Plant Circular RNA Database

Detail information of AT4G08920_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G08920_circ_g.3
					
						ID in PlantcircBase
						ath_circ_029992
					
						Alias
						At_ciR2541
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 5724761-5726551  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT4G08920						
					
						Parent gene annotation
						
							Cryptochrome-1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G08920_circ_g.1 AT4G08920_circ_g.2 4_circ_ag.4 AT4G08920_circ_g.5 AT4G08920_circ_g.6 AT4G08920_circ_g.7 						
					
						Support reads
						3/47/5
					
						Tissues
						leaf/leaf, aerial, whole_plant/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
						AT4G08920.1:2

General Information
CircRNA Name	AT4G08920_circ_g.3
ID in PlantcircBase	ath_circ_029992
Alias	At_ciR2541
Organism	Arabidpsis thaliana
Position	chr4: 5724761-5726551 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT4G08920
Parent gene annotation	Cryptochrome-1
Parent gene strand	+
Alternative splicing	AT4G08920_circ_g.1 AT4G08920_circ_g.2 4_circ_ag.4 AT4G08920_circ_g.5 AT4G08920_circ_g.6 AT4G08920_circ_g.7
Support reads	3/47/5
Tissues	leaf/leaf, aerial, whole_plant/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	AT4G08920.1:2

			
						 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  
						
							TCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTACAACGTCTAGCTACTTGCAGAATCACCA
TGAAATACTGAACTGGAGACGGCTTTCACAAACCGGatccattgtctttggtgcgtgatcaccg
agctaaagatgttttgacggcgcaaggcatagcggttcgatcattcaacgcagacttgctttat
gagccatg

									
								

					

						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: 1708
Transcript exons: 5724761-5724979,5725063-5726551
ATCCATTGTCTTTGGTGCGTGATCACCGAGCTAAAGATGTTTTGACGGCGCAAGGCATAGCGGT
TCGATCATTCAACGCAGACTTGCTTTATGAGCCATGGGAAGTGACTGATGAATTAGGCCGTCCT
TTCTCTATGTTTGCTGCGTTTTGGGAGAGATGTCTTAGTATGCCTTATGACCCTGAGTCTCCTC
TTCTTCCACCTAAGAAGATCATTTCAGGGGATGTGTCTAAATGTGTTGCGGATCCATTGGTGTT
TGAGGATGACTCTGAGAAAGGAAGCAATGCACTTCTGGCTCGTGCTTGGTCTCCTGGATGGAGT
AATGGTGATAAAGCTCTCACAACGTTTATAAACGGTCCATTGCTTGAATACTCTAAGAACCGCA
GAAAAGCCGATAGTGCTACAACCTCGTTTCTTTCTCCACACTTGCATTTTGGGGAAGTGAGTGT
GAGAAAAGTTTTTCATCTTGTTCGGATCAAACAGGTCGCGTGGGCAAACGAAGGAAACGAGGCC
GGGGAAGAAAGCGTGAATCTTTTCCTGAAATCTATTGGTCTCAGGGAGTATTCTAGGTACATAA
GTTTTAACCATCCATATTCCCATGAAAGACCACTTCTTGGCCATCTAAAGTTCTTCCCTTGGGC
TGTGGATGAGAACTATTTCAAGGCATGGAGGCAAGGCCGGACTGGATATCCGTTGGTCGATGCC
GGGATGAGAGAGTTATGGGCTACTGGTTGGTTGCATGATCGCATAAGAGTAGTTGTTTCAAGCT
TCTTTGTTAAAGTGCTTCAATTACCATGGAGATGGGGGATGAAGTATTTCTGGGACACACTTCT
TGATGCGGATTTAGAAAGCGATGCTCTTGGTTGGCAATACATTACCGGTACTCTCCCGGATAGC
CGGGAGTTTGATCGCATAGATAACCCTCAGTTTGAAGGGTACAAGTTTGATCCAAATGGTGAAT
ACGTAAGGCGATGGCTTCCTGAACTCTCTAGACTCCCGACAGACTGGATACATCATCCGTGGAA
CGCACCTGAGTCCGTTCTTCAAGCTGCTGGTATCGAGCTTGGATCAAACTATCCTCTACCAATT
GTAGGATTAGACGAAGCAAAAGCACGGCTTCATGAAGCGCTTTCACAGATGTGGCAACTAGAAG
CTGCTTCAAGAGCTGCAATAGAGAACGGATCCGAAGAAGGACTTGGAGATTCTGCTGAGGTAGA
GGAAGCTCCTATAGAGTTCCCAAGGGACATTACAATGGAAGAGACTGAACCAACCAGACTCAAC
CCAAACAGGAGATATGAGGATCAGATGGTTCCAAGCATTACTTCTTCTTTGATCAGACCTGAAG
AAGACGAAGAGTCGTCTCTTAATTTGAGAAATTCAGTAGGAGATAGCAGAGCAGAGGTTCCAAG
GAACATGGTTAACACCAACCAAGCTCAGCAGCGGAGAGCAGAACCGGCTTCAAACCAAGTCACT
GCTATGATTCCAGAATTTAATATCAGAATTGTTGCAGAGAGCACTGAAGACTCAACAGCGGAAT
CTTCCAGCAGCGGAAGGAGAGAAAGAAGCGGAGGCATAGTCCCCGAGTGGTCTCCAGGGTACTC
AGAGCAGTTCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTACAACGTCTAGCTACTTGCAG
AATCACCATGAAATACTGAACTGGAGACGGCTTTCACAAACCGG
Transcript length: 183
Transcript exons: 5724761-5724811,5726420-5726551
ATCCATTGTCTTTGGTGCGTGATCACCGAGCTAAAGATGTTTTGACGGCGCCCCCGAGTGGTCT
CCAGGGTACTCAGAGCAGTTCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTACAACGTCTA
GCTACTTGCAGAATCACCATGAAATACTGAACTGGAGACGGCTTTCACAAACCGG
						
					

						Genomic sequence
						
							ATCCATTGTCTTTGGTGCGTGATCACCGAGCTAAAGATGTTTTGACGGCGCAAGGCATAGCGGT
TCGATCATTCAACGCAGACTTGCTTTATGAGCCATGGGAAGTGACTGATGAATTAGGCCGTCCT
TTCTCTATGTTTGCTGCGTTTTGGGAGAGATGTCTTAGTATGCCTTATGACCCTGAGTCTCCTC
TTCTTCCACCTAAGAAGATCATTTCAGGTTTGTTTCTTTGCCACTCTCTCTTGTGGGTTTTCGT
TTTTTCCAAATCTGTATCATTCAATAATGTTTCTTTTATGTTGCAGGGGATGTGTCTAAATGTG
TTGCGGATCCATTGGTGTTTGAGGATGACTCTGAGAAAGGAAGCAATGCACTTCTGGCTCGTGC
TTGGTCTCCTGGATGGAGTAATGGTGATAAAGCTCTCACAACGTTTATAAACGGTCCATTGCTT
GAATACTCTAAGAACCGCAGAAAAGCCGATAGTGCTACAACCTCGTTTCTTTCTCCACACTTGC
ATTTTGGGGAAGTGAGTGTGAGAAAAGTTTTTCATCTTGTTCGGATCAAACAGGTCGCGTGGGC
AAACGAAGGAAACGAGGCCGGGGAAGAAAGCGTGAATCTTTTCCTGAAATCTATTGGTCTCAGG
GAGTATTCTAGGTACATAAGTTTTAACCATCCATATTCCCATGAAAGACCACTTCTTGGCCATC
TAAAGTTCTTCCCTTGGGCTGTGGATGAGAACTATTTCAAGGCATGGAGGCAAGGCCGGACTGG
ATATCCGTTGGTCGATGCCGGGATGAGAGAGTTATGGGCTACTGGTTGGTTGCATGATCGCATA
AGAGTAGTTGTTTCAAGCTTCTTTGTTAAAGTGCTTCAATTACCATGGAGATGGGGGATGAAGT
ATTTCTGGGACACACTTCTTGATGCGGATTTAGAAAGCGATGCTCTTGGTTGGCAATACATTAC
CGGTACTCTCCCGGATAGCCGGGAGTTTGATCGCATAGATAACCCTCAGTTTGAAGGGTACAAG
TTTGATCCAAATGGTGAATACGTAAGGCGATGGCTTCCTGAACTCTCTAGACTCCCGACAGACT
GGATACATCATCCGTGGAACGCACCTGAGTCCGTTCTTCAAGCTGCTGGTATCGAGCTTGGATC
AAACTATCCTCTACCAATTGTAGGATTAGACGAAGCAAAAGCACGGCTTCATGAAGCGCTTTCA
CAGATGTGGCAACTAGAAGCTGCTTCAAGAGCTGCAATAGAGAACGGATCCGAAGAAGGACTTG
GAGATTCTGCTGAGGTAGAGGAAGCTCCTATAGAGTTCCCAAGGGACATTACAATGGAAGAGAC
TGAACCAACCAGACTCAACCCAAACAGGAGATATGAGGATCAGATGGTTCCAAGCATTACTTCT
TCTTTGATCAGACCTGAAGAAGACGAAGAGTCGTCTCTTAATTTGAGAAATTCAGTAGGAGATA
GCAGAGCAGAGGTTCCAAGGAACATGGTTAACACCAACCAAGCTCAGCAGCGGAGAGCAGAACC
GGCTTCAAACCAAGTCACTGCTATGATTCCAGAATTTAATATCAGAATTGTTGCAGAGAGCACT
GAAGACTCAACAGCGGAATCTTCCAGCAGCGGAAGGAGAGAAAGAAGCGGAGGCATAGTCCCCG
AGTGGTCTCCAGGGTACTCAGAGCAGTTCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTAC
AACGTCTAGCTACTTGCAGAATCACCATGAAATACTGAACTGGAGACGGCTTTCACAAACCGG
						
					

			
		

Sequences
Splice junction sequence	TCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTACAACGTCTAGCTACTTGCAGAATCACCA TGAAATACTGAACTGGAGACGGCTTTCACAAACCGGatccattgtctttggtgcgtgatcaccg agctaaagatgttttgacggcgcaaggcatagcggttcgatcattcaacgcagacttgctttat gagccatg
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: 1708 Transcript exons: 5724761-5724979,5725063-5726551 ATCCATTGTCTTTGGTGCGTGATCACCGAGCTAAAGATGTTTTGACGGCGCAAGGCATAGCGGT TCGATCATTCAACGCAGACTTGCTTTATGAGCCATGGGAAGTGACTGATGAATTAGGCCGTCCT TTCTCTATGTTTGCTGCGTTTTGGGAGAGATGTCTTAGTATGCCTTATGACCCTGAGTCTCCTC TTCTTCCACCTAAGAAGATCATTTCAGGGGATGTGTCTAAATGTGTTGCGGATCCATTGGTGTT TGAGGATGACTCTGAGAAAGGAAGCAATGCACTTCTGGCTCGTGCTTGGTCTCCTGGATGGAGT AATGGTGATAAAGCTCTCACAACGTTTATAAACGGTCCATTGCTTGAATACTCTAAGAACCGCA GAAAAGCCGATAGTGCTACAACCTCGTTTCTTTCTCCACACTTGCATTTTGGGGAAGTGAGTGT GAGAAAAGTTTTTCATCTTGTTCGGATCAAACAGGTCGCGTGGGCAAACGAAGGAAACGAGGCC GGGGAAGAAAGCGTGAATCTTTTCCTGAAATCTATTGGTCTCAGGGAGTATTCTAGGTACATAA GTTTTAACCATCCATATTCCCATGAAAGACCACTTCTTGGCCATCTAAAGTTCTTCCCTTGGGC TGTGGATGAGAACTATTTCAAGGCATGGAGGCAAGGCCGGACTGGATATCCGTTGGTCGATGCC GGGATGAGAGAGTTATGGGCTACTGGTTGGTTGCATGATCGCATAAGAGTAGTTGTTTCAAGCT TCTTTGTTAAAGTGCTTCAATTACCATGGAGATGGGGGATGAAGTATTTCTGGGACACACTTCT TGATGCGGATTTAGAAAGCGATGCTCTTGGTTGGCAATACATTACCGGTACTCTCCCGGATAGC CGGGAGTTTGATCGCATAGATAACCCTCAGTTTGAAGGGTACAAGTTTGATCCAAATGGTGAAT ACGTAAGGCGATGGCTTCCTGAACTCTCTAGACTCCCGACAGACTGGATACATCATCCGTGGAA CGCACCTGAGTCCGTTCTTCAAGCTGCTGGTATCGAGCTTGGATCAAACTATCCTCTACCAATT GTAGGATTAGACGAAGCAAAAGCACGGCTTCATGAAGCGCTTTCACAGATGTGGCAACTAGAAG CTGCTTCAAGAGCTGCAATAGAGAACGGATCCGAAGAAGGACTTGGAGATTCTGCTGAGGTAGA GGAAGCTCCTATAGAGTTCCCAAGGGACATTACAATGGAAGAGACTGAACCAACCAGACTCAAC CCAAACAGGAGATATGAGGATCAGATGGTTCCAAGCATTACTTCTTCTTTGATCAGACCTGAAG AAGACGAAGAGTCGTCTCTTAATTTGAGAAATTCAGTAGGAGATAGCAGAGCAGAGGTTCCAAG GAACATGGTTAACACCAACCAAGCTCAGCAGCGGAGAGCAGAACCGGCTTCAAACCAAGTCACT GCTATGATTCCAGAATTTAATATCAGAATTGTTGCAGAGAGCACTGAAGACTCAACAGCGGAAT CTTCCAGCAGCGGAAGGAGAGAAAGAAGCGGAGGCATAGTCCCCGAGTGGTCTCCAGGGTACTC AGAGCAGTTCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTACAACGTCTAGCTACTTGCAG AATCACCATGAAATACTGAACTGGAGACGGCTTTCACAAACCGG Transcript length: 183 Transcript exons: 5724761-5724811,5726420-5726551 ATCCATTGTCTTTGGTGCGTGATCACCGAGCTAAAGATGTTTTGACGGCGCCCCCGAGTGGTCT CCAGGGTACTCAGAGCAGTTCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTACAACGTCTA GCTACTTGCAGAATCACCATGAAATACTGAACTGGAGACGGCTTTCACAAACCGG
Genomic sequence	ATCCATTGTCTTTGGTGCGTGATCACCGAGCTAAAGATGTTTTGACGGCGCAAGGCATAGCGGT TCGATCATTCAACGCAGACTTGCTTTATGAGCCATGGGAAGTGACTGATGAATTAGGCCGTCCT TTCTCTATGTTTGCTGCGTTTTGGGAGAGATGTCTTAGTATGCCTTATGACCCTGAGTCTCCTC TTCTTCCACCTAAGAAGATCATTTCAGGTTTGTTTCTTTGCCACTCTCTCTTGTGGGTTTTCGT TTTTTCCAAATCTGTATCATTCAATAATGTTTCTTTTATGTTGCAGGGGATGTGTCTAAATGTG TTGCGGATCCATTGGTGTTTGAGGATGACTCTGAGAAAGGAAGCAATGCACTTCTGGCTCGTGC TTGGTCTCCTGGATGGAGTAATGGTGATAAAGCTCTCACAACGTTTATAAACGGTCCATTGCTT GAATACTCTAAGAACCGCAGAAAAGCCGATAGTGCTACAACCTCGTTTCTTTCTCCACACTTGC ATTTTGGGGAAGTGAGTGTGAGAAAAGTTTTTCATCTTGTTCGGATCAAACAGGTCGCGTGGGC AAACGAAGGAAACGAGGCCGGGGAAGAAAGCGTGAATCTTTTCCTGAAATCTATTGGTCTCAGG GAGTATTCTAGGTACATAAGTTTTAACCATCCATATTCCCATGAAAGACCACTTCTTGGCCATC TAAAGTTCTTCCCTTGGGCTGTGGATGAGAACTATTTCAAGGCATGGAGGCAAGGCCGGACTGG ATATCCGTTGGTCGATGCCGGGATGAGAGAGTTATGGGCTACTGGTTGGTTGCATGATCGCATA AGAGTAGTTGTTTCAAGCTTCTTTGTTAAAGTGCTTCAATTACCATGGAGATGGGGGATGAAGT ATTTCTGGGACACACTTCTTGATGCGGATTTAGAAAGCGATGCTCTTGGTTGGCAATACATTAC CGGTACTCTCCCGGATAGCCGGGAGTTTGATCGCATAGATAACCCTCAGTTTGAAGGGTACAAG TTTGATCCAAATGGTGAATACGTAAGGCGATGGCTTCCTGAACTCTCTAGACTCCCGACAGACT GGATACATCATCCGTGGAACGCACCTGAGTCCGTTCTTCAAGCTGCTGGTATCGAGCTTGGATC AAACTATCCTCTACCAATTGTAGGATTAGACGAAGCAAAAGCACGGCTTCATGAAGCGCTTTCA CAGATGTGGCAACTAGAAGCTGCTTCAAGAGCTGCAATAGAGAACGGATCCGAAGAAGGACTTG GAGATTCTGCTGAGGTAGAGGAAGCTCCTATAGAGTTCCCAAGGGACATTACAATGGAAGAGAC TGAACCAACCAGACTCAACCCAAACAGGAGATATGAGGATCAGATGGTTCCAAGCATTACTTCT TCTTTGATCAGACCTGAAGAAGACGAAGAGTCGTCTCTTAATTTGAGAAATTCAGTAGGAGATA GCAGAGCAGAGGTTCCAAGGAACATGGTTAACACCAACCAAGCTCAGCAGCGGAGAGCAGAACC GGCTTCAAACCAAGTCACTGCTATGATTCCAGAATTTAATATCAGAATTGTTGCAGAGAGCACT GAAGACTCAACAGCGGAATCTTCCAGCAGCGGAAGGAGAGAAAGAAGCGGAGGCATAGTCCCCG AGTGGTCTCCAGGGTACTCAGAGCAGTTCCCTAGTGAAGAAAATGGTATTGGAGGAGGAAGTAC AACGTCTAGCTACTTGCAGAATCACCATGAAATACTGAACTGGAGACGGCTTTCACAAACCGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.480975249

Conservation Information
Conserved circRNAs	NA
PMCS	0.480975249

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to heat stress

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to heat stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017

circRNA

Detail information of AT4G08920_circ_g.3

Address

Any questions?

Supported by