Plant Circular RNA Database

Detail information of Zm00001d051856_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d051856_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008147
					
						Alias
						zma_circ_0001588
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 172482910-172484062  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d051856						
					
						Parent gene annotation
						
							O-fucosyltransferase family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d051856_circ_g.2 						
					
						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
						Zm00001d051856_T011:2
Zm00001d051856_T014:2
Zm00001d051856_T013:2
Zm00001d051856_T012:2
Zm00001d051856_T009:2
Zm00001d051856_T015:2
Zm00001d051856_T016:2
Zm00001d051856_T003:2
Zm00001d051856_T017:2
Zm00001d051856_T004:2
Zm00001d051856_T008:2
Zm00001d051856_T002:2
Zm00001d051856_T010:2

General Information
CircRNA Name	Zm00001d051856_circ_g.3
ID in PlantcircBase	zma_circ_008147
Alias	zma_circ_0001588
Organism	Zea mays
Position	chr4: 172482910-172484062 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d051856
Parent gene annotation	O-fucosyltransferase family protein
Parent gene strand	-
Alternative splicing	Zm00001d051856_circ_g.2
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	Zm00001d051856_T011:2 Zm00001d051856_T014:2 Zm00001d051856_T013:2 Zm00001d051856_T012:2 Zm00001d051856_T009:2 Zm00001d051856_T015:2 Zm00001d051856_T016:2 Zm00001d051856_T003:2 Zm00001d051856_T017:2 Zm00001d051856_T004:2 Zm00001d051856_T008:2 Zm00001d051856_T002:2 Zm00001d051856_T010:2

			
						 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  
						
							CCATCTTCCTGGACACTGAATCAACTGCTAGCTGCTCCTTTACTGTTCCTCGTTTAATCATCTG
ATTCCTTCTATACTGAATAAGCTCTGTATGAATATCctgtccggcctgtaggttataccggaag
gtgtttggtacaaccggtgccccatgaccaaacttgagtagtctggccaaccactaccgtcatt
gtgaaacc

									
								

					

						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: 683
Transcript exons: 172482910-172483463,172483934-172484062
CTGTCCGGCCTGTAGGTTATACCGGAAGGTGTTTGGTACAACCGGTGCCCCATGACCAAACTTG
AGTAGTCTGGCCAACCACTACCGTCATTGTGAAACCCGGGGAAGAAGGCATCAGCTTCAACAGA
AACAAAATAATCAAGTGCATCCCAGAGCAACTGGTGTGCTTGCCTCCTGAACTCGATCAGTGAA
GCATCCGGTTCTGTGTCATTCTCACCAATCCAACCATACCAGCCTTCCTTCTCATGTGCATAGA
ATGGCCTTGCAGGAGGTGGAGGCAGCGGCCTTGGACGAGGCCCTGCTCTCCTCCATTCTTCAAT
AAGTTGTTTTTCACTTTTGGGAGGTGGAGGCTGTGGCAAATCTGGGGTTCGAGGATCTTCTGGC
CCAACTAAATCAAACAGCTCCCTCTGACTACATAATGAAGTGCGGTCTACTAGGTTAGCGAACA
TAGCTCGTAGAGGAATAAGCATTCTTTGTCCACCAAAAGTCTCAGAACCGGCCAAGAATATTAT
TGTAGTTGGTGGGTAACCTACTGCTTGAAGTAGAAGTCCAACCTCTTCTGGCATGAGTGGACAC
AAACCAGCCATCTTCCTGGACACTGAATCAACTGCTAGCTGCTCCTTTACTGTTCCTCGTTTAA
TCATCTGATTCCTTCTATACTGAATAAGCTCTGTATGAATATC
						
					

						Genomic sequence
						
							CTGTCCGGCCTGTAGGTTATACCGGAAGGTGTTTGGTACAACCGGTGCCCCATGACCAAACTTG
AGTAGTCTGGCCAACCACTACCGTCATTGTGAAACCCGGGGAAGAAGGCATCAGCTTCAACAGA
AACAAAATAATCAAGTGCATCCCAGAGCAACTGGTGTGCTTGCCTCCTGAACTCGATCAGTGAA
GCATCCGGTTCTGTGTCATTCTCACCAATCCAACCATACCAGCCTTCCTTCTCATGTGCATAGA
ATGGCCTTGCAGGAGGTGGAGGCAGCGGCCTTGGACGAGGCCCTGCTCTCCTCCATTCTTCAAT
AAGTTGTTTTTCACTTTTGGGAGGTGGAGGCTGTGGCAAATCTGGGGTTCGAGGATCTTCTGGC
CCAACTAAATCAAACAGCTCCCTCTGACTACATAATGAAGTGCGGTCTACTAGGTTAGCGAACA
TAGCTCGTAGAGGAATAAGCATTCTTTGTCCACCAAAAGTCTCAGAACCGGCCAAGAATATTAT
TGTAGTTGGTGGGTAACCTACTGCTTGAAGTAGAAGTCCAACCTAGAAACACAGGATTGTTTAC
ATCACAGCATTAGCAATCAAAATGAAACAGTAACCTGGTGTTGTAAACCAGGCATAGTGCTAAG
CAGATTATATCGTGCAGCACGATGTGTGCCACAGGACCAAAAAATTGAAAGAATAAAGGAAGTC
TTTCTAGTTAACTTTTCTTTCTTTAAACTTCTTTGTCTTGAGCTTGATTTCCATAATGATGATT
GATACAAACAATGATGCTTAAAAGCAAAACGTGAAGTTCAAATTCCGAAGGTAAAGGTCCATAT
GGTAAAGGAAAATTATCATCTAGTTTTCTTTTGTTTGGTTGCTTATATTTTGTCAGCCTCAGAT
TTCTTCTATATGAACTCTCTTGGTGCAGAACAGTAATATAACACCAGCTTACCTAATATAAATA
AACATGAAGAAGTTGCATCCAGATTTAGTGAGCAAACATACAAGACTGTAATAAGCAAGCTCAC
CTCTTCTGGCATGAGTGGACACAAACCAGCCATCTTCCTGGACACTGAATCAACTGCTAGCTGC
TCCTTTACTGTTCCTCGTTTAATCATCTGATTCCTTCTATACTGAATAAGCTCTGTATGAATAT
C
						
					

			
		

Sequences
Splice junction sequence	CCATCTTCCTGGACACTGAATCAACTGCTAGCTGCTCCTTTACTGTTCCTCGTTTAATCATCTG ATTCCTTCTATACTGAATAAGCTCTGTATGAATATCctgtccggcctgtaggttataccggaag gtgtttggtacaaccggtgccccatgaccaaacttgagtagtctggccaaccactaccgtcatt gtgaaacc
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: 683 Transcript exons: 172482910-172483463,172483934-172484062 CTGTCCGGCCTGTAGGTTATACCGGAAGGTGTTTGGTACAACCGGTGCCCCATGACCAAACTTG AGTAGTCTGGCCAACCACTACCGTCATTGTGAAACCCGGGGAAGAAGGCATCAGCTTCAACAGA AACAAAATAATCAAGTGCATCCCAGAGCAACTGGTGTGCTTGCCTCCTGAACTCGATCAGTGAA GCATCCGGTTCTGTGTCATTCTCACCAATCCAACCATACCAGCCTTCCTTCTCATGTGCATAGA ATGGCCTTGCAGGAGGTGGAGGCAGCGGCCTTGGACGAGGCCCTGCTCTCCTCCATTCTTCAAT AAGTTGTTTTTCACTTTTGGGAGGTGGAGGCTGTGGCAAATCTGGGGTTCGAGGATCTTCTGGC CCAACTAAATCAAACAGCTCCCTCTGACTACATAATGAAGTGCGGTCTACTAGGTTAGCGAACA TAGCTCGTAGAGGAATAAGCATTCTTTGTCCACCAAAAGTCTCAGAACCGGCCAAGAATATTAT TGTAGTTGGTGGGTAACCTACTGCTTGAAGTAGAAGTCCAACCTCTTCTGGCATGAGTGGACAC AAACCAGCCATCTTCCTGGACACTGAATCAACTGCTAGCTGCTCCTTTACTGTTCCTCGTTTAA TCATCTGATTCCTTCTATACTGAATAAGCTCTGTATGAATATC
Genomic sequence	CTGTCCGGCCTGTAGGTTATACCGGAAGGTGTTTGGTACAACCGGTGCCCCATGACCAAACTTG AGTAGTCTGGCCAACCACTACCGTCATTGTGAAACCCGGGGAAGAAGGCATCAGCTTCAACAGA AACAAAATAATCAAGTGCATCCCAGAGCAACTGGTGTGCTTGCCTCCTGAACTCGATCAGTGAA GCATCCGGTTCTGTGTCATTCTCACCAATCCAACCATACCAGCCTTCCTTCTCATGTGCATAGA ATGGCCTTGCAGGAGGTGGAGGCAGCGGCCTTGGACGAGGCCCTGCTCTCCTCCATTCTTCAAT AAGTTGTTTTTCACTTTTGGGAGGTGGAGGCTGTGGCAAATCTGGGGTTCGAGGATCTTCTGGC CCAACTAAATCAAACAGCTCCCTCTGACTACATAATGAAGTGCGGTCTACTAGGTTAGCGAACA TAGCTCGTAGAGGAATAAGCATTCTTTGTCCACCAAAAGTCTCAGAACCGGCCAAGAATATTAT TGTAGTTGGTGGGTAACCTACTGCTTGAAGTAGAAGTCCAACCTAGAAACACAGGATTGTTTAC ATCACAGCATTAGCAATCAAAATGAAACAGTAACCTGGTGTTGTAAACCAGGCATAGTGCTAAG CAGATTATATCGTGCAGCACGATGTGTGCCACAGGACCAAAAAATTGAAAGAATAAAGGAAGTC TTTCTAGTTAACTTTTCTTTCTTTAAACTTCTTTGTCTTGAGCTTGATTTCCATAATGATGATT GATACAAACAATGATGCTTAAAAGCAAAACGTGAAGTTCAAATTCCGAAGGTAAAGGTCCATAT GGTAAAGGAAAATTATCATCTAGTTTTCTTTTGTTTGGTTGCTTATATTTTGTCAGCCTCAGAT TTCTTCTATATGAACTCTCTTGGTGCAGAACAGTAATATAACACCAGCTTACCTAATATAAATA AACATGAAGAAGTTGCATCCAGATTTAGTGAGCAAACATACAAGACTGTAATAAGCAAGCTCAC CTCTTCTGGCATGAGTGGACACAAACCAGCCATCTTCCTGGACACTGAATCAACTGCTAGCTGC TCCTTTACTGTTCCTCGTTTAATCATCTGATTCCTTCTATACTGAATAAGCTCTGTATGAATAT C

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.168678712

Conservation Information
Conserved circRNAs	NA
PMCS	0.168678712

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							172484025-172484022(-)
						
						Potential amino acid sequence
						
							MIKRGTVKEQLAVDSVSRKMAGLCPLMPEEVGLLLQAVGYPPTTIIFLAGSETFGGQRMLIPLR
AMFANLVDRTSLCSQRELFDLVGPEDPRTPDLPQPPPPKSEKQLIEEWRRAGPRPRPLPPPPAR
PFYAHEKEGWYGWIGENDTEPDASLIEFRRQAHQLLWDALDYFVSVEADAFFPGFHNDGSGWPD
YSSLVMGHRLYQTPSGITYRPDRIFIQSLFSIEGIR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	172484025-172484022(-)
Potential amino acid sequence	MIKRGTVKEQLAVDSVSRKMAGLCPLMPEEVGLLLQAVGYPPTTIIFLAGSETFGGQRMLIPLR AMFANLVDRTSLCSQRELFDLVGPEDPRTPDLPQPPPPKSEKQLIEEWRRAGPRPRPLPPPPAR PFYAHEKEGWYGWIGENDTEPDASLIEFRRQAHQLLWDALDYFVSVEADAFFPGFHNDGSGWPD YSSLVMGHRLYQTPSGITYRPDRIFIQSLFSIEGIR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d051856_circ_g.3

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