Plant Circular RNA Database

Detail information of Zm00001d025011_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d025011_circ_g.1
					
						ID in PlantcircBase
						zma_circ_010264
					
						Alias
						Zm10circ00033, GRMZM2G019246_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 99636972-99637622  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d025011						
					
						Parent gene annotation
						
							Polyketide cyclase/dehydrase and lipid transport superfamily pro
tein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d025011_T001:3
Zm00001d025011_T003:2
Zm00001d025011_T002:3

General Information
CircRNA Name	Zm00001d025011_circ_g.1
ID in PlantcircBase	zma_circ_010264
Alias	Zm10circ00033, GRMZM2G019246_C1
Organism	Zea mays
Position	chr10: 99636972-99637622 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d025011
Parent gene annotation	Polyketide cyclase/dehydrase and lipid transport superfamily pro tein
Parent gene strand	-
Alternative splicing	NA
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	Zm00001d025011_T001:3 Zm00001d025011_T003:2 Zm00001d025011_T002:3

			
						 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  
						
							GTCCTTCTCGTCGACGAGCCGCCAGAGGTGCAGCAAGTCACCGGTGTTGACCGCCAGCTGCTGC
TGCTCGTCCTCGGCCGCCGCATGAGCCACCACAGTTcttggtcacacagtaaaatgtcttccca
gacgcccatatcctgcggcctatgatgtactccctgtcgctgcagaagaacgggaactgcacgc
gagaacca

						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: 445
Transcript exons: 99636972-99637055,99637158-99637340,99637445-99637622
CTTGGTCACACAGTAAAATGTCTTCCCAGACGCCCATATCCTGCGGCCTATGATGTACTCCCTG
TCGCTGCAGAAGAACGGGAACTTCCTGACCCACCGGACCACCATGGTTCCAGTCTCGGTGCACT
CCTCCAGCGTCTCGTGCTGAAGAAGCATGTCGTCCCAGCTGTTCTTCATCCGGAACTCATCGTC
CCAGAAGAAATCTCTCACAACCTCCGGTGACGCGTCCTCGAAGATTGTGCTGCTGCGGTACTGT
GGTGGACCACTCGGTGGGTCTCTCCGCCAGGCTTGGTACCTCATGGTTGGTAAGGTGCGGTCCA
TCATGTGAATCCACGACGGGCCACCGTCCTTCTCGTCGACGAGCCGCCAGAGGTGCAGCAAGTC
ACCGGTGTTGACCGCCAGCTGCTGCTGCTCGTCCTCGGCCGCCGCATGAGCCACCACAGTT
						
						Genomic sequence
						
							CTTGGTCACACAGTAAAATGTCTTCCCAGACGCCCATATCCTGCGGCCTATGATGTACTCCCTG
TCGCTGCAGAAGAACGGGAACTGCACGCGAGAACCACGCATCGTCGGTTTATATAAGCAGCCTG
CGCCATGGTTTGAGCTCAATAATCACCAGCAGAGATGTGTGGATGCAGAACGGCTCACCTTCCT
GACCCACCGGACCACCATGGTTCCAGTCTCGGTGCACTCCTCCAGCGTCTCGTGCTGAAGAAGC
ATGTCGTCCCAGCTGTTCTTCATCCGGAACTCATCGTCCCAGAAGAAATCTCTCACAACCTCCG
GTGACGCGTCCTCGAAGATTGTGCTGCTGCGGTACTGTGGTGGACCACTCTGGAATGAAACAAA
CACACACACACACAAATAAATAAATCAATTCGACGAGTTCTCTCTAGCCATTTAACAGTGGGAT
GAAGAAAAGACTTGCTGCTGCATACCGGTGGGTCTCTCCGCCAGGCTTGGTACCTCATGGTTGG
TAAGGTGCGGTCCATCATGTGAATCCACGACGGGCCACCGTCCTTCTCGTCGACGAGCCGCCAG
AGGTGCAGCAAGTCACCGGTGTTGACCGCCAGCTGCTGCTGCTCGTCCTCGGCCGCCGCATGAG
CCACCACAGTT

Sequences
Splice junction sequence	GTCCTTCTCGTCGACGAGCCGCCAGAGGTGCAGCAAGTCACCGGTGTTGACCGCCAGCTGCTGC TGCTCGTCCTCGGCCGCCGCATGAGCCACCACAGTTcttggtcacacagtaaaatgtcttccca gacgcccatatcctgcggcctatgatgtactccctgtcgctgcagaagaacgggaactgcacgc gagaacca
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: 445 Transcript exons: 99636972-99637055,99637158-99637340,99637445-99637622 CTTGGTCACACAGTAAAATGTCTTCCCAGACGCCCATATCCTGCGGCCTATGATGTACTCCCTG TCGCTGCAGAAGAACGGGAACTTCCTGACCCACCGGACCACCATGGTTCCAGTCTCGGTGCACT CCTCCAGCGTCTCGTGCTGAAGAAGCATGTCGTCCCAGCTGTTCTTCATCCGGAACTCATCGTC CCAGAAGAAATCTCTCACAACCTCCGGTGACGCGTCCTCGAAGATTGTGCTGCTGCGGTACTGT GGTGGACCACTCGGTGGGTCTCTCCGCCAGGCTTGGTACCTCATGGTTGGTAAGGTGCGGTCCA TCATGTGAATCCACGACGGGCCACCGTCCTTCTCGTCGACGAGCCGCCAGAGGTGCAGCAAGTC ACCGGTGTTGACCGCCAGCTGCTGCTGCTCGTCCTCGGCCGCCGCATGAGCCACCACAGTT
Genomic sequence	CTTGGTCACACAGTAAAATGTCTTCCCAGACGCCCATATCCTGCGGCCTATGATGTACTCCCTG TCGCTGCAGAAGAACGGGAACTGCACGCGAGAACCACGCATCGTCGGTTTATATAAGCAGCCTG CGCCATGGTTTGAGCTCAATAATCACCAGCAGAGATGTGTGGATGCAGAACGGCTCACCTTCCT GACCCACCGGACCACCATGGTTCCAGTCTCGGTGCACTCCTCCAGCGTCTCGTGCTGAAGAAGC ATGTCGTCCCAGCTGTTCTTCATCCGGAACTCATCGTCCCAGAAGAAATCTCTCACAACCTCCG GTGACGCGTCCTCGAAGATTGTGCTGCTGCGGTACTGTGGTGGACCACTCTGGAATGAAACAAA CACACACACACACAAATAAATAAATCAATTCGACGAGTTCTCTCTAGCCATTTAACAGTGGGAT GAAGAAAAGACTTGCTGCTGCATACCGGTGGGTCTCTCCGCCAGGCTTGGTACCTCATGGTTGG TAAGGTGCGGTCCATCATGTGAATCCACGACGGGCCACCGTCCTTCTCGTCGACGAGCCGCCAG AGGTGCAGCAAGTCACCGGTGTTGACCGCCAGCTGCTGCTGCTCGTCCTCGGCCGCCGCATGAG CCACCACAGTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.313225666

Conservation Information
Conserved circRNAs	NA
PMCS	0.313225666

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							99637608-99637021(+)
99637010-99637500(-)
99637503-99637562(-)
						
						Potential amino acid sequence
						
							MSHHSSWSHSKMSSQTPISCGL*(+)
MGVWEDILLCDQELWWLMRRPRTSSSSWRSTPVTCCTSGGSSTRRTVARRGFT*(-)
MMDRTLPTMRYQAWRRDPPSGPPQYRSSTIFEDASPEVVRDFFWDDEFRMKNSWDDMLLQHETL
EECTETGTMVVRWVRKFPFFCSDREYIIGRRIWASGKTFYCVTKNCGGSCGGRGRAAAAGGQHR
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	99637608-99637021(+) 99637010-99637500(-) 99637503-99637562(-)
Potential amino acid sequence	MSHHSSWSHSKMSSQTPISCGL(+) MGVWEDILLCDQELWWLMRRPRTSSSSWRSTPVTCCTSGGSSTRRTVARRGFT(-) MMDRTLPTMRYQAWRRDPPSGPPQYRSSTIFEDASPEVVRDFFWDDEFRMKNSWDDMLLQHETL EECTETGTMVVRWVRKFPFFCSDREYIIGRRIWASGKTFYCVTKNCGGSCGGRGRAAAAGGQHR *(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d025011_circ_g.1

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