Plant Circular RNA Database

Detail information of AT2G27170_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT2G27170_circ_g.2
					
						ID in PlantcircBase
						ath_circ_015148
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 11610308-11611492  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT2G27170						
					
						Parent gene annotation
						
							Structural maintenance of chromosomes protein 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G27170_circ_g.1 AT2G27170_circ_g.3 AT2G27170_circ_g.4 AT2G27170_circ_g.5 AT2G27170_circ_g.6 						
					
						Support reads
						3
					
						Tissues
						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-GC							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
						AT2G27170.3:5
AT2G27170.1:5
AT2G27170.2:5
AT2G27170.4:5

General Information
CircRNA Name	AT2G27170_circ_g.2
ID in PlantcircBase	ath_circ_015148
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 11610308-11611492 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT2G27170
Parent gene annotation	Structural maintenance of chromosomes protein 3
Parent gene strand	-
Alternative splicing	AT2G27170_circ_g.1 AT2G27170_circ_g.3 AT2G27170_circ_g.4 AT2G27170_circ_g.5 AT2G27170_circ_g.6
Support reads	3
Tissues	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-GC 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	AT2G27170.3:5 AT2G27170.1:5 AT2G27170.2:5 AT2G27170.4:5

			
						 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  
						
							TATCATCGTCGATGGAAGCTATAGTAGCCTGTAACTCAGTTATTCTCCTCTTTAAGTTGGTAGC
AATATTAGCCTCCAACTCTGCTTTTCTTGTCTCCCTctttttcttcataatgataaggttacca
tatccatcttgcacaagctcagagaatacatccctgaagtgatgtgcaacccctttgaaagtac
gttctata

									
								

					

						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: 723
Transcript exons: 11610308-11610454,11610536-11610704,11610909-11611060,11
611132-11611202,11611309-11611492
CTTTTTCTTCATAATGATAAGGTTACCATATCCATCTTGCACAAGCTCAGAGAATACATCCCTG
AAGTGATGTGCAACCCCTTTGAAAGTACGTTCTATAGATTCGTCTTTCCGCTGATCCAGAACTG
TTATCAGCTCTTTAATTTTCTCATCTCCTGCATCAAGCTCTGCTTGCCGATTTTGAAGTTCTTC
TCGCTGTTCTGTGAAATTCACATATTGATCCAGCGCTTTCTTGTTGACATGGCTGAATTGTTGC
AGCTGTTCACTGCACCGGTGTAGCATCTTCTGCAGCTCCTTGATATTTTTTCGTTTATACGTGT
CAAAAGCGTCAGATGACAATGGACCCAATCCCCTAATCTTCTTAGTATACTCATCTTGCTTAGC
AAGGAGCGTGTTGCGAAGGCTAAACAGTTCCTCCAACTTTTTATCTAAATCTTGTAGTGTCCCT
TTACAATCATCTTCCAATGTCTTTAACTTTGCTTTCTCATCTTTAATTTTCTTGATTTGCTTTG
TCTTCTCATCAATGCTGTCACAGACACTTTTGAGCTCTTTTGCAGCCTCATTGACCGACAATTT
TGCATCATCAAGTTCCTGTTCTTTTGTGCCAGCTGAACTAGGCAAACTATCATCGTCGATGGAA
GCTATAGTAGCCTGTAACTCAGTTATTCTCCTCTTTAAGTTGGTAGCAATATTAGCCTCCAACT
CTGCTTTTCTTGTCTCCCT
						
					

						Genomic sequence
						
							CTTTTTCTTCATAATGATAAGGTTACCATATCCATCTTGCACAAGCTCAGAGAATACATCCCTG
AAGTGATGTGCAACCCCTTTGAAAGTACGTTCTATAGATTCGTCTTTCCGCTGATCCAGAACTG
TTATCAGCTCTTTAATTTTCTGCGGAAACGATCATGAGTCAGTCAAGCTCTACTTTCTACATAG
AATTTGGCAAAGTGTATGAAACCTCCTATTATTTACCTCATCTCCTGCATCAAGCTCTGCTTGC
CGATTTTGAAGTTCTTCTCGCTGTTCTGTGAAATTCACATATTGATCCAGCGCTTTCTTGTTGA
CATGGCTGAATTGTTGCAGCTGTTCACTGCACCGGTGTAGCATCTTCTGCAGCTCCTTGATATT
TTTTCGTTTATACCTATAATGTTCAATAGCTTGTATATATTATAGAACTCCTAGGATAAAACTC
TCATGATACAACAATTGTCCACCAATGATGACTAAGAACTAACTGGACAAGATAAATGAAAATT
GGGACAGTATAACTATAAAAGTTCTAACTAGACTGAGTGCTGAACTTTCTGGATGCATAACCAA
TAAGAAAGAGAAGAAGCAAACATACGTGTCAAAAGCGTCAGATGACAATGGACCCAATCCCCTA
ATCTTCTTAGTATACTCATCTTGCTTAGCAAGGAGCGTGTTGCGAAGGCTAAACAGTTCCTCCA
ACTTTTTATCTAAATCTTGTAGTGTCCCTTTACAATCATCTTCCAATGTCTGAGAGAACAAGAA
ACTTTTGTTAGATAGAGAAAAACGCAGGTCTCTTACTTTATGATATATTATACTACCTTTAACT
TTGCTTTCTCATCTTTAATTTTCTTGATTTGCTTTGTCTTCTCATCAATGCTGTCACAGACACC
TAAAACACACAAAATGGCATTGAGTGTACTCGTCTGGATAGTAAATAGTAAAAGACCAAGATCA
AGCAATGCCAAGCAAAGTAGTTCAGAATGTTTGGGACCCACTTTTGAGCTCTTTTGCAGCCTCA
TTGACCGACAATTTTGCATCATCAAGTTCCTGTTCTTTTGTGCCAGCTGAACTAGGCAAACTAT
CATCGTCGATGGAAGCTATAGTAGCCTGTAACTCAGTTATTCTCCTCTTTAAGTTGGTAGCAAT
ATTAGCCTCCAACTCTGCTTTTCTTGTCTCCCT
						
					

			
		

Sequences
Splice junction sequence	TATCATCGTCGATGGAAGCTATAGTAGCCTGTAACTCAGTTATTCTCCTCTTTAAGTTGGTAGC AATATTAGCCTCCAACTCTGCTTTTCTTGTCTCCCTctttttcttcataatgataaggttacca tatccatcttgcacaagctcagagaatacatccctgaagtgatgtgcaacccctttgaaagtac gttctata
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: 723 Transcript exons: 11610308-11610454,11610536-11610704,11610909-11611060,11 611132-11611202,11611309-11611492 CTTTTTCTTCATAATGATAAGGTTACCATATCCATCTTGCACAAGCTCAGAGAATACATCCCTG AAGTGATGTGCAACCCCTTTGAAAGTACGTTCTATAGATTCGTCTTTCCGCTGATCCAGAACTG TTATCAGCTCTTTAATTTTCTCATCTCCTGCATCAAGCTCTGCTTGCCGATTTTGAAGTTCTTC TCGCTGTTCTGTGAAATTCACATATTGATCCAGCGCTTTCTTGTTGACATGGCTGAATTGTTGC AGCTGTTCACTGCACCGGTGTAGCATCTTCTGCAGCTCCTTGATATTTTTTCGTTTATACGTGT CAAAAGCGTCAGATGACAATGGACCCAATCCCCTAATCTTCTTAGTATACTCATCTTGCTTAGC AAGGAGCGTGTTGCGAAGGCTAAACAGTTCCTCCAACTTTTTATCTAAATCTTGTAGTGTCCCT TTACAATCATCTTCCAATGTCTTTAACTTTGCTTTCTCATCTTTAATTTTCTTGATTTGCTTTG TCTTCTCATCAATGCTGTCACAGACACTTTTGAGCTCTTTTGCAGCCTCATTGACCGACAATTT TGCATCATCAAGTTCCTGTTCTTTTGTGCCAGCTGAACTAGGCAAACTATCATCGTCGATGGAA GCTATAGTAGCCTGTAACTCAGTTATTCTCCTCTTTAAGTTGGTAGCAATATTAGCCTCCAACT CTGCTTTTCTTGTCTCCCT
Genomic sequence	CTTTTTCTTCATAATGATAAGGTTACCATATCCATCTTGCACAAGCTCAGAGAATACATCCCTG AAGTGATGTGCAACCCCTTTGAAAGTACGTTCTATAGATTCGTCTTTCCGCTGATCCAGAACTG TTATCAGCTCTTTAATTTTCTGCGGAAACGATCATGAGTCAGTCAAGCTCTACTTTCTACATAG AATTTGGCAAAGTGTATGAAACCTCCTATTATTTACCTCATCTCCTGCATCAAGCTCTGCTTGC CGATTTTGAAGTTCTTCTCGCTGTTCTGTGAAATTCACATATTGATCCAGCGCTTTCTTGTTGA CATGGCTGAATTGTTGCAGCTGTTCACTGCACCGGTGTAGCATCTTCTGCAGCTCCTTGATATT TTTTCGTTTATACCTATAATGTTCAATAGCTTGTATATATTATAGAACTCCTAGGATAAAACTC TCATGATACAACAATTGTCCACCAATGATGACTAAGAACTAACTGGACAAGATAAATGAAAATT GGGACAGTATAACTATAAAAGTTCTAACTAGACTGAGTGCTGAACTTTCTGGATGCATAACCAA TAAGAAAGAGAAGAAGCAAACATACGTGTCAAAAGCGTCAGATGACAATGGACCCAATCCCCTA ATCTTCTTAGTATACTCATCTTGCTTAGCAAGGAGCGTGTTGCGAAGGCTAAACAGTTCCTCCA ACTTTTTATCTAAATCTTGTAGTGTCCCTTTACAATCATCTTCCAATGTCTGAGAGAACAAGAA ACTTTTGTTAGATAGAGAAAAACGCAGGTCTCTTACTTTATGATATATTATACTACCTTTAACT TTGCTTTCTCATCTTTAATTTTCTTGATTTGCTTTGTCTTCTCATCAATGCTGTCACAGACACC TAAAACACACAAAATGGCATTGAGTGTACTCGTCTGGATAGTAAATAGTAAAAGACCAAGATCA AGCAATGCCAAGCAAAGTAGTTCAGAATGTTTGGGACCCACTTTTGAGCTCTTTTGCAGCCTCA TTGACCGACAATTTTGCATCATCAAGTTCCTGTTCTTTTGTGCCAGCTGAACTAGGCAAACTAT CATCGTCGATGGAAGCTATAGTAGCCTGTAACTCAGTTATTCTCCTCTTTAAGTTGGTAGCAAT ATTAGCCTCCAACTCTGCTTTTCTTGTCTCCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.203950936

Conservation Information
Conserved circRNAs	NA
PMCS	0.203950936

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11610671-11610310(-)
						
						Potential amino acid sequence
						
							MLHRCSEQLQQFSHVNKKALDQYVNFTEQREELQNRQAELDAGDEKIKELITVLDQRKDESIER
TFKGVAHHFRDVFSELVQDGYGNLIIMKKKRETRKAELEANIATNLKRRITELQATIASIDDDS
LPSSAGTKEQELDDAKLSVNEAAKELKSVCDSIDEKTKQIKKIKDEKAKLKTLEDDCKGTLQDL
DKKLEELFSLRNTLLAKQDEYTKKIRGLGPLSSDAFDTYKRKNIKELQKMLHRCSEQLQQFSHV
NKKALDQYVNFTEQREELQNRQAELDAGDEKIKELITVLDQRKDESIERTFKGVAHHFRDVFSE
LVQDGYGNLIIMKKKRETRKAELEANIATNLKRRITELQATIASIDDDSLPSSAGTKEQELDDA
KLSVNEAAKELKSVCDSIDEKTKQIKKIKDEKAKLKTLEDDCKGTLQDLDKKLEELFSLRNTLL
AKQDEYTKKIRGLGPLSSDAFDTYKRKNIKELQKMLHRCSEQLQQFSHVNKKALDQYVNFTEQR
EELQNRQAELDAGDEKIKELITVLDQRKDESIERTFKGVAHHFRDVFSELVQDGYGNLIIMKKK
RETRKAELEANIATNLKRRITELQATIASIDDDSLPSSAGTKEQELDDAKLSVNEAAKELKSVC
DSIDEKTKQIKKIKDEKAKLKTLEDDCKGTLQDLDKKLEELFSLRNTLLAKQDEYTKKIRGLGP
LSSDAFDTYKRKNIKELQKMLHRCSEQLQQFSHVNKKALDQYVNFTEQREELQNRQAELDAGDE
KIKELITVLDQRKDESIERTFKGVAHHFRDVFSELVQDGYGNLIIMKKK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11610671-11610310(-)
Potential amino acid sequence	MLHRCSEQLQQFSHVNKKALDQYVNFTEQREELQNRQAELDAGDEKIKELITVLDQRKDESIER TFKGVAHHFRDVFSELVQDGYGNLIIMKKKRETRKAELEANIATNLKRRITELQATIASIDDDS LPSSAGTKEQELDDAKLSVNEAAKELKSVCDSIDEKTKQIKKIKDEKAKLKTLEDDCKGTLQDL DKKLEELFSLRNTLLAKQDEYTKKIRGLGPLSSDAFDTYKRKNIKELQKMLHRCSEQLQQFSHV NKKALDQYVNFTEQREELQNRQAELDAGDEKIKELITVLDQRKDESIERTFKGVAHHFRDVFSE LVQDGYGNLIIMKKKRETRKAELEANIATNLKRRITELQATIASIDDDSLPSSAGTKEQELDDA KLSVNEAAKELKSVCDSIDEKTKQIKKIKDEKAKLKTLEDDCKGTLQDLDKKLEELFSLRNTLL AKQDEYTKKIRGLGPLSSDAFDTYKRKNIKELQKMLHRCSEQLQQFSHVNKKALDQYVNFTEQR EELQNRQAELDAGDEKIKELITVLDQRKDESIERTFKGVAHHFRDVFSELVQDGYGNLIIMKKK RETRKAELEANIATNLKRRITELQATIASIDDDSLPSSAGTKEQELDDAKLSVNEAAKELKSVC DSIDEKTKQIKKIKDEKAKLKTLEDDCKGTLQDLDKKLEELFSLRNTLLAKQDEYTKKIRGLGP LSSDAFDTYKRKNIKELQKMLHRCSEQLQQFSHVNKKALDQYVNFTEQREELQNRQAELDAGDE KIKELITVLDQRKDESIERTFKGVAHHFRDVFSELVQDGYGNLIIMKKK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT2G27170_circ_g.2

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