Plant Circular RNA Database

Detail information of AT5G62165_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G62165_circ_g.2
					
						ID in PlantcircBase
						ath_circ_045329
					
						Alias
						5:24965038-24967427
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 24965038-24967427  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G62165						
					
						Parent gene annotation
						
							MADS-box protein AGL42
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G62165_circ_g.1 AT5G62165_circ_g.3 AT5G62165_circ_g.4 AT5G62165_circ_g.5 AT5G62165_circ_g.6 AT5G62165_circ_g.7 AT5G62165_circ_g.8 						
					
						Support reads
						1/1
					
						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  
						
							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
						AT5G62165.8:4
AT5G62165.1:4
AT5G62165.6:4
AT5G62165.3:4
AT5G62165.16:3
AT5G62165.4:4
AT5G62165.10:4
AT5G62165.9:4
AT5G62165.14:3
AT5G62165.2:4
AT5G62165.11:4
AT5G62165.7:4
AT5G62165.13:4
AT5G62165.5:3
AT5G62165.12:4
AT5G62165.15:3
AT5G62165.17:4

General Information
CircRNA Name	AT5G62165_circ_g.2
ID in PlantcircBase	ath_circ_045329
Alias	5:24965038-24967427
Organism	Arabidpsis thaliana
Position	chr5: 24965038-24967427 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G62165
Parent gene annotation	MADS-box protein AGL42
Parent gene strand	+
Alternative splicing	AT5G62165_circ_g.1 AT5G62165_circ_g.3 AT5G62165_circ_g.4 AT5G62165_circ_g.5 AT5G62165_circ_g.6 AT5G62165_circ_g.7 AT5G62165_circ_g.8
Support reads	1/1
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	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	AT5G62165.8:4 AT5G62165.1:4 AT5G62165.6:4 AT5G62165.3:4 AT5G62165.16:3 AT5G62165.4:4 AT5G62165.10:4 AT5G62165.9:4 AT5G62165.14:3 AT5G62165.2:4 AT5G62165.11:4 AT5G62165.7:4 AT5G62165.13:4 AT5G62165.5:3 AT5G62165.12:4 AT5G62165.15:3 AT5G62165.17:4

			
						 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  
						
							GAAGCTATTGGGACAAGGAATTGCTTCTTGTTCTCTAGAAGAGCTTCAAGAAATCGATAGTCAA
CTCCAAAGAAGTCTGGGAAAGGTCCGAGAAAGAAAGatcttgtggcagaaaaaatcaagtcaaa
gcaagaaaaatggttagaggaaagatagagatgaagaaaatagaaaacgcaacgagtagacaag
tgactttc

									
								

					

						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: 463
Transcript exons: 24965038-24965256,24966362-24966443,24966818-24966879,24
967328-24967427
ATCTTGTGGCAGAAAAAATCAAGTCAAAGCAAGAAAAATGGTTAGAGGAAAGATAGAGATGAAG
AAAATAGAAAACGCAACGAGTAGACAAGTGACTTTCTCAAAAAGAAGAAATGGTTTGTTGAAGA
AAGCTTATGAGCTCTCAGTACTCTGCGATGCTCAACTCTCTCTCATCATCTTCTCCCAGAGAGG
AAGGCTTTATGAATTCTCTAGCTCTGATATGCAGAAGACGATCGAACGCTACCGCAAGTACACA
AAAGATCATGAAACCAGCAATCACGACTCACAAATTCACTTGCAGCAATTGAAACAAGAAGCAA
GCCACATGATAACAAAGATTGAACTCCTTGAGTTTCACAAGCGGAAGCTATTGGGACAAGGAAT
TGCTTCTTGTTCTCTAGAAGAGCTTCAAGAAATCGATAGTCAACTCCAAAGAAGTCTGGGAAAG
GTCCGAGAAAGAAAG
						
					

						Genomic sequence
						
							ATCTTGTGGCAGAAAAAATCAAGTCAAAGCAAGAAAAATGGTTAGAGGAAAGATAGAGATGAAG
AAAATAGAAAACGCAACGAGTAGACAAGTGACTTTCTCAAAAAGAAGAAATGGTTTGTTGAAGA
AAGCTTATGAGCTCTCAGTACTCTGCGATGCTCAACTCTCTCTCATCATCTTCTCCCAGAGAGG
AAGGCTTTATGAATTCTCTAGCTCTGAGTATGTTTTCTTCAATTTCTTCTTGATTCTTTTAATT
CATCTTCTTTTACTTTTCCGATCGTACTTTTTTTGGGGGGTTAATTAGGCTTTTAGGTCATGTG
TTTGTGTCTGTTCTGATTTATTTTCTGAATCGTTATTGACTAAAGCAACCTTCTCAGATTTTGG
TACTTGAGAGATTCGATCCTTGTCTGAATCCTAAAGATTTCTTTCTTCTCTTCCCCTATCAGTC
TAATTTCATTTTTCTATTTTTATAATAGTCATTTGGTTAGAAATCTAGACAAACTCCTTTTTTC
TGATCTACCAAAACTTTACATCCAAACTAAATTGTGTGCGTATATATTGATATATGTGTGTGTA
TGTTTCTAGGGTTTCCAAATTCTTGAAAGTATATATGAACAGAAAACAACATCGGAAGTAGATC
TAAATGGGATTTATTCTATAATTTGATGATTATTTATTGTGATCCGTACCAAGTTGCACATATT
TTTACCCATTTCTTTGGTGATAATATAAAATAAGTTTACTTTTTCTTGCCCCTAGTTAATTAGG
TTGTGTACTATCGTTTTTGGTTTTCGTTATGTCTTTATTTGGGCTCTACTTTTGCAGCCATGTA
GTAATAATGCTTGCTCTTCCTCGTTTGATTCAGGTGTCCAGTGCATACATAGTTCCCTATATAT
ATATATGTTTAACACATTCACATCCTTAAGTTTTTGCTATAATCAATGTTAGAACCAAGTAGCT
AAAGTTGTGATTTGTTATTCTCTATAGTAATATATATTGTTGATTAGAGGTTTCCTAATGGGTT
AATGGATCTAGATTCAATTATTTGATGTGAGAAAAAAAAGAGTTCAATAAATGGACAAAAAAGG
GCCCGGTGAATCATAGGGCATGGATTTGAATAGTTACCTAGCTATAGAGATATTAACCAACAGC
AAAGAAGATATTGTAGTACAATCTAAGAATCATACTACAGTCAAACAAAATTTTCATATCTCGT
TGCGATAAGATGTTATTTCAAATATAGTAGAGCTATAGATAAAACAAATACGAAGATAAGTACG
TTAGTTCATATTTCTGAAAATATATGTCTATTTTTGATCATCAGTATGCAGAAGACGATCGAAC
GCTACCGCAAGTACACAAAAGATCATGAAACCAGCAATCACGACTCACAAATTCACTTGCAGGT
TTGTTAGCAAACTCTTTTTTTTTCACTTGATGACTTTCACGGTTTTATCCTTGGTAAAAATAAT
CAAACTTAAACTTTACATGATTTCCATGCTATTGATATTAGACTGTGGGCTTCCAACTTAAAAC
CAATTGGCAATAGGTGGAGAGACCCATATCTTATATATACCACTTAAGATCCTACTCAACTTCC
GATGTGGGACATTGTCCCTAATAATTGATTCTTTGACTTTCAATGGCCAACAAAACCAAATCTT
ATGAGATCAATTACTACATCACAAAACAACTGATGGATCGATGGTCACAAAGATTACATACTGA
TCTGTTTTACTTCTTTTGCATCCTATGATTTTATTTTGTGGGCGTATTGTAGCAATTGAAACAA
GAAGCAAGCCACATGATAACAAAGATTGAACTCCTTGAGTTTCACAAGCGGTATAATGTCTTAG
ACTTTTTGTTTCTTTTTCTTTTCGTTGCTACTTCTCTTAGATCACAATCTTGATTATTATTCCT
TTAATTTCATTTACGGTATTTTGTTTCGTTTTATATATAAAACCATATAAGCTTAGACTTTTTA
ACCAAACTTTCTTTATTAATTGTAGATCCATATCCTTAAGACTTCATTAACCATTTTTTATTTA
TTTCAATACTATAATTTTTAACCTTTTTGTTAGTATTTCAAGAATTTTTTTTATAAAATTTGAA
ACCTTTAGTCGTTTAGATTTAAAAGTCCTTTTAGTTGTTTCCGTATGTAAAGGTACGCATGTAA
TCAAAGACCATACTATAGTAATATCATTAATGTATTTGTTAGTGATCTCAAATAGGAGAACTAC
TTTGGAGATTTACAAAATTTGTTCATGAACCCTCCTCTGCGTGTGTATAGGAAGCTATTGGGAC
AAGGAATTGCTTCTTGTTCTCTAGAAGAGCTTCAAGAAATCGATAGTCAACTCCAAAGAAGTCT
GGGAAAGGTCCGAGAAAGAAAG
						
					

			
		

Sequences
Splice junction sequence	GAAGCTATTGGGACAAGGAATTGCTTCTTGTTCTCTAGAAGAGCTTCAAGAAATCGATAGTCAA CTCCAAAGAAGTCTGGGAAAGGTCCGAGAAAGAAAGatcttgtggcagaaaaaatcaagtcaaa gcaagaaaaatggttagaggaaagatagagatgaagaaaatagaaaacgcaacgagtagacaag tgactttc
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: 463 Transcript exons: 24965038-24965256,24966362-24966443,24966818-24966879,24 967328-24967427 ATCTTGTGGCAGAAAAAATCAAGTCAAAGCAAGAAAAATGGTTAGAGGAAAGATAGAGATGAAG AAAATAGAAAACGCAACGAGTAGACAAGTGACTTTCTCAAAAAGAAGAAATGGTTTGTTGAAGA AAGCTTATGAGCTCTCAGTACTCTGCGATGCTCAACTCTCTCTCATCATCTTCTCCCAGAGAGG AAGGCTTTATGAATTCTCTAGCTCTGATATGCAGAAGACGATCGAACGCTACCGCAAGTACACA AAAGATCATGAAACCAGCAATCACGACTCACAAATTCACTTGCAGCAATTGAAACAAGAAGCAA GCCACATGATAACAAAGATTGAACTCCTTGAGTTTCACAAGCGGAAGCTATTGGGACAAGGAAT TGCTTCTTGTTCTCTAGAAGAGCTTCAAGAAATCGATAGTCAACTCCAAAGAAGTCTGGGAAAG GTCCGAGAAAGAAAG
Genomic sequence	ATCTTGTGGCAGAAAAAATCAAGTCAAAGCAAGAAAAATGGTTAGAGGAAAGATAGAGATGAAG AAAATAGAAAACGCAACGAGTAGACAAGTGACTTTCTCAAAAAGAAGAAATGGTTTGTTGAAGA AAGCTTATGAGCTCTCAGTACTCTGCGATGCTCAACTCTCTCTCATCATCTTCTCCCAGAGAGG AAGGCTTTATGAATTCTCTAGCTCTGAGTATGTTTTCTTCAATTTCTTCTTGATTCTTTTAATT CATCTTCTTTTACTTTTCCGATCGTACTTTTTTTGGGGGGTTAATTAGGCTTTTAGGTCATGTG TTTGTGTCTGTTCTGATTTATTTTCTGAATCGTTATTGACTAAAGCAACCTTCTCAGATTTTGG TACTTGAGAGATTCGATCCTTGTCTGAATCCTAAAGATTTCTTTCTTCTCTTCCCCTATCAGTC TAATTTCATTTTTCTATTTTTATAATAGTCATTTGGTTAGAAATCTAGACAAACTCCTTTTTTC TGATCTACCAAAACTTTACATCCAAACTAAATTGTGTGCGTATATATTGATATATGTGTGTGTA TGTTTCTAGGGTTTCCAAATTCTTGAAAGTATATATGAACAGAAAACAACATCGGAAGTAGATC TAAATGGGATTTATTCTATAATTTGATGATTATTTATTGTGATCCGTACCAAGTTGCACATATT TTTACCCATTTCTTTGGTGATAATATAAAATAAGTTTACTTTTTCTTGCCCCTAGTTAATTAGG TTGTGTACTATCGTTTTTGGTTTTCGTTATGTCTTTATTTGGGCTCTACTTTTGCAGCCATGTA GTAATAATGCTTGCTCTTCCTCGTTTGATTCAGGTGTCCAGTGCATACATAGTTCCCTATATAT ATATATGTTTAACACATTCACATCCTTAAGTTTTTGCTATAATCAATGTTAGAACCAAGTAGCT AAAGTTGTGATTTGTTATTCTCTATAGTAATATATATTGTTGATTAGAGGTTTCCTAATGGGTT AATGGATCTAGATTCAATTATTTGATGTGAGAAAAAAAAGAGTTCAATAAATGGACAAAAAAGG GCCCGGTGAATCATAGGGCATGGATTTGAATAGTTACCTAGCTATAGAGATATTAACCAACAGC AAAGAAGATATTGTAGTACAATCTAAGAATCATACTACAGTCAAACAAAATTTTCATATCTCGT TGCGATAAGATGTTATTTCAAATATAGTAGAGCTATAGATAAAACAAATACGAAGATAAGTACG TTAGTTCATATTTCTGAAAATATATGTCTATTTTTGATCATCAGTATGCAGAAGACGATCGAAC GCTACCGCAAGTACACAAAAGATCATGAAACCAGCAATCACGACTCACAAATTCACTTGCAGGT TTGTTAGCAAACTCTTTTTTTTTCACTTGATGACTTTCACGGTTTTATCCTTGGTAAAAATAAT CAAACTTAAACTTTACATGATTTCCATGCTATTGATATTAGACTGTGGGCTTCCAACTTAAAAC CAATTGGCAATAGGTGGAGAGACCCATATCTTATATATACCACTTAAGATCCTACTCAACTTCC GATGTGGGACATTGTCCCTAATAATTGATTCTTTGACTTTCAATGGCCAACAAAACCAAATCTT ATGAGATCAATTACTACATCACAAAACAACTGATGGATCGATGGTCACAAAGATTACATACTGA TCTGTTTTACTTCTTTTGCATCCTATGATTTTATTTTGTGGGCGTATTGTAGCAATTGAAACAA GAAGCAAGCCACATGATAACAAAGATTGAACTCCTTGAGTTTCACAAGCGGTATAATGTCTTAG ACTTTTTGTTTCTTTTTCTTTTCGTTGCTACTTCTCTTAGATCACAATCTTGATTATTATTCCT TTAATTTCATTTACGGTATTTTGTTTCGTTTTATATATAAAACCATATAAGCTTAGACTTTTTA ACCAAACTTTCTTTATTAATTGTAGATCCATATCCTTAAGACTTCATTAACCATTTTTTATTTA TTTCAATACTATAATTTTTAACCTTTTTGTTAGTATTTCAAGAATTTTTTTTATAAAATTTGAA ACCTTTAGTCGTTTAGATTTAAAAGTCCTTTTAGTTGTTTCCGTATGTAAAGGTACGCATGTAA TCAAAGACCATACTATAGTAATATCATTAATGTATTTGTTAGTGATCTCAAATAGGAGAACTAC TTTGGAGATTTACAAAATTTGTTCATGAACCCTCCTCTGCGTGTGTATAGGAAGCTATTGGGAC AAGGAATTGCTTCTTGTTCTCTAGAAGAGCTTCAAGAAATCGATAGTCAACTCCAAAGAAGTCT GGGAAAGGTCCGAGAAAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.176429719

Conservation Information
Conserved circRNAs	NA
PMCS	0.176429719

			
						 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 AT5G62165_circ_g.2

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