Plant Circular RNA Database

Detail information of AT3G48860_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G48860_circ_g.1
					
						ID in PlantcircBase
						ath_circ_026601
					
						Alias
						3:18118134-18121852
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 18118134-18121852  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G48860						
					
						Parent gene annotation
						
							Coiled-coil domain-containing protein SCD2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G48860_circ_g.2 AT3G48860_circ_g.3 AT3G48860_circ_g.4 AT3G48860_circ_g.5 AT3G48860_circ_g.6 AT3G48860_circ_g.7 AT3G48860_circ_g.8 						
					
						Support reads
						2
					
						Tissues
						seedling
					
						Exon boundary  
						
							Yes-No							"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
						AT3G48860.2:16
AT3G48860.3:16
AT3G48860.1:13

General Information
CircRNA Name	AT3G48860_circ_g.1
ID in PlantcircBase	ath_circ_026601
Alias	3:18118134-18121852
Organism	Arabidpsis thaliana
Position	chr3: 18118134-18121852 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G48860
Parent gene annotation	Coiled-coil domain-containing protein SCD2
Parent gene strand	+
Alternative splicing	AT3G48860_circ_g.2 AT3G48860_circ_g.3 AT3G48860_circ_g.4 AT3G48860_circ_g.5 AT3G48860_circ_g.6 AT3G48860_circ_g.7 AT3G48860_circ_g.8
Support reads	2
Tissues	seedling
Exon boundary	Yes-No "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	AT3G48860.2:16 AT3G48860.3:16 AT3G48860.1:13

			
						 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  
						
							AACTGGGAATAGAGCAACAGTTGTGGGAAGCTTCTCGACGAGAAATCGATCAGCTTCCCTCGCC
TACTTCTTCGAATCACGATCTCGATGCTGATTCATAttaggcaggaacttcgccgagcaagtac
cttcttcagtgcggtctgcttcagccggaaggccgtcaatgtctgctagatctacgactccgac
tccgattc

									
								

					

						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
						
							TTAGGCAGGAACTTCGCCGAGCAAGTACCTTCTTCAGTGCGGTCTGCTTCAGCCGGAAGGCCGT
CAATGTCTGCTAGATCTACGACTCCGACTCCGATTCCTAATCTAATGCCGCCTAGTAGGGTGTC
GGTGAAAACTCCGGTTTCTATTCCTCCACTTGATCCTCCAACTCGGAGCAGAGATAAAAGGTGA
TAACATTTTGAAGTTCTTAAAAATTGTGCTTCTTATTATAGTTCTCAAATCTTGGTAGTCAAGG
GAACGTGTGACTTAGTGGAATATGTCAAAACCAGTTTGGTTGCTCTTTGGAGTTGGTGTATAAT
ATGATTTTTCGTTGACTAAATATTTATCCTCAAAGCCTAATAATAGAGGTTGCTATAAAGGTTC
ATGAGAAATGGGATCCTTGCTCCAAGAATTAGAGATCCCTGCTGGTTTTTGGTTGTGCGTCTTG
CGTTTGATTTCGGATATTTGATGTTTTTAGGTTCTTTGCTGATGTACCATCAGTAAATTCAAAA
GAAAAGGGTGATCAGCGGGAAGCTTCAGCTCTTCGTGATGAAGTATGTGATTGTTTCTTTTGAA
CCTTTTGCGGTATCTCGTCAATTTAGTTATTGTAAATTTTAGTCAAATTAGAATTTGTGTATGA
GTCATAAGAGTTGACTTGGGGCTGATTCATTTTTATATGCAGCTGGATATGCTACAAGAGGAGA
ATGAGAATGTACTGGAGAAGGTTTGATCTCTGCGATTGAATTTTATATTATGTAATAAAGCTGT
TTACTTCTGTTGTTCATAAAATTTATTCTTGATTACAGCTTCGTCGTGCGGAAGAAAAAAGGGT
GGAAGCAGAAGCTAGGGCTAAGGAGCTCGAGAAACAGGTTTTTGAACTGGTTGTCTTGAGTAGT
CCATTTTTCACTTATGTTGCGTCTTGAAATTCTGACTGAAAAAAATACTCCACTTGTTTAAATC
TCTTTGTATATCTTGTTGTTATCTTTTTGAAACAGCATCCCACCTCGTTGTTTAAATTTACTTT
AAATCATATATTTCTAATGTATTGGCATCTGTTCAAGGTTTCATTTGTTTTTATTTTTGGTTCC
AAAAGGTTGCCTCTCTTGGAGAAGGAGTTTCCTTGGAGGCGAAATTGTTAAGCAGGTGGGAGCC
TGTGCCTTCTTTAGCTTCTCTTTTCTTGCTCTCTTTTTCAGAAACCAAGGTGGTAGTTTTTAAT
CGCTCATGTTGAATATGTCTTTGTATAGGAAAGAAGCAGCATTGCGTCAAAGAGAGGTTAATAC
CCTCAATCTATTTTGCTGCTCAGATGTAGTCTTCTTTTAATCGAGTCATTATGTAAAACATACA
ATTTAAGCTGTGCAGAAAATTTGTACCTGTTACAGGCTGCTCTAAATGTTGCTAAACAAAAAAA
GAGTGGAAAGGATGAGGAAATTGTTTCCCTACGTTCGGAGCTTGAGGTAAGGTTCACTGATGTA
CTGTTTTCTATGAGATGTACCACTTTTATTTGCATTATGAAACCATGTCTTATTTTTCTCTGCT
ATGTTCAGAACTTGAAAGATGAGGCTACAACTGCTGCAGAACGGCTTCAAGAAGCAGAGTCTGA
AGCGAAGTCTCTTCGCACAATGACTCAGAGGATGATTTTAACACAGGATGAAATGGTTTGTCAA
AAAATCTTGGGTCTCGTAATGTACCAATAATTGATAAGGTTCTGAGGTTCTGACTTTATGAATG
ATTGAATTATCTAGGAAGAAGTAGTTCTGAAGAGATGCTGGCTTGCTCGGTATTGGGGCTTGGC
TGTGCAACATGGTAGGTGATTCATCCATTCTTAAGAAAAAGAGTTTATATTCTGAACCAGAGAA
AATATTATCATAATATTCTTTGTATCTTCCGTCAACATGGCATATACTTGTGGTAGTAATAAAT
CAAATTTACAGATATTTGCTTTTCCTATGGTGTGCTTCTGTAGGCATTTGTGCGGATATAGCAC
CATCCAGGCAAGAGCACTGGTCAAAGTTGGCTCCTCTTCCATTTGAGCTCGTCACTTCAGCAGC
ACAGAAGGCGAAGGAGTTATCTTGGGATAAAGGCTCGTCTATTGTCTGCTATAGTTTAAAAAAA
TTCTTTGCTTGCTGTTGTTGTAAATTTTTTTACTTATCAACATATGAAATAATGCAGGTGGGAA
TGATCGGAGTAAGGCGGCTAGAGATTTGAGTGATCTAACTGGAGAAGGAAATATTGAAAGTATG
CTTTCAGTTGAGATGGGTTTGAGAGAGCTAGCATCATTAAAGGTATCCATAATTCTTTCTGAGT
TACCTACAAGTGTTGTCACCTAGCAGATATCTCCAAGGACTACGTTTTCAAATCTTCTTCTCTC
TTTTGAATATCAGGTGGAGGATGCTGTTGTGCTTATATTCGCCCAGCAGAGAAAGTTGAGTTTG
GTTCGCCACACTGTTTCCGGTATGTAATGTATTTGCGAGCTATAACACCACAATGACAAATATA
TGCTTCTTTCGCTTCTATTCTTAAAAGTTTAAACGATGGATGAGTAATCTGTTTTCTGTTTAGA
TACTTAACGCTTATAAGCTCTTAATAAGAAGGCATAACTAAAAGCAATTTAACTTTTGTTTTCT
CTGTATCTTACAGACTCCAAAGGTCATGGAGAATCCAGATTTATCGATGCATATGGTAACGGAA
AAGTCTCACTAACTCTTTTCTCTTTGTTTTCCACCCTTATGTAGAGGTTCTTGGGGTCGAACCC
TCAACACCTTGAATGTTGTGGAAGGGTTTCACTAGTATAGCCACATCTTTAACCCAAAAAAAGA
GTCTAGCCACATCCTCTCGGTCTTTGACATAGTGCATGCGTTGTTGATTTAGTAGGAGTAAATT
GCATCTATGTCCCCTACCTTGAAGGATTTTCTGTGGTTTCAAATTTTACCTTTACTCAACGCAT
AAAATCATCTTCTGTAGACGTAATCAACCATATCGTGAAATCTTATACAATGTTCTCTTGTTGT
TATAAATGCAGAACTGGGTGAAGCGGAACAAGAAGATGTTGCCTTTAAGCAGGTACTTTAACAC
TTACACTCATCATGATATACACCTTCCAGCTAAAAGCCTAAATCATCCATCGAGTGACTTGATT
TTGAGACGACCACACATTATCAATGTTGTATATCATCACATAGAAAGAAAATATCCGACAAAAA
GTAACCACACCGAAACATCTTTTGAAACGTGTCTAGATCTATGTGCTGGATGACGAAACTTATG
AATCCAAACACTGTAGAACCGTTACTTATCAGTTTAAATCAAGATATCGTCTTGATTCCTACAA
TTACATAATGCAGGCATGGCTGATGTACTTCTGGGGAAGAGCTAAGTTGCACGGTGTGGAAGAT
GACATCGCAGAGGAACGTGTCCAGTTATGGATCAGCCGTAGCAGTGGGAAATCTCAGACGACTT
CTCATGATGCCTTGGATGGTAAAACCGGACTTAAGCCATTTCGTTATAATATCTGATTCTTTTG
CTTTAAAGCTTTAGCGAGGAGTAGATTTATAATGATGATAAAACTAAAGTTTCCCATTTTGCTT
GTCTTCAGTGGAAAGAGGGTTGATAGAGCTACGAAAACTGGGAATAGAGCAACAGTTGTGGGAA
GCTTCTCGACGAGAAATCGATCAGCTTCCCTCGCCTACTTCTTCGAATCACGATCTCGATGCTG
ATTCATA
						
					

			
		

Sequences
Splice junction sequence	AACTGGGAATAGAGCAACAGTTGTGGGAAGCTTCTCGACGAGAAATCGATCAGCTTCCCTCGCC TACTTCTTCGAATCACGATCTCGATGCTGATTCATAttaggcaggaacttcgccgagcaagtac cttcttcagtgcggtctgcttcagccggaaggccgtcaatgtctgctagatctacgactccgac tccgattc
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	TTAGGCAGGAACTTCGCCGAGCAAGTACCTTCTTCAGTGCGGTCTGCTTCAGCCGGAAGGCCGT CAATGTCTGCTAGATCTACGACTCCGACTCCGATTCCTAATCTAATGCCGCCTAGTAGGGTGTC GGTGAAAACTCCGGTTTCTATTCCTCCACTTGATCCTCCAACTCGGAGCAGAGATAAAAGGTGA TAACATTTTGAAGTTCTTAAAAATTGTGCTTCTTATTATAGTTCTCAAATCTTGGTAGTCAAGG GAACGTGTGACTTAGTGGAATATGTCAAAACCAGTTTGGTTGCTCTTTGGAGTTGGTGTATAAT ATGATTTTTCGTTGACTAAATATTTATCCTCAAAGCCTAATAATAGAGGTTGCTATAAAGGTTC ATGAGAAATGGGATCCTTGCTCCAAGAATTAGAGATCCCTGCTGGTTTTTGGTTGTGCGTCTTG CGTTTGATTTCGGATATTTGATGTTTTTAGGTTCTTTGCTGATGTACCATCAGTAAATTCAAAA GAAAAGGGTGATCAGCGGGAAGCTTCAGCTCTTCGTGATGAAGTATGTGATTGTTTCTTTTGAA CCTTTTGCGGTATCTCGTCAATTTAGTTATTGTAAATTTTAGTCAAATTAGAATTTGTGTATGA GTCATAAGAGTTGACTTGGGGCTGATTCATTTTTATATGCAGCTGGATATGCTACAAGAGGAGA ATGAGAATGTACTGGAGAAGGTTTGATCTCTGCGATTGAATTTTATATTATGTAATAAAGCTGT TTACTTCTGTTGTTCATAAAATTTATTCTTGATTACAGCTTCGTCGTGCGGAAGAAAAAAGGGT GGAAGCAGAAGCTAGGGCTAAGGAGCTCGAGAAACAGGTTTTTGAACTGGTTGTCTTGAGTAGT CCATTTTTCACTTATGTTGCGTCTTGAAATTCTGACTGAAAAAAATACTCCACTTGTTTAAATC TCTTTGTATATCTTGTTGTTATCTTTTTGAAACAGCATCCCACCTCGTTGTTTAAATTTACTTT AAATCATATATTTCTAATGTATTGGCATCTGTTCAAGGTTTCATTTGTTTTTATTTTTGGTTCC AAAAGGTTGCCTCTCTTGGAGAAGGAGTTTCCTTGGAGGCGAAATTGTTAAGCAGGTGGGAGCC TGTGCCTTCTTTAGCTTCTCTTTTCTTGCTCTCTTTTTCAGAAACCAAGGTGGTAGTTTTTAAT CGCTCATGTTGAATATGTCTTTGTATAGGAAAGAAGCAGCATTGCGTCAAAGAGAGGTTAATAC CCTCAATCTATTTTGCTGCTCAGATGTAGTCTTCTTTTAATCGAGTCATTATGTAAAACATACA ATTTAAGCTGTGCAGAAAATTTGTACCTGTTACAGGCTGCTCTAAATGTTGCTAAACAAAAAAA GAGTGGAAAGGATGAGGAAATTGTTTCCCTACGTTCGGAGCTTGAGGTAAGGTTCACTGATGTA CTGTTTTCTATGAGATGTACCACTTTTATTTGCATTATGAAACCATGTCTTATTTTTCTCTGCT ATGTTCAGAACTTGAAAGATGAGGCTACAACTGCTGCAGAACGGCTTCAAGAAGCAGAGTCTGA AGCGAAGTCTCTTCGCACAATGACTCAGAGGATGATTTTAACACAGGATGAAATGGTTTGTCAA AAAATCTTGGGTCTCGTAATGTACCAATAATTGATAAGGTTCTGAGGTTCTGACTTTATGAATG ATTGAATTATCTAGGAAGAAGTAGTTCTGAAGAGATGCTGGCTTGCTCGGTATTGGGGCTTGGC TGTGCAACATGGTAGGTGATTCATCCATTCTTAAGAAAAAGAGTTTATATTCTGAACCAGAGAA AATATTATCATAATATTCTTTGTATCTTCCGTCAACATGGCATATACTTGTGGTAGTAATAAAT CAAATTTACAGATATTTGCTTTTCCTATGGTGTGCTTCTGTAGGCATTTGTGCGGATATAGCAC CATCCAGGCAAGAGCACTGGTCAAAGTTGGCTCCTCTTCCATTTGAGCTCGTCACTTCAGCAGC ACAGAAGGCGAAGGAGTTATCTTGGGATAAAGGCTCGTCTATTGTCTGCTATAGTTTAAAAAAA TTCTTTGCTTGCTGTTGTTGTAAATTTTTTTACTTATCAACATATGAAATAATGCAGGTGGGAA TGATCGGAGTAAGGCGGCTAGAGATTTGAGTGATCTAACTGGAGAAGGAAATATTGAAAGTATG CTTTCAGTTGAGATGGGTTTGAGAGAGCTAGCATCATTAAAGGTATCCATAATTCTTTCTGAGT TACCTACAAGTGTTGTCACCTAGCAGATATCTCCAAGGACTACGTTTTCAAATCTTCTTCTCTC TTTTGAATATCAGGTGGAGGATGCTGTTGTGCTTATATTCGCCCAGCAGAGAAAGTTGAGTTTG GTTCGCCACACTGTTTCCGGTATGTAATGTATTTGCGAGCTATAACACCACAATGACAAATATA TGCTTCTTTCGCTTCTATTCTTAAAAGTTTAAACGATGGATGAGTAATCTGTTTTCTGTTTAGA TACTTAACGCTTATAAGCTCTTAATAAGAAGGCATAACTAAAAGCAATTTAACTTTTGTTTTCT CTGTATCTTACAGACTCCAAAGGTCATGGAGAATCCAGATTTATCGATGCATATGGTAACGGAA AAGTCTCACTAACTCTTTTCTCTTTGTTTTCCACCCTTATGTAGAGGTTCTTGGGGTCGAACCC TCAACACCTTGAATGTTGTGGAAGGGTTTCACTAGTATAGCCACATCTTTAACCCAAAAAAAGA GTCTAGCCACATCCTCTCGGTCTTTGACATAGTGCATGCGTTGTTGATTTAGTAGGAGTAAATT GCATCTATGTCCCCTACCTTGAAGGATTTTCTGTGGTTTCAAATTTTACCTTTACTCAACGCAT AAAATCATCTTCTGTAGACGTAATCAACCATATCGTGAAATCTTATACAATGTTCTCTTGTTGT TATAAATGCAGAACTGGGTGAAGCGGAACAAGAAGATGTTGCCTTTAAGCAGGTACTTTAACAC TTACACTCATCATGATATACACCTTCCAGCTAAAAGCCTAAATCATCCATCGAGTGACTTGATT TTGAGACGACCACACATTATCAATGTTGTATATCATCACATAGAAAGAAAATATCCGACAAAAA GTAACCACACCGAAACATCTTTTGAAACGTGTCTAGATCTATGTGCTGGATGACGAAACTTATG AATCCAAACACTGTAGAACCGTTACTTATCAGTTTAAATCAAGATATCGTCTTGATTCCTACAA TTACATAATGCAGGCATGGCTGATGTACTTCTGGGGAAGAGCTAAGTTGCACGGTGTGGAAGAT GACATCGCAGAGGAACGTGTCCAGTTATGGATCAGCCGTAGCAGTGGGAAATCTCAGACGACTT CTCATGATGCCTTGGATGGTAAAACCGGACTTAAGCCATTTCGTTATAATATCTGATTCTTTTG CTTTAAAGCTTTAGCGAGGAGTAGATTTATAATGATGATAAAACTAAAGTTTCCCATTTTGCTT GTCTTCAGTGGAAAGAGGGTTGATAGAGCTACGAAAACTGGGAATAGAGCAACAGTTGTGGGAA GCTTCTCGACGAGAAATCGATCAGCTTCCCTCGCCTACTTCTTCGAATCACGATCTCGATGCTG ATTCATA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171760715

Conservation Information
Conserved circRNAs	NA
PMCS	0.171760715

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

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G48860_circ_g.1

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