Plant Circular RNA Database

Detail information of Zm00001d004036_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d004036_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007209
					
						Alias
						Zm02circ00061
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 77707085-77708054  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d004036						
					
						Parent gene annotation
						
							Protein XRI1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d004036_circ_g.1 Zm00001d004036_circ_g.2 Zm00001d004036_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  
						
							GT-AG							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
						Zm00001d004036_T003:6
Zm00001d004036_T001:4
Zm00001d004036_T006:6
Zm00001d004036_T002:6
Zm00001d004036_T004:6
Zm00001d004036_T007:5
Zm00001d004036_T008:5

General Information
CircRNA Name	Zm00001d004036_circ_g.3
ID in PlantcircBase	zma_circ_007209
Alias	Zm02circ00061
Organism	Zea mays
Position	chr2: 77707085-77708054 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d004036
Parent gene annotation	Protein XRI1
Parent gene strand	+
Alternative splicing	Zm00001d004036_circ_g.1 Zm00001d004036_circ_g.2 Zm00001d004036_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	GT-AG 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	Zm00001d004036_T003:6 Zm00001d004036_T001:4 Zm00001d004036_T006:6 Zm00001d004036_T002:6 Zm00001d004036_T004:6 Zm00001d004036_T007:5 Zm00001d004036_T008:5

			
						 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  
						
							CTCATTTATTTGTTAGTCGTGATATATTCATCTCCTGCTTGCTGTAGACCTTGTAGCCAGCAGA
GCATTGCATGTACAAATGATCAAGCTGGTATTTCAGtctttgggattggacagaacagcattgt
gaacctaacgattcaagtcatggtactttcattcacatccataacctgcatctatgtcacaaac
aaacttta

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TCTTTGGGATTGGACAGAACAGCATTGTGAACCTAACGATTCAAGTCATGGTACTTTCATTCAC
ATCCATAACCTGCATCTATGTCACAAACAAACTTTAAAGTACCTGTTTGGACTTCCTTTTTCAT
CATGTCTCATCTTTTTTTTACAGCAGATGCTACTAAATTTGTGTGGGATTGCCTCAATCAAGAT
GACAATGAGCTGTTGGGATTGCTTGGAAATCAAACCCCATTGAGATACTGCCGTGATTTCTTCG
CTGACCTTGATGGTACAAAGCTTTTTGTTGTGGCAATTATCATTGCTAGCACTCTTGAATGCAT
AGCTTAAAGTGTCCGTTACTTGAGTAGATATCACATGCAAGGAGACCCTGGACCTGGAGGAATC
TCGGGAATCAAAGCGGCGGCGCACATTGGAGTACCCTTTGGAGTCTAGTCAGTCAGAAGTTGGG
ACTCATGAAACCGGTTCACCTTTCGTCACACCTGAGGTTGTTCACCAGCTCCTAGCTATGTTTC
AAAATCCCTCTCTTCTGCTAATCTTTGCTATCATAGTTATGCATGTTTCTGTTGTTCCATATTT
CAGGTAGCAGAAATTTCATTGCTCTGCACTGATAAACCACAGAGCTTAAATTGTGGTATGCACC
ACACTTTAAATAATCTAGGTTTGTATTTTTCATTATATATGCTTAAACAGTGCCTCTAGTATTT
GCTAATTGAAAATTTTACATCAGATACAATAAATTCCTTGTCAGATGAAGCACCCTACCAGCAA
GAAGATATCCTTTTGGAACATTGCTCTTATGGAACGGCAGTGTACCTTGAGCCAGATCAAACGT
TTGTCCCTCTCTGGTTCCACTGAAACCACTTTATTTGGCTCATTTATTTGTTAGTCGTGATATA
TTCATCTCCTGCTTGCTGTAGACCTTGTAGCCAGCAGAGCATTGCATGTACAAATGATCAAGCT
GGTATTTCAG

Sequences
Splice junction sequence	CTCATTTATTTGTTAGTCGTGATATATTCATCTCCTGCTTGCTGTAGACCTTGTAGCCAGCAGA GCATTGCATGTACAAATGATCAAGCTGGTATTTCAGtctttgggattggacagaacagcattgt gaacctaacgattcaagtcatggtactttcattcacatccataacctgcatctatgtcacaaac aaacttta
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TCTTTGGGATTGGACAGAACAGCATTGTGAACCTAACGATTCAAGTCATGGTACTTTCATTCAC ATCCATAACCTGCATCTATGTCACAAACAAACTTTAAAGTACCTGTTTGGACTTCCTTTTTCAT CATGTCTCATCTTTTTTTTACAGCAGATGCTACTAAATTTGTGTGGGATTGCCTCAATCAAGAT GACAATGAGCTGTTGGGATTGCTTGGAAATCAAACCCCATTGAGATACTGCCGTGATTTCTTCG CTGACCTTGATGGTACAAAGCTTTTTGTTGTGGCAATTATCATTGCTAGCACTCTTGAATGCAT AGCTTAAAGTGTCCGTTACTTGAGTAGATATCACATGCAAGGAGACCCTGGACCTGGAGGAATC TCGGGAATCAAAGCGGCGGCGCACATTGGAGTACCCTTTGGAGTCTAGTCAGTCAGAAGTTGGG ACTCATGAAACCGGTTCACCTTTCGTCACACCTGAGGTTGTTCACCAGCTCCTAGCTATGTTTC AAAATCCCTCTCTTCTGCTAATCTTTGCTATCATAGTTATGCATGTTTCTGTTGTTCCATATTT CAGGTAGCAGAAATTTCATTGCTCTGCACTGATAAACCACAGAGCTTAAATTGTGGTATGCACC ACACTTTAAATAATCTAGGTTTGTATTTTTCATTATATATGCTTAAACAGTGCCTCTAGTATTT GCTAATTGAAAATTTTACATCAGATACAATAAATTCCTTGTCAGATGAAGCACCCTACCAGCAA GAAGATATCCTTTTGGAACATTGCTCTTATGGAACGGCAGTGTACCTTGAGCCAGATCAAACGT TTGTCCCTCTCTGGTTCCACTGAAACCACTTTATTTGGCTCATTTATTTGTTAGTCGTGATATA TTCATCTCCTGCTTGCTGTAGACCTTGTAGCCAGCAGAGCATTGCATGTACAAATGATCAAGCT GGTATTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.130313187

Conservation Information
Conserved circRNAs	NA
PMCS	0.130313187

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							77707834-77707111(+)
77707133-77708051(+)
						
						Potential amino acid sequence
						
							MKHPTSKKISFWNIALMERQCTLSQIKHLVASRALHVQMIKLVFQSLGLDRTAL*(+)
MVAEISLLCTDKPQSLNCGMHHTLNNLDEAPYQQEDILLEHCSYGTAVYLEPDQTPCSQQSIAC
TNDQAGISVFGIGQNSIVNLTIQVMVAEISLLCTDKPQSLNCGMHHTLNNLDEAPYQQEDILLE
HCSYGTAVYLEPDQTPCSQQSIACTNDQAGISVFGIGQNSIVNLTIQVMVAEISLLCTDKPQSL
NCGMHHTLNNLDEAPYQQEDILLEHCSYGTAVYLEPDQTPCSQQSIACTNDQAGISVFGIGQNS
IVNLTIQVMVAEISLLCTDKPQSLNCGMHHTLNNLDEAPYQQEDILLEHCSYGTAVYLEPDQTP
CSQQSIACTNDQAGIS(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	77707834-77707111(+) 77707133-77708051(+)
Potential amino acid sequence	MKHPTSKKISFWNIALMERQCTLSQIKHLVASRALHVQMIKLVFQSLGLDRTAL*(+) MVAEISLLCTDKPQSLNCGMHHTLNNLDEAPYQQEDILLEHCSYGTAVYLEPDQTPCSQQSIAC TNDQAGISVFGIGQNSIVNLTIQVMVAEISLLCTDKPQSLNCGMHHTLNNLDEAPYQQEDILLE HCSYGTAVYLEPDQTPCSQQSIACTNDQAGISVFGIGQNSIVNLTIQVMVAEISLLCTDKPQSL NCGMHHTLNNLDEAPYQQEDILLEHCSYGTAVYLEPDQTPCSQQSIACTNDQAGISVFGIGQNS IVNLTIQVMVAEISLLCTDKPQSLNCGMHHTLNNLDEAPYQQEDILLEHCSYGTAVYLEPDQTP CSQQSIACTNDQAGIS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d004036_circ_g.3

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