Plant Circular RNA Database

Detail information of Zm00001d043948_circ_g.9

			
						 General Information
					
						CircRNA Name
						Zm00001d043948_circ_g.9
					
						ID in PlantcircBase
						zma_circ_007839
					
						Alias
						zma_circ_0001334
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 214458994-214476152  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d043948						
					
						Parent gene annotation
						
							Transducin/WD40 repeat-like superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d043948_circ_g.1 Zm00001d043948_circ_g.2 Zm00001d043948_circ_g.3 Zm00001d043948_circ_g.4 Zm00001d043948_circ_g.5 Zm00001d043948_circ_g.6 Zm00001d043948_circ_g.7 Zm00001d043948_circ_g.8 						
					
						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
						Zm00001d043948_T006:3
Zm00001d043948_T002:4
Zm00001d043948_T010:1
Zm00001d043948_T001:4
Zm00001d043948_T005:4
Zm00001d043948_T008:5
Zm00001d043948_T004:3
Zm00001d043948_T007:1
Zm00001d043948_T003:5
Zm00001d043948_T009:1

General Information
CircRNA Name	Zm00001d043948_circ_g.9
ID in PlantcircBase	zma_circ_007839
Alias	zma_circ_0001334
Organism	Zea mays
Position	chr3: 214458994-214476152 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d043948
Parent gene annotation	Transducin/WD40 repeat-like superfamily protein
Parent gene strand	-
Alternative splicing	Zm00001d043948_circ_g.1 Zm00001d043948_circ_g.2 Zm00001d043948_circ_g.3 Zm00001d043948_circ_g.4 Zm00001d043948_circ_g.5 Zm00001d043948_circ_g.6 Zm00001d043948_circ_g.7 Zm00001d043948_circ_g.8
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	Zm00001d043948_T006:3 Zm00001d043948_T002:4 Zm00001d043948_T010:1 Zm00001d043948_T001:4 Zm00001d043948_T005:4 Zm00001d043948_T008:5 Zm00001d043948_T004:3 Zm00001d043948_T007:1 Zm00001d043948_T003:5 Zm00001d043948_T009:1

			
						 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  
						
							TTCCTTCGTGTCCTTTACATTCCCCTAGGTACTGTCCGGTTTCTGGAGAATAAAACTTTAGTGC
ATTTGTTGACAAGGAAACTGCAAGCGTTGAGATCTCcttaatgtctcaatatgggttaaacacc
aaagcttcttatacttgttcccaaaaaaacccaccttggcaacagatgtttccgcattcataac
ctatggga

									
								

					

						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: 1918
Transcript exons: 214458994-214459085,214459486-214459596,214465819-214465
893,214474513-214476152
CTTAATGTCTCAATATGGGTTAAACACCAAAGCTTCTTATACTTGTTCCCAAAAAAACCCACCT
TGGCAACAGATGTTTCCGCATTCATAACAGATAACAGATGATTGTCATCATCAATATCACCATC
AGTGTCAAAAACACATATTAATCCATCAACTGCTGCAGAAATGAGTTTACTTTGTTGATCTGGT
GTGAATTTGACTTGTGTCACATCATCCATGTGGGATTCCTCTAAGCATGCAATTTGTCTTGAAC
TTCTCCAATCCCAGAATAGAACCTGGGCATTAGAGCCCGCAGCAAGTAGGCTACCATTTGATCC
ACCAAAAGCGAAGGTGAACATTTCTTGTGACACGCCTCCTCTTAGCAAAGATATCTGGCAACAT
TTAGAGACAGTGAACAGTTGGATTTAGAACATAGAGAACTTCAGACAAACAGGTGTACTTACTG
GTACAAAAAAGAGAAACAAAAAAGCTTGGCATACAAGCACACTAATCATTAATGGCATATCAAA
TGCTGAAATGCATGCTAAGTGGTAAAACTCTTGACAAGACACATGTAGCATATAATGAAGTGCT
ATATCATTACATTAGTAGCTACTTAGATAAAAAATATAAAACCTATTCAACATACAATAATATT
TTTCACATTGGAATGAAGAATTCATACTGTCATAAAGCTGTAAGAAAACTCTGTTAGCTAAGTT
CAGCAAACTGCATAAGTTCATTGTAATGTTGGTCACAAAGGCAATCACAAAAATGACATCACCT
TATTGAGTTGAACTTCCATTTACTTATCTTTTTTTTCTTTCTTTTGGCGAAAAGGCATCTAGCC
GAGTTGGTTAGACGGTCTGAGTCCTCAAGTCCCGACTTCGACTACCGTGGAAGCGGATTTCAGG
CTGTGGTTAAAAAAACCTTGTCTATCCCACGCCAAAGCACGAGTCTAAGGCCCGGCCCCAGTCG
CGGTCATTCTCACATGGGCTACGGTGCCGTTGTGTATGGGTGGGACAGAGGTTCAGGAGTTTCT
CGACCTGTGTGAGAAGGTCTTCTTTTTAATACAATGCCCAGGGGCTGTCTTACCTCCCGTAGGT
CGAGTTTTTCTTTTGAACCGGAAGAAAGTTTTGAGTTGCCCAGTATAAAGAAAAAGTAGGTACA
AACTACGGATAAATATACTCATGTTCCATCAAATGGGATCAATGGCCAACCCAAATTCAAGCAT
GAAAATAAAAACAGAACTTGTTTTAGTAGTAGAATTTACAAAGCGAACAGAAGAATTAGTCATG
GCGCTGTAACGATTTTAAGCAGAAGTAGGGCAGTGTTCCAATATGAATGCATAAGCAGTAGCAA
TAAAGTGCATACGGCAACATATATTAATCTAAACGTAGGACAAATGACTAAATGAAGTGAACAA
GAATATAGTCATTATGTTAACAGGAACATGAAAAAATCGAACATAAGAGAACAAAACAGAAATG
TTGACTAATTTCCATTAGCATGAACAATATCATAACCATTTTAGGAGCACACAATCATGGGCAC
AATGTTCAGATGTTCTACACCTTTAGCCTGTAGGGTAATATGGATATATGATTATCTTTTTCAT
TTTGATTGTGAAATAAGTAGATGTGGTAGTCTTATTAAGCAACCATACACACATACAAGGAAAA
TTGAAATGCTGACAAGAATTTTCAATAAACATAAAGTATTAGAAAACAACCTGCTTAAAGTTTC
TTGTATCCCAAGCTCTGACAGTTCCATCAGAAGAACAAGAGCAGATTACTTGTGGTGACGATGG
AGCTGAGAAGGAGATTTCATGGATTGTTCCTTCGTGTCCTTTACATTCCCCTAGGTACTGTCCG
GTTTCTGGAGAATAAAACTTTAGTGCATTTGTTGACAAGGAAACTGCAAGCGTTGAGATCTC
						
					

						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	TTCCTTCGTGTCCTTTACATTCCCCTAGGTACTGTCCGGTTTCTGGAGAATAAAACTTTAGTGC ATTTGTTGACAAGGAAACTGCAAGCGTTGAGATCTCcttaatgtctcaatatgggttaaacacc aaagcttcttatacttgttcccaaaaaaacccaccttggcaacagatgtttccgcattcataac ctatggga
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: 1918 Transcript exons: 214458994-214459085,214459486-214459596,214465819-214465 893,214474513-214476152 CTTAATGTCTCAATATGGGTTAAACACCAAAGCTTCTTATACTTGTTCCCAAAAAAACCCACCT TGGCAACAGATGTTTCCGCATTCATAACAGATAACAGATGATTGTCATCATCAATATCACCATC AGTGTCAAAAACACATATTAATCCATCAACTGCTGCAGAAATGAGTTTACTTTGTTGATCTGGT GTGAATTTGACTTGTGTCACATCATCCATGTGGGATTCCTCTAAGCATGCAATTTGTCTTGAAC TTCTCCAATCCCAGAATAGAACCTGGGCATTAGAGCCCGCAGCAAGTAGGCTACCATTTGATCC ACCAAAAGCGAAGGTGAACATTTCTTGTGACACGCCTCCTCTTAGCAAAGATATCTGGCAACAT TTAGAGACAGTGAACAGTTGGATTTAGAACATAGAGAACTTCAGACAAACAGGTGTACTTACTG GTACAAAAAAGAGAAACAAAAAAGCTTGGCATACAAGCACACTAATCATTAATGGCATATCAAA TGCTGAAATGCATGCTAAGTGGTAAAACTCTTGACAAGACACATGTAGCATATAATGAAGTGCT ATATCATTACATTAGTAGCTACTTAGATAAAAAATATAAAACCTATTCAACATACAATAATATT TTTCACATTGGAATGAAGAATTCATACTGTCATAAAGCTGTAAGAAAACTCTGTTAGCTAAGTT CAGCAAACTGCATAAGTTCATTGTAATGTTGGTCACAAAGGCAATCACAAAAATGACATCACCT TATTGAGTTGAACTTCCATTTACTTATCTTTTTTTTCTTTCTTTTGGCGAAAAGGCATCTAGCC GAGTTGGTTAGACGGTCTGAGTCCTCAAGTCCCGACTTCGACTACCGTGGAAGCGGATTTCAGG CTGTGGTTAAAAAAACCTTGTCTATCCCACGCCAAAGCACGAGTCTAAGGCCCGGCCCCAGTCG CGGTCATTCTCACATGGGCTACGGTGCCGTTGTGTATGGGTGGGACAGAGGTTCAGGAGTTTCT CGACCTGTGTGAGAAGGTCTTCTTTTTAATACAATGCCCAGGGGCTGTCTTACCTCCCGTAGGT CGAGTTTTTCTTTTGAACCGGAAGAAAGTTTTGAGTTGCCCAGTATAAAGAAAAAGTAGGTACA AACTACGGATAAATATACTCATGTTCCATCAAATGGGATCAATGGCCAACCCAAATTCAAGCAT GAAAATAAAAACAGAACTTGTTTTAGTAGTAGAATTTACAAAGCGAACAGAAGAATTAGTCATG GCGCTGTAACGATTTTAAGCAGAAGTAGGGCAGTGTTCCAATATGAATGCATAAGCAGTAGCAA TAAAGTGCATACGGCAACATATATTAATCTAAACGTAGGACAAATGACTAAATGAAGTGAACAA GAATATAGTCATTATGTTAACAGGAACATGAAAAAATCGAACATAAGAGAACAAAACAGAAATG TTGACTAATTTCCATTAGCATGAACAATATCATAACCATTTTAGGAGCACACAATCATGGGCAC AATGTTCAGATGTTCTACACCTTTAGCCTGTAGGGTAATATGGATATATGATTATCTTTTTCAT TTTGATTGTGAAATAAGTAGATGTGGTAGTCTTATTAAGCAACCATACACACATACAAGGAAAA TTGAAATGCTGACAAGAATTTTCAATAAACATAAAGTATTAGAAAACAACCTGCTTAAAGTTTC TTGTATCCCAAGCTCTGACAGTTCCATCAGAAGAACAAGAGCAGATTACTTGTGGTGACGATGG AGCTGAGAAGGAGATTTCATGGATTGTTCCTTCGTGTCCTTTACATTCCCCTAGGTACTGTCCG GTTTCTGGAGAATAAAACTTTAGTGCATTTGTTGACAAGGAAACTGCAAGCGTTGAGATCTC
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
						0.072027716

Conservation Information
Conserved circRNAs	NA
PMCS	0.072027716

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							214476024-214458995(+)
214474577-214476112(-)
						
						Potential amino acid sequence
						
							MELRRRFHGLFLRVLYIPLGTVRFLENKTLVHLLTRKLQALRSP*(+)
MFTFAFGGSNGSLLAAGSNAQVLFWDWRSSRQIACLEESHMDDVTQVKFTPDQQSKLISAAVDG
LICVFDTDGDIDDDNHLLSVMNAETSVAKVGFFGNKYKKLWCLTHIETLRRSQRLQFPCQQMH*
(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	214476024-214458995(+) 214474577-214476112(-)
Potential amino acid sequence	MELRRRFHGLFLRVLYIPLGTVRFLENKTLVHLLTRKLQALRSP(+) MFTFAFGGSNGSLLAAGSNAQVLFWDWRSSRQIACLEESHMDDVTQVKFTPDQQSKLISAAVDG LICVFDTDGDIDDDNHLLSVMNAETSVAKVGFFGNKYKKLWCLTHIETLRRSQRLQFPCQQMH (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d043948_circ_g.9

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