Plant Circular RNA Database

Detail information of Zm00001d036986_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d036986_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009001
					
						Alias
						zma_circ_0002289, GRMZM2G029506_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 108329536-108330183  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d036986						
					
						Parent gene annotation
						
							ABC transporter G family member 29
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d036986_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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  
						
							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
						Zm00001d036986_T009:2
Zm00001d036986_T003:2
Zm00001d036986_T010:1
Zm00001d036986_T005:2
Zm00001d036986_T002:2
Zm00001d036986_T007:2
Zm00001d036986_T001:2

General Information
CircRNA Name	Zm00001d036986_circ_g.2
ID in PlantcircBase	zma_circ_009001
Alias	zma_circ_0002289, GRMZM2G029506_C1
Organism	Zea mays
Position	chr6: 108329536-108330183 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d036986
Parent gene annotation	ABC transporter G family member 29
Parent gene strand	+
Alternative splicing	Zm00001d036986_circ_g.1
Support reads	NA
Tissues	leaf, 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	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	Zm00001d036986_T009:2 Zm00001d036986_T003:2 Zm00001d036986_T010:1 Zm00001d036986_T005:2 Zm00001d036986_T002:2 Zm00001d036986_T007:2 Zm00001d036986_T001:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F:CTTATGACGGAGCTGGCCAG
 R:CGGAACCCGTTGTAGGAGAC
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	Yes 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	F:CTTATGACGGAGCTGGCCAG R:CGGAACCCGTTGTAGGAGAC 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  
						
							ATGCGTGCCGTGTCGACCATCAGATCTTATGACGGAGCTGGCCAGGAGGGAGAAGGGGGCCGGC
ATCCGGCCGGAGCCTGAAGTCGACCTCTTCATGAAGggtgggcatcgagctgccgacggtggag
gtgcggttcgagcggctgacggtggaggccaggtgccacgtgggcagccgcgcgctgccgacgc
tgctgaac

						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: 541
Transcript exons: 108329536-108329999,108330107-108330183
GGTGGGCATCGAGCTGCCGACGGTGGAGGTGCGGTTCGAGCGGCTGACGGTGGAGGCCAGGTGC
CACGTGGGCAGCCGCGCGCTGCCGACGCTGCTGAACACGGCGCGCAACGTCGCGGAGGCGGCGC
TGGGCCTGTGCGGCGTGCGGCTGGGGGGCCGGCAGGCCAGGCTGACCATCCTCAGGGACGTGTC
CGGCGCCGTCCGCCCGTCCAGGATGACGCTGCTGCTTGGCCCGCCGTCGTCCGGGAAGACCACG
CTGCTGCTGGCCCTCGCGGGCAAGCTGGACCCGGCGCTGGTCGTCGCCGGCGGCGGCGAGGTCT
CCTACAACGGGTTCCGCCTCGGCGAGTTCGTGCCGCAGAAGACGGCGGCGTACATCAGCCAGAC
GGACGTGCACGTCGGCGAGATGACGGTCAAGGAGACGCTCGACTTCTCCGCCCGGTGCCAGGGC
GTCGGCACCAAATACGATCTTATGACGGAGCTGGCCAGGAGGGAGAAGGGGGCCGGCATCCGGC
CGGAGCCTGAAGTCGACCTCTTCATGAAG
						
						Genomic sequence
						
							GGTGGGCATCGAGCTGCCGACGGTGGAGGTGCGGTTCGAGCGGCTGACGGTGGAGGCCAGGTGC
CACGTGGGCAGCCGCGCGCTGCCGACGCTGCTGAACACGGCGCGCAACGTCGCGGAGGCGGCGC
TGGGCCTGTGCGGCGTGCGGCTGGGGGGCCGGCAGGCCAGGCTGACCATCCTCAGGGACGTGTC
CGGCGCCGTCCGCCCGTCCAGGATGACGCTGCTGCTTGGCCCGCCGTCGTCCGGGAAGACCACG
CTGCTGCTGGCCCTCGCGGGCAAGCTGGACCCGGCGCTGGTCGTCGCCGGCGGCGGCGAGGTCT
CCTACAACGGGTTCCGCCTCGGCGAGTTCGTGCCGCAGAAGACGGCGGCGTACATCAGCCAGAC
GGACGTGCACGTCGGCGAGATGACGGTCAAGGAGACGCTCGACTTCTCCGCCCGGTGCCAGGGC
GTCGGCACCAAATACGGTACGCCGGCGGCCTTATTGTGTTTTCGATTTGACGTACGGACGACGG
CACGATGCACGGTGCCAGGGCGTTTTTTGACGATGGATGCGTGCCGTGTCGACCATCAGATCTT
ATGACGGAGCTGGCCAGGAGGGAGAAGGGGGCCGGCATCCGGCCGGAGCCTGAAGTCGACCTCT
TCATGAAG

Sequences
Splice junction sequence	ATGCGTGCCGTGTCGACCATCAGATCTTATGACGGAGCTGGCCAGGAGGGAGAAGGGGGCCGGC ATCCGGCCGGAGCCTGAAGTCGACCTCTTCATGAAGggtgggcatcgagctgccgacggtggag gtgcggttcgagcggctgacggtggaggccaggtgccacgtgggcagccgcgcgctgccgacgc tgctgaac
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: 541 Transcript exons: 108329536-108329999,108330107-108330183 GGTGGGCATCGAGCTGCCGACGGTGGAGGTGCGGTTCGAGCGGCTGACGGTGGAGGCCAGGTGC CACGTGGGCAGCCGCGCGCTGCCGACGCTGCTGAACACGGCGCGCAACGTCGCGGAGGCGGCGC TGGGCCTGTGCGGCGTGCGGCTGGGGGGCCGGCAGGCCAGGCTGACCATCCTCAGGGACGTGTC CGGCGCCGTCCGCCCGTCCAGGATGACGCTGCTGCTTGGCCCGCCGTCGTCCGGGAAGACCACG CTGCTGCTGGCCCTCGCGGGCAAGCTGGACCCGGCGCTGGTCGTCGCCGGCGGCGGCGAGGTCT CCTACAACGGGTTCCGCCTCGGCGAGTTCGTGCCGCAGAAGACGGCGGCGTACATCAGCCAGAC GGACGTGCACGTCGGCGAGATGACGGTCAAGGAGACGCTCGACTTCTCCGCCCGGTGCCAGGGC GTCGGCACCAAATACGATCTTATGACGGAGCTGGCCAGGAGGGAGAAGGGGGCCGGCATCCGGC CGGAGCCTGAAGTCGACCTCTTCATGAAG
Genomic sequence	GGTGGGCATCGAGCTGCCGACGGTGGAGGTGCGGTTCGAGCGGCTGACGGTGGAGGCCAGGTGC CACGTGGGCAGCCGCGCGCTGCCGACGCTGCTGAACACGGCGCGCAACGTCGCGGAGGCGGCGC TGGGCCTGTGCGGCGTGCGGCTGGGGGGCCGGCAGGCCAGGCTGACCATCCTCAGGGACGTGTC CGGCGCCGTCCGCCCGTCCAGGATGACGCTGCTGCTTGGCCCGCCGTCGTCCGGGAAGACCACG CTGCTGCTGGCCCTCGCGGGCAAGCTGGACCCGGCGCTGGTCGTCGCCGGCGGCGGCGAGGTCT CCTACAACGGGTTCCGCCTCGGCGAGTTCGTGCCGCAGAAGACGGCGGCGTACATCAGCCAGAC GGACGTGCACGTCGGCGAGATGACGGTCAAGGAGACGCTCGACTTCTCCGCCCGGTGCCAGGGC GTCGGCACCAAATACGGTACGCCGGCGGCCTTATTGTGTTTTCGATTTGACGTACGGACGACGG CACGATGCACGGTGCCAGGGCGTTTTTTGACGATGGATGCGTGCCGTGTCGACCATCAGATCTT ATGACGGAGCTGGCCAGGAGGGAGAAGGGGGCCGGCATCCGGCCGGAGCCTGAAGTCGACCTCT TCATGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.273537013

Conservation Information
Conserved circRNAs	NA
PMCS	0.273537013

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							108329751-108330161(+)
108329714-108330178(-)
						
						Potential amino acid sequence
						
							MTLLLGPPSSGKTTLLLALAGKLDPALVVAGGGEVSYNGFRLGEFVPQKTAAYISQTDVHVGEM
TVKETLDFSARCQGVGTKYDLMTELARREKGAGIRPEPEVDLFMKGGHRAADGGGAVRAADGGG
QVPRGQPRAADAAEHGAQRRGGGAGPVRRAAGGPAGQADHPQGRVRRRPPVQDDAAAWPAVVRE
DHAAAGPRGQAGPGAGRRRRRRGLLQRVPPRRVRAAEDGGVHQPDGRARRRDDGQGDARLLRPV
PGRRHQIRSYDGAGQEGEGGRHPAGA*(+)
MVSLACRPPSRTPHRPSAASATLRAVFSSVGSARLPTWHLASTVSRSNRTSTVGSSMPTLHEEV
DFRLRPDAGPLLPPGQLRHKIVFGADALAPGGEVERLLDRHLADVHVRLADVRRRLLRHELAEA
EPVVGDLAAAGDDQRRVQLAREGQQQRGLPGRRRAKQQRHPGRADGAGHVPEDGQPGLPAPQPH
AAQAQRRLRDVARRVQQRRQRAAAHVAPGLHRQPLEPHLHRRQLDAHPS*(-)
						
						Sponge-miRNAs
						
							zma-miR394b-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	108329751-108330161(+) 108329714-108330178(-)
Potential amino acid sequence	MTLLLGPPSSGKTTLLLALAGKLDPALVVAGGGEVSYNGFRLGEFVPQKTAAYISQTDVHVGEM TVKETLDFSARCQGVGTKYDLMTELARREKGAGIRPEPEVDLFMKGGHRAADGGGAVRAADGGG QVPRGQPRAADAAEHGAQRRGGGAGPVRRAAGGPAGQADHPQGRVRRRPPVQDDAAAWPAVVRE DHAAAGPRGQAGPGAGRRRRRRGLLQRVPPRRVRAAEDGGVHQPDGRARRRDDGQGDARLLRPV PGRRHQIRSYDGAGQEGEGGRHPAGA(+) MVSLACRPPSRTPHRPSAASATLRAVFSSVGSARLPTWHLASTVSRSNRTSTVGSSMPTLHEEV DFRLRPDAGPLLPPGQLRHKIVFGADALAPGGEVERLLDRHLADVHVRLADVRRRLLRHELAEA EPVVGDLAAAGDDQRRVQLAREGQQQRGLPGRRRAKQQRHPGRADGAGHVPEDGQPGLPAPQPH AAQAQRRLRDVARRVQQRRQRAAAHVAPGLHRQPLEPHLHRRQLDAHPS(-)
Sponge-miRNAs	zma-miR394b-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d036986_circ_g.2

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