Plant Circular RNA Database

Detail information of AT2G41100_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT2G41100_circ_g.4
					
						ID in PlantcircBase
						ath_circ_017731
					
						Alias
						At_ciR3895, Ath_circ_FC1615
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 17138307-17138943  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder, circseq_cup, find_circ
					
						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.3 AT2G41100_circ_g.5 AT2G41100_circ_g.6 AT2G41100_circ_g.7 AT2G41100_circ_g.8 						
					
						Support reads
						2/52
					
						Tissues
						leaf/aerial, inflorescences
					
						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
						AT2G41100.2:1
AT2G41100.3:2
AT2G41100.6:2
AT2G41100.7:2
AT2G41100.1:2
AT2G41100.4:2

General Information
CircRNA Name	AT2G41100_circ_g.4
ID in PlantcircBase	ath_circ_017731
Alias	At_ciR3895, Ath_circ_FC1615
Organism	Arabidpsis thaliana
Position	chr2: 17138307-17138943 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder, circseq_cup, find_circ
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.3 AT2G41100_circ_g.5 AT2G41100_circ_g.6 AT2G41100_circ_g.7 AT2G41100_circ_g.8
Support reads	2/52
Tissues	leaf/aerial, inflorescences
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	AT2G41100.2:1 AT2G41100.3:2 AT2G41100.6:2 AT2G41100.7:2 AT2G41100.1:2 AT2G41100.4:2

			
						 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  
						
							CCGCGTCACACTAAAAAAACAATGGTGGATTATCAGCTCACTGACGATCAGATCTTAGAATTCA
GGGAAGCCTTCCGCGTATTCGACAAGAATGGTGATGgttccattacgaaaaaggagctcggtac
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: 464
Transcript exons: 17138307-17138575,17138672-17138866
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATGGTAGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAA
AAACCGGACAAAAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACC
ATCGATTTCCCTGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTC
ACACTAAAAAAACAAT
Transcript length: 537
Transcript exons: 17138307-17138573,17138674-17138943
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAAC
CGGACAAAAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCATCG
ATTTCCCTGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACAC
TAAAAAAACAATGGTGGATTATCAGCTCACTGACGATCAGATCTTAGAATTCAGGGAAGCCTTC
CGCGTATTCGACAAGAATGGTGATG
Transcript length: 540
Transcript exons: 17138307-17138575,17138673-17138943
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATGGTGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAA
AACCGGACAAAAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCA
TCGATTTCCCTGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCA
CACTAAAAAAACAATGGTGGATTATCAGCTCACTGACGATCAGATCTTAGAATTCAGGGAAGCC
TTCCGCGTATTCGACAAGAATGGTGATG
Transcript length: 561
Transcript exons: 17138307-17138575,17138619-17138888,17138922-17138943
GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATGGTGATCATCTTCAAAGCAATGAAATGACTAACACTAGTCCTTGATTACTTTTT
GTAGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAACCGGACAA
AAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCATCGATTTCCC
TGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAA
ACAATGGTGGATTATCAGCTCACTGACGTATTCGACAAGAATGGTGATG
Transcript length: 267
Transcript exons: 17138307-17138943
GTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAACCGGACAAAAGC
TGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATG
						
					

						Genomic sequence
						
							GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC
TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG
TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA
TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA
GAATGGTGATGGTATGGTTCATCAACTCTTTCCATTTAATCGTAATGTTGGATCATGATCATCT
TCAAAGCAATGAAATGACTAACACTAGTCCTTGATTACTTTTTGTAGGTTCCATTACGAAAAAG
GAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAACCGGACAAAAGCTGATCTTCAGGACATGA
TGAACGAAGTGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAGTTCTTGTACCTAATGGC
TAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAATGGTGGATTATCAGCTC
ACTGACGATCAGATCTTAGAATTCAGGGAAGCCTTCCGCGTATTCGACAAGAATGGTGATG
						
					

			
		

Sequences
Splice junction sequence	CCGCGTCACACTAAAAAAACAATGGTGGATTATCAGCTCACTGACGATCAGATCTTAGAATTCA GGGAAGCCTTCCGCGTATTCGACAAGAATGGTGATGgttccattacgaaaaaggagctcggtac 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: 464 Transcript exons: 17138307-17138575,17138672-17138866 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATGGTAGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAA AAACCGGACAAAAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACC ATCGATTTCCCTGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTC ACACTAAAAAAACAAT Transcript length: 537 Transcript exons: 17138307-17138573,17138674-17138943 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAAC CGGACAAAAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCATCG ATTTCCCTGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACAC TAAAAAAACAATGGTGGATTATCAGCTCACTGACGATCAGATCTTAGAATTCAGGGAAGCCTTC CGCGTATTCGACAAGAATGGTGATG Transcript length: 540 Transcript exons: 17138307-17138575,17138673-17138943 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATGGTGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAA AACCGGACAAAAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCA TCGATTTCCCTGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCA CACTAAAAAAACAATGGTGGATTATCAGCTCACTGACGATCAGATCTTAGAATTCAGGGAAGCC TTCCGCGTATTCGACAAGAATGGTGATG Transcript length: 561 Transcript exons: 17138307-17138575,17138619-17138888,17138922-17138943 GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATGGTGATCATCTTCAAAGCAATGAAATGACTAACACTAGTCCTTGATTACTTTTT GTAGGTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAACCGGACAA AAGCTGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCATCGATTTCCC TGAGTTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAA ACAATGGTGGATTATCAGCTCACTGACGTATTCGACAAGAATGGTGATG Transcript length: 267 Transcript exons: 17138307-17138943 GTTCCATTACGAAAAAGGAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAACCGGACAAAAGC TGATCTTCAGGACATGATGAACGAAGTGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTACCTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATG
Genomic sequence	GTTCCATTACGAAAAAGGAGCTCGGTACCATGATGCGTTCAATCGGTGAAAAACCGACAAAAGC TGATCTTCAGGACTTGATGAACGAAGCGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAG TTCTTGTGCGTAATGGCTAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAA TGGCGGATAAGCTCACTGACGATCAGATTACAGAGTACAGGGAATCTTTCAGGTTATTCGACAA GAATGGTGATGGTATGGTTCATCAACTCTTTCCATTTAATCGTAATGTTGGATCATGATCATCT TCAAAGCAATGAAATGACTAACACTAGTCCTTGATTACTTTTTGTAGGTTCCATTACGAAAAAG GAGCTCCGTACCGTGATGTTTTCCCTCGGTAAAAACCGGACAAAAGCTGATCTTCAGGACATGA TGAACGAAGTGGATTTAGATGGTGATGGAACCATCGATTTCCCTGAGTTCTTGTACCTAATGGC TAAGAATCAAGGTCATGATCAAGCGCCGCGTCACACTAAAAAAACAATGGTGGATTATCAGCTC ACTGACGATCAGATCTTAGAATTCAGGGAAGCCTTCCGCGTATTCGACAAGAATGGTGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.714537706

Conservation Information
Conserved circRNAs	NA
PMCS	0.714537706

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17138336-17138940(+)
						
						Potential amino acid sequence
						
							MMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQI
TEYRESFRLFDKNGDGSITKKELRTVMFSLGKNRTKADLQDMMNEVDLDGDGTIDFPEFLYLMA
KNQGHDQAPRHTKKTMVDYQLTDDQILEFREAFRVFDKNGDGSITKKELGTMMRSIGEKPTKAD
LQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKN
GDGSITKKELRTVMFSLGKNRTKADLQDMMNEVDLDGDGTIDFPEFLYLMAKNQGHDQAPRHTK
KTMVDYQLTDDQILEFREAFRVFDKNGDGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGD
GTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNGDGSITKKELRTV
MFSLGKNRTKADLQDMMNEVDLDGDGTIDFPEFLYLMAKNQGHDQAPRHTKKTMVDYQLTDDQI
LEFREAFRVFDKNGDGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMA
KNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNGDGSITKKELRTVMFSLGKNRTKADL
QDMMNEVDLDGDGTIDFPEFLYLMAKNQGHDQAPRHTKKTMVDYQLTDDQILEFREAFRVFDKN
GD(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17138336-17138940(+)
Potential amino acid sequence	MMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQI TEYRESFRLFDKNGDGSITKKELRTVMFSLGKNRTKADLQDMMNEVDLDGDGTIDFPEFLYLMA KNQGHDQAPRHTKKTMVDYQLTDDQILEFREAFRVFDKNGDGSITKKELGTMMRSIGEKPTKAD LQDLMNEADLDGDGTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKN GDGSITKKELRTVMFSLGKNRTKADLQDMMNEVDLDGDGTIDFPEFLYLMAKNQGHDQAPRHTK KTMVDYQLTDDQILEFREAFRVFDKNGDGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGD GTIDFPEFLCVMAKNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNGDGSITKKELRTV MFSLGKNRTKADLQDMMNEVDLDGDGTIDFPEFLYLMAKNQGHDQAPRHTKKTMVDYQLTDDQI LEFREAFRVFDKNGDGSITKKELGTMMRSIGEKPTKADLQDLMNEADLDGDGTIDFPEFLCVMA KNQGHDQAPRHTKKTMADKLTDDQITEYRESFRLFDKNGDGSITKKELRTVMFSLGKNRTKADL QDMMNEVDLDGDGTIDFPEFLYLMAKNQGHDQAPRHTKKTMVDYQLTDDQILEFREAFRVFDKN GD(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT2G41100_circ_g.4

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