zm00001d027259_T015:3 Zm00001d027259_T056:3 Zm00001d027259_T016:3 Zm00001d027259_T032:3 Zm00001d027259_T042:3 Zm00001d027259_T025:3 Zm00001d027259_T038:3 Zm00001d027259_T011:3 Zm00001d027259_T007:3 Zm00001d027259_T029:3 Zm00001d027259_T049:1 Zm00001d027259_T004:3 Zm00001d027259_T064:3 Zm00001d027259_T060:3 Zm00001d027259_T058:3 Zm00001d027259_T035:3 Zm00001d027259_T062:3 Zm00001d027259_T027:3 Zm00001d027259_T034:3 Zm00001d027259_T018:3 Zm00001d027259_T003:3

			
						 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  
						
							AGAAGTCCCATAGCACGGAAAATGCAGAAGAAACAGAATCATCGGAGTTGTAAGGATTACACCA
TGAGGCAACAGAACTAACACATCGCATTGACCAAATctttcgataatatcaagaaaaatgcatc
ggagggttgaatcagaaaataaaggttccaacctcttcatttgagattcattgtcactatagca
gcttgaaa

						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: 497
Transcript exons: 700404-700531,700613-700843,700968-701105
CTTTCGATAATATCAAGAAAAATGCATCGGAGGGTTGAATCAGAAAATAAAGGTTCCAACCTCT
TCATTTGAGATTCATTGTCACTATAGCAGCTTGAAATAGATAGAAGAGAATCCATACAAAGCCA
CTTCCAAGTCATCAAAACAGCTCTTCTGCTTCGCGTCAGAGTTCCCTCTGTAAGAAGATGGTTG
ATGTTGTCAAGGAAAGTGGTGACCAAAATGTCCAATGAAAACTTGTGGGCTTGATCTGTCTGCT
TCGCTTCCACAAAATCCAAAAACTGAGTACTGGAAGCAGTAGATAGAACTGCCAGAACATAGGC
AAGAGCTTCATAAGCTGCCAGGTGAAGTTCAGCTCCGATCTCATTGGCAATAGTGGAGTGATGG
GTAACATTCAAATAGAAGTCCCATAGCACGGAAAATGCAGAAGAAACAGAATCATCGGAGTTGT
AAGGATTACACCATGAGGCAACAGAACTAACACATCGCATTGACCAAAT
						
						Genomic sequence
						
							CTTTCGATAATATCAAGAAAAATGCATCGGAGGGTTGAATCAGAAAATAAAGGTTCCAACCTCT
TCATTTGAGATTCATTGTCACTATAGCAGCTTGAAATAGATAGAAGAGAATCCATACAAAGCCA
CTGAAATAAAAATTAAGAATTAGGAGCCATCCAAACTGACTTCTTTGTGTACTGCAAAAAGAGG
CAAGATATTATCCTAACCTTCCAAGTCATCAAAACAGCTCTTCTGCTTCGCGTCAGAGTTCCCT
CTGTAAGAAGATGGTTGATGTTGTCAAGGAAAGTGGTGACCAAAATGTCCAATGAAAACTTGTG
GGCTTGATCTGTCTGCTTCGCTTCCACAAAATCCAAAAACTGAGTACTGGAAGCAGTAGATAGA
ACTGCCAGAACATAGGCAAGAGCTTCATAAGCTGCCAGGTGAAGTTCAGCTCCGATCTTGTACA
GGGGAAAAAAAGAGAAAGACTGACTTTAGAATTTATGTAAAGAAAGCTAACAGAAAGGACAATG
AAAAAGAATAATTAAGTAAATCAGTAAAAAGTTGTTTAAAATAGCAACATACCTCATTGGCAAT
AGTGGAGTGATGGGTAACATTCAAATAGAAGTCCCATAGCACGGAAAATGCAGAAGAAACAGAA
TCATCGGAGTTGTAAGGATTACACCATGAGGCAACAGAACTAACACATCGCATTGACCAAAT

Sequences
Splice junction sequence	AGAAGTCCCATAGCACGGAAAATGCAGAAGAAACAGAATCATCGGAGTTGTAAGGATTACACCA TGAGGCAACAGAACTAACACATCGCATTGACCAAATctttcgataatatcaagaaaaatgcatc ggagggttgaatcagaaaataaaggttccaacctcttcatttgagattcattgtcactatagca gcttgaaa
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: 497 Transcript exons: 700404-700531,700613-700843,700968-701105 CTTTCGATAATATCAAGAAAAATGCATCGGAGGGTTGAATCAGAAAATAAAGGTTCCAACCTCT TCATTTGAGATTCATTGTCACTATAGCAGCTTGAAATAGATAGAAGAGAATCCATACAAAGCCA CTTCCAAGTCATCAAAACAGCTCTTCTGCTTCGCGTCAGAGTTCCCTCTGTAAGAAGATGGTTG ATGTTGTCAAGGAAAGTGGTGACCAAAATGTCCAATGAAAACTTGTGGGCTTGATCTGTCTGCT TCGCTTCCACAAAATCCAAAAACTGAGTACTGGAAGCAGTAGATAGAACTGCCAGAACATAGGC AAGAGCTTCATAAGCTGCCAGGTGAAGTTCAGCTCCGATCTCATTGGCAATAGTGGAGTGATGG GTAACATTCAAATAGAAGTCCCATAGCACGGAAAATGCAGAAGAAACAGAATCATCGGAGTTGT AAGGATTACACCATGAGGCAACAGAACTAACACATCGCATTGACCAAAT
Genomic sequence	CTTTCGATAATATCAAGAAAAATGCATCGGAGGGTTGAATCAGAAAATAAAGGTTCCAACCTCT TCATTTGAGATTCATTGTCACTATAGCAGCTTGAAATAGATAGAAGAGAATCCATACAAAGCCA CTGAAATAAAAATTAAGAATTAGGAGCCATCCAAACTGACTTCTTTGTGTACTGCAAAAAGAGG CAAGATATTATCCTAACCTTCCAAGTCATCAAAACAGCTCTTCTGCTTCGCGTCAGAGTTCCCT CTGTAAGAAGATGGTTGATGTTGTCAAGGAAAGTGGTGACCAAAATGTCCAATGAAAACTTGTG GGCTTGATCTGTCTGCTTCGCTTCCACAAAATCCAAAAACTGAGTACTGGAAGCAGTAGATAGA ACTGCCAGAACATAGGCAAGAGCTTCATAAGCTGCCAGGTGAAGTTCAGCTCCGATCTTGTACA GGGGAAAAAAAGAGAAAGACTGACTTTAGAATTTATGTAAAGAAAGCTAACAGAAAGGACAATG AAAAAGAATAATTAAGTAAATCAGTAAAAAGTTGTTTAAAATAGCAACATACCTCATTGGCAAT AGTGGAGTGATGGGTAACATTCAAATAGAAGTCCCATAGCACGGAAAATGCAGAAGAAACAGAA TCATCGGAGTTGTAAGGATTACACCATGAGGCAACAGAACTAACACATCGCATTGACCAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.22653545

Conservation Information
Conserved circRNAs	NA
PMCS	0.22653545

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							701098-701002(-)
						
						Potential amino acid sequence
						
							MRCVSSVASWCNPYNSDDSVSSAFSVLWDFYLNVTHHSTIANESFSFFPLYKIGAELHLAAYEA
LAYVLAVLSTASSTQFLDFVEAKQTDQAHKFSLDILVTTFLDNINHLLTEGTLTRSRRAVLMTW
KWLCMDSLLSISSCYSDNESQMKRLEPLFSDSTLRCIFLDIIERFGQCDVLVLLPHGVILTTPM
ILFLLHFPCYGTSI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	701098-701002(-)
Potential amino acid sequence	MRCVSSVASWCNPYNSDDSVSSAFSVLWDFYLNVTHHSTIANESFSFFPLYKIGAELHLAAYEA LAYVLAVLSTASSTQFLDFVEAKQTDQAHKFSLDILVTTFLDNINHLLTEGTLTRSRRAVLMTW KWLCMDSLLSISSCYSDNESQMKRLEPLFSDSTLRCIFLDIIERFGQCDVLVLLPHGVILTTPM ILFLLHFPCYGTSI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d027259_circ_g.2

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