Plant Circular RNA Database

Detail information of AT1G03860_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G03860_circ_g.3
					
						ID in PlantcircBase
						ath_circ_000496
					
						Alias
						Ath_circ_FC0160, AT1G03860_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 980778-981160  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT1G03860						
					
						Parent gene annotation
						
							PHB2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G03860_circ_g.1 AT1G03860_circ_g.2 						
					
						Support reads
						25
					
						Tissues
						root, leaf, aerial, inflorescences, 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
						AT1G03860.2:1
AT1G03860.3:2
AT1G03860.1:2

General Information
CircRNA Name	AT1G03860_circ_g.3
ID in PlantcircBase	ath_circ_000496
Alias	Ath_circ_FC0160, AT1G03860_C1
Organism	Arabidpsis thaliana
Position	chr1: 980778-981160 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
Parent gene	AT1G03860
Parent gene annotation	PHB2
Parent gene strand	-
Alternative splicing	AT1G03860_circ_g.1 AT1G03860_circ_g.2
Support reads	25
Tissues	root, leaf, aerial, inflorescences, 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	AT1G03860.2:1 AT1G03860.3:2 AT1G03860.1:2

			
						 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  
						
							TAAGGGCATAGACACCGAGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGC
TCCAGGAATGTTGGGAACTTTGTTGAAACTCATTTCcatctgaagatcatgactaccagtggtg
ctctctacaaggtaaggtcgtgcacgaacgtcatagatgattggcctttcaaaccatggcacca
taaaatgt

									
								

					

						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: 207
Transcript exons: 980778-980884,981061-981160
CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG
ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTTAAGGGCATAGACACCGAGCC
CACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAACTTT
GTTGAAACTCATTTC
Transcript length: 227
Transcript exons: 980778-980880,981037-981160
CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG
ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCATCGACATTGTAGAGACTATTAGT
AAGGGCATAGACACCGAGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCT
CCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC
Transcript length: 275
Transcript exons: 980778-980878,980987-981160
CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG
ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGCTTTTCCTTGATACCAGTTAATCGGTT
GAACATGACAGCACGGTGTCCTCCATCGACATTGTAGAGACTATTAGTAAGGGCATAGACACCG
AGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAA
CTTTGTTGAAACTCATTTC
Transcript length: 291
Transcript exons: 980778-980894,980987-981160
CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG
ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTCTGGGTACACCTTTTCCTTGA
TACCAGTTAATCGGTTGAACATGACAGCACGGTGTCCTCCATCGACATTGTAGAGACTATTAGT
AAGGGCATAGACACCGAGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCT
CCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC
Transcript length: 383
Transcript exons: 980778-981160
CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG
ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTCTGGGTACACCTGAAAACACA
AATCCAAGTAAAAGTAACGCTTTCTTAGAATTCAAAGCCTCAGATATAAAAGTACATCTTGTTA
GTTTGAGAAATACAAACCTTTTCCTTGATACCAGTTAATCGGTTGAACATGACAGCACGGTGTC
CTCCATCGACATTGTAGAGACTATTAGTAAGGGCATAGACACCGAGCCCACCAATAACGCTGAC
CTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC
						
					

						Genomic sequence
						
							CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG
ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTCTGGGTACACCTGAAAACACA
AATCCAAGTAAAAGTAACGCTTTCTTAGAATTCAAAGCCTCAGATATAAAAGTACATCTTGTTA
GTTTGAGAAATACAAACCTTTTCCTTGATACCAGTTAATCGGTTGAACATGACAGCACGGTGTC
CTCCATCGACATTGTAGAGACTATTAGTAAGGGCATAGACACCGAGCCCACCAATAACGCTGAC
CTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC
						
					

			
		

Sequences
Splice junction sequence	TAAGGGCATAGACACCGAGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGC TCCAGGAATGTTGGGAACTTTGTTGAAACTCATTTCcatctgaagatcatgactaccagtggtg ctctctacaaggtaaggtcgtgcacgaacgtcatagatgattggcctttcaaaccatggcacca taaaatgt
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: 207 Transcript exons: 980778-980884,981061-981160 CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTTAAGGGCATAGACACCGAGCC CACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAACTTT GTTGAAACTCATTTC Transcript length: 227 Transcript exons: 980778-980880,981037-981160 CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCATCGACATTGTAGAGACTATTAGT AAGGGCATAGACACCGAGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCT CCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC Transcript length: 275 Transcript exons: 980778-980878,980987-981160 CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGCTTTTCCTTGATACCAGTTAATCGGTT GAACATGACAGCACGGTGTCCTCCATCGACATTGTAGAGACTATTAGTAAGGGCATAGACACCG AGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAA CTTTGTTGAAACTCATTTC Transcript length: 291 Transcript exons: 980778-980894,980987-981160 CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTCTGGGTACACCTTTTCCTTGA TACCAGTTAATCGGTTGAACATGACAGCACGGTGTCCTCCATCGACATTGTAGAGACTATTAGT AAGGGCATAGACACCGAGCCCACCAATAACGCTGACCTTAAGAAGGGCAGAGAGAGCAGGAGCT CCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC Transcript length: 383 Transcript exons: 980778-981160 CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTCTGGGTACACCTGAAAACACA AATCCAAGTAAAAGTAACGCTTTCTTAGAATTCAAAGCCTCAGATATAAAAGTACATCTTGTTA GTTTGAGAAATACAAACCTTTTCCTTGATACCAGTTAATCGGTTGAACATGACAGCACGGTGTC CTCCATCGACATTGTAGAGACTATTAGTAAGGGCATAGACACCGAGCCCACCAATAACGCTGAC CTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC
Genomic sequence	CATCTGAAGATCATGACTACCAGTGGTGCTCTCTACAAGGTAAGGTCGTGCACGAACGTCATAG ATGATTGGCCTTTCAAACCATGGCACCATAAAATGTGTGCCTTCTGGGTACACCTGAAAACACA AATCCAAGTAAAAGTAACGCTTTCTTAGAATTCAAAGCCTCAGATATAAAAGTACATCTTGTTA GTTTGAGAAATACAAACCTTTTCCTTGATACCAGTTAATCGGTTGAACATGACAGCACGGTGTC CTCCATCGACATTGTAGAGACTATTAGTAAGGGCATAGACACCGAGCCCACCAATAACGCTGAC CTTAAGAAGGGCAGAGAGAGCAGGAGCTCCAGGAATGTTGGGAACTTTGTTGAAACTCATTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.561597313

Conservation Information
Conserved circRNAs	NA
PMCS	0.561597313

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							981158-980780(-)
						
						Potential amino acid sequence
						
							MSFNKVPNIPGAPALSALLKVSVIGGLGVYALTNSLYNVDGGHRAVMFNRLTGIKEKVYPEGTH
FMVPWFERPIIYDVRARPYLVESTTGSHDLQMEMSFNKVPNIPGAPALSALLKVSVIGGLGVYA
LTNSLYNVDGGHRAVMFNRLTGIKEKVYPEGTHFMVPWFERPIIYDVRARPYLVESTTGSHDLQ
MEMSFNKVPNIPGAPALSALLKVSVIGGLGVYALTNSLYNVDGGHRAVMFNRLTGIKEKVYPEG
THFMVPWFERPIIYDVRARPYLVESTTGSHDLQMEMSFNKVPNIPGAPALSALLKVSVIGGLGV
YALTNSLYNVDGGHRAVMFNRLTGIKEKVYPEGTHFMVPWFERPIIYDVRARPYLVESTTGSHD
LQM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	981158-980780(-)
Potential amino acid sequence	MSFNKVPNIPGAPALSALLKVSVIGGLGVYALTNSLYNVDGGHRAVMFNRLTGIKEKVYPEGTH FMVPWFERPIIYDVRARPYLVESTTGSHDLQMEMSFNKVPNIPGAPALSALLKVSVIGGLGVYA LTNSLYNVDGGHRAVMFNRLTGIKEKVYPEGTHFMVPWFERPIIYDVRARPYLVESTTGSHDLQ MEMSFNKVPNIPGAPALSALLKVSVIGGLGVYALTNSLYNVDGGHRAVMFNRLTGIKEKVYPEG THFMVPWFERPIIYDVRARPYLVESTTGSHDLQMEMSFNKVPNIPGAPALSALLKVSVIGGLGV YALTNSLYNVDGGHRAVMFNRLTGIKEKVYPEGTHFMVPWFERPIIYDVRARPYLVESTTGSHD LQM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT1G03860_circ_g.3

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