Plant Circular RNA Database

Detail information of AT5G01920_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G01920_circ_g.4
					
						ID in PlantcircBase
						ath_circ_035948
					
						Alias
						At_ciR4762, Ath_circ_FC3102, AT5G01920_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 359784-360446  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT5G01920						
					
						Parent gene annotation
						
							Serine/threonine-protein kinase STN8, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G01920_circ_g.2 AT5G01920_circ_g.3 AT5G01920_circ_g.5 						
					
						Support reads
						2/23/9
					
						Tissues
						leaf/root, aerial, inflorescences, 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
						AT5G01920.2:2
AT5G01920.1:2

General Information
CircRNA Name	AT5G01920_circ_g.4
ID in PlantcircBase	ath_circ_035948
Alias	At_ciR4762, Ath_circ_FC3102, AT5G01920_C1
Organism	Arabidpsis thaliana
Position	chr5: 359784-360446 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI2
Parent gene	AT5G01920
Parent gene annotation	Serine/threonine-protein kinase STN8, chloroplastic
Parent gene strand	+
Alternative splicing	AT5G01920_circ_g.2 AT5G01920_circ_g.3 AT5G01920_circ_g.5
Support reads	2/23/9
Tissues	leaf/root, aerial, inflorescences, 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	AT5G01920.2:2 AT5G01920.1:2

			
						 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  
						
							TCCTGACTACTGTCCTCCTGAGCTCTATGTCCTCCCGGAGGAAACGCCAAGCCCTCCTCCGGAG
CCTATAGCCGCTTTGCTTTCCCCGATTCTCTGGCAGgtcaaggtgggagtacgaggggccgagg
aatttggcgagtacgaagagtggttcaactaccgactctcaagggccgctcctgacacctgcgc
tgagtttc

									
								

					

						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: 282
Transcript exons: 359784-359912,360294-360446
GTCAAGGTGGGAGTACGAGGGGCCGAGGAATTTGGCGAGTACGAAGAGTGGTTCAACTACCGAC
TCTCAAGGGCCGCTCCTGACACCTGCGCTGAGTTTCTCGGAAGCTTTGTCGCCGACAAGACCAA
TGCTGCTGATCTTCGCATTGGCAAGAATTACATCCCGGAACGCACTTTACTCGATCCTGACTAC
TGTCCTCCTGAGCTCTATGTCCTCCCGGAGGAAACGCCAAGCCCTCCTCCGGAGCCTATAGCCG
CTTTGCTTTCCCCGATTCTCTGGCAG
Transcript length: 579
Transcript exons: 359784-359957,360042-360446
GTCAAGGTGGGAGTACGAGGGGCCGAGGAATTTGGCGAGTACGAAGAGTGGTTCAACTACCGAC
TCTCAAGGGCCGCTCCTGACACCTGCGCTGAGTTTCTCGGAAGCTTTGTCGCCGACAAGACCAA
TACTATGTTTACTAAAGGCGGCAAATGGCTTGTCTGGAGGTTCGAGGGAGACCGTGATCTCGCT
GATTACATGAAAGATCGGAGCTTTCCTTCTAATTTGGAGTCCATCATGTTTGGGCGCGTTCTCC
AAGGAGTCGAGTCTGTGAAACGTCGTGCACTGATCATTAAGCAGATTATGCGCCAGATCATTAC
ATCTCTCAGGAAAATCCATGGCACGGGCATTGTTCACCGGGACGTGAAGCCTGCCAACTTGGTG
GTTACAAAGAAGGGCCAGATTAAGCTCATCGACTTTGGTGCCGCTGCTGATCTTCGCATTGGCA
AGAATTACATCCCGGAACGCACTTTACTCGATCCTGACTACTGTCCTCCTGAGCTCTATGTCCT
CCCGGAGGAAACGCCAAGCCCTCCTCCGGAGCCTATAGCCGCTTTGCTTTCCCCGATTCTCTGG
CAG
						
					

						Genomic sequence
						
							GTCAAGGTGGGAGTACGAGGGGCCGAGGAATTTGGCGAGTACGAAGAGTGGTTCAACTACCGAC
TCTCAAGGGCCGCTCCTGACACCTGCGCTGAGTTTCTCGGAAGCTTTGTCGCCGACAAGACCAA
TACTATGTTTACTAAAGGCGGCAAATGGCTTGTCTGGAGGTTCGAGGTGTGGTCTTCTTACTTA
CCCTTACAATGAATCTGCTGTTTATAGTTGCGATGATGATGATGAATGAAATGTTTTCTTCAAC
AGGGAGACCGTGATCTCGCTGATTACATGAAAGATCGGAGCTTTCCTTCTAATTTGGAGTCCAT
CATGTTTGGGCGCGTTCTCCAAGGAGTCGAGTCTGTGAAACGTCGTGCACTGATCATTAAGCAG
ATTATGCGCCAGATCATTACATCTCTCAGGAAAATCCATGGCACGGGCATTGTTCACCGGGACG
TGAAGCCTGCCAACTTGGTGGTTACAAAGAAGGGCCAGATTAAGCTCATCGACTTTGGTGCCGC
TGCTGATCTTCGCATTGGCAAGAATTACATCCCGGAACGCACTTTACTCGATCCTGACTACTGT
CCTCCTGAGCTCTATGTCCTCCCGGAGGAAACGCCAAGCCCTCCTCCGGAGCCTATAGCCGCTT
TGCTTTCCCCGATTCTCTGGCAG
						
					

			
		

Sequences
Splice junction sequence	TCCTGACTACTGTCCTCCTGAGCTCTATGTCCTCCCGGAGGAAACGCCAAGCCCTCCTCCGGAG CCTATAGCCGCTTTGCTTTCCCCGATTCTCTGGCAGgtcaaggtgggagtacgaggggccgagg aatttggcgagtacgaagagtggttcaactaccgactctcaagggccgctcctgacacctgcgc tgagtttc
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: 282 Transcript exons: 359784-359912,360294-360446 GTCAAGGTGGGAGTACGAGGGGCCGAGGAATTTGGCGAGTACGAAGAGTGGTTCAACTACCGAC TCTCAAGGGCCGCTCCTGACACCTGCGCTGAGTTTCTCGGAAGCTTTGTCGCCGACAAGACCAA TGCTGCTGATCTTCGCATTGGCAAGAATTACATCCCGGAACGCACTTTACTCGATCCTGACTAC TGTCCTCCTGAGCTCTATGTCCTCCCGGAGGAAACGCCAAGCCCTCCTCCGGAGCCTATAGCCG CTTTGCTTTCCCCGATTCTCTGGCAG Transcript length: 579 Transcript exons: 359784-359957,360042-360446 GTCAAGGTGGGAGTACGAGGGGCCGAGGAATTTGGCGAGTACGAAGAGTGGTTCAACTACCGAC TCTCAAGGGCCGCTCCTGACACCTGCGCTGAGTTTCTCGGAAGCTTTGTCGCCGACAAGACCAA TACTATGTTTACTAAAGGCGGCAAATGGCTTGTCTGGAGGTTCGAGGGAGACCGTGATCTCGCT GATTACATGAAAGATCGGAGCTTTCCTTCTAATTTGGAGTCCATCATGTTTGGGCGCGTTCTCC AAGGAGTCGAGTCTGTGAAACGTCGTGCACTGATCATTAAGCAGATTATGCGCCAGATCATTAC ATCTCTCAGGAAAATCCATGGCACGGGCATTGTTCACCGGGACGTGAAGCCTGCCAACTTGGTG GTTACAAAGAAGGGCCAGATTAAGCTCATCGACTTTGGTGCCGCTGCTGATCTTCGCATTGGCA AGAATTACATCCCGGAACGCACTTTACTCGATCCTGACTACTGTCCTCCTGAGCTCTATGTCCT CCCGGAGGAAACGCCAAGCCCTCCTCCGGAGCCTATAGCCGCTTTGCTTTCCCCGATTCTCTGG CAG
Genomic sequence	GTCAAGGTGGGAGTACGAGGGGCCGAGGAATTTGGCGAGTACGAAGAGTGGTTCAACTACCGAC TCTCAAGGGCCGCTCCTGACACCTGCGCTGAGTTTCTCGGAAGCTTTGTCGCCGACAAGACCAA TACTATGTTTACTAAAGGCGGCAAATGGCTTGTCTGGAGGTTCGAGGTGTGGTCTTCTTACTTA CCCTTACAATGAATCTGCTGTTTATAGTTGCGATGATGATGATGAATGAAATGTTTTCTTCAAC AGGGAGACCGTGATCTCGCTGATTACATGAAAGATCGGAGCTTTCCTTCTAATTTGGAGTCCAT CATGTTTGGGCGCGTTCTCCAAGGAGTCGAGTCTGTGAAACGTCGTGCACTGATCATTAAGCAG ATTATGCGCCAGATCATTACATCTCTCAGGAAAATCCATGGCACGGGCATTGTTCACCGGGACG TGAAGCCTGCCAACTTGGTGGTTACAAAGAAGGGCCAGATTAAGCTCATCGACTTTGGTGCCGC TGCTGATCTTCGCATTGGCAAGAATTACATCCCGGAACGCACTTTACTCGATCCTGACTACTGT CCTCCTGAGCTCTATGTCCTCCCGGAGGAAACGCCAAGCCCTCCTCCGGAGCCTATAGCCGCTT TGCTTTCCCCGATTCTCTGGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.654484273

Conservation Information
Conserved circRNAs	NA
PMCS	0.654484273

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							359916-360443(+)
						
						Potential amino acid sequence
						
							MFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQIITS
LRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELYVLP
EETPSPPPEPIAALLSPILWQVKVGVRGAEEFGEYEEWFNYRLSRAAPDTCAEFLGSFVADKTN
TMFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQIIT
SLRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELYVL
PEETPSPPPEPIAALLSPILWQVKVGVRGAEEFGEYEEWFNYRLSRAAPDTCAEFLGSFVADKT
NTMFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQII
TSLRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELYV
LPEETPSPPPEPIAALLSPILWQVKVGVRGAEEFGEYEEWFNYRLSRAAPDTCAEFLGSFVADK
TNTMFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQI
ITSLRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELY
VLPEETPSPPPEPIAALLSPILWQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	359916-360443(+)
Potential amino acid sequence	MFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQIITS LRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELYVLP EETPSPPPEPIAALLSPILWQVKVGVRGAEEFGEYEEWFNYRLSRAAPDTCAEFLGSFVADKTN TMFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQIIT SLRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELYVL PEETPSPPPEPIAALLSPILWQVKVGVRGAEEFGEYEEWFNYRLSRAAPDTCAEFLGSFVADKT NTMFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQII TSLRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELYV LPEETPSPPPEPIAALLSPILWQVKVGVRGAEEFGEYEEWFNYRLSRAAPDTCAEFLGSFVADK TNTMFTKGGKWLVWRFEGDRDLADYMKDRSFPSNLESIMFGRVLQGVESVKRRALIIKQIMRQI ITSLRKIHGTGIVHRDVKPANLVVTKKGQIKLIDFGAAADLRIGKNYIPERTLLDPDYCPPELY VLPEETPSPPPEPIAALLSPILWQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of AT5G01920_circ_g.4

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