Plant Circular RNA Database

Detail information of AT4G23100_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT4G23100_circ_g.5
					
						ID in PlantcircBase
						ath_circ_032275
					
						Alias
						At_ciR1496, AT4G23100_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 12104893-12106255  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT4G23100						
					
						Parent gene annotation
						
							Glutamate--cysteine ligase, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G23100_circ_g.2 AT4G23100_circ_g.3 AT4G23100_circ_g.4 AT4G23100_circ_g.6 AT4G23100_circ_g.7 AT4G23100_circ_g.8 						
					
						Support reads
						8/34
					
						Tissues
						leaf/root, aerial, 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  
						
							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
						AT4G23100.1:7
AT4G23100.3:7
AT4G23100.2:7

General Information
CircRNA Name	AT4G23100_circ_g.5
ID in PlantcircBase	ath_circ_032275
Alias	At_ciR1496, AT4G23100_C1
Organism	Arabidpsis thaliana
Position	chr4: 12104893-12106255 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT4G23100
Parent gene annotation	Glutamate--cysteine ligase, chloroplastic
Parent gene strand	-
Alternative splicing	AT4G23100_circ_g.2 AT4G23100_circ_g.3 AT4G23100_circ_g.4 AT4G23100_circ_g.6 AT4G23100_circ_g.7 AT4G23100_circ_g.8
Support reads	8/34
Tissues	leaf/root, aerial, 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	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	AT4G23100.1:7 AT4G23100.3:7 AT4G23100.2:7

			
						 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  
						
							TCTTTCAGCGATACCATTAAGAAGCTCGGCTATTTGATCATACTTCATAGGGCGCAAAGTATTG
ACCTCAAAACCAAATTTCTCATGTTCTGTACCTATTccaaaagagtcatcgaaaacaaatggta
gcattcctgtgcggtccttgtcagtgtctgtccatatgtggctgtcaaaacataccagagttat
aaggtggg

									
								

					

						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: 645
Transcript exons: 12104893-12104961,12105046-12105116,12105207-12105275,12
105395-12105478,12105658-12105750,12105828-12105935,1210
6105-12106255
CCAAAAGAGTCATCGAAAACAAATGGTAGCATTCCTGTGCGGTCCTTGTCAGTGTCTGTCCATA
TGTGGCTTCTCATGCTGAGAAATCCGTTTGGCTTTCCTTCTGTAAAAGGGGAATTCGCAAATAG
AGCCGTTGCTATAGGTTGTAAAGCAAGACCAGCACGAAACTTCCTGATCATATCAGCTTCTGAG
CTAAAATCCAGATTAACCTGAACAGTACACGTTCGGAGCATCATATCAAGACCAAGGGTACCAA
CTTTCGGCATGTAGTTTCTCATAATGTCGTATCTCCCCTTTGGCATGATGGGTATATCCTCCCG
ACGCCATTTGGGCTGGAAGCCAATTCCTAAGAAACCAATTCCCATTTCCTCAGCAACTGCTTTT
ACCTGATAAAGATGTGAATTGACTTCAGCACAAGTTTGATGCAAAGTCTCAAGAGGTGCACCAC
TAAGCTCGAACTGACCCCCAGGTTCAAGTGAAATGCTTTGCTTTCCCTGCTTCAGACCAATGAT
CTTGTCACCTTCCATTACTTTTTCCCATTCAAATCTTTCAGCGATACCATTAAGAAGCTCGGCT
ATTTGATCATACTTCATAGGGCGCAAAGTATTGACCTCAAAACCAAATTTCTCATGTTCTGTAC
CTATT
Transcript length: 328
Transcript exons: 12104893-12106255
CCAAAAGAGTCATCGAAAACAAATGGTAGCATTCCTGTGCGGTCCTTGTCAGTGTCTGTCCATA
TGTGGCTGATAAAGATGTGAATTGACTTCAGCACAAGTTTGATGCAAAGTCTCAAGAGGTGCAC
CACTAAGCTCGAACTGACCCCCAGGTTCAAGTGAAATGCTTTGCTTTCCCTGCTTCAGACCAAT
GATCTTGTCACCTTCCATTACTTTTTCCCATTCAAATCTTTCAGCGATACCATTAAGAAGCTCG
GCTATTTGATCATACTTCATAGGGCGCAAAGTATTGACCTCAAAACCAAATTTCTCATGTTCTG
TACCTATT
						
					

						Genomic sequence
						
							CCAAAAGAGTCATCGAAAACAAATGGTAGCATTCCTGTGCGGTCCTTGTCAGTGTCTGTCCATA
TGTGGCTGTCAAAACATACCAGAGTTATAAGGTGGGAGGGAAACTAATTCAAAAAGATATCGGG
GATCATAACAACTGAATCTAGATACCTTCTCATGCTGAGAAATCCGTTTGGCTTTCCTTCTGTA
AAAGGGGAATTCGCAAATAGAGCCGTTGCTATCTGTTGAATTTAGATAATAGTGAGGCAATGGT
TAGTCAAAATCGTTAATAAAAGTTTCTGGTTATGCCACAAAGAGATCGAGCTTCTCACAGGTTG
TAAAGCAAGACCAGCACGAAACTTCCTGATCATATCAGCTTCTGAGCTAAAATCCAGATTAACC
TGTCAAGATTGCAAGTAATGCAGTTTCTATAAGTTTCAAAATAAGATTATTGATGAGAACTGGA
AAGTTTAGTTTAAGGAAATTATGAAAAGGCGCAAAGTCAGAATATTAATCTAACCTGAACAGTA
CACGTTCGGAGCATCATATCAAGACCAAGGGTACCAACTTTCGGCATGTAGTTTCTCATAATGT
CGTATCTCCCCTGCACAGAACACATTACACTATGTCAAATCTTACTGCCTGACTCGTCATAGGA
AAACTTAACACAAACACCAAGAAATAATCCGAACGTTGGCTATGTAGAATCAGATAATATTATC
TGAATTAGAAACAAACAGATGTTAACTTTCTTCAATCTTAAGAATAGAGAAAGCGTCATACCTT
TGGCATGATGGGTATATCCTCCCGACGCCATTTGGGCTGGAAGCCAATTCCTAAGAAACCAATT
CCCATTTCCTCAGCAACTGCTTTTACCTGTGACATCCGTAGATAGTTGGTTATTTGTCACGTTT
TAGGGTGAGAGCATTGGCAATAATTATCTTTGAAATTACCTGATAAAGATGTGAATTGACTTCA
GCACAAGTTTGATGCAAAGTCTCAAGAGGTGCACCACTAAGCTCGAACTGACCCCCAGGTTCAA
GTGAAATGCTTTGCTTTCCCTGGTCAACAAAAGGACAGAACGAGTTATCTACAGCAAAAAAAAA
AAAAAGACTGAAACCTTATAATATACCGATCATTGTGTTGTATATGAAGCTAACATGTTCTACA
GGCTGAAAATGTATATAAATAATAAACGGCTCAAAAGATGAAACACAGGAGAATGTTAACCTGC
TTCAGACCAATGATCTTGTCACCTTCCATTACTTTTTCCCATTCAAATCTTTCAGCGATACCAT
TAAGAAGCTCGGCTATTTGATCATACTTCATAGGGCGCAAAGTATTGACCTCAAAACCAAATTT
CTCATGTTCTGTACCTATT
						
					

			
		

Sequences
Splice junction sequence	TCTTTCAGCGATACCATTAAGAAGCTCGGCTATTTGATCATACTTCATAGGGCGCAAAGTATTG ACCTCAAAACCAAATTTCTCATGTTCTGTACCTATTccaaaagagtcatcgaaaacaaatggta gcattcctgtgcggtccttgtcagtgtctgtccatatgtggctgtcaaaacataccagagttat aaggtggg
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: 645 Transcript exons: 12104893-12104961,12105046-12105116,12105207-12105275,12 105395-12105478,12105658-12105750,12105828-12105935,1210 6105-12106255 CCAAAAGAGTCATCGAAAACAAATGGTAGCATTCCTGTGCGGTCCTTGTCAGTGTCTGTCCATA TGTGGCTTCTCATGCTGAGAAATCCGTTTGGCTTTCCTTCTGTAAAAGGGGAATTCGCAAATAG AGCCGTTGCTATAGGTTGTAAAGCAAGACCAGCACGAAACTTCCTGATCATATCAGCTTCTGAG CTAAAATCCAGATTAACCTGAACAGTACACGTTCGGAGCATCATATCAAGACCAAGGGTACCAA CTTTCGGCATGTAGTTTCTCATAATGTCGTATCTCCCCTTTGGCATGATGGGTATATCCTCCCG ACGCCATTTGGGCTGGAAGCCAATTCCTAAGAAACCAATTCCCATTTCCTCAGCAACTGCTTTT ACCTGATAAAGATGTGAATTGACTTCAGCACAAGTTTGATGCAAAGTCTCAAGAGGTGCACCAC TAAGCTCGAACTGACCCCCAGGTTCAAGTGAAATGCTTTGCTTTCCCTGCTTCAGACCAATGAT CTTGTCACCTTCCATTACTTTTTCCCATTCAAATCTTTCAGCGATACCATTAAGAAGCTCGGCT ATTTGATCATACTTCATAGGGCGCAAAGTATTGACCTCAAAACCAAATTTCTCATGTTCTGTAC CTATT Transcript length: 328 Transcript exons: 12104893-12106255 CCAAAAGAGTCATCGAAAACAAATGGTAGCATTCCTGTGCGGTCCTTGTCAGTGTCTGTCCATA TGTGGCTGATAAAGATGTGAATTGACTTCAGCACAAGTTTGATGCAAAGTCTCAAGAGGTGCAC CACTAAGCTCGAACTGACCCCCAGGTTCAAGTGAAATGCTTTGCTTTCCCTGCTTCAGACCAAT GATCTTGTCACCTTCCATTACTTTTTCCCATTCAAATCTTTCAGCGATACCATTAAGAAGCTCG GCTATTTGATCATACTTCATAGGGCGCAAAGTATTGACCTCAAAACCAAATTTCTCATGTTCTG TACCTATT
Genomic sequence	CCAAAAGAGTCATCGAAAACAAATGGTAGCATTCCTGTGCGGTCCTTGTCAGTGTCTGTCCATA TGTGGCTGTCAAAACATACCAGAGTTATAAGGTGGGAGGGAAACTAATTCAAAAAGATATCGGG GATCATAACAACTGAATCTAGATACCTTCTCATGCTGAGAAATCCGTTTGGCTTTCCTTCTGTA AAAGGGGAATTCGCAAATAGAGCCGTTGCTATCTGTTGAATTTAGATAATAGTGAGGCAATGGT TAGTCAAAATCGTTAATAAAAGTTTCTGGTTATGCCACAAAGAGATCGAGCTTCTCACAGGTTG TAAAGCAAGACCAGCACGAAACTTCCTGATCATATCAGCTTCTGAGCTAAAATCCAGATTAACC TGTCAAGATTGCAAGTAATGCAGTTTCTATAAGTTTCAAAATAAGATTATTGATGAGAACTGGA AAGTTTAGTTTAAGGAAATTATGAAAAGGCGCAAAGTCAGAATATTAATCTAACCTGAACAGTA CACGTTCGGAGCATCATATCAAGACCAAGGGTACCAACTTTCGGCATGTAGTTTCTCATAATGT CGTATCTCCCCTGCACAGAACACATTACACTATGTCAAATCTTACTGCCTGACTCGTCATAGGA AAACTTAACACAAACACCAAGAAATAATCCGAACGTTGGCTATGTAGAATCAGATAATATTATC TGAATTAGAAACAAACAGATGTTAACTTTCTTCAATCTTAAGAATAGAGAAAGCGTCATACCTT TGGCATGATGGGTATATCCTCCCGACGCCATTTGGGCTGGAAGCCAATTCCTAAGAAACCAATT CCCATTTCCTCAGCAACTGCTTTTACCTGTGACATCCGTAGATAGTTGGTTATTTGTCACGTTT TAGGGTGAGAGCATTGGCAATAATTATCTTTGAAATTACCTGATAAAGATGTGAATTGACTTCA GCACAAGTTTGATGCAAAGTCTCAAGAGGTGCACCACTAAGCTCGAACTGACCCCCAGGTTCAA GTGAAATGCTTTGCTTTCCCTGGTCAACAAAAGGACAGAACGAGTTATCTACAGCAAAAAAAAA AAAAAGACTGAAACCTTATAATATACCGATCATTGTGTTGTATATGAAGCTAACATGTTCTACA GGCTGAAAATGTATATAAATAATAAACGGCTCAAAAGATGAAACACAGGAGAATGTTAACCTGC TTCAGACCAATGATCTTGTCACCTTCCATTACTTTTTCCCATTCAAATCTTTCAGCGATACCAT TAAGAAGCTCGGCTATTTGATCATACTTCATAGGGCGCAAAGTATTGACCTCAAAACCAAATTT CTCATGTTCTGTACCTATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.564060077

Conservation Information
Conserved circRNAs	NA
PMCS	0.564060077

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12106204-12104895(-)
						
						Potential amino acid sequence
						
							MKYDQIAELLNGIAERFEWEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQTCAEVN
SHLYQVKAVAEEMGIGFLGIGFQPKWRREDIPIMPKGRYDIMRNYMPKVGTLGLDMMLRTCTVQ
VNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTGMLPFV
FDDSFGIGTEHEKFGFEVNTLRPMKYDQIAELLNGIAERFEWEKVMEGDKIIGLKQGKQSISLE
PGGQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFLGIGFQPKWRREDIPIMPKGRYDI
MRNYMPKVGTLGLDMMLRTCTVQVNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNG
FLSMRSHIWTDTDKDRTGMLPFVFDDSFGIGTEHEKFGFEVNTLRPMKYDQIAELLNGIAERFE
WEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFL
GIGFQPKWRREDIPIMPKGRYDIMRNYMPKVGTLGLDMMLRTCTVQVNLDFSSEADMIRKFRAG
LALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTGMLPFVFDDSFGIGTEHEKFGFEV
NTLRPMKYDQIAELLNGIAERFEWEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQT
CAEVNSHLYQVKAVAEEMGIGFLGIGFQPKWRREDIPIMPKGRYDIMRNYMPKVGTLGLDMMLR
TCTVQVNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTG
MLPFVFDDSF(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to methyl jasmonate

Functional Information
Coding potential	Y
Potential coding position	12106204-12104895(-)
Potential amino acid sequence	MKYDQIAELLNGIAERFEWEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQTCAEVN SHLYQVKAVAEEMGIGFLGIGFQPKWRREDIPIMPKGRYDIMRNYMPKVGTLGLDMMLRTCTVQ VNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTGMLPFV FDDSFGIGTEHEKFGFEVNTLRPMKYDQIAELLNGIAERFEWEKVMEGDKIIGLKQGKQSISLE PGGQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFLGIGFQPKWRREDIPIMPKGRYDI MRNYMPKVGTLGLDMMLRTCTVQVNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNG FLSMRSHIWTDTDKDRTGMLPFVFDDSFGIGTEHEKFGFEVNTLRPMKYDQIAELLNGIAERFE WEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFL GIGFQPKWRREDIPIMPKGRYDIMRNYMPKVGTLGLDMMLRTCTVQVNLDFSSEADMIRKFRAG LALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTGMLPFVFDDSFGIGTEHEKFGFEV NTLRPMKYDQIAELLNGIAERFEWEKVMEGDKIIGLKQGKQSISLEPGGQFELSGAPLETLHQT CAEVNSHLYQVKAVAEEMGIGFLGIGFQPKWRREDIPIMPKGRYDIMRNYMPKVGTLGLDMMLR TCTVQVNLDFSSEADMIRKFRAGLALQPIATALFANSPFTEGKPNGFLSMRSHIWTDTDKDRTG MLPFVFDDSF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to methyl jasmonate

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

circRNA

Detail information of AT4G23100_circ_g.5

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