Plant Circular RNA Database

Detail information of AT1G55520_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT1G55520_circ_g.9
					
						ID in PlantcircBase
						ath_circ_007543
					
						Alias
						At_ciR1109, AT1G55520_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20726904-20727486  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT1G55520						
					
						Parent gene annotation
						
							TATA-box-binding protein 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G55520_circ_g.1 AT1G55520_circ_g.2 AT1G55520_circ_g.3 AT1G55520_circ_g.4 AT1G55520_circ_g.5 AT1G55520_circ_g.6 AT1G55520_circ_g.7 AT1G55520_circ_g.8 AT1G55520_circ_g.10 AT1G55520_circ_g.11 AT1G55520_circ_g.12 AT1G55520_circ_g.13 						
					
						Support reads
						5/8/5
					
						Tissues
						leaf/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  
						
							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
						AT1G55520.3:4
AT1G55520.1:4
AT1G55520.2:4
AT1G55520.4:4

General Information
CircRNA Name	AT1G55520_circ_g.9
ID in PlantcircBase	ath_circ_007543
Alias	At_ciR1109, AT1G55520_C1
Organism	Arabidpsis thaliana
Position	chr1: 20726904-20727486 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT1G55520
Parent gene annotation	TATA-box-binding protein 2
Parent gene strand	-
Alternative splicing	AT1G55520_circ_g.1 AT1G55520_circ_g.2 AT1G55520_circ_g.3 AT1G55520_circ_g.4 AT1G55520_circ_g.5 AT1G55520_circ_g.6 AT1G55520_circ_g.7 AT1G55520_circ_g.8 AT1G55520_circ_g.10 AT1G55520_circ_g.11 AT1G55520_circ_g.12 AT1G55520_circ_g.13
Support reads	5/8/5
Tissues	leaf/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	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	AT1G55520.3:4 AT1G55520.1:4 AT1G55520.2:4 AT1G55520.4:4

			
						 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  
						
							ACACAAAAGAGAGAACTCACTGAAGAGTAGGAACAATCCCTGAAGGATGTTTAGTAAGGTCAAC
TGGCTGGCTCCCTTCCGTTCCTTGATCAGCCATTCTctttcttgcagcaagctttgaaagatgt
tcacttttagctccggtacacacctaatattggacagcatagatgccacgtcaaaacaaggaca
tggaagat

						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: 291
Transcript exons: 20726904-20727486
CTTTCTTGCAGCAAGCTTTGAAAGATGTTCACTTTTAGCTCCGGTACACACCATTTTCCCAGAA
GCAAAAATTAACGCTGTGGTCTTTGGCTCTCTGATCCTCATGATTACAGCAGCGAAACGCTTGG
GGTTATATTCAGCATTCCTAGCTTGCAAAGCTATGGCTTTAAGATCAAGCTTGCAGTCTAAGTT
CACTGTTGAGACAATATTTTGAAGAGTAGGAACAATCCCTGAAGGATGTTTAGTAAGGTCAACT
GGCTGGCTCCCTTCCGTTCCTTGATCAGCCATTCT
						
						Genomic sequence
						
							CTTTCTTGCAGCAAGCTTTGAAAGATGTTCACTTTTAGCTCCGGTACACACCTAATATTGGACA
GCATAGATGCCACGTCAAAACAAGGACATGGAAGATTAGGCCATAAGAGAAAAAGTGACAAAGG
AAAACATACCATTTTCCCAGAAGCAAAAATTAACGCTGTGGTCTTTGGCTCTCTGATCCTCATG
ATTACAGCAGCGAAACGCTGGAACATAAAACACAGATTAAAACCAAATCCGAAAATACAAACCA
AAGTGGTGGAGACCAAACAAAATGATCGATTACTAAAACACGAATATCACAAAGAAAGCAAAAC
CTTGGGGTTATATTCAGCATTCCTAGCTTGCAAAGCTATGGCTTTAAGATCAAGCTTGCAGTCT
AAGTTCACTGTTGAGACAATATTTCTGAAACAAACCAAAAAAGAAAAAGGTAAGATCTTGTGAT
TCACAAAAGCACAAACTCAGAATCTTAAAACAGAGACACAAAAGAGAGAACTCACTGAAGAGTA
GGAACAATCCCTGAAGGATGTTTAGTAAGGTCAACTGGCTGGCTCCCTTCCGTTCCTTGATCAG
CCATTCT

Sequences
Splice junction sequence	ACACAAAAGAGAGAACTCACTGAAGAGTAGGAACAATCCCTGAAGGATGTTTAGTAAGGTCAAC TGGCTGGCTCCCTTCCGTTCCTTGATCAGCCATTCTctttcttgcagcaagctttgaaagatgt tcacttttagctccggtacacacctaatattggacagcatagatgccacgtcaaaacaaggaca tggaagat
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: 291 Transcript exons: 20726904-20727486 CTTTCTTGCAGCAAGCTTTGAAAGATGTTCACTTTTAGCTCCGGTACACACCATTTTCCCAGAA GCAAAAATTAACGCTGTGGTCTTTGGCTCTCTGATCCTCATGATTACAGCAGCGAAACGCTTGG GGTTATATTCAGCATTCCTAGCTTGCAAAGCTATGGCTTTAAGATCAAGCTTGCAGTCTAAGTT CACTGTTGAGACAATATTTTGAAGAGTAGGAACAATCCCTGAAGGATGTTTAGTAAGGTCAACT GGCTGGCTCCCTTCCGTTCCTTGATCAGCCATTCT
Genomic sequence	CTTTCTTGCAGCAAGCTTTGAAAGATGTTCACTTTTAGCTCCGGTACACACCTAATATTGGACA GCATAGATGCCACGTCAAAACAAGGACATGGAAGATTAGGCCATAAGAGAAAAAGTGACAAAGG AAAACATACCATTTTCCCAGAAGCAAAAATTAACGCTGTGGTCTTTGGCTCTCTGATCCTCATG ATTACAGCAGCGAAACGCTGGAACATAAAACACAGATTAAAACCAAATCCGAAAATACAAACCA AAGTGGTGGAGACCAAACAAAATGATCGATTACTAAAACACGAATATCACAAAGAAAGCAAAAC CTTGGGGTTATATTCAGCATTCCTAGCTTGCAAAGCTATGGCTTTAAGATCAAGCTTGCAGTCT AAGTTCACTGTTGAGACAATATTTCTGAAACAAACCAAAAAAGAAAAAGGTAAGATCTTGTGAT TCACAAAAGCACAAACTCAGAATCTTAAAACAGAGACACAAAAGAGAGAACTCACTGAAGAGTA GGAACAATCCCTGAAGGATGTTTAGTAAGGTCAACTGGCTGGCTCCCTTCCGTTCCTTGATCAG CCATTCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.168027115

Conservation Information
Conserved circRNAs	NA
PMCS	0.168027115

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20727484-20726906(-)
						
						Potential amino acid sequence
						
							MADQGTEGSQPVDLTKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRI
REPKTTALIFASGKMVCTGAKSEHLSKLAARKRMADQGTEGSQPVDLTKHPSGIVPTLQNIVST
VNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHLSKLAAR
KRMADQGTEGSQPVDLTKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIM
RIREPKTTALIFASGKMVCTGAKSEHLSKLAARKRMADQGTEGSQPVDLTKHPSGIVPTLQNIV
STVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHLSKLA
ARK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to heat stress

Functional Information
Coding potential	Y
Potential coding position	20727484-20726906(-)
Potential amino acid sequence	MADQGTEGSQPVDLTKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRI REPKTTALIFASGKMVCTGAKSEHLSKLAARKRMADQGTEGSQPVDLTKHPSGIVPTLQNIVST VNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHLSKLAAR KRMADQGTEGSQPVDLTKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIM RIREPKTTALIFASGKMVCTGAKSEHLSKLAARKRMADQGTEGSQPVDLTKHPSGIVPTLQNIV STVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHLSKLA ARK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to heat stress

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

circRNA

Detail information of AT1G55520_circ_g.9

Address

Any questions?

Supported by