Plant Circular RNA Database

Detail information of Zm00001d010309_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d010309_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009661
					
						Alias
						zma_circ_0002786
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 109072072-109072540  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d010309						
					
						Parent gene annotation
						
							Squamosa promoter-binding protein-like (SBP domain) transcriptio
n factor family protein  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d010309_circ_g.1 Zm00001d010309_circ_g.3 						
					
						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
						Zm00001d010309_T004:2
Zm00001d010309_T001:2
Zm00001d010309_T005:2
Zm00001d010309_T008:2
Zm00001d010309_T003:2
Zm00001d010309_T002:2
Zm00001d010309_T009:2
Zm00001d010309_T006:2
Zm00001d010309_T007:2

General Information
CircRNA Name	Zm00001d010309_circ_g.2
ID in PlantcircBase	zma_circ_009661
Alias	zma_circ_0002786
Organism	Zea mays
Position	chr8: 109072072-109072540 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d010309
Parent gene annotation	Squamosa promoter-binding protein-like (SBP domain) transcriptio n factor family protein
Parent gene strand	+
Alternative splicing	Zm00001d010309_circ_g.1 Zm00001d010309_circ_g.3
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	Zm00001d010309_T004:2 Zm00001d010309_T001:2 Zm00001d010309_T005:2 Zm00001d010309_T008:2 Zm00001d010309_T003:2 Zm00001d010309_T002:2 Zm00001d010309_T009:2 Zm00001d010309_T006:2 Zm00001d010309_T007:2

			
						 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  
						
							AGTAATGTTATACTGTCCATTCTAGTGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGG
AATCCTGCAGAATTTCCTCGACGACTACGACACCAGagaacatggaaggcataaccagtgagat
tcttgagactgttcttagcaacaaggtgatggacagagaaacacctgtgggatctgaagatgtg
cttagttc

						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: 329
Transcript exons: 109072072-109072325,109072466-109072540
AGAACATGGAAGGCATAACCAGTGAGATTCTTGAGACTGTTCTTAGCAACAAGGTGATGGACAG
AGAAACACCTGTGGGATCTGAAGATGTGCTTAGTTCACCAACCTGTACACAACCTTGTTTGCAA
AATGACCAAAGTAAAAGTGTAGTTACCTTTGCAGCTTCTGTTGAAGCCTGCATTGGTGCAAAGC
AGGAAAGCATAAAACTTGCCAATTCCCCAATGCATGACACCAAGAGTGCATATTCATCCTCGTG
TCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTTCCTCGACGACTA
CGACACCAG
						
						Genomic sequence
						
							AGAACATGGAAGGCATAACCAGTGAGATTCTTGAGACTGTTCTTAGCAACAAGGTGATGGACAG
AGAAACACCTGTGGGATCTGAAGATGTGCTTAGTTCACCAACCTGTACACAACCTTGTTTGCAA
AATGACCAAAGTAAAAGTGTAGTTACCTTTGCAGCTTCTGTTGAAGCCTGCATTGGTGCAAAGC
AGGAAAGCATAAAACTTGCCAATTCCCCAATGCATGACACCAAGAGTGCATATTCATCCTCGGT
AGGACCTTTTCTTTGTTCTCATGAAGTTGTTTATTTTTATAATATGTACGATTTTGCAGTTGCA
ATCTGTTTAGGTTGATGGAATTTTTTATCCCTTCCACTCTAATGGTTGTAGTAATGTTATACTG
TCCATTCTAGTGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTT
CCTCGACGACTACGACACCAG

Sequences
Splice junction sequence	AGTAATGTTATACTGTCCATTCTAGTGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGG AATCCTGCAGAATTTCCTCGACGACTACGACACCAGagaacatggaaggcataaccagtgagat tcttgagactgttcttagcaacaaggtgatggacagagaaacacctgtgggatctgaagatgtg cttagttc
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: 329 Transcript exons: 109072072-109072325,109072466-109072540 AGAACATGGAAGGCATAACCAGTGAGATTCTTGAGACTGTTCTTAGCAACAAGGTGATGGACAG AGAAACACCTGTGGGATCTGAAGATGTGCTTAGTTCACCAACCTGTACACAACCTTGTTTGCAA AATGACCAAAGTAAAAGTGTAGTTACCTTTGCAGCTTCTGTTGAAGCCTGCATTGGTGCAAAGC AGGAAAGCATAAAACTTGCCAATTCCCCAATGCATGACACCAAGAGTGCATATTCATCCTCGTG TCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTTCCTCGACGACTA CGACACCAG
Genomic sequence	AGAACATGGAAGGCATAACCAGTGAGATTCTTGAGACTGTTCTTAGCAACAAGGTGATGGACAG AGAAACACCTGTGGGATCTGAAGATGTGCTTAGTTCACCAACCTGTACACAACCTTGTTTGCAA AATGACCAAAGTAAAAGTGTAGTTACCTTTGCAGCTTCTGTTGAAGCCTGCATTGGTGCAAAGC AGGAAAGCATAAAACTTGCCAATTCCCCAATGCATGACACCAAGAGTGCATATTCATCCTCGGT AGGACCTTTTCTTTGTTCTCATGAAGTTGTTTATTTTTATAATATGTACGATTTTGCAGTTGCA ATCTGTTTAGGTTGATGGAATTTTTTATCCCTTCCACTCTAATGGTTGTAGTAATGTTATACTG TCCATTCTAGTGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTT CCTCGACGACTACGACACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.218902583

Conservation Information
Conserved circRNAs	NA
PMCS	0.218902583

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							109072298-109072093(+)
109072078-109072086(+)
109072484-109072490(-)
						
						Potential amino acid sequence
						
							MTPRVHIHPRVQQGASHSSCMIGILQNFLDDYDTREHGRHNQ*(+)
MEGITSEILETVLSNKVMDRETPVGSEDVLSSPTCTQPCLQNDQSKSVVTFAASVEACIGAKQE
SIKLANSPMHDTKSAYSSSCPTGRISFKLYDWNPAEFPRRLRHQRTWKA*(+)
MRPVGHEDEYALLVSCIGELASFMLSCFAPMQASTEAAKVTTLLLWSFCKQGCVQVGELSTSSD
PTGVSLSITLLLRTVSRISLVMPSMFSGVVVVEEILQDSNHTT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	109072298-109072093(+) 109072078-109072086(+) 109072484-109072490(-)
Potential amino acid sequence	MTPRVHIHPRVQQGASHSSCMIGILQNFLDDYDTREHGRHNQ(+) MEGITSEILETVLSNKVMDRETPVGSEDVLSSPTCTQPCLQNDQSKSVVTFAASVEACIGAKQE SIKLANSPMHDTKSAYSSSCPTGRISFKLYDWNPAEFPRRLRHQRTWKA(+) MRPVGHEDEYALLVSCIGELASFMLSCFAPMQASTEAAKVTTLLLWSFCKQGCVQVGELSTSSD PTGVSLSITLLLRTVSRISLVMPSMFSGVVVVEEILQDSNHTT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d010309_circ_g.2

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