Plant Circular RNA Database

Detail information of Zm00001d003401_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d003401_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007162
					
						Alias
						Zm02circ00044, zma_circ_0000725, GRMZM2G102499_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 43090791-43091650  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d003401						
					
						Parent gene annotation
						
							14-3-3-like protein GF14-6  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d003401_circ_g.2 Zm00001d003401_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d003401_T010:3
Zm00001d003401_T001:3
Zm00001d003401_T004:3
Zm00001d003401_T005:3
Zm00001d003401_T006:3
Zm00001d003401_T003:3
Zm00001d003401_T007:2
Zm00001d003401_T002:3
Zm00001d003401_T011:3
Zm00001d003401_T009:3

General Information
CircRNA Name	Zm00001d003401_circ_g.3
ID in PlantcircBase	zma_circ_007162
Alias	Zm02circ00044, zma_circ_0000725, GRMZM2G102499_C1
Organism	Zea mays
Position	chr2: 43090791-43091650 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d003401
Parent gene annotation	14-3-3-like protein GF14-6
Parent gene strand	-
Alternative splicing	Zm00001d003401_circ_g.2 Zm00001d003401_circ_g.4
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d003401_T010:3 Zm00001d003401_T001:3 Zm00001d003401_T004:3 Zm00001d003401_T005:3 Zm00001d003401_T006:3 Zm00001d003401_T003:3 Zm00001d003401_T007:2 Zm00001d003401_T002:3 Zm00001d003401_T011:3 Zm00001d003401_T009:3

			
						 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  
						
							GCCTGCTCAGCGAGCTTCGCCATGTACACATTTTCCTCACGGGAAAGCTCTGCTGATGCCATCT
TACAGTTCAGTTTTCAAAATTTGCAGTACGCCGGATctgctttgcaagactgcaggcgcgatca
ggtgagttcagaatctcatagtagaacactgagaagttaagtgccagtccaagcctaatagggt
gagttgga

									
								

					

						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: 647
Transcript exons: 43090791-43090913,43091040-43091118,43091206-43091650
CTGCTTTGCAAGACTGCAGGCGCGATCAGGTGAGTTCAGAATCTCATAGTAGAACACTGAGAAG
TTAAGTGCCAGTCCAAGCCTAATAGGGTGAGTTGGAGCAAGCTCAGCCAGAGCAATGTCCTGGG
CAGCCTTGTATGCCACCATCGTGTTCTCAGCGGCGTCCTTTCTCTCAGCTCCAGTCTTGAACTC
AGCAAGGTATCTGTAGTAATCACCCTTCATCTTGAGATAGAAGACCTTGGACTCGGGGGCAGTG
GAAGACGGCACAAGATGGGTCTCAAGCAGCTTGAGGATGCCATCACAGATCTTGGTCAGCTCAG
TCTCAATCTTGCCACGATAATCCTTGATGAGTGTTACTCGGTCCTCATTGCCTCGGCCCTCCTC
CTTCTGCTCGATGGAGGAGATGATGCGCCATGAGGCGCGGCGGGCTCCAATGACGTTCTTGTAT
GCAACAGACAAGAGGTTTCGCTCCTCCACAGTGAGCTCCTCCGAGTCAACAGTCTTGGCTACCT
TCTCCATGAACTCAACCATCTCCTCGTACCTCTCCGCCTGCTCAGCGAGCTTCGCCATGTACAC
ATTTTCCTCACGGGAAAGCTCTGCTGATGCCATCTTACAGTTCAGTTTTCAAAATTTGCAGTAC
GCCGGAT
						
					

						Genomic sequence
						
							CTGCTTTGCAAGACTGCAGGCGCGATCAGGTGAGTTCAGAATCTCATAGTAGAACACTGAGAAG
TTAAGTGCCAGTCCAAGCCTAATAGGGTGAGTTGGAGCAAGCTCAGCCAGAGCAATGTCCTGAA
TGCACCACAAACCCCTTTTCAGCAAACTTGTAATAAAATATGACGTGAAAAAAAACTACAAGCA
TATTGCTTCATGAACAAAATTGCACACTGATTAAGAATGAAACAAAAAATTGTTGACCTGGGCA
GCCTTGTATGCCACCATCGTGTTCTCAGCGGCGTCCTTTCTCTCAGCTCCAGTCTTGAACTCAG
CAAGGTATCTAATCATGACAACTGAATCAGTCAAACAGAAACGTAATCTCACAGCATATGAGAA
AGTCTTACTGGGATCCATACAATCATATTACCTGTAGTAATCACCCTTCATCTTGAGATAGAAG
ACCTTGGACTCGGGGGCAGTGGAAGACGGCACAAGATGGGTCTCAAGCAGCTTGAGGATGCCAT
CACAGATCTTGGTCAGCTCAGTCTCAATCTTGCCACGATAATCCTTGATGAGTGTTACTCGGTC
CTCATTGCCTCGGCCCTCCTCCTTCTGCTCGATGGAGGAGATGATGCGCCATGAGGCGCGGCGG
GCTCCAATGACGTTCTTGTATGCAACAGACAAGAGGTTTCGCTCCTCCACAGTGAGCTCCTCCG
AGTCAACAGTCTTGGCTACCTTCTCCATGAACTCAACCATCTCCTCGTACCTCTCCGCCTGCTC
AGCGAGCTTCGCCATGTACACATTTTCCTCACGGGAAAGCTCTGCTGATGCCATCTTACAGTTC
AGTTTTCAAAATTTGCAGTACGCCGGAT
						
					

			
		

Sequences
Splice junction sequence	GCCTGCTCAGCGAGCTTCGCCATGTACACATTTTCCTCACGGGAAAGCTCTGCTGATGCCATCT TACAGTTCAGTTTTCAAAATTTGCAGTACGCCGGATctgctttgcaagactgcaggcgcgatca ggtgagttcagaatctcatagtagaacactgagaagttaagtgccagtccaagcctaatagggt gagttgga
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: 647 Transcript exons: 43090791-43090913,43091040-43091118,43091206-43091650 CTGCTTTGCAAGACTGCAGGCGCGATCAGGTGAGTTCAGAATCTCATAGTAGAACACTGAGAAG TTAAGTGCCAGTCCAAGCCTAATAGGGTGAGTTGGAGCAAGCTCAGCCAGAGCAATGTCCTGGG CAGCCTTGTATGCCACCATCGTGTTCTCAGCGGCGTCCTTTCTCTCAGCTCCAGTCTTGAACTC AGCAAGGTATCTGTAGTAATCACCCTTCATCTTGAGATAGAAGACCTTGGACTCGGGGGCAGTG GAAGACGGCACAAGATGGGTCTCAAGCAGCTTGAGGATGCCATCACAGATCTTGGTCAGCTCAG TCTCAATCTTGCCACGATAATCCTTGATGAGTGTTACTCGGTCCTCATTGCCTCGGCCCTCCTC CTTCTGCTCGATGGAGGAGATGATGCGCCATGAGGCGCGGCGGGCTCCAATGACGTTCTTGTAT GCAACAGACAAGAGGTTTCGCTCCTCCACAGTGAGCTCCTCCGAGTCAACAGTCTTGGCTACCT TCTCCATGAACTCAACCATCTCCTCGTACCTCTCCGCCTGCTCAGCGAGCTTCGCCATGTACAC ATTTTCCTCACGGGAAAGCTCTGCTGATGCCATCTTACAGTTCAGTTTTCAAAATTTGCAGTAC GCCGGAT
Genomic sequence	CTGCTTTGCAAGACTGCAGGCGCGATCAGGTGAGTTCAGAATCTCATAGTAGAACACTGAGAAG TTAAGTGCCAGTCCAAGCCTAATAGGGTGAGTTGGAGCAAGCTCAGCCAGAGCAATGTCCTGAA TGCACCACAAACCCCTTTTCAGCAAACTTGTAATAAAATATGACGTGAAAAAAAACTACAAGCA TATTGCTTCATGAACAAAATTGCACACTGATTAAGAATGAAACAAAAAATTGTTGACCTGGGCA GCCTTGTATGCCACCATCGTGTTCTCAGCGGCGTCCTTTCTCTCAGCTCCAGTCTTGAACTCAG CAAGGTATCTAATCATGACAACTGAATCAGTCAAACAGAAACGTAATCTCACAGCATATGAGAA AGTCTTACTGGGATCCATACAATCATATTACCTGTAGTAATCACCCTTCATCTTGAGATAGAAG ACCTTGGACTCGGGGGCAGTGGAAGACGGCACAAGATGGGTCTCAAGCAGCTTGAGGATGCCAT CACAGATCTTGGTCAGCTCAGTCTCAATCTTGCCACGATAATCCTTGATGAGTGTTACTCGGTC CTCATTGCCTCGGCCCTCCTCCTTCTGCTCGATGGAGGAGATGATGCGCCATGAGGCGCGGCGG GCTCCAATGACGTTCTTGTATGCAACAGACAAGAGGTTTCGCTCCTCCACAGTGAGCTCCTCCG AGTCAACAGTCTTGGCTACCTTCTCCATGAACTCAACCATCTCCTCGTACCTCTCCGCCTGCTC AGCGAGCTTCGCCATGTACACATTTTCCTCACGGGAAAGCTCTGCTGATGCCATCTTACAGTTC AGTTTTCAAAATTTGCAGTACGCCGGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_024089 osi_circ_005529 						
					
						PMCS
						0.478386673

Conservation Information
Conserved circRNAs	osa_circ_024089 osi_circ_005529
PMCS	0.478386673

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							43091351-43090855(+)
43091607-43090820(+)
43091614-43091623(-)
						
						Potential amino acid sequence
						
							MSVTRSSLPRPSSFCSMEEMMRHEARRAPMTFLYATDKRFRSSTVSSSESTVLATFSMNSTISS
YLSACSASFAMYTFSSRESSADAILQFSFQNLQYAGSALQDCRRDQVSSESHSRTLRS*(+)
MPSYSSVFKICSTPDLLCKTAGAIR*(+)
MASAELSREENVYMAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARRA
SWRIISSIEQKEEGRGNEDRVTLIKDYRGKIETELTKICDGILKLLETHLVPSSTAPESKVFYL
KMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYYEILN
SPDRACSLAKQIRRTANFEN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	43091351-43090855(+) 43091607-43090820(+) 43091614-43091623(-)
Potential amino acid sequence	MSVTRSSLPRPSSFCSMEEMMRHEARRAPMTFLYATDKRFRSSTVSSSESTVLATFSMNSTISS YLSACSASFAMYTFSSRESSADAILQFSFQNLQYAGSALQDCRRDQVSSESHSRTLRS(+) MPSYSSVFKICSTPDLLCKTAGAIR(+) MASAELSREENVYMAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARRA SWRIISSIEQKEEGRGNEDRVTLIKDYRGKIETELTKICDGILKLLETHLVPSSTAPESKVFYL KMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYYEILN SPDRACSLAKQIRRTANFEN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d003401_circ_g.3

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