Plant Circular RNA Database

Detail information of AT4G16310_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G16310_circ_g.1
					
						ID in PlantcircBase
						ath_circ_031191
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 9222876-9224311  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT4G16310						
					
						Parent gene annotation
						
							Lysine-specific histone demethylase 1 homolog 3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						seedlings
					
						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
						AT4G16310.4:3
AT4G16310.5:3
AT4G16310.1:3
AT4G16310.3:3
AT4G16310.2:3

General Information
CircRNA Name	AT4G16310_circ_g.1
ID in PlantcircBase	ath_circ_031191
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 9222876-9224311 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT4G16310
Parent gene annotation	Lysine-specific histone demethylase 1 homolog 3
Parent gene strand	+
Alternative splicing	NA
Support reads	3
Tissues	seedlings
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	AT4G16310.4:3 AT4G16310.5:3 AT4G16310.1:3 AT4G16310.3:3 AT4G16310.2:3

			
						 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  
						
							AGTTGTAGATTTTGTTGCATCGTTGCTTATGGCCCCGTATAGAGCAAAGAAAATTGATAGAGAT
GTATACAAGTCAATTATGAAGAAGACAGCAACAAAGgattcgatgggtaagaatggaacccagc
ttttacgtcactgtgtacatattcttgttcgagttacgagtgacctctttgccttgaggctatc
aggtattg

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							GATTCGATGGGTAAGAATGGAACCCAGCTTTTACGTCACTGTGTACATATTCTTGTTCGAGTTA
CGAGTGACCTCTTTGCCTTGAGGCTATCAGGTATTGGTTTTTCTTCCAAGTACACTTTTTGTCC
CAACCTAATATATCACATGCAATCAGTTCTGTCTTAAGACTCGACATCATGTGCTATCTGTTTT
GGGATTTCAGCCCTGTTTGATTTTCTCTAAGTTGGTTACTTTCCACTTGCTGATGCAGGTATTG
GGAAGACTGTGAAAGAAAAGGTTTGTGCACACACGAGCCGTGATATTCGTGCCATTGCAAGTCA
GCTTGTTAATGTGTGGCTGGATCTATACCGGAAAGAAAAAGCTAATAGTGGAAAGAAATCGTTG
AGACAAGCGAATACTACAAACACCTCTAGAATAAGAAGAAAACTGAATAGTCCGGACACAGACA
GTAAGGGAAAGCTGAGCAATGGCAACGATGTGAAAACAGATGAAGAGTTTGAGGACAACCAGCT
ACCTATGTCAGAGGAAGAGAAGGCTGTGTTTGCTGAAGCTGAGGCGGCTCGTGCAGCAGCAGAA
GCAGCTGCAAAGGCAAGTTTTTTTTAATCTCTAAATTAGTGAAAGGCATTTATGGATGCTTACT
GAATGTTTTTGTTTTCTCTGAGGCCGTTAACTCTTTATTTATCTGTTTGTTAACGAATAAATTA
TATGTTTCTGTCTTGCAGGCATTTTCTGAGGCCTATCATAATACTTCATTGCAGCTTCCTAAGA
TCCCCTCATTTCATAAGTTTGCCAGGCGAGAGCAGTATGCAAAGATGGACGAATCTGATTTCAG
GAAAAAGTTTCCTGGAAATGTCTTAGGAAGACAAGATTGTATGTCAGAGATTGACTCGAGGAAC
TGCAAAGTTAGGGACTGGTATGATTTTCCTGCCTCGTGCCTTGACCTTGACAGTGCAAGGATTC
CAGTTGATAACTATTCACAGCCTAGCCATTCGAATGAGCTTGTATCTCATTCGAAGTTCAGAGA
ATGTTCTGGAGAAAGTGTGGCTGCGGATACCAGTTTCTTAACTGGGGCATGGGTTGATACTGGT
GGTAGTAGCGATGGTTTCAAGGATTCTCAGGCTATAGATAGATGGCAATCTCAAGCTGCTGCTG
CTGATCCTGAATTTTTCAATCGTACTTTGCATATAAAGGATGAAGAAGATTCGATTGCTTGTTC
GACTGGCCCTCCTAGTTGGAAGCATGACCAACGAGCGAATGAATGTTCCGTGTCACAGGTTACA
GTGAATAAAGAGCCACATAAAAATCATATCCGGAGTGCAGATCGTTTGAAACAGGGAGTTGTAG
ATTTTGTTGCATCGTTGCTTATGGCCCCGTATAGAGCAAAGAAAATTGATAGAGATGTATACAA
GTCAATTATGAAGAAGACAGCAACAAAG

Sequences
Splice junction sequence	AGTTGTAGATTTTGTTGCATCGTTGCTTATGGCCCCGTATAGAGCAAAGAAAATTGATAGAGAT GTATACAAGTCAATTATGAAGAAGACAGCAACAAAGgattcgatgggtaagaatggaacccagc ttttacgtcactgtgtacatattcttgttcgagttacgagtgacctctttgccttgaggctatc aggtattg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GATTCGATGGGTAAGAATGGAACCCAGCTTTTACGTCACTGTGTACATATTCTTGTTCGAGTTA CGAGTGACCTCTTTGCCTTGAGGCTATCAGGTATTGGTTTTTCTTCCAAGTACACTTTTTGTCC CAACCTAATATATCACATGCAATCAGTTCTGTCTTAAGACTCGACATCATGTGCTATCTGTTTT GGGATTTCAGCCCTGTTTGATTTTCTCTAAGTTGGTTACTTTCCACTTGCTGATGCAGGTATTG GGAAGACTGTGAAAGAAAAGGTTTGTGCACACACGAGCCGTGATATTCGTGCCATTGCAAGTCA GCTTGTTAATGTGTGGCTGGATCTATACCGGAAAGAAAAAGCTAATAGTGGAAAGAAATCGTTG AGACAAGCGAATACTACAAACACCTCTAGAATAAGAAGAAAACTGAATAGTCCGGACACAGACA GTAAGGGAAAGCTGAGCAATGGCAACGATGTGAAAACAGATGAAGAGTTTGAGGACAACCAGCT ACCTATGTCAGAGGAAGAGAAGGCTGTGTTTGCTGAAGCTGAGGCGGCTCGTGCAGCAGCAGAA GCAGCTGCAAAGGCAAGTTTTTTTTAATCTCTAAATTAGTGAAAGGCATTTATGGATGCTTACT GAATGTTTTTGTTTTCTCTGAGGCCGTTAACTCTTTATTTATCTGTTTGTTAACGAATAAATTA TATGTTTCTGTCTTGCAGGCATTTTCTGAGGCCTATCATAATACTTCATTGCAGCTTCCTAAGA TCCCCTCATTTCATAAGTTTGCCAGGCGAGAGCAGTATGCAAAGATGGACGAATCTGATTTCAG GAAAAAGTTTCCTGGAAATGTCTTAGGAAGACAAGATTGTATGTCAGAGATTGACTCGAGGAAC TGCAAAGTTAGGGACTGGTATGATTTTCCTGCCTCGTGCCTTGACCTTGACAGTGCAAGGATTC CAGTTGATAACTATTCACAGCCTAGCCATTCGAATGAGCTTGTATCTCATTCGAAGTTCAGAGA ATGTTCTGGAGAAAGTGTGGCTGCGGATACCAGTTTCTTAACTGGGGCATGGGTTGATACTGGT GGTAGTAGCGATGGTTTCAAGGATTCTCAGGCTATAGATAGATGGCAATCTCAAGCTGCTGCTG CTGATCCTGAATTTTTCAATCGTACTTTGCATATAAAGGATGAAGAAGATTCGATTGCTTGTTC GACTGGCCCTCCTAGTTGGAAGCATGACCAACGAGCGAATGAATGTTCCGTGTCACAGGTTACA GTGAATAAAGAGCCACATAAAAATCATATCCGGAGTGCAGATCGTTTGAAACAGGGAGTTGTAG ATTTTGTTGCATCGTTGCTTATGGCCCCGTATAGAGCAAAGAAAATTGATAGAGATGTATACAA GTCAATTATGAAGAAGACAGCAACAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171205751

Conservation Information
Conserved circRNAs	NA
PMCS	0.171205751

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							9222882-9224308(+)
						
					

						Potential amino acid sequence
						
							MGKNGTQLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRK
EKANSGKKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFA
EAEAARAAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDC
MSEIDSRNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFL
TGAWVDTGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRAN
ECSVSQVTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATKDSMG
KNGTQLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRKEK
ANSGKKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFAEA
EAARAAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDCMS
EIDSRNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFLTG
AWVDTGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRANEC
SVSQVTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATKDSMGKN
GTQLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRKEKAN
SGKKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFAEAEA
ARAAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDCMSEI
DSRNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFLTGAW
VDTGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRANECSV
SQVTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATKDSMGKNGT
QLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRKEKANSG
KKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFAEAEAAR
AAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDCMSEIDS
RNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFLTGAWVD
TGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRANECSVSQ
VTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATK(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	9222882-9224308(+)
Potential amino acid sequence	MGKNGTQLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRK EKANSGKKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFA EAEAARAAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDC MSEIDSRNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFL TGAWVDTGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRAN ECSVSQVTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATKDSMG KNGTQLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRKEK ANSGKKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFAEA EAARAAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDCMS EIDSRNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFLTG AWVDTGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRANEC SVSQVTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATKDSMGKN GTQLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRKEKAN SGKKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFAEAEA ARAAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDCMSEI DSRNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFLTGAW VDTGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRANECSV SQVTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATKDSMGKNGT QLLRHCVHILVRVTSDLFALRLSGIGKTVKEKVCAHTSRDIRAIASQLVNVWLDLYRKEKANSG KKSLRQANTTNTSRIRRKLNSPDTDSKGKLSNGNDVKTDEEFEDNQLPMSEEEKAVFAEAEAAR AAAEAAAKAFSEAYHNTSLQLPKIPSFHKFARREQYAKMDESDFRKKFPGNVLGRQDCMSEIDS RNCKVRDWYDFPASCLDLDSARIPVDNYSQPSHSNELVSHSKFRECSGESVAADTSFLTGAWVD TGGSSDGFKDSQAIDRWQSQAAAADPEFFNRTLHIKDEEDSIACSTGPPSWKHDQRANECSVSQ VTVNKEPHKNHIRSADRLKQGVVDFVASLLMAPYRAKKIDRDVYKSIMKKTATK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Pan et al., 2017

circRNA

Detail information of AT4G16310_circ_g.1

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