Plant Circular RNA Database

Detail information of Zm00001d011713_circ_g.9

			
						 General Information
					
						CircRNA Name
						Zm00001d011713_circ_g.9
					
						ID in PlantcircBase
						zma_circ_009760
					
						Alias
						Zm08circ00069, zma_circ_0002845, GRMZM2G058155_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 159566345-159566900  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d011713						
					
						Parent gene annotation
						
							Myosin family protein with Dil domain
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d011713_circ_g.8 Zm00001d011713_circ_g.10 Zm00001d011713_circ_g.11 						
					
						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
						Zm00001d011713_T003:3
Zm00001d011713_T004:3
Zm00001d011713_T008:3
Zm00001d011713_T016:3
Zm00001d011713_T017:3
Zm00001d011713_T013:3
Zm00001d011713_T006:3
Zm00001d011713_T015:3
Zm00001d011713_T007:3

General Information
CircRNA Name	Zm00001d011713_circ_g.9
ID in PlantcircBase	zma_circ_009760
Alias	Zm08circ00069, zma_circ_0002845, GRMZM2G058155_C2
Organism	Zea mays
Position	chr8: 159566345-159566900 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d011713
Parent gene annotation	Myosin family protein with Dil domain
Parent gene strand	-
Alternative splicing	Zm00001d011713_circ_g.8 Zm00001d011713_circ_g.10 Zm00001d011713_circ_g.11
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	Zm00001d011713_T003:3 Zm00001d011713_T004:3 Zm00001d011713_T008:3 Zm00001d011713_T016:3 Zm00001d011713_T017:3 Zm00001d011713_T013:3 Zm00001d011713_T006:3 Zm00001d011713_T015:3 Zm00001d011713_T007:3

			
						 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  
						
							GATGCATGTATTCACAAAACTGATGCAAGAATGAAAATCATTGATTAATATGTGAAACTCACCA
GGCTTCATCAAGAAGTGCAATAATGCCACCTGGTTTcttaaagcgagttgcaattgatgatttt
gatgattttgtgttctcttctgttgctggtggaaataatcctgatacaaaagagcacttagaac
cattaagt

						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: 333
Transcript exons: 159566345-159566512,159566631-159566757,159566863-159566
900
CTTAAAGCGAGTTGCAATTGATGATTTTGATGATTTTGTGTTCTCTTCTGTTGCTGGTGGAAAT
AATCCTGATACAAAAGAGCACTTAGAACCATTAAGTAATTCTTGATGCTCTGCAACCACGTAGT
CCTTGTTCTTGTCCAGGAATTGATCAGATTGATATGTTACATCCCCAGCATAATGTTGAATTGT
AAATGCAGTACGAGAAAGCTTTGGTTTGGTAAATCTTTTGTGGGTCTTGAACTTTTCATACAGC
TTCTGAGACAATGTCTCGTGTGTGGACTTTGGAAACATGCAGGCTTCATCAAGAAGTGCAATAA
TGCCACCTGGTTT
						
						Genomic sequence
						
							CTTAAAGCGAGTTGCAATTGATGATTTTGATGATTTTGTGTTCTCTTCTGTTGCTGGTGGAAAT
AATCCTGATACAAAAGAGCACTTAGAACCATTAAGTAATTCTTGATGCTCTGCAACCACGTAGT
CCTTGTTCTTGTCCAGGAATTGATCAGATTGATATGTTACCTAGGAAATAAAGAAGAAAAATGA
TCATACTCATGCAAAAACATGAAAACTGAACAACAAGGAGTCGTATATATGGGTCAATATGTTT
TTTTCTAAAATATGAGTGGGAAATACTTACATCCCCAGCATAATGTTGAATTGTAAATGCAGTA
CGAGAAAGCTTTGGTTTGGTAAATCTTTTGTGGGTCTTGAACTTTTCATACAGCTTCTGAGACA
ATGTCTCGTGTGTGGACTTTGGAAACATGCTGATGGATGCATTTCAGCACAGAAAGAAGGTAAC
TGTCGTTAGATGCATGTATTCACAAAACTGATGCAAGAATGAAAATCATTGATTAATATGTGAA
ACTCACCAGGCTTCATCAAGAAGTGCAATAATGCCACCTGGTTT

Sequences
Splice junction sequence	GATGCATGTATTCACAAAACTGATGCAAGAATGAAAATCATTGATTAATATGTGAAACTCACCA GGCTTCATCAAGAAGTGCAATAATGCCACCTGGTTTcttaaagcgagttgcaattgatgatttt gatgattttgtgttctcttctgttgctggtggaaataatcctgatacaaaagagcacttagaac cattaagt
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: 333 Transcript exons: 159566345-159566512,159566631-159566757,159566863-159566 900 CTTAAAGCGAGTTGCAATTGATGATTTTGATGATTTTGTGTTCTCTTCTGTTGCTGGTGGAAAT AATCCTGATACAAAAGAGCACTTAGAACCATTAAGTAATTCTTGATGCTCTGCAACCACGTAGT CCTTGTTCTTGTCCAGGAATTGATCAGATTGATATGTTACATCCCCAGCATAATGTTGAATTGT AAATGCAGTACGAGAAAGCTTTGGTTTGGTAAATCTTTTGTGGGTCTTGAACTTTTCATACAGC TTCTGAGACAATGTCTCGTGTGTGGACTTTGGAAACATGCAGGCTTCATCAAGAAGTGCAATAA TGCCACCTGGTTT
Genomic sequence	CTTAAAGCGAGTTGCAATTGATGATTTTGATGATTTTGTGTTCTCTTCTGTTGCTGGTGGAAAT AATCCTGATACAAAAGAGCACTTAGAACCATTAAGTAATTCTTGATGCTCTGCAACCACGTAGT CCTTGTTCTTGTCCAGGAATTGATCAGATTGATATGTTACCTAGGAAATAAAGAAGAAAAATGA TCATACTCATGCAAAAACATGAAAACTGAACAACAAGGAGTCGTATATATGGGTCAATATGTTT TTTTCTAAAATATGAGTGGGAAATACTTACATCCCCAGCATAATGTTGAATTGTAAATGCAGTA CGAGAAAGCTTTGGTTTGGTAAATCTTTTGTGGGTCTTGAACTTTTCATACAGCTTCTGAGACA ATGTCTCGTGTGTGGACTTTGGAAACATGCTGATGGATGCATTTCAGCACAGAAAGAAGGTAAC TGTCGTTAGATGCATGTATTCACAAAACTGATGCAAGAATGAAAATCATTGATTAATATGTGAA ACTCACCAGGCTTCATCAAGAAGTGCAATAATGCCACCTGGTTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.283271673

Conservation Information
Conserved circRNAs	NA
PMCS	0.283271673

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							159566454-159566362(+)
159566756-159566450(+)
159566758-159566347(-)
159566441-159566511(-)
						
						Potential amino acid sequence
						
							MLCNHVVLVLVQELIRLICYIPSIMLNCKCSTRKLWFGKSFVGLELFIQLLRQCLVCGLWKHAG
FIKKCNNATWFLKASCN*(+)
MQASSRSAIMPPGFLKRVAIDDFDDFVFSSVAGGNNPDTKEHLEPLSNS*(+)
MFPKSTHETLSQKLYEKFKTHKRFTKPKLSRTAFTIQHYAGDVTYQSDQFLDKNKDYVVAEHQE
LLNGSKCSFVSGLFPPATEENTKSSKSSIATRFKKPGGIIALLDEACMFPKSTHETLSQKLYEK
FKTHKRFTKPKLSRTAFTIQHYAGDVTYQSDQFLDKNKDYVVAEHQELLNGSKCSFVSGLFPPA
TEENTKSSKSSIATRFKKPGGIIALLDEACMFPKSTHETLSQKLYEKFKTHKRFTKPKLSRTAF
TIQHYAGDVTYQSDQFLDKNKDYVVAEHQELLNGSKCSFVSGLFPPATEENTKSSKSSIATRFK
KPGGIIALLDEACMFPKSTHETLSQKLYEKFKTHKRFTKPKLSRTAFTIQHYAGDVTYQSDQFL
DKNKDYVVAEHQELLNGSKCSFVSGLFPPATEENTKSSKSSIATRFK(-)
MVLSALLYQDYFHQQQKRTQNHQNHQLQLALRNQVALLHFLMKPACFQSPHTRHCLRSCMKSSR
PTKDLPNQSFLVLHLQFNIMLGM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	159566454-159566362(+) 159566756-159566450(+) 159566758-159566347(-) 159566441-159566511(-)
Potential amino acid sequence	MLCNHVVLVLVQELIRLICYIPSIMLNCKCSTRKLWFGKSFVGLELFIQLLRQCLVCGLWKHAG FIKKCNNATWFLKASCN(+) MQASSRSAIMPPGFLKRVAIDDFDDFVFSSVAGGNNPDTKEHLEPLSNS(+) MFPKSTHETLSQKLYEKFKTHKRFTKPKLSRTAFTIQHYAGDVTYQSDQFLDKNKDYVVAEHQE LLNGSKCSFVSGLFPPATEENTKSSKSSIATRFKKPGGIIALLDEACMFPKSTHETLSQKLYEK FKTHKRFTKPKLSRTAFTIQHYAGDVTYQSDQFLDKNKDYVVAEHQELLNGSKCSFVSGLFPPA TEENTKSSKSSIATRFKKPGGIIALLDEACMFPKSTHETLSQKLYEKFKTHKRFTKPKLSRTAF TIQHYAGDVTYQSDQFLDKNKDYVVAEHQELLNGSKCSFVSGLFPPATEENTKSSKSSIATRFK KPGGIIALLDEACMFPKSTHETLSQKLYEKFKTHKRFTKPKLSRTAFTIQHYAGDVTYQSDQFL DKNKDYVVAEHQELLNGSKCSFVSGLFPPATEENTKSSKSSIATRFK(-) MVLSALLYQDYFHQQQKRTQNHQNHQLQLALRNQVALLHFLMKPACFQSPHTRHCLRSCMKSSR PTKDLPNQSFLVLHLQFNIMLGM*(-)
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 Zm00001d011713_circ_g.9

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