Plant Circular RNA Database

Detail information of Zm00001d002390_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d002390_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007064
					
						Alias
						Zm02circ00014
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 11675375-11677174  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d002390						
					
						Parent gene annotation
						
							DNA ligase 4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d002390_circ_g.2 Zm00001d002390_circ_g.3 Zm00001d002390_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d002390_T003:7
Zm00001d002390_T011:8
Zm00001d002390_T014:8
Zm00001d002390_T025:8
Zm00001d002390_T013:8
Zm00001d002390_T021:8
Zm00001d002390_T017:8
Zm00001d002390_T023:8
Zm00001d002390_T005:7
Zm00001d002390_T016:8
Zm00001d002390_T010:8
Zm00001d002390_T008:8
Zm00001d002390_T020:8
Zm00001d002390_T019:8
Zm00001d002390_T022:8
Zm00001d002390_T006:8
Zm00001d002390_T024:8
Zm00001d002390_T018:8
Zm00001d002390_T001:8
Zm00001d002390_T015:8
Zm00001d002390_T004:7
Zm00001d002390_T012:8

General Information
CircRNA Name	Zm00001d002390_circ_g.1
ID in PlantcircBase	zma_circ_007064
Alias	Zm02circ00014
Organism	Zea mays
Position	chr2: 11675375-11677174 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d002390
Parent gene annotation	DNA ligase 4
Parent gene strand	-
Alternative splicing	Zm00001d002390_circ_g.2 Zm00001d002390_circ_g.3 Zm00001d002390_circ_g.4
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d002390_T003:7 Zm00001d002390_T011:8 Zm00001d002390_T014:8 Zm00001d002390_T025:8 Zm00001d002390_T013:8 Zm00001d002390_T021:8 Zm00001d002390_T017:8 Zm00001d002390_T023:8 Zm00001d002390_T005:7 Zm00001d002390_T016:8 Zm00001d002390_T010:8 Zm00001d002390_T008:8 Zm00001d002390_T020:8 Zm00001d002390_T019:8 Zm00001d002390_T022:8 Zm00001d002390_T006:8 Zm00001d002390_T024:8 Zm00001d002390_T018:8 Zm00001d002390_T001:8 Zm00001d002390_T015:8 Zm00001d002390_T004:7 Zm00001d002390_T012:8

			
						 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  
						
							AATCAAAGTTGAATACCTGAAATAAGGGTTCAGTTTGGTGACAAGAGCATCACGCTCTTCATCA
GAGAGGCCAGTACCAACTCGGCAAAACGAAAGGAACctgcttgaggtcagcaatttcaatgtcc
cagtagtaatagtcagcgtatgaatcgatctcttcaggaaatttgtgcctagcgaaatcagcaa
taaatagt

									
								

					

						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: 847
Transcript exons: 11675375-11675480,11675559-11675658,11675750-11675875,11
676144-11676344,11676487-11676574,11676717-11676765,1167
6854-11676946,11677091-11677174
CTGCTTGAGGTCAGCAATTTCAATGTCCCAGTAGTAATAGTCAGCGTATGAATCGATCTCTTCA
GGAAATTTGTGCCTAGCGAAATCAGCAATAAATAGTATATACCTAGGATGCAAATGAAGAAGAT
GTTTTTCCTTGCAACAGTCTAATATCCACTCATAGTGAATGATTCTTCCCTGTCGTAAAGCTGC
CTGATATTTGATACCTTTCTTCTCCGCAGCTATGCAGTGTGTAACAGAGTCATTGAGATTCATG
GAGAAAGATCCCCCATTTTCCACAACCAGTTTATGAAAATATTCGAGATTATATGATGATGGAA
TGTTGACAAAATAGAAAATCAGGTTGGCAAATATCAAGGTTTCTCCCTTGAGACCTGATACATC
AGTTTTCATGAAATGTGAAGGGATGATTGAGACACACTTCTCTACTTTTTTGTTTGTTCTTGAA
TGTTTTGTGTCATCATTCTTCAGGCTATTATCATCTGCCACCCTTTGTATTGTACCATTATTTG
AATGCACAATGTCCACAAATGCCTGCACATCAAGGCACTCATGCCATGGCTTGTCATATCTCAC
TCGCTGAATACGGGGGAACCTCAAACAGTATGGAGCAGCAAATACCTCAGACTTGATTGTACGA
ATGTCACTTGTTACAGATATTATGACTGACTTATCAGGACTTTCAATCCAAACATCTGGTCTCT
CCTTTGAGTTATTTGTAACTTCATAGAATTTTGGTGGTTTTTTGGGGTACTCATTTTTCCTGAA
ATAAGGGTTCAGTTTGGTGACAAGAGCATCACGCTCTTCATCAGAGAGGCCAGTACCAACTCGG
CAAAACGAAAGGAAC
						
					

						Genomic sequence
						
							CTGCTTGAGGTCAGCAATTTCAATGTCCCAGTAGTAATAGTCAGCGTATGAATCGATCTCTTCA
GGAAATTTGTGCCTAGCGAAATCAGCAATAAATAGTATATACCTGTACAATTATAATTGCATTA
GAATTATTTTCTAAATAAGTTATGAGGTAAATGTGGTTAAGTAAAAGGGGTCCAACCTAGGATG
CAAATGAAGAAGATGTTTTTCCTTGCAACAGTCTAATATCCACTCATAGTGAATGATTCTTCCC
TGTCGTAAAGCTGCCTGATATTTGATACCTGGAAAATATAACAGGCAAATATACTTCAAACTAT
GTATTCAATATCCCATTATCAAAGAAAAAGGAACTCCTAAAACAAAGGTAAATACCTTTCTTCT
CCGCAGCTATGCAGTGTGTAACAGAGTCATTGAGATTCATGGAGAAAGATCCCCCATTTTCCAC
AACCAGTTTATGAAAATATTCGAGATTATATGATGATGGAATGTTGACAAAATCTAAGTAAGAT
AAGGAATACTCCTACTTTATACAATTTTCTGGCCTTTGTCTTGTAAATAAGTATAGCTAGCTCT
GTTCTTAAGGCGTCGCCTAGGCGACGCCTAGGCGTCCGGGCGGTGGTCTAACGCCTAGGCGCCT
TGCCCGCCTACCTCGCCTAGGCGTCGCCTAGGCGCCGTCTAGGCGTCCAGGCGGTGGTCCAACG
CCTTGGACCGCCTTACCGCTTTAAAAACCATGATAGCTAGCAAAGAATAACACTGGAAAGGATA
CAGAAAATCAGGTTGGCAAATATCAAGGTTTCTCCCTTGAGACCTGATACATCAGTTTTCATGA
AATGTGAAGGGATGATTGAGACACACTTCTCTACTTTTTTGTTTGTTCTTGAATGTTTTGTGTC
ATCATTCTTCAGGCTATTATCATCTGCCACCCTTTGTATTGTACCATTATTTGAATGCACAATG
TCCACAAATGCTGCAATGATCAGCGTGTTATAGAGAAATCATCTTCGAGATATAACCTAGATTA
GGGCATCACGAGGGATGTAGCTTATTGTAAGCTACTAAAAGAACAAAGAATACAGACACAAAAT
ATTAAGTATAAGAAAAACAATTACCCTGCACATCAAGGCACTCATGCCATGGCTTGTCATATCT
CACTCGCTGAATACGGGGGAACCTCAAACAGTATGGAGCAGCAAATACCTGCATAAGGTTGAAA
ACATTAAAAGTAAGTTAGAAGAGAAAATACACCAGCTGACTGCACAAGAGAAATCAGTCCAAGA
ATTAATGCTTTTAAAGACAGAACTGCAGAACATATAAGTATTTGATTCTTTAAATCAAATACCT
CAGACTTGATTGTACGAATGTCACTTGTTACAGATATTATGACTGACCTGAAAATGCAATTAGT
GATTTAGCATATCATGTGCTTCCTATATCTAAGAAAATGGCTCTCAATCAAAGAATTAAAAAAA
AACTTACTTATCAGGACTTTCAATCCAAACATCTGGTCTCTCCTTTGAGTTATTTGTAACTTCA
TAGAATTTTGGTGGTTTTTTGGGGTACTCATTTTTCCTGATTCAAAAAATAGCACAATATGACA
GAATGAGAAGGAACTTTAATTCCTTAGTAATAAATAGGTTTTGAAGCTTCAAGGAAACGTACTT
ACACAAAATACTGATTCAGTAAATATGAAACATAATAATCAAAGTTGAATACCTGAAATAAGGG
TTCAGTTTGGTGACAAGAGCATCACGCTCTTCATCAGAGAGGCCAGTACCAACTCGGCAAAACG
AAAGGAAC
						
					

			
		

Sequences
Splice junction sequence	AATCAAAGTTGAATACCTGAAATAAGGGTTCAGTTTGGTGACAAGAGCATCACGCTCTTCATCA GAGAGGCCAGTACCAACTCGGCAAAACGAAAGGAACctgcttgaggtcagcaatttcaatgtcc cagtagtaatagtcagcgtatgaatcgatctcttcaggaaatttgtgcctagcgaaatcagcaa taaatagt
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: 847 Transcript exons: 11675375-11675480,11675559-11675658,11675750-11675875,11 676144-11676344,11676487-11676574,11676717-11676765,1167 6854-11676946,11677091-11677174 CTGCTTGAGGTCAGCAATTTCAATGTCCCAGTAGTAATAGTCAGCGTATGAATCGATCTCTTCA GGAAATTTGTGCCTAGCGAAATCAGCAATAAATAGTATATACCTAGGATGCAAATGAAGAAGAT GTTTTTCCTTGCAACAGTCTAATATCCACTCATAGTGAATGATTCTTCCCTGTCGTAAAGCTGC CTGATATTTGATACCTTTCTTCTCCGCAGCTATGCAGTGTGTAACAGAGTCATTGAGATTCATG GAGAAAGATCCCCCATTTTCCACAACCAGTTTATGAAAATATTCGAGATTATATGATGATGGAA TGTTGACAAAATAGAAAATCAGGTTGGCAAATATCAAGGTTTCTCCCTTGAGACCTGATACATC AGTTTTCATGAAATGTGAAGGGATGATTGAGACACACTTCTCTACTTTTTTGTTTGTTCTTGAA TGTTTTGTGTCATCATTCTTCAGGCTATTATCATCTGCCACCCTTTGTATTGTACCATTATTTG AATGCACAATGTCCACAAATGCCTGCACATCAAGGCACTCATGCCATGGCTTGTCATATCTCAC TCGCTGAATACGGGGGAACCTCAAACAGTATGGAGCAGCAAATACCTCAGACTTGATTGTACGA ATGTCACTTGTTACAGATATTATGACTGACTTATCAGGACTTTCAATCCAAACATCTGGTCTCT CCTTTGAGTTATTTGTAACTTCATAGAATTTTGGTGGTTTTTTGGGGTACTCATTTTTCCTGAA ATAAGGGTTCAGTTTGGTGACAAGAGCATCACGCTCTTCATCAGAGAGGCCAGTACCAACTCGG CAAAACGAAAGGAAC
Genomic sequence	CTGCTTGAGGTCAGCAATTTCAATGTCCCAGTAGTAATAGTCAGCGTATGAATCGATCTCTTCA GGAAATTTGTGCCTAGCGAAATCAGCAATAAATAGTATATACCTGTACAATTATAATTGCATTA GAATTATTTTCTAAATAAGTTATGAGGTAAATGTGGTTAAGTAAAAGGGGTCCAACCTAGGATG CAAATGAAGAAGATGTTTTTCCTTGCAACAGTCTAATATCCACTCATAGTGAATGATTCTTCCC TGTCGTAAAGCTGCCTGATATTTGATACCTGGAAAATATAACAGGCAAATATACTTCAAACTAT GTATTCAATATCCCATTATCAAAGAAAAAGGAACTCCTAAAACAAAGGTAAATACCTTTCTTCT CCGCAGCTATGCAGTGTGTAACAGAGTCATTGAGATTCATGGAGAAAGATCCCCCATTTTCCAC AACCAGTTTATGAAAATATTCGAGATTATATGATGATGGAATGTTGACAAAATCTAAGTAAGAT AAGGAATACTCCTACTTTATACAATTTTCTGGCCTTTGTCTTGTAAATAAGTATAGCTAGCTCT GTTCTTAAGGCGTCGCCTAGGCGACGCCTAGGCGTCCGGGCGGTGGTCTAACGCCTAGGCGCCT TGCCCGCCTACCTCGCCTAGGCGTCGCCTAGGCGCCGTCTAGGCGTCCAGGCGGTGGTCCAACG CCTTGGACCGCCTTACCGCTTTAAAAACCATGATAGCTAGCAAAGAATAACACTGGAAAGGATA CAGAAAATCAGGTTGGCAAATATCAAGGTTTCTCCCTTGAGACCTGATACATCAGTTTTCATGA AATGTGAAGGGATGATTGAGACACACTTCTCTACTTTTTTGTTTGTTCTTGAATGTTTTGTGTC ATCATTCTTCAGGCTATTATCATCTGCCACCCTTTGTATTGTACCATTATTTGAATGCACAATG TCCACAAATGCTGCAATGATCAGCGTGTTATAGAGAAATCATCTTCGAGATATAACCTAGATTA GGGCATCACGAGGGATGTAGCTTATTGTAAGCTACTAAAAGAACAAAGAATACAGACACAAAAT ATTAAGTATAAGAAAAACAATTACCCTGCACATCAAGGCACTCATGCCATGGCTTGTCATATCT CACTCGCTGAATACGGGGGAACCTCAAACAGTATGGAGCAGCAAATACCTGCATAAGGTTGAAA ACATTAAAAGTAAGTTAGAAGAGAAAATACACCAGCTGACTGCACAAGAGAAATCAGTCCAAGA ATTAATGCTTTTAAAGACAGAACTGCAGAACATATAAGTATTTGATTCTTTAAATCAAATACCT CAGACTTGATTGTACGAATGTCACTTGTTACAGATATTATGACTGACCTGAAAATGCAATTAGT GATTTAGCATATCATGTGCTTCCTATATCTAAGAAAATGGCTCTCAATCAAAGAATTAAAAAAA AACTTACTTATCAGGACTTTCAATCCAAACATCTGGTCTCTCCTTTGAGTTATTTGTAACTTCA TAGAATTTTGGTGGTTTTTTGGGGTACTCATTTTTCCTGATTCAAAAAATAGCACAATATGACA GAATGAGAAGGAACTTTAATTCCTTAGTAATAAATAGGTTTTGAAGCTTCAAGGAAACGTACTT ACACAAAATACTGATTCAGTAAATATGAAACATAATAATCAAAGTTGAATACCTGAAATAAGGG TTCAGTTTGGTGACAAGAGCATCACGCTCTTCATCAGAGAGGCCAGTACCAACTCGGCAAAACG AAAGGAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110957316

Conservation Information
Conserved circRNAs	NA
PMCS	0.110957316

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11676206-11677138(-)
						
						Potential amino acid sequence
						
							MKTDVSGLKGETLIFANLIFYFVNIPSSYNLEYFHKLVVENGGSFSMNLNDSVTHCIAAEKKGI
KYQAALRQGRIIHYEWILDCCKEKHLLHLHPRYILFIADFARHKFPEEIDSYADYYYWDIEIAD
LKQVPFVLPSWYWPL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11676206-11677138(-)
Potential amino acid sequence	MKTDVSGLKGETLIFANLIFYFVNIPSSYNLEYFHKLVVENGGSFSMNLNDSVTHCIAAEKKGI KYQAALRQGRIIHYEWILDCCKEKHLLHLHPRYILFIADFARHKFPEEIDSYADYYYWDIEIAD LKQVPFVLPSWYWPL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d002390_circ_g.1

Address

Any questions?

Supported by