Plant Circular RNA Database

Detail information of AT5G18230_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT5G18230_circ_g.5
					
						ID in PlantcircBase
						ath_circ_038947
					
						Alias
						AT5G18230_C3
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6022253-6022516  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, CIRI2
					
						Parent gene
						
							AT5G18230						
					
						Parent gene annotation
						
							transcription regulator NOT2/NOT3/NOT5 family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G18230_circ_g.6 AT5G18230_circ_g.7 AT5G18230_circ_g.8 AT5G18230_circ_g.9 AT5G18230_circ_g.10 AT5G18230_circ_g.11 AT5G18230_circ_g.12 AT5G18230_circ_g.13 AT5G18230_circ_g.14 AT5G18230_circ_g.15 AT5G18230_circ_g.16 AT5G18230_circ_g.17 AT5G18230_circ_g.18 AT5G18230_circ_g.19 						
					
						Support reads
						28
					
						Tissues
						leaf, whole_plant
					
						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
						AT5G18230.3:1
AT5G18230.1:1
AT5G18230.2:1
AT5G18230.4:1

General Information
CircRNA Name	AT5G18230_circ_g.5
ID in PlantcircBase	ath_circ_038947
Alias	AT5G18230_C3
Organism	Arabidpsis thaliana
Position	chr5: 6022253-6022516 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, CIRI2
Parent gene	AT5G18230
Parent gene annotation	transcription regulator NOT2/NOT3/NOT5 family protein
Parent gene strand	-
Alternative splicing	AT5G18230_circ_g.6 AT5G18230_circ_g.7 AT5G18230_circ_g.8 AT5G18230_circ_g.9 AT5G18230_circ_g.10 AT5G18230_circ_g.11 AT5G18230_circ_g.12 AT5G18230_circ_g.13 AT5G18230_circ_g.14 AT5G18230_circ_g.15 AT5G18230_circ_g.16 AT5G18230_circ_g.17 AT5G18230_circ_g.18 AT5G18230_circ_g.19
Support reads	28
Tissues	leaf, whole_plant
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	AT5G18230.3:1 AT5G18230.1:1 AT5G18230.2:1 AT5G18230.4:1

			
						 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  
						
							GGCTACTTGAAGATTGACCCGGTTGTATAGGTTGTCCAGGAGAGAAATCAGGACCGCTAGATAC
TTGTACTGGATCCAACATGTAGCTGGGCATTCCCGAcggagaatagggtctaggacgttctgaa
tctgagggttgaggacgtttgtaaaaagcagcttcaagcatctggagattgtgcatttgatcat
gcattggc

						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: 239
Transcript exons: 6022253-6022307,6022328-6022452,6022458-6022516
CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAATTGTGCAT
TTGATCATGCATTGGCCCTACAGCTGAAGGGTCACCAATGGCTCCTAACTCAGAGTTACTTCTC
CGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTATAGGTTGTCGAGAAATCAGGA
CCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGCATTCCCGA
Transcript length: 244
Transcript exons: 6022253-6022364,6022385-6022516
CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAGCAGCTTCA
AGCATCTGGAGATTGTGCATTTGATCATGCATTGGCCCTACAGCTGAACTCAGAGTTACTTCTC
CGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTATAGGTTGTCCAGGAGAGAAAT
CAGGACCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGCATTCCCGA
Transcript length: 264
Transcript exons: 6022253-6022516
CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAGCAGCTTCA
AGCATCTGGAGATTGTGCATTTGATCATGCATTGGCCCTACAGCTGAAGGGTCACCAATGGCTC
CTAACTCAGAGTTACTTCTCCGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTAT
AGGTTGTCCAGGAGAGAAATCAGGACCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGC
ATTCCCGA
						
						Genomic sequence
						
							CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAGCAGCTTCA
AGCATCTGGAGATTGTGCATTTGATCATGCATTGGCCCTACAGCTGAAGGGTCACCAATGGCTC
CTAACTCAGAGTTACTTCTCCGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTAT
AGGTTGTCCAGGAGAGAAATCAGGACCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGC
ATTCCCGA

Sequences
Splice junction sequence	GGCTACTTGAAGATTGACCCGGTTGTATAGGTTGTCCAGGAGAGAAATCAGGACCGCTAGATAC TTGTACTGGATCCAACATGTAGCTGGGCATTCCCGAcggagaatagggtctaggacgttctgaa tctgagggttgaggacgtttgtaaaaagcagcttcaagcatctggagattgtgcatttgatcat gcattggc
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: 239 Transcript exons: 6022253-6022307,6022328-6022452,6022458-6022516 CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAATTGTGCAT TTGATCATGCATTGGCCCTACAGCTGAAGGGTCACCAATGGCTCCTAACTCAGAGTTACTTCTC CGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTATAGGTTGTCGAGAAATCAGGA CCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGCATTCCCGA Transcript length: 244 Transcript exons: 6022253-6022364,6022385-6022516 CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAGCAGCTTCA AGCATCTGGAGATTGTGCATTTGATCATGCATTGGCCCTACAGCTGAACTCAGAGTTACTTCTC CGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTATAGGTTGTCCAGGAGAGAAAT CAGGACCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGCATTCCCGA Transcript length: 264 Transcript exons: 6022253-6022516 CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAGCAGCTTCA AGCATCTGGAGATTGTGCATTTGATCATGCATTGGCCCTACAGCTGAAGGGTCACCAATGGCTC CTAACTCAGAGTTACTTCTCCGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTAT AGGTTGTCCAGGAGAGAAATCAGGACCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGC ATTCCCGA
Genomic sequence	CGGAGAATAGGGTCTAGGACGTTCTGAATCTGAGGGTTGAGGACGTTTGTAAAAAGCAGCTTCA AGCATCTGGAGATTGTGCATTTGATCATGCATTGGCCCTACAGCTGAAGGGTCACCAATGGCTC CTAACTCAGAGTTACTTCTCCGTCCAATGACCCCGAGGCTACTTGAAGATTGACCCGGTTGTAT AGGTTGTCCAGGAGAGAAATCAGGACCGCTAGATACTTGTACTGGATCCAACATGTAGCTGGGC ATTCCCGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.670573527

Conservation Information
Conserved circRNAs	NA
PMCS	0.670573527

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6022511-6022255(-)
						
						Potential amino acid sequence
						
							MPSYMLDPVQVSSGPDFSPGQPIQPGQSSSSLGVIGRRSNSELGAIGDPSAVGPMHDQMHNLQM
LEAAFYKRPQPSDSERPRPYSPSGMPSYMLDPVQVSSGPDFSPGQPIQPGQSSSSLGVIGRRSN
SELGAIGDPSAVGPMHDQMHNLQMLEAAFYKRPQPSDSERPRPYSPSGMPSYMLDPVQVSSGPD
FSPGQPIQPGQSSSSLGVIGRRSNSELGAIGDPSAVGPMHDQMHNLQMLEAAFYKRPQPSDSER
PRPYSPSGMPSYMLDPVQVSSGPDFSPGQPIQPGQSSSSLGVIGRRSNSELGAIGDPSAVGPMH
DQMHNLQMLEAAFYKRPQPSDSERPRPYSP(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	6022511-6022255(-)
Potential amino acid sequence	MPSYMLDPVQVSSGPDFSPGQPIQPGQSSSSLGVIGRRSNSELGAIGDPSAVGPMHDQMHNLQM LEAAFYKRPQPSDSERPRPYSPSGMPSYMLDPVQVSSGPDFSPGQPIQPGQSSSSLGVIGRRSN SELGAIGDPSAVGPMHDQMHNLQMLEAAFYKRPQPSDSERPRPYSPSGMPSYMLDPVQVSSGPD FSPGQPIQPGQSSSSLGVIGRRSNSELGAIGDPSAVGPMHDQMHNLQMLEAAFYKRPQPSDSER PRPYSPSGMPSYMLDPVQVSSGPDFSPGQPIQPGQSSSSLGVIGRRSNSELGAIGDPSAVGPMH DQMHNLQMLEAAFYKRPQPSDSERPRPYSP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Chu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT5G18230_circ_g.5

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