Plant Circular RNA Database

Detail information of Zm00001d025153_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d025153_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010288
					
						Alias
						Zm10circ00042
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 106783213-106798402  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d025153						
					
						Parent gene annotation
						
							Phospholipid-transporting ATPase 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025153_circ_g.1 Zm00001d025153_circ_g.2 Zm00001d025153_circ_g.4 Zm00001d025153_circ_g.5 						
					
						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
						Zm00001d025153_T012:6
Zm00001d025153_T005:5
Zm00001d025153_T002:6
Zm00001d025153_T001:4
Zm00001d025153_T010:6
Zm00001d025153_T006:6
Zm00001d025153_T007:6
Zm00001d025153_T011:6
Zm00001d025153_T004:6
Zm00001d025153_T003:6
Zm00001d025153_T009:6
Zm00001d025153_T008:4
Zm00001d025153_T013:6

General Information
CircRNA Name	Zm00001d025153_circ_g.3
ID in PlantcircBase	zma_circ_010288
Alias	Zm10circ00042
Organism	Zea mays
Position	chr10: 106783213-106798402 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d025153
Parent gene annotation	Phospholipid-transporting ATPase 2
Parent gene strand	-
Alternative splicing	Zm00001d025153_circ_g.1 Zm00001d025153_circ_g.2 Zm00001d025153_circ_g.4 Zm00001d025153_circ_g.5
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	Zm00001d025153_T012:6 Zm00001d025153_T005:5 Zm00001d025153_T002:6 Zm00001d025153_T001:4 Zm00001d025153_T010:6 Zm00001d025153_T006:6 Zm00001d025153_T007:6 Zm00001d025153_T011:6 Zm00001d025153_T004:6 Zm00001d025153_T003:6 Zm00001d025153_T009:6 Zm00001d025153_T008:4 Zm00001d025153_T013:6

			
						 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  
						
							TGCCTTTTGATAGGGACCACTGTATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAG
GATCATTACTTGAGACCGCATTTACAAGTCTGACATcagaagttatgaggttacagagaagtcc
aatctgaattgctgtattttgcttatcaccggttagcatccacacattaattccagcattcctc
aacaattt

						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: 729
Transcript exons: 106783213-106783333,106783440-106783520,106783626-106783
780,106797878-106798042,106798125-106798234,106798306-10
6798402
CAGAAGTTATGAGGTTACAGAGAAGTCCAATCTGAATTGCTGTATTTTGCTTATCACCGGTTAG
CATCCACACATTAATTCCAGCATTCCTCAACAATTTAATGGTTTCAGGAACACCATCCTGAAGA
CGATCCTCTATAGCAGTAACACCAAGAATTTGAAGGTCTTGCTCTAAGCTATTACAAACTTCAG
CAATTTTAAACTCTCTATTGTCCAATGAGCAGCTAGCCTTTTGAAAGTTTTTGGACCATTCCTT
ATATTCATTTTCTTTTAAATCACGCCACCCCAAACATAAGGTTCGCAATCCCAACTGAGAATAC
ATTTCTACTGCTTCAAGATATCTCTGTATTTGTTGTCCTGGACAGGCACGAGGCAGGAGAGCTT
CATCAGCACCTTTTGATAAAAGAAGGATCTTACCAGTCTCCCCTTCCTTTACCACTACAGACAT
TCTTTTGCGATCAGAAGTGAATTCCAAAATGTCCAACAACTCATACCAAAACTTAGACCCATTG
AAACAAATCTCAGCTGTAATGGTGTCTTTACTGATGAGCATCATATTCAGCTTTGCTGCAGCGT
TAACTAAAGCTTCCTCATCTTGGGATTGTGCTTTGTATGACACAGTACCATCATTGCTTTTGAT
AGGGACCACTGTATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAGGATCATTACTT
GAGACCGCATTTACAAGTCTGACAT
						
						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	TGCCTTTTGATAGGGACCACTGTATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAG GATCATTACTTGAGACCGCATTTACAAGTCTGACATcagaagttatgaggttacagagaagtcc aatctgaattgctgtattttgcttatcaccggttagcatccacacattaattccagcattcctc aacaattt
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: 729 Transcript exons: 106783213-106783333,106783440-106783520,106783626-106783 780,106797878-106798042,106798125-106798234,106798306-10 6798402 CAGAAGTTATGAGGTTACAGAGAAGTCCAATCTGAATTGCTGTATTTTGCTTATCACCGGTTAG CATCCACACATTAATTCCAGCATTCCTCAACAATTTAATGGTTTCAGGAACACCATCCTGAAGA CGATCCTCTATAGCAGTAACACCAAGAATTTGAAGGTCTTGCTCTAAGCTATTACAAACTTCAG CAATTTTAAACTCTCTATTGTCCAATGAGCAGCTAGCCTTTTGAAAGTTTTTGGACCATTCCTT ATATTCATTTTCTTTTAAATCACGCCACCCCAAACATAAGGTTCGCAATCCCAACTGAGAATAC ATTTCTACTGCTTCAAGATATCTCTGTATTTGTTGTCCTGGACAGGCACGAGGCAGGAGAGCTT CATCAGCACCTTTTGATAAAAGAAGGATCTTACCAGTCTCCCCTTCCTTTACCACTACAGACAT TCTTTTGCGATCAGAAGTGAATTCCAAAATGTCCAACAACTCATACCAAAACTTAGACCCATTG AAACAAATCTCAGCTGTAATGGTGTCTTTACTGATGAGCATCATATTCAGCTTTGCTGCAGCGT TAACTAAAGCTTCCTCATCTTGGGATTGTGCTTTGTATGACACAGTACCATCATTGCTTTTGAT AGGGACCACTGTATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAGGATCATTACTT GAGACCGCATTTACAAGTCTGACAT
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
						0.131934711

Conservation Information
Conserved circRNAs	NA
PMCS	0.131934711

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							106797998-106783244(+)
106798342-106783215(-)
						
						Potential amino acid sequence
						
							MSNNSYQNLDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAI
TNRNLMTSGSLLETAFTSLTSEVMRLQRSPI*(+)
MALCNTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDI
LEFTSDRKRMSVVVKEGETGKILLLSKGADEALLPRACPGQQIQRYLEAVEMYSQLGLRTLCLG
WRDLKENEYKEWSKNFQKASCSLDNREFKIAEVCNSLEQDLQILGVTAIEDRLQDGVPETIKLL
RNAGINVWMLTGDKQNTAIQIGLLCNLITSDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKSN
DGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSVV
VKEGETGKILLLSKGADEALLPRACPGQQIQRYLEAVEMYSQLGLRTLCLGWRDLKENEYKEWS
KNFQKASCSLDNREFKIAEVCNSLEQDLQILGVTAIEDRLQDGVPETIKLLRNAGINVWMLTGD
KQNTAIQIGLLCNLITSDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKSNDGTVSYKAQSQDE
EALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSVVVKEGETGKILLLS
KGADEALLPRACPGQQIQRYLEAVEMYSQLGLRTLCLGWRDLKENEYKEWSKNFQKASCSLDNR
EFKIAEVCNSLEQDLQILGVTAIEDRLQDGVPETIKLLRNAGINVWMLTGDKQNTAIQIGLLCN
LITSDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMM
LISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSVVVKEGETGKILLLSKGADEALLPRACP
GQQIQRYLEAVEMYSQLGLRTLCLGWRDLKENEYKEWSKNFQKASCSLDNREFKIAEVCNSLEQ
DLQILGVTAIEDRLQDGVPETIKLLRNAGINVWMLTGDKQNTAIQIGLLCNLITS(-)
						
						Sponge-miRNAs
						
							zma-miR172a zma-miR172c-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	106797998-106783244(+) 106798342-106783215(-)
Potential amino acid sequence	MSNNSYQNLDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAI TNRNLMTSGSLLETAFTSLTSEVMRLQRSPI*(+) MALCNTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDI LEFTSDRKRMSVVVKEGETGKILLLSKGADEALLPRACPGQQIQRYLEAVEMYSQLGLRTLCLG WRDLKENEYKEWSKNFQKASCSLDNREFKIAEVCNSLEQDLQILGVTAIEDRLQDGVPETIKLL RNAGINVWMLTGDKQNTAIQIGLLCNLITSDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKSN DGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSVV VKEGETGKILLLSKGADEALLPRACPGQQIQRYLEAVEMYSQLGLRTLCLGWRDLKENEYKEWS KNFQKASCSLDNREFKIAEVCNSLEQDLQILGVTAIEDRLQDGVPETIKLLRNAGINVWMLTGD KQNTAIQIGLLCNLITSDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKSNDGTVSYKAQSQDE EALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSVVVKEGETGKILLLS KGADEALLPRACPGQQIQRYLEAVEMYSQLGLRTLCLGWRDLKENEYKEWSKNFQKASCSLDNR EFKIAEVCNSLEQDLQILGVTAIEDRLQDGVPETIKLLRNAGINVWMLTGDKQNTAIQIGLLCN LITSDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMM LISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSVVVKEGETGKILLLSKGADEALLPRACP GQQIQRYLEAVEMYSQLGLRTLCLGWRDLKENEYKEWSKNFQKASCSLDNREFKIAEVCNSLEQ DLQILGVTAIEDRLQDGVPETIKLLRNAGINVWMLTGDKQNTAIQIGLLCNLITS(-)
Sponge-miRNAs	zma-miR172a zma-miR172c-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d025153_circ_g.3

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