Plant Circular RNA Database

Detail information of AT4G03250_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G03250_circ_g.2
					
						ID in PlantcircBase
						ath_circ_029550
					
						Alias
						At_ciR722
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 1425539-1426335  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT4G03250						
					
						Parent gene annotation
						
							Homeodomain-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							4_circ_ag.6 4_circ_ag.7 4_circ_ag.8 4_circ_ag.9 ENSRNA049493837_circ_g.1 AT4G02980_circ_g.1 AT4G02980_circ_g.2 AT4G02980_circ_g.3 AT4G02990_circ_g.1 AT4G03000_circ_g.1 AT4G03020_circ_g.1 AT4G03020_circ_g.2 AT4G03020_circ_g.3 AT4G03020_circ_g.4 AT4G03050_circ_g.1 AT4G03080_circ_g.1 AT4G03080_circ_g.2 AT4G03080_circ_g.3 AT4G03080_circ_g.4 AT4G03080_circ_g.5 AT4G03080_circ_g.6 AT4G03080_circ_g.7 AT4G03080_circ_g.8 AT4G03080_circ_g.9 AT4G03080_circ_g.10 AT4G03080_circ_g.11 AT4G03080_circ_g.12 AT4G03090_circ_g.1 AT4G03090_circ_g.2 AT4G03110_circ_g.1 AT4G03110_circ_g.2 AT4G03115_circ_g.1 AT4G03120_circ_g.1 AT4G03180_circ_g.1 AT4G03190_circ_g.1 AT4G03200_circ_g.1 AT4G03200_circ_g.2 AT4G03200_circ_g.3 AT4G03200_circ_g.4 AT4G03200_circ_g.5 AT4G03200_circ_g.6 AT4G03200_circ_g.7 AT4G03200_circ_g.8 AT4G03200_circ_g.9 AT4G03200_circ_g.10 AT4G03210_circ_g.1 AT4G03210_circ_g.2 AT4G03210_circ_g.3 AT4G03230_circ_g.1 AT4G03240_circ_g.1 AT4G03250_circ_g.1 AT4G03250_circ_g.3 AT4G03260_circ_g.1 AT4G03270_circ_g.1 AT4G03280_circ_g.1 AT4G03280_circ_g.2 AT4G03280_circ_g.3 AT4G03280_circ_g.4 AT4G03280_circ_g.5 AT4G03290_circ_g.1 4_circ_igg.2 4_circ_ag.3 4_circ_ag.4 4_circ_ag.5 ENSRNA049493832_circ_g.1 4_circ_ag.2 ENSRNA049493835_circ_g.1 ENSRNA049493835_circ_g.2 ENSRNA049493835_circ_g.3 ENSRNA049493835_circ_g.4 ENSRNA049493835_circ_g.5 ENSRNA049493835_circ_g.6 ENSRNA049493835_circ_g.7 ENSRNA049493835_circ_g.8 AT4G03390_circ_g.1 AT4G03390_circ_g.2 AT4G03390_circ_g.3 AT4G03390_circ_g.4 AT4G03400_circ_g.1 AT4G03400_circ_g.2 AT4G03400_circ_g.3 AT4G03400_circ_g.4 AT4G03410_circ_g.1 AT4G03410_circ_g.2 AT4G03410_circ_g.3 AT4G03410_circ_g.4 AT4G03420_circ_g.1 AT4G03420_circ_g.2 AT4G03420_circ_g.3 						
					
						Support reads
						12/1
					
						Tissues
						leaf/leaf
					
						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
						AT4G03250.1:2

General Information
CircRNA Name	AT4G03250_circ_g.2
ID in PlantcircBase	ath_circ_029550
Alias	At_ciR722
Organism	Arabidpsis thaliana
Position	chr4: 1425539-1426335 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, find_circ
Parent gene	AT4G03250
Parent gene annotation	Homeodomain-like superfamily protein
Parent gene strand	+
Alternative splicing	4_circ_ag.6 4_circ_ag.7 4_circ_ag.8 4_circ_ag.9 ENSRNA049493837_circ_g.1 AT4G02980_circ_g.1 AT4G02980_circ_g.2 AT4G02980_circ_g.3 AT4G02990_circ_g.1 AT4G03000_circ_g.1 AT4G03020_circ_g.1 AT4G03020_circ_g.2 AT4G03020_circ_g.3 AT4G03020_circ_g.4 AT4G03050_circ_g.1 AT4G03080_circ_g.1 AT4G03080_circ_g.2 AT4G03080_circ_g.3 AT4G03080_circ_g.4 AT4G03080_circ_g.5 AT4G03080_circ_g.6 AT4G03080_circ_g.7 AT4G03080_circ_g.8 AT4G03080_circ_g.9 AT4G03080_circ_g.10 AT4G03080_circ_g.11 AT4G03080_circ_g.12 AT4G03090_circ_g.1 AT4G03090_circ_g.2 AT4G03110_circ_g.1 AT4G03110_circ_g.2 AT4G03115_circ_g.1 AT4G03120_circ_g.1 AT4G03180_circ_g.1 AT4G03190_circ_g.1 AT4G03200_circ_g.1 AT4G03200_circ_g.2 AT4G03200_circ_g.3 AT4G03200_circ_g.4 AT4G03200_circ_g.5 AT4G03200_circ_g.6 AT4G03200_circ_g.7 AT4G03200_circ_g.8 AT4G03200_circ_g.9 AT4G03200_circ_g.10 AT4G03210_circ_g.1 AT4G03210_circ_g.2 AT4G03210_circ_g.3 AT4G03230_circ_g.1 AT4G03240_circ_g.1 AT4G03250_circ_g.1 AT4G03250_circ_g.3 AT4G03260_circ_g.1 AT4G03270_circ_g.1 AT4G03280_circ_g.1 AT4G03280_circ_g.2 AT4G03280_circ_g.3 AT4G03280_circ_g.4 AT4G03280_circ_g.5 AT4G03290_circ_g.1 4_circ_igg.2 4_circ_ag.3 4_circ_ag.4 4_circ_ag.5 ENSRNA049493832_circ_g.1 4_circ_ag.2 ENSRNA049493835_circ_g.1 ENSRNA049493835_circ_g.2 ENSRNA049493835_circ_g.3 ENSRNA049493835_circ_g.4 ENSRNA049493835_circ_g.5 ENSRNA049493835_circ_g.6 ENSRNA049493835_circ_g.7 ENSRNA049493835_circ_g.8 AT4G03390_circ_g.1 AT4G03390_circ_g.2 AT4G03390_circ_g.3 AT4G03390_circ_g.4 AT4G03400_circ_g.1 AT4G03400_circ_g.2 AT4G03400_circ_g.3 AT4G03400_circ_g.4 AT4G03410_circ_g.1 AT4G03410_circ_g.2 AT4G03410_circ_g.3 AT4G03410_circ_g.4 AT4G03420_circ_g.1 AT4G03420_circ_g.2 AT4G03420_circ_g.3
Support reads	12/1
Tissues	leaf/leaf
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	AT4G03250.1:2

			
						 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  
						
							TTAGGAAGACAATACCAAGAGGATGGTCCACCTCTGGGGGTTGAATTTGATCCTCTTCCTCCCG
GTGCATTTGAGCCTCAGACTAATCCTATAGTTCACGattcaggcgaagcgaccgctgatggcga
taaagcttctacagaaaacagcaaaaaacggaagcttaagactcctatgcaagttatggcgctt
gagaattt

									
								

					

						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: 714
Transcript exons: 1425539-1425646,1425730-1426335
ATTCAGGCGAAGCGACCGCTGATGGCGATAAAGCTTCTACAGAAAACAGCAAAAAACGGAAGCT
TAAGACTCCTATGCAAGTTATGGCGCTTGAGAATTTCTACAATGAGCATAAGTATCCGACTGAA
GAAATGAAGGGCAAGTTAGCAGAGGAAGTTGGATTAACTGAGAAGCAAGTTTCAGGTTGGTTCT
GCCATAGAAGGTTAAAAGACAAACGTCATGTAAAAGAAGATGGGAATGCCATTGGGAGCCAAGA
TCGGTCAAGCGTTGTTCTTCAGGATCGTGGAAGTGGGCTTCGACAGGATTCATGTGGTAGTACA
AAGCAAACGGATTATTGGAACCCCAAGCCTAGGGAAGTTGAAAGTCAAAGGCTTTATATGGGAA
ATGCTGATGGTGAAGATAGTACATCTTCTGATCGTAGCTCATCATTACGTAAGAATCTTGTCTC
TAGCAAAGATGGAATTCGCGATGTGGAAAGTTCTAGATATGTTGCACATAAAGACGTTATTCAG
CATCCTCAGTTCATGAGAAGCTATGGGTATAATAAGCCTTCGGGATACTTGAAAGTGAAGGGAG
AGAGTGAGAATTTTGCTATCACTGCCGTAAAGAGACAATTAGGAAGACAATACCAAGAGGATGG
TCCACCTCTGGGGGTTGAATTTGATCCTCTTCCTCCCGGTGCATTTGAGCCTCAGACTAATCCT
ATAGTTCACG
						
					

						Genomic sequence
						
							ATTCAGGCGAAGCGACCGCTGATGGCGATAAAGCTTCTACAGAAAACAGCAAAAAACGGAAGCT
TAAGACTCCTATGCAAGTTATGGCGCTTGAGAATTTCTACAATGGTAAATTATGGCTTTGTTGT
TTGCATATGTTCCTTTATACCAAGTTGTATATGCTTTACAGGTGTGATTTGGTTTTTCTACAGA
GCATAAGTATCCGACTGAAGAAATGAAGGGCAAGTTAGCAGAGGAAGTTGGATTAACTGAGAAG
CAAGTTTCAGGTTGGTTCTGCCATAGAAGGTTAAAAGACAAACGTCATGTAAAAGAAGATGGGA
ATGCCATTGGGAGCCAAGATCGGTCAAGCGTTGTTCTTCAGGATCGTGGAAGTGGGCTTCGACA
GGATTCATGTGGTAGTACAAAGCAAACGGATTATTGGAACCCCAAGCCTAGGGAAGTTGAAAGT
CAAAGGCTTTATATGGGAAATGCTGATGGTGAAGATAGTACATCTTCTGATCGTAGCTCATCAT
TACGTAAGAATCTTGTCTCTAGCAAAGATGGAATTCGCGATGTGGAAAGTTCTAGATATGTTGC
ACATAAAGACGTTATTCAGCATCCTCAGTTCATGAGAAGCTATGGGTATAATAAGCCTTCGGGA
TACTTGAAAGTGAAGGGAGAGAGTGAGAATTTTGCTATCACTGCCGTAAAGAGACAATTAGGAA
GACAATACCAAGAGGATGGTCCACCTCTGGGGGTTGAATTTGATCCTCTTCCTCCCGGTGCATT
TGAGCCTCAGACTAATCCTATAGTTCACG
						
					

			
		

Sequences
Splice junction sequence	TTAGGAAGACAATACCAAGAGGATGGTCCACCTCTGGGGGTTGAATTTGATCCTCTTCCTCCCG GTGCATTTGAGCCTCAGACTAATCCTATAGTTCACGattcaggcgaagcgaccgctgatggcga taaagcttctacagaaaacagcaaaaaacggaagcttaagactcctatgcaagttatggcgctt gagaattt
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: 714 Transcript exons: 1425539-1425646,1425730-1426335 ATTCAGGCGAAGCGACCGCTGATGGCGATAAAGCTTCTACAGAAAACAGCAAAAAACGGAAGCT TAAGACTCCTATGCAAGTTATGGCGCTTGAGAATTTCTACAATGAGCATAAGTATCCGACTGAA GAAATGAAGGGCAAGTTAGCAGAGGAAGTTGGATTAACTGAGAAGCAAGTTTCAGGTTGGTTCT GCCATAGAAGGTTAAAAGACAAACGTCATGTAAAAGAAGATGGGAATGCCATTGGGAGCCAAGA TCGGTCAAGCGTTGTTCTTCAGGATCGTGGAAGTGGGCTTCGACAGGATTCATGTGGTAGTACA AAGCAAACGGATTATTGGAACCCCAAGCCTAGGGAAGTTGAAAGTCAAAGGCTTTATATGGGAA ATGCTGATGGTGAAGATAGTACATCTTCTGATCGTAGCTCATCATTACGTAAGAATCTTGTCTC TAGCAAAGATGGAATTCGCGATGTGGAAAGTTCTAGATATGTTGCACATAAAGACGTTATTCAG CATCCTCAGTTCATGAGAAGCTATGGGTATAATAAGCCTTCGGGATACTTGAAAGTGAAGGGAG AGAGTGAGAATTTTGCTATCACTGCCGTAAAGAGACAATTAGGAAGACAATACCAAGAGGATGG TCCACCTCTGGGGGTTGAATTTGATCCTCTTCCTCCCGGTGCATTTGAGCCTCAGACTAATCCT ATAGTTCACG
Genomic sequence	ATTCAGGCGAAGCGACCGCTGATGGCGATAAAGCTTCTACAGAAAACAGCAAAAAACGGAAGCT TAAGACTCCTATGCAAGTTATGGCGCTTGAGAATTTCTACAATGGTAAATTATGGCTTTGTTGT TTGCATATGTTCCTTTATACCAAGTTGTATATGCTTTACAGGTGTGATTTGGTTTTTCTACAGA GCATAAGTATCCGACTGAAGAAATGAAGGGCAAGTTAGCAGAGGAAGTTGGATTAACTGAGAAG CAAGTTTCAGGTTGGTTCTGCCATAGAAGGTTAAAAGACAAACGTCATGTAAAAGAAGATGGGA ATGCCATTGGGAGCCAAGATCGGTCAAGCGTTGTTCTTCAGGATCGTGGAAGTGGGCTTCGACA GGATTCATGTGGTAGTACAAAGCAAACGGATTATTGGAACCCCAAGCCTAGGGAAGTTGAAAGT CAAAGGCTTTATATGGGAAATGCTGATGGTGAAGATAGTACATCTTCTGATCGTAGCTCATCAT TACGTAAGAATCTTGTCTCTAGCAAAGATGGAATTCGCGATGTGGAAAGTTCTAGATATGTTGC ACATAAAGACGTTATTCAGCATCCTCAGTTCATGAGAAGCTATGGGTATAATAAGCCTTCGGGA TACTTGAAAGTGAAGGGAGAGAGTGAGAATTTTGCTATCACTGCCGTAAAGAGACAATTAGGAA GACAATACCAAGAGGATGGTCCACCTCTGGGGGTTGAATTTGATCCTCTTCCTCCCGGTGCATT TGAGCCTCAGACTAATCCTATAGTTCACG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.22269396

Conservation Information
Conserved circRNAs	NA
PMCS	0.22269396

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1425613-1426332(+)
						
						Potential amino acid sequence
						
							MQVMALENFYNEHKYPTEEMKGKLAEEVGLTEKQVSGWFCHRRLKDKRHVKEDGNAIGSQDRSS
VVLQDRGSGLRQDSCGSTKQTDYWNPKPREVESQRLYMGNADGEDSTSSDRSSSLRKNLVSSKD
GIRDVESSRYVAHKDVIQHPQFMRSYGYNKPSGYLKVKGESENFAITAVKRQLGRQYQEDGPPL
GVEFDPLPPGAFEPQTNPIVHDSGEATADGDKASTENSKKRKLKTPMQVMALENFYNEHKYPTE
EMKGKLAEEVGLTEKQVSGWFCHRRLKDKRHVKEDGNAIGSQDRSSVVLQDRGSGLRQDSCGST
KQTDYWNPKPREVESQRLYMGNADGEDSTSSDRSSSLRKNLVSSKDGIRDVESSRYVAHKDVIQ
HPQFMRSYGYNKPSGYLKVKGESENFAITAVKRQLGRQYQEDGPPLGVEFDPLPPGAFEPQTNP
IVHDSGEATADGDKASTENSKKRKLKTPMQVMALENFYNEHKYPTEEMKGKLAEEVGLTEKQVS
GWFCHRRLKDKRHVKEDGNAIGSQDRSSVVLQDRGSGLRQDSCGSTKQTDYWNPKPREVESQRL
YMGNADGEDSTSSDRSSSLRKNLVSSKDGIRDVESSRYVAHKDVIQHPQFMRSYGYNKPSGYLK
VKGESENFAITAVKRQLGRQYQEDGPPLGVEFDPLPPGAFEPQTNPIVHDSGEATADGDKASTE
NSKKRKLKTPMQVMALENFYNEHKYPTEEMKGKLAEEVGLTEKQVSGWFCHRRLKDKRHVKEDG
NAIGSQDRSSVVLQDRGSGLRQDSCGSTKQTDYWNPKPREVESQRLYMGNADGEDSTSSDRSSS
LRKNLVSSKDGIRDVESSRYVAHKDVIQHPQFMRSYGYNKPSGYLKVKGESENFAITAVKRQLG
RQYQEDGPPLGVEFDPLPPGAFEPQTNPIVH(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1425613-1426332(+)
Potential amino acid sequence	MQVMALENFYNEHKYPTEEMKGKLAEEVGLTEKQVSGWFCHRRLKDKRHVKEDGNAIGSQDRSS VVLQDRGSGLRQDSCGSTKQTDYWNPKPREVESQRLYMGNADGEDSTSSDRSSSLRKNLVSSKD GIRDVESSRYVAHKDVIQHPQFMRSYGYNKPSGYLKVKGESENFAITAVKRQLGRQYQEDGPPL GVEFDPLPPGAFEPQTNPIVHDSGEATADGDKASTENSKKRKLKTPMQVMALENFYNEHKYPTE EMKGKLAEEVGLTEKQVSGWFCHRRLKDKRHVKEDGNAIGSQDRSSVVLQDRGSGLRQDSCGST KQTDYWNPKPREVESQRLYMGNADGEDSTSSDRSSSLRKNLVSSKDGIRDVESSRYVAHKDVIQ HPQFMRSYGYNKPSGYLKVKGESENFAITAVKRQLGRQYQEDGPPLGVEFDPLPPGAFEPQTNP IVHDSGEATADGDKASTENSKKRKLKTPMQVMALENFYNEHKYPTEEMKGKLAEEVGLTEKQVS GWFCHRRLKDKRHVKEDGNAIGSQDRSSVVLQDRGSGLRQDSCGSTKQTDYWNPKPREVESQRL YMGNADGEDSTSSDRSSSLRKNLVSSKDGIRDVESSRYVAHKDVIQHPQFMRSYGYNKPSGYLK VKGESENFAITAVKRQLGRQYQEDGPPLGVEFDPLPPGAFEPQTNPIVHDSGEATADGDKASTE NSKKRKLKTPMQVMALENFYNEHKYPTEEMKGKLAEEVGLTEKQVSGWFCHRRLKDKRHVKEDG NAIGSQDRSSVVLQDRGSGLRQDSCGSTKQTDYWNPKPREVESQRLYMGNADGEDSTSSDRSSS LRKNLVSSKDGIRDVESSRYVAHKDVIQHPQFMRSYGYNKPSGYLKVKGESENFAITAVKRQLG RQYQEDGPPLGVEFDPLPPGAFEPQTNPIVH(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT4G03250_circ_g.2

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