Plant Circular RNA Database

Detail information of Zm00001d025153_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d025153_circ_g.5
					
						ID in PlantcircBase
						zma_circ_010290
					
						Alias
						Zm10circ00044, zma_circ_0003224, ZmciR421
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 106797878-106798402  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						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.3 Zm00001d025153_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
						Zm00001d025153_T003:3
Zm00001d025153_T004:3
Zm00001d025153_T013:3
Zm00001d025153_T011:3
Zm00001d025153_T002:3
Zm00001d025153_T009:3
Zm00001d025153_T010:3
Zm00001d025153_T007:3
Zm00001d025153_T005:2
Zm00001d025153_T012:3
Zm00001d025153_T006:3

General Information
CircRNA Name	Zm00001d025153_circ_g.5
ID in PlantcircBase	zma_circ_010290
Alias	Zm10circ00044, zma_circ_0003224, ZmciR421
Organism	Zea mays
Position	chr10: 106797878-106798402 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
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.3 Zm00001d025153_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	Zm00001d025153_T003:3 Zm00001d025153_T004:3 Zm00001d025153_T013:3 Zm00001d025153_T011:3 Zm00001d025153_T002:3 Zm00001d025153_T009:3 Zm00001d025153_T010:3 Zm00001d025153_T007:3 Zm00001d025153_T005:2 Zm00001d025153_T012:3 Zm00001d025153_T006:3

			
						 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  
						
							TGCCTTTTGATAGGGACCACTGTATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAG
GATCATTACTTGAGACCGCATTTACAAGTCTGACATctggacaggcacgaggcaggagagcttc
atcagcaccttttgataaaagaaggatcttaccagtctccccttcctttaccactacagacatt
cttttgcg

						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: 372
Transcript exons: 106797878-106798042,106798125-106798234,106798306-106798
402
CTGGACAGGCACGAGGCAGGAGAGCTTCATCAGCACCTTTTGATAAAAGAAGGATCTTACCAGT
CTCCCCTTCCTTTACCACTACAGACATTCTTTTGCGATCAGAAGTGAATTCCAAAATGTCCAAC
AACTCATACCAAAACTTAGACCCATTGAAACAAATCTCAGCTGTAATGGTGTCTTTACTGATGA
GCATCATATTCAGCTTTGCTGCAGCGTTAACTAAAGCTTCCTCATCTTGGGATTGTGCTTTGTA
TGACACAGTACCATCATTGCTTTTGATAGGGACCACTGTATTGCAAAGAGCCATAACCAACAGA
AATTTGATGACATCAGGATCATTACTTGAGACCGCATTTACAAGTCTGACAT
						
						Genomic sequence
						
							CTGGACAGGCACGAGGCAGGAGAGCTTCATCAGCACCTTTTGATAAAAGAAGGATCTTACCAGT
CTCCCCTTCCTTTACCACTACAGACATTCTTTTGCGATCAGAAGTGAATTCCAAAATGTCCAAC
AACTCATACCAAAACTTAGACCCATTGAAACAAATCTCTGAAGAAACAAAAGGGAATTCAATCA
AACAGCTTAATGGAATTGTAATAATCTCATCACAAACCGATGAACATTCACTAACCAGCTGTAA
TGGTGTCTTTACTGATGAGCATCATATTCAGCTTTGCTGCAGCGTTAACTAAAGCTTCCTCATC
TTGGGATTGTGCTTTGTATGACACAGTACCATCATTGCTGAAAGTATGAAAATTTTATAAATAA
CAGCTTAATACCATGCAGAGTAACGAAAAGAAACTGTGACTTGCCTTTTGATAGGGACCACTGT
ATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAGGATCATTACTTGAGACCGCATTT
ACAAGTCTGACAT

Sequences
Splice junction sequence	TGCCTTTTGATAGGGACCACTGTATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAG GATCATTACTTGAGACCGCATTTACAAGTCTGACATctggacaggcacgaggcaggagagcttc atcagcaccttttgataaaagaaggatcttaccagtctccccttcctttaccactacagacatt cttttgcg
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: 372 Transcript exons: 106797878-106798042,106798125-106798234,106798306-106798 402 CTGGACAGGCACGAGGCAGGAGAGCTTCATCAGCACCTTTTGATAAAAGAAGGATCTTACCAGT CTCCCCTTCCTTTACCACTACAGACATTCTTTTGCGATCAGAAGTGAATTCCAAAATGTCCAAC AACTCATACCAAAACTTAGACCCATTGAAACAAATCTCAGCTGTAATGGTGTCTTTACTGATGA GCATCATATTCAGCTTTGCTGCAGCGTTAACTAAAGCTTCCTCATCTTGGGATTGTGCTTTGTA TGACACAGTACCATCATTGCTTTTGATAGGGACCACTGTATTGCAAAGAGCCATAACCAACAGA AATTTGATGACATCAGGATCATTACTTGAGACCGCATTTACAAGTCTGACAT
Genomic sequence	CTGGACAGGCACGAGGCAGGAGAGCTTCATCAGCACCTTTTGATAAAAGAAGGATCTTACCAGT CTCCCCTTCCTTTACCACTACAGACATTCTTTTGCGATCAGAAGTGAATTCCAAAATGTCCAAC AACTCATACCAAAACTTAGACCCATTGAAACAAATCTCTGAAGAAACAAAAGGGAATTCAATCA AACAGCTTAATGGAATTGTAATAATCTCATCACAAACCGATGAACATTCACTAACCAGCTGTAA TGGTGTCTTTACTGATGAGCATCATATTCAGCTTTGCTGCAGCGTTAACTAAAGCTTCCTCATC TTGGGATTGTGCTTTGTATGACACAGTACCATCATTGCTGAAAGTATGAAAATTTTATAAATAA CAGCTTAATACCATGCAGAGTAACGAAAAGAAACTGTGACTTGCCTTTTGATAGGGACCACTGT ATTGCAAAGAGCCATAACCAACAGAAATTTGATGACATCAGGATCATTACTTGAGACCGCATTT ACAAGTCTGACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.197148814

Conservation Information
Conserved circRNAs	NA
PMCS	0.197148814

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							106797998-106798399(+)
106798342-106797880(-)
						
						Potential amino acid sequence
						
							MSNNSYQNLDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAI
TNRNLMTSGSLLETAFTSLTSGQARGRRASSAPFDKRRILPVSPSFTTTDILLRSEVNSKMSNN
SYQNLDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAITNRN
LMTSGSLLETAFTSLTSGQARGRRASSAPFDKRRILPVSPSFTTTDILLRSEVNSKMSNNSYQN
LDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAITNRNLMTS
GSLLETAFTSLTSGQARGRRASSAPFDKRRILPVSPSFTTTDILLRSEVNSKMSNNSYQNLDPL
KQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAITNRNLMTSGSLL
ETAFTSLT(+)
MALCNTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDI
LEFTSDRKRMSVVVKEGETGKILLLSKGADEALLPRACPDVRLVNAVSSNDPDVIKFLLVMALC
NTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFT
SDRKRMSVVVKEGETGKILLLSKGADEALLPRACPDVRLVNAVSSNDPDVIKFLLVMALCNTVV
PIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRK
RMSVVVKEGETGKILLLSKGADEALLPRACPDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKS
NDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSV
VVKEGETGKILLLSKGADEALLPRACP(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	106797998-106798399(+) 106798342-106797880(-)
Potential amino acid sequence	MSNNSYQNLDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAI TNRNLMTSGSLLETAFTSLTSGQARGRRASSAPFDKRRILPVSPSFTTTDILLRSEVNSKMSNN SYQNLDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAITNRN LMTSGSLLETAFTSLTSGQARGRRASSAPFDKRRILPVSPSFTTTDILLRSEVNSKMSNNSYQN LDPLKQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAITNRNLMTS GSLLETAFTSLTSGQARGRRASSAPFDKRRILPVSPSFTTTDILLRSEVNSKMSNNSYQNLDPL KQISAVMVSLLMSIIFSFAAALTKASSSWDCALYDTVPSLLLIGTTVLQRAITNRNLMTSGSLL ETAFTSLT(+) MALCNTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDI LEFTSDRKRMSVVVKEGETGKILLLSKGADEALLPRACPDVRLVNAVSSNDPDVIKFLLVMALC NTVVPIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFT SDRKRMSVVVKEGETGKILLLSKGADEALLPRACPDVRLVNAVSSNDPDVIKFLLVMALCNTVV PIKSNDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRK RMSVVVKEGETGKILLLSKGADEALLPRACPDVRLVNAVSSNDPDVIKFLLVMALCNTVVPIKS NDGTVSYKAQSQDEEALVNAAAKLNMMLISKDTITAEICFNGSKFWYELLDILEFTSDRKRMSV VVKEGETGKILLLSKGADEALLPRACP(-)
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 Zm00001d025153_circ_g.5

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