Plant Circular RNA Database

Detail information of AT2G41100_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G41100_circ_g.3
					
						ID in PlantcircBase
						ath_circ_017730
					
						Alias
						At_ciR10, AT2G41100_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 17138307-17138573  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, CIRI-full, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ, CIRI2
					
						Parent gene
						
							AT2G41100						
					
						Parent gene annotation
						
							Calmodulin-like protein 12
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G41090_circ_g.1 AT2G41090_circ_g.2 AT2G41090_circ_g.3 2_circ_ag.4 2_circ_ag.5 2_circ_ag.6 AT2G41090_circ_g.7 AT2G41100_circ_g.1 AT2G41100_circ_g.2 AT2G41100_circ_g.4 AT2G41100_circ_g.5 AT2G41100_circ_g.6 AT2G41100_circ_g.7 AT2G41100_circ_g.8 						
					
						Support reads
						5/1319/1001
					
						Tissues
						siliques and seeds/leaf/root, leaf, aerial, inflorescences, seed, whole_plant
					
						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
						AT2G41100.3:1
AT2G41100.1:1
AT2G41100.2:1
AT2G41100.4:1
AT2G41100.6:1
AT2G41100.7:1

General Information
CircRNA Name	AT2G41100_circ_g.3
ID in PlantcircBase	ath_circ_017730
Alias	At_ciR10, AT2G41100_C1
Organism	Arabidpsis thaliana
Position	chr2: 17138307-17138573 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, CIRI, CIRI-full, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ, CIRI2
Parent gene	AT2G41100
Parent gene annotation	Calmodulin-like protein 12
Parent gene strand	+
Alternative splicing	AT2G41090_circ_g.1 AT2G41090_circ_g.2 AT2G41090_circ_g.3 2_circ_ag.4 2_circ_ag.5 2_circ_ag.6 AT2G41090_circ_g.7 AT2G41100_circ_g.1 AT2G41100_circ_g.2 AT2G41100_circ_g.4 AT2G41100_circ_g.5 AT2G41100_circ_g.6 AT2G41100_circ_g.7 AT2G41100_circ_g.8
Support reads	5/1319/1001
Tissues	siliques and seeds/leaf/root, leaf, aerial, inflorescences, seed, whole_plant
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	AT2G41100.3:1 AT2G41100.1:1 AT2G41100.2:1 AT2G41100.4:1 AT2G41100.6:1 AT2G41100.7:1

			
						 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  
						
							GCGCCGCGTCACACTAAAAAAACAATGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACA
GGGAATCTTTCAGGTTATTCGACAAGAATGGTGATGgttccattacgaaaaaggagctcggtac
catgatgcgttcaatcggtgaaaaaccgacaaaagctgatcttcaggacttgatgaacgaagcg
gatttaga

									
								

					

						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: 198
Transcript exons: 17138307-17138504
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGG
Transcript length: 267
Transcript exons: 17138307-17138573
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAATACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATG
Transcript length: 267
Transcript exons: 17138307-17138573
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATG
Transcript length: 801
Transcript exons: 17138307-17138573
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAATACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATGGTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAA
CCGACAAAAGCTGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCG
ATTTCCCTGAGTTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACAC
TAAAAAAACAATGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGG
TTATTCGACAAGAATGGTGATGGTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAA
TCGGTGAAAAACCGACAAAAGCTGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGA
TGGAACCATCGATTTCCCTGAGTTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCG
CCGCGTCACACTAAAAAAACAATGGCGGATAAGCTCACTGACGATCAGATTACAGAATACAGGG
AATCTTTCAGGTTATTCGACAAGAATGGTGATG
						
					

						Genomic sequence
						
							GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATG
						
					

			
		

Sequences
Splice junction sequence	GCGCCGCGTCACACTAAAAAAACAATGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACA GGGAATCTTTCAGGTTATTCGACAAGAATGGTGATGgttccattacgaaaaaggagctcggtac catgatgcgttcaatcggtgaaaaaccgacaaaagctgatcttcaggacttgatgaacgaagcg gatttaga
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: 198 Transcript exons: 17138307-17138504 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGG Transcript length: 267 Transcript exons: 17138307-17138573 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAATACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATG Transcript length: 267 Transcript exons: 17138307-17138573 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATG Transcript length: 801 Transcript exons: 17138307-17138573 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAATACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATGGTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAA CCGACAAAAGCTGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCG ATTTCCCTGAGTTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACAC TAAAAAAACAATGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGG TTATTCGACAAGAATGGTGATGGTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAA TCGGTGAAAAACCGACAAAAGCTGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGA TGGAACCATCGATTTCCCTGAGTTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCG CCGCGTCACACTAAAAAAACAATGGCGGATAAGCTCACTGACGATCAGATTACAGAATACAGGG AATCTTTCAGGTTATTCGACAAGAATGGTGATG
Genomic sequence	GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.976501907

Conservation Information
Conserved circRNAs	NA
PMCS	0.976501907

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17138336-17138570(+)
						
						Potential amino acid sequence
						
							MMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQI
TEYRESFRLFDKNGDGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMA
KNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNGDGSITKKELGTMMRSIGEKPTKADL
QDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNG
DGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKK
TMADKLTDDQITEYRESFRLFDKNGD(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	17138336-17138570(+)
Potential amino acid sequence	MMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQI TEYRESFRLFDKNGDGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMA KNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNGDGSITKKELGTMMRSIGEKPTKADL QDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNG DGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKK TMADKLTDDQITEYRESFRLFDKNGD(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

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

circRNA

Detail information of AT2G41100_circ_g.3

Address

Any questions?

Supported by