Plant Circular RNA Database

Detail information of AT1G55490_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G55490_circ_g.2
					
						ID in PlantcircBase
						ath_circ_007511
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20716046-20717754  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT1G55490						
					
						Parent gene annotation
						
							LEN1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G55490_circ_g.1 AT1G55490_circ_g.3 AT1G55490_circ_g.4 AT1G55490_circ_g.5 AT1G55490_circ_g.6 AT1G55490_circ_g.7 AT1G55490_circ_g.8 AT1G55490_circ_g.9 AT1G55490_circ_g.10 AT1G55490_circ_g.11 AT1G55490_circ_g.12 AT1G55490_circ_g.13 AT1G55490_circ_g.14 AT1G55490_circ_g.15 AT1G55490_circ_g.16 AT1G55490_circ_g.17 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						AT1G55490.5:8
AT1G55490.1:8
AT1G55490.2:8
AT1G55490.4:8
AT1G55490.3:8

General Information
CircRNA Name	AT1G55490_circ_g.2
ID in PlantcircBase	ath_circ_007511
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 20716046-20717754 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT1G55490
Parent gene annotation	LEN1
Parent gene strand	-
Alternative splicing	AT1G55490_circ_g.1 AT1G55490_circ_g.3 AT1G55490_circ_g.4 AT1G55490_circ_g.5 AT1G55490_circ_g.6 AT1G55490_circ_g.7 AT1G55490_circ_g.8 AT1G55490_circ_g.9 AT1G55490_circ_g.10 AT1G55490_circ_g.11 AT1G55490_circ_g.12 AT1G55490_circ_g.13 AT1G55490_circ_g.14 AT1G55490_circ_g.15 AT1G55490_circ_g.16 AT1G55490_circ_g.17
Support reads	1
Tissues	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	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	AT1G55490.5:8 AT1G55490.1:8 AT1G55490.2:8 AT1G55490.4:8 AT1G55490.3:8

			
						 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  
						
							TCCTGCCCACTTTGCTCATTGCTTCAGCAATCATATTTCCAATTTCGTCGTTGTTACCCGCACT
AACAGCTGCAACATCTGCAAGTTCACTGTCTTCAACctttgttggatcgatgattcctgcagcc
atcaaatcctcgtacttgccggttgcagcattgtaaccgaatttcacgttatcgttggaaagca
cctgccaa

									
								

					

						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
						
							CTTTGTTGGATCGATGATTCCTGCAGCCATCAAATCCTCGTACTTGCCGGTTGCAGCATTGTAA
CCGAATTTCACGTTATCGTTGGAAAGCACCTGCCAATGAATAGAGACATCTCTTCAAGCATCTG
ACTTGAAATCTAGAGATAAAAAAGTGGGAATTATGTTATCTGTTGTTATTACCTTCTCGCTAAC
TACACTTCCATTAACACCAGCATTCTTGGCGATTAGTTTTAGGGGGTAACTTAGTGCTCTTTTA
ACTATATCCGCTCCAACCTAAAGGGAATCATCAGCAAAGTTAGAGAAACCGAAGGTTCATGAGT
TAAAATCTGAAGACTTGATTGATTTACCTTTTCTTCATCATTATCAAGCGTGGCTTTAATGGCA
TCAACCTTGGAAGCAAGACGAAGCAGAGTGCAACCACCACCAACAACAATACCTTCCTCGACAG
CGGCCTGAAGAATTAAAATCCTGATTAGTTATAGTTCACGAGTATGCAAATAACACGCTTCTCA
AGCCTCAGAAATACAAAATCACCTTTGTTGCATTAAGAGCATCTTCAACTCTCAACTTCTTCTC
TTTGAGTTCTGTCTCAGTTTGTGCTCCAACCTTTAACCAATACATAACGAGCTTAACTTAATAT
CTCTGAAACACATCTTAATCAGACAAAGGAAACTTAAATAGTTTTTAGTTTACCTGAATCACAG
CAACTCCACCAGAGAGCTTTGCAATTCTCTCATTGAGTTTCTCCTTCTCGTAATCTTGCTCCGC
TTGCTGCACAAACCAATTACCATTGCAATGTAACTACACTATCCACAAAAAGTAAAAGAGGTCC
CATATATGCTATACTCTTTTACTATACCTCAATAAGATTTTTAATCTGTGTAACACGCTTTTTC
ACTGCATCCTGTGTGCTTCCATCACCCACTATGGTCGAGGTCTCCTTTGTGAGGACAACCTTTG
AAGCATTACCAAGAACCTCTTTTCCAGCTTTGTCAAGTGAAAGACCAACTTCCTCACGGATCAC
AGTTGCTGCAAGCGAAGATAGAAAATTAGGACAAGATAAAAACTACAAATATATGCGTAAACAT
AGGGCTCATCAATGCAGACAGAACTTACCTCCAGTTAGAATGGCAATATCATCAAGGTATTGGC
TCTTGCGCTCTCCAAACCCTGGAGCTCTGAGAGCTGCTATCTTCAGTGTACCTCTAAGCTTGTT
TACAACAAGAGTCGCTAAAGCTTCTTGTTCAATGTCTTCAGCAATAATTAATATTGGGTATCCG
CCTCTAATTGCATCCTCCAAAACACCAACAAGATCCCTTGCATTGGTAATTTTCTTGTCAACGA
GAAGTAACTGCAATCATACCAAAACATTAAAGATCGTTGTTATACTCATATATAAATATCTTTA
GTGGCTAAATAGTCTGCCAACAAAATTCATCTTCTACTCAGATTCAAGAAACATCTACCTTGCA
ATTGTCGAACTCGACGGACATTTTCTCGCTGTCTGTCACAAAGTAAGGAGAGATATAACCACGG
TCAAATTGCATTCCTTCTACGACGTAGAGGTTGTTCTCGGCACTTTTACCCTCCTCAAGGGTCA
CCACACCTTTCCTGCCCACTTTGCTCATTGCTTCAGCAATCATATTTCCAATTTCGTCGTTGTT
ACCCGCACTAACAGCTGCAACATCTGCAAGTTCACTGTCTTCAAC
						
					

			
		

Sequences
Splice junction sequence	TCCTGCCCACTTTGCTCATTGCTTCAGCAATCATATTTCCAATTTCGTCGTTGTTACCCGCACT AACAGCTGCAACATCTGCAAGTTCACTGTCTTCAACctttgttggatcgatgattcctgcagcc atcaaatcctcgtacttgccggttgcagcattgtaaccgaatttcacgttatcgttggaaagca cctgccaa
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	CTTTGTTGGATCGATGATTCCTGCAGCCATCAAATCCTCGTACTTGCCGGTTGCAGCATTGTAA CCGAATTTCACGTTATCGTTGGAAAGCACCTGCCAATGAATAGAGACATCTCTTCAAGCATCTG ACTTGAAATCTAGAGATAAAAAAGTGGGAATTATGTTATCTGTTGTTATTACCTTCTCGCTAAC TACACTTCCATTAACACCAGCATTCTTGGCGATTAGTTTTAGGGGGTAACTTAGTGCTCTTTTA ACTATATCCGCTCCAACCTAAAGGGAATCATCAGCAAAGTTAGAGAAACCGAAGGTTCATGAGT TAAAATCTGAAGACTTGATTGATTTACCTTTTCTTCATCATTATCAAGCGTGGCTTTAATGGCA TCAACCTTGGAAGCAAGACGAAGCAGAGTGCAACCACCACCAACAACAATACCTTCCTCGACAG CGGCCTGAAGAATTAAAATCCTGATTAGTTATAGTTCACGAGTATGCAAATAACACGCTTCTCA AGCCTCAGAAATACAAAATCACCTTTGTTGCATTAAGAGCATCTTCAACTCTCAACTTCTTCTC TTTGAGTTCTGTCTCAGTTTGTGCTCCAACCTTTAACCAATACATAACGAGCTTAACTTAATAT CTCTGAAACACATCTTAATCAGACAAAGGAAACTTAAATAGTTTTTAGTTTACCTGAATCACAG CAACTCCACCAGAGAGCTTTGCAATTCTCTCATTGAGTTTCTCCTTCTCGTAATCTTGCTCCGC TTGCTGCACAAACCAATTACCATTGCAATGTAACTACACTATCCACAAAAAGTAAAAGAGGTCC CATATATGCTATACTCTTTTACTATACCTCAATAAGATTTTTAATCTGTGTAACACGCTTTTTC ACTGCATCCTGTGTGCTTCCATCACCCACTATGGTCGAGGTCTCCTTTGTGAGGACAACCTTTG AAGCATTACCAAGAACCTCTTTTCCAGCTTTGTCAAGTGAAAGACCAACTTCCTCACGGATCAC AGTTGCTGCAAGCGAAGATAGAAAATTAGGACAAGATAAAAACTACAAATATATGCGTAAACAT AGGGCTCATCAATGCAGACAGAACTTACCTCCAGTTAGAATGGCAATATCATCAAGGTATTGGC TCTTGCGCTCTCCAAACCCTGGAGCTCTGAGAGCTGCTATCTTCAGTGTACCTCTAAGCTTGTT TACAACAAGAGTCGCTAAAGCTTCTTGTTCAATGTCTTCAGCAATAATTAATATTGGGTATCCG CCTCTAATTGCATCCTCCAAAACACCAACAAGATCCCTTGCATTGGTAATTTTCTTGTCAACGA GAAGTAACTGCAATCATACCAAAACATTAAAGATCGTTGTTATACTCATATATAAATATCTTTA GTGGCTAAATAGTCTGCCAACAAAATTCATCTTCTACTCAGATTCAAGAAACATCTACCTTGCA ATTGTCGAACTCGACGGACATTTTCTCGCTGTCTGTCACAAAGTAAGGAGAGATATAACCACGG TCAAATTGCATTCCTTCTACGACGTAGAGGTTGTTCTCGGCACTTTTACCCTCCTCAAGGGTCA CCACACCTTTCCTGCCCACTTTGCTCATTGCTTCAGCAATCATATTTCCAATTTCGTCGTTGTT ACCCGCACTAACAGCTGCAACATCTGCAAGTTCACTGTCTTCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.263716063

Conservation Information
Conserved circRNAs	NA
PMCS	0.263716063

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							20717689-20716048(-)
						
					

						Potential amino acid sequence
						
							MIAEAMSKVGRKGVVTLEEGKSAENNLYVVEGMQFDRGYISPYFVTDSEKMSVEFDNCKLLLVD
KKITNARDLVGVLEDAIRGGYPILIIAEDIEQEALATLVVNKLRGTLKIAALRAPGFGERKSQY
LDDIAILTGATVIREEVGLSLDKAGKEVLGNASKVVLTKETSTIVGDGSTQDAVKKRVTQIKNL
IEQAEQDYEKEKLNERIAKLSGGVAVIQVGAQTETELKEKKLRVEDALNATKAAVEEGIVVGGG
CTLLRLASKVDAIKATLDNDEEKVGADIVKRALSYPLKLIAKNAGVNGSVVSEKVLSNDNVKFG
YNAATGKYEDLMAAGIIDPTKVEDSELADVAAVSAGNNDEIGNMIAEAMSKVGRKGVVTLEEGK
SAENNLYVVEGMQFDRGYISPYFVTDSEKMSVEFDNCKLLLVDKKITNARDLVGVLEDAIRGGY
PILIIAEDIEQEALATLVVNKLRGTLKIAALRAPGFGERKSQYLDDIAILTGATVIREEVGLSL
DKAGKEVLGNASKVVLTKETSTIVGDGSTQDAVKKRVTQIKNLIEQAEQDYEKEKLNERIAKLS
GGVAVIQVGAQTETELKEKKLRVEDALNATKAAVEEGIVVGGGCTLLRLASKVDAIKATLDNDE
EKVGADIVKRALSYPLKLIAKNAGVNGSVVSEKVLSNDNVKFGYNAATGKYEDLMAAGIIDPTK
VEDSELADVAAVSAGNNDEIGNMIAEAMSKVGRKGVVTLEEGKSAENNLYVVEGMQFDRGYISP
YFVTDSEKMSVEFDNCKLLLVDKKITNARDLVGVLEDAIRGGYPILIIAEDIEQEALATLVVNK
LRGTLKIAALRAPGFGERKSQYLDDIAILTGATVIREEVGLSLDKAGKEVLGNASKVVLTKETS
TIVGDGSTQDAVKKRVTQIKNLIEQAEQDYEKEKLNERIAKLSGGVAVIQVGAQTETELKEKKL
RVEDALNATKAAVEEGIVVGGGCTLLRLASKVDAIKATLDNDEEKVGADIVKRALSYPLKLIAK
NAGVNGSVVSEKVLSNDNVKFGYNAATGKYEDLMAAGIIDPTKVEDSELADVAAVSAGNNDEIG
NMIAEAMSKVGRKGVVTLEEGKSAENNLYVVEGMQFDRGYISPYFVTDSEKMSVEFDNCKLLLV
DKKITNARDLVGVLEDAIRGGYPILIIAEDIEQEALATLVVNKLRGTLKIAALRAPGFGERKSQ
YLDDIAILTGATVIREEVGLSLDKAGKEVLGNASKVVLTKETSTIVGDGSTQDAVKKRVTQIKN
LIEQAEQDYEKEKLNERIAKLSGGVAVIQVGAQTETELKEKKLRVEDALNATKAAVEEGIVVGG
GCTLLRLASKVDAIKATLDNDEEKVGADIVKRALSYPLKLIAKNAGVNGSVVSEKVLSNDNVKF
GYNAATGKYEDLMAAGIIDPTK(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	20717689-20716048(-)
Potential amino acid sequence	MIAEAMSKVGRKGVVTLEEGKSAENNLYVVEGMQFDRGYISPYFVTDSEKMSVEFDNCKLLLVD KKITNARDLVGVLEDAIRGGYPILIIAEDIEQEALATLVVNKLRGTLKIAALRAPGFGERKSQY LDDIAILTGATVIREEVGLSLDKAGKEVLGNASKVVLTKETSTIVGDGSTQDAVKKRVTQIKNL IEQAEQDYEKEKLNERIAKLSGGVAVIQVGAQTETELKEKKLRVEDALNATKAAVEEGIVVGGG CTLLRLASKVDAIKATLDNDEEKVGADIVKRALSYPLKLIAKNAGVNGSVVSEKVLSNDNVKFG YNAATGKYEDLMAAGIIDPTKVEDSELADVAAVSAGNNDEIGNMIAEAMSKVGRKGVVTLEEGK SAENNLYVVEGMQFDRGYISPYFVTDSEKMSVEFDNCKLLLVDKKITNARDLVGVLEDAIRGGY PILIIAEDIEQEALATLVVNKLRGTLKIAALRAPGFGERKSQYLDDIAILTGATVIREEVGLSL DKAGKEVLGNASKVVLTKETSTIVGDGSTQDAVKKRVTQIKNLIEQAEQDYEKEKLNERIAKLS GGVAVIQVGAQTETELKEKKLRVEDALNATKAAVEEGIVVGGGCTLLRLASKVDAIKATLDNDE EKVGADIVKRALSYPLKLIAKNAGVNGSVVSEKVLSNDNVKFGYNAATGKYEDLMAAGIIDPTK VEDSELADVAAVSAGNNDEIGNMIAEAMSKVGRKGVVTLEEGKSAENNLYVVEGMQFDRGYISP YFVTDSEKMSVEFDNCKLLLVDKKITNARDLVGVLEDAIRGGYPILIIAEDIEQEALATLVVNK LRGTLKIAALRAPGFGERKSQYLDDIAILTGATVIREEVGLSLDKAGKEVLGNASKVVLTKETS TIVGDGSTQDAVKKRVTQIKNLIEQAEQDYEKEKLNERIAKLSGGVAVIQVGAQTETELKEKKL RVEDALNATKAAVEEGIVVGGGCTLLRLASKVDAIKATLDNDEEKVGADIVKRALSYPLKLIAK NAGVNGSVVSEKVLSNDNVKFGYNAATGKYEDLMAAGIIDPTKVEDSELADVAAVSAGNNDEIG NMIAEAMSKVGRKGVVTLEEGKSAENNLYVVEGMQFDRGYISPYFVTDSEKMSVEFDNCKLLLV DKKITNARDLVGVLEDAIRGGYPILIIAEDIEQEALATLVVNKLRGTLKIAALRAPGFGERKSQ YLDDIAILTGATVIREEVGLSLDKAGKEVLGNASKVVLTKETSTIVGDGSTQDAVKKRVTQIKN LIEQAEQDYEKEKLNERIAKLSGGVAVIQVGAQTETELKEKKLRVEDALNATKAAVEEGIVVGG GCTLLRLASKVDAIKATLDNDEEKVGADIVKRALSYPLKLIAKNAGVNGSVVSEKVLSNDNVKF GYNAATGKYEDLMAAGIIDPTK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G55490_circ_g.2

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