Plant Circular RNA Database

Detail information of AT4G04350_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G04350_circ_g.4
					
						ID in PlantcircBase
						ath_circ_029629
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 2128714-2130289  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT4G04350						
					
						Parent gene annotation
						
							Leucine--tRNA ligase, chloroplastic/mitochondrial
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G04350_circ_g.1 AT4G04350_circ_g.2 AT4G04350_circ_g.3 AT4G04350_circ_g.5 AT4G04350_circ_g.6 AT4G04350_circ_g.7 AT4G04350_circ_g.8 AT4G04350_circ_g.9 AT4G04350_circ_g.10 AT4G04350_circ_g.11 AT4G04350_circ_g.12 AT4G04350_circ_g.13 AT4G04350_circ_g.14 AT4G04350_circ_g.15 AT4G04350_circ_g.16 AT4G04350_circ_g.17 AT4G04350_circ_g.18 AT4G04350_circ_g.19 AT4G04350_circ_g.20 						
					
						Support reads
						2
					
						Tissues
						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
						AT4G04350.1:7

General Information
CircRNA Name	AT4G04350_circ_g.4
ID in PlantcircBase	ath_circ_029629
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 2128714-2130289 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT4G04350
Parent gene annotation	Leucine--tRNA ligase, chloroplastic/mitochondrial
Parent gene strand	+
Alternative splicing	AT4G04350_circ_g.1 AT4G04350_circ_g.2 AT4G04350_circ_g.3 AT4G04350_circ_g.5 AT4G04350_circ_g.6 AT4G04350_circ_g.7 AT4G04350_circ_g.8 AT4G04350_circ_g.9 AT4G04350_circ_g.10 AT4G04350_circ_g.11 AT4G04350_circ_g.12 AT4G04350_circ_g.13 AT4G04350_circ_g.14 AT4G04350_circ_g.15 AT4G04350_circ_g.16 AT4G04350_circ_g.17 AT4G04350_circ_g.18 AT4G04350_circ_g.19 AT4G04350_circ_g.20
Support reads	2
Tissues	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	AT4G04350.1:7

			
						 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  
						
							TTCAGAAGGACAAGACGGGCGTATTTACGGGATGTTATGCGAAAAATCCAGCTAATGGAGATGC
TATTCCCATATGGGTAGCTGATTATGTTCTAGCTAGtggagcaggattacatgtgggacatcca
ttgggttatacagcaactgatattctagcgaggcttaggcgtatgcaaggttacaatgtgttgc
atcctatg

									
								

					

						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: 873
Transcript exons: 2128714-2128858,2128950-2129006,2129264-2129383,2129466-
2129570,2129687-2129910,2129995-2130061,2130135-2130289
TGGAGCAGGATTACATGTGGGACATCCATTGGGTTATACAGCAACTGATATTCTAGCGAGGCTT
AGGCGTATGCAAGGTTACAATGTGTTGCATCCTATGGGTTGGGATGCTTTTGGATTGCCTGCTG
AACAATATGCTATTGAGACAGGAACCCATCCGAAAACTACGACATTGAAGAACATTGACCGCTT
TCGATTGCAGCTCAAATCATTGGGCTTCTCATACGATTGGGACCGTGAACTTTCTACAACAGAG
CCAGACTACTACAAATGGACACAATGGATCTTTCTTCAGCTTTATAAGAAAGGTTTGGCATATC
AGGCTGAAGTACCGGTCAATTGGTGCCCGGCTCTTGGTACTGTTTTGGCCAATGAAGAAGTGGT
GGATGGTGTTAGTGAGCGTGGTGGCCACCCGGTTATAAGAAAGCCGATGAGGCAATGGATGCTG
AAGATTACTGCGTACGCTGATCGTCTTCTAGAAGATTTGGACGAGCTTGAGTGGCCTGAAAGTA
TAAAGGAAATGCAAAGAAACTGGATAGGAAGATCCGAAGGAGCTGAGTTGAACTTTTCAATTCT
TGATGGGGAAGGCCGAGAAACTGACAAAGAGATTACAGTGTACACCACGAGGCCAGATACACTT
TTTGGAGCAACTTACATGGTTGTGGCACCAGAGCATCAGTTGTTGTCTTACTTTGTAACCGCAG
AACAGAAACAGCAAGTTGAGGAATACAAAGATTTCGCTTCGAGGAAAAGTGATCTTGAGAGAAC
AGAACTTCAGAAGGACAAGACGGGCGTATTTACGGGATGTTATGCGAAAAATCCAGCTAATGGA
GATGCTATTCCCATATGGGTAGCTGATTATGTTCTAGCTAG
						
					

						Genomic sequence
						
							TGGAGCAGGATTACATGTGGGACATCCATTGGGTTATACAGCAACTGATATTCTAGCGAGGCTT
AGGCGTATGCAAGGTTACAATGTGTTGCATCCTATGGGTTGGGATGCTTTTGGATTGCCTGCTG
AACAATATGCTATTGAGGTCCATTTTTTTTCTCTGTTCTCAAGTCATTATGTATGGATGTTTTT
GTTGATAAAATTTGTGTCCTTAGTATTTGTAATCTGCATTGCAGACAGGAACCCATCCGAAAAC
TACGACATTGAAGAACATTGACCGCTTTCGATTGCAGGTGATATATTTCTTTCAATCTAGCACT
AGCCTAGAAAAGTTACTATTCTCTTCTATTCATCATTTCCCTAACAGAAGAAATTTCTCAGTTT
TGTTATCGGTTTCGTTGTGAGAAATTTATGCTTGTTTCATGGTTTAGGATTACTGATCCTTGAA
GATTATGCAAAAGCCATTACTTTGGACTGTTTTGCTTAGGTCTTACCATGGGAGTAAAGATCTG
GGGACCTTAACAATTGTAGTTCTTTTGTTTGTTTGCAGCTCAAATCATTGGGCTTCTCATACGA
TTGGGACCGTGAACTTTCTACAACAGAGCCAGACTACTACAAATGGACACAATGGATCTTTCTT
CAGCTTTATAAGAAAGGTTTGGCATATCAGGTCAACAAAATCAATGTCTAGTTCACATGTTAAA
ACCGTGCATTTGTGTATAGAAAAGTTCTTTGAAAGATTGTAAACTCAGGCTGAAGTACCGGTCA
ATTGGTGCCCGGCTCTTGGTACTGTTTTGGCCAATGAAGAAGTGGTGGATGGTGTTAGTGAGCG
TGGTGGCCACCCGGTTATAAGAAAGGTACTATCTATTACCATCTGGGAATATTATGTCGTTTTT
CCCCTTTCGAAATCTGTATTTCCTCTGTTTTGAAAATTCTCATGAATTTTACAGTGACATTGTT
TATTACCAAGCAGCCGATGAGGCAATGGATGCTGAAGATTACTGCGTACGCTGATCGTCTTCTA
GAAGATTTGGACGAGCTTGAGTGGCCTGAAAGTATAAAGGAAATGCAAAGAAACTGGATAGGAA
GATCCGAAGGAGCTGAGTTGAACTTTTCAATTCTTGATGGGGAAGGCCGAGAAACTGACAAAGA
GATTACAGTGTACACCACGAGGCCAGATACACTTTTTGGAGCAACGTATGCTTAAAGGATTAAT
TATATATTCAACATCTGAAATCTTGATCTTGATTGTCTTAATATGATATTTGCTTCCATTCGCA
GTTACATGGTTGTGGCACCAGAGCATCAGTTGTTGTCTTACTTTGTAACCGCAGAACAGAAACA
GCAAGTAAGAGTTTTTTCTTCTTTCGATTATTCAACTTGCCTTTCAGATTTTCATGAGTTCTCT
CTTATGGTTGCAGGTTGAGGAATACAAAGATTTCGCTTCGAGGAAAAGTGATCTTGAGAGAACA
GAACTTCAGAAGGACAAGACGGGCGTATTTACGGGATGTTATGCGAAAAATCCAGCTAATGGAG
ATGCTATTCCCATATGGGTAGCTGATTATGTTCTAGCTAG
						
					

			
		

Sequences
Splice junction sequence	TTCAGAAGGACAAGACGGGCGTATTTACGGGATGTTATGCGAAAAATCCAGCTAATGGAGATGC TATTCCCATATGGGTAGCTGATTATGTTCTAGCTAGtggagcaggattacatgtgggacatcca ttgggttatacagcaactgatattctagcgaggcttaggcgtatgcaaggttacaatgtgttgc atcctatg
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: 873 Transcript exons: 2128714-2128858,2128950-2129006,2129264-2129383,2129466- 2129570,2129687-2129910,2129995-2130061,2130135-2130289 TGGAGCAGGATTACATGTGGGACATCCATTGGGTTATACAGCAACTGATATTCTAGCGAGGCTT AGGCGTATGCAAGGTTACAATGTGTTGCATCCTATGGGTTGGGATGCTTTTGGATTGCCTGCTG AACAATATGCTATTGAGACAGGAACCCATCCGAAAACTACGACATTGAAGAACATTGACCGCTT TCGATTGCAGCTCAAATCATTGGGCTTCTCATACGATTGGGACCGTGAACTTTCTACAACAGAG CCAGACTACTACAAATGGACACAATGGATCTTTCTTCAGCTTTATAAGAAAGGTTTGGCATATC AGGCTGAAGTACCGGTCAATTGGTGCCCGGCTCTTGGTACTGTTTTGGCCAATGAAGAAGTGGT GGATGGTGTTAGTGAGCGTGGTGGCCACCCGGTTATAAGAAAGCCGATGAGGCAATGGATGCTG AAGATTACTGCGTACGCTGATCGTCTTCTAGAAGATTTGGACGAGCTTGAGTGGCCTGAAAGTA TAAAGGAAATGCAAAGAAACTGGATAGGAAGATCCGAAGGAGCTGAGTTGAACTTTTCAATTCT TGATGGGGAAGGCCGAGAAACTGACAAAGAGATTACAGTGTACACCACGAGGCCAGATACACTT TTTGGAGCAACTTACATGGTTGTGGCACCAGAGCATCAGTTGTTGTCTTACTTTGTAACCGCAG AACAGAAACAGCAAGTTGAGGAATACAAAGATTTCGCTTCGAGGAAAAGTGATCTTGAGAGAAC AGAACTTCAGAAGGACAAGACGGGCGTATTTACGGGATGTTATGCGAAAAATCCAGCTAATGGA GATGCTATTCCCATATGGGTAGCTGATTATGTTCTAGCTAG
Genomic sequence	TGGAGCAGGATTACATGTGGGACATCCATTGGGTTATACAGCAACTGATATTCTAGCGAGGCTT AGGCGTATGCAAGGTTACAATGTGTTGCATCCTATGGGTTGGGATGCTTTTGGATTGCCTGCTG AACAATATGCTATTGAGGTCCATTTTTTTTCTCTGTTCTCAAGTCATTATGTATGGATGTTTTT GTTGATAAAATTTGTGTCCTTAGTATTTGTAATCTGCATTGCAGACAGGAACCCATCCGAAAAC TACGACATTGAAGAACATTGACCGCTTTCGATTGCAGGTGATATATTTCTTTCAATCTAGCACT AGCCTAGAAAAGTTACTATTCTCTTCTATTCATCATTTCCCTAACAGAAGAAATTTCTCAGTTT TGTTATCGGTTTCGTTGTGAGAAATTTATGCTTGTTTCATGGTTTAGGATTACTGATCCTTGAA GATTATGCAAAAGCCATTACTTTGGACTGTTTTGCTTAGGTCTTACCATGGGAGTAAAGATCTG GGGACCTTAACAATTGTAGTTCTTTTGTTTGTTTGCAGCTCAAATCATTGGGCTTCTCATACGA TTGGGACCGTGAACTTTCTACAACAGAGCCAGACTACTACAAATGGACACAATGGATCTTTCTT CAGCTTTATAAGAAAGGTTTGGCATATCAGGTCAACAAAATCAATGTCTAGTTCACATGTTAAA ACCGTGCATTTGTGTATAGAAAAGTTCTTTGAAAGATTGTAAACTCAGGCTGAAGTACCGGTCA ATTGGTGCCCGGCTCTTGGTACTGTTTTGGCCAATGAAGAAGTGGTGGATGGTGTTAGTGAGCG TGGTGGCCACCCGGTTATAAGAAAGGTACTATCTATTACCATCTGGGAATATTATGTCGTTTTT CCCCTTTCGAAATCTGTATTTCCTCTGTTTTGAAAATTCTCATGAATTTTACAGTGACATTGTT TATTACCAAGCAGCCGATGAGGCAATGGATGCTGAAGATTACTGCGTACGCTGATCGTCTTCTA GAAGATTTGGACGAGCTTGAGTGGCCTGAAAGTATAAAGGAAATGCAAAGAAACTGGATAGGAA GATCCGAAGGAGCTGAGTTGAACTTTTCAATTCTTGATGGGGAAGGCCGAGAAACTGACAAAGA GATTACAGTGTACACCACGAGGCCAGATACACTTTTTGGAGCAACGTATGCTTAAAGGATTAAT TATATATTCAACATCTGAAATCTTGATCTTGATTGTCTTAATATGATATTTGCTTCCATTCGCA GTTACATGGTTGTGGCACCAGAGCATCAGTTGTTGTCTTACTTTGTAACCGCAGAACAGAAACA GCAAGTAAGAGTTTTTTCTTCTTTCGATTATTCAACTTGCCTTTCAGATTTTCATGAGTTCTCT CTTATGGTTGCAGGTTGAGGAATACAAAGATTTCGCTTCGAGGAAAAGTGATCTTGAGAGAACA GAACTTCAGAAGGACAAGACGGGCGTATTTACGGGATGTTATGCGAAAAATCCAGCTAATGGAG ATGCTATTCCCATATGGGTAGCTGATTATGTTCTAGCTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.268698353

Conservation Information
Conserved circRNAs	NA
PMCS	0.268698353

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2128784-2130286(+)
						
						Potential amino acid sequence
						
							MQGYNVLHPMGWDAFGLPAEQYAIETGTHPKTTTLKNIDRFRLQLKSLGFSYDWDRELSTTEPD
YYKWTQWIFLQLYKKGLAYQAEVPVNWCPALGTVLANEEVVDGVSERGGHPVIRKPMRQWMLKI
TAYADRLLEDLDELEWPESIKEMQRNWIGRSEGAELNFSILDGEGRETDKEITVYTTRPDTLFG
ATYMVVAPEHQLLSYFVTAEQKQQVEEYKDFASRKSDLERTELQKDKTGVFTGCYAKNPANGDA
IPIWVADYVLASGAGLHVGHPLGYTATDILARLRRMQGYNVLHPMGWDAFGLPAEQYAIETGTH
PKTTTLKNIDRFRLQLKSLGFSYDWDRELSTTEPDYYKWTQWIFLQLYKKGLAYQAEVPVNWCP
ALGTVLANEEVVDGVSERGGHPVIRKPMRQWMLKITAYADRLLEDLDELEWPESIKEMQRNWIG
RSEGAELNFSILDGEGRETDKEITVYTTRPDTLFGATYMVVAPEHQLLSYFVTAEQKQQVEEYK
DFASRKSDLERTELQKDKTGVFTGCYAKNPANGDAIPIWVADYVLASGAGLHVGHPLGYTATDI
LARLRRMQGYNVLHPMGWDAFGLPAEQYAIETGTHPKTTTLKNIDRFRLQLKSLGFSYDWDREL
STTEPDYYKWTQWIFLQLYKKGLAYQAEVPVNWCPALGTVLANEEVVDGVSERGGHPVIRKPMR
QWMLKITAYADRLLEDLDELEWPESIKEMQRNWIGRSEGAELNFSILDGEGRETDKEITVYTTR
PDTLFGATYMVVAPEHQLLSYFVTAEQKQQVEEYKDFASRKSDLERTELQKDKTGVFTGCYAKN
PANGDAIPIWVADYVLASGAGLHVGHPLGYTATDILARLRRMQGYNVLHPMGWDAFGLPAEQYA
IETGTHPKTTTLKNIDRFRLQLKSLGFSYDWDRELSTTEPDYYKWTQWIFLQLYKKGLAYQAEV
PVNWCPALGTVLANEEVVDGVSERGGHPVIRKPMRQWMLKITAYADRLLEDLDELEWPESIKEM
QRNWIGRSEGAELNFSILDGEGRETDKEITVYTTRPDTLFGATYMVVAPEHQLLSYFVTAEQKQ
QVEEYKDFASRKSDLERTELQKDKTGVFTGCYAKNPANGDAIPIWVADYVLA(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2128784-2130286(+)
Potential amino acid sequence	MQGYNVLHPMGWDAFGLPAEQYAIETGTHPKTTTLKNIDRFRLQLKSLGFSYDWDRELSTTEPD YYKWTQWIFLQLYKKGLAYQAEVPVNWCPALGTVLANEEVVDGVSERGGHPVIRKPMRQWMLKI TAYADRLLEDLDELEWPESIKEMQRNWIGRSEGAELNFSILDGEGRETDKEITVYTTRPDTLFG ATYMVVAPEHQLLSYFVTAEQKQQVEEYKDFASRKSDLERTELQKDKTGVFTGCYAKNPANGDA IPIWVADYVLASGAGLHVGHPLGYTATDILARLRRMQGYNVLHPMGWDAFGLPAEQYAIETGTH PKTTTLKNIDRFRLQLKSLGFSYDWDRELSTTEPDYYKWTQWIFLQLYKKGLAYQAEVPVNWCP ALGTVLANEEVVDGVSERGGHPVIRKPMRQWMLKITAYADRLLEDLDELEWPESIKEMQRNWIG RSEGAELNFSILDGEGRETDKEITVYTTRPDTLFGATYMVVAPEHQLLSYFVTAEQKQQVEEYK DFASRKSDLERTELQKDKTGVFTGCYAKNPANGDAIPIWVADYVLASGAGLHVGHPLGYTATDI LARLRRMQGYNVLHPMGWDAFGLPAEQYAIETGTHPKTTTLKNIDRFRLQLKSLGFSYDWDREL STTEPDYYKWTQWIFLQLYKKGLAYQAEVPVNWCPALGTVLANEEVVDGVSERGGHPVIRKPMR QWMLKITAYADRLLEDLDELEWPESIKEMQRNWIGRSEGAELNFSILDGEGRETDKEITVYTTR PDTLFGATYMVVAPEHQLLSYFVTAEQKQQVEEYKDFASRKSDLERTELQKDKTGVFTGCYAKN PANGDAIPIWVADYVLASGAGLHVGHPLGYTATDILARLRRMQGYNVLHPMGWDAFGLPAEQYA IETGTHPKTTTLKNIDRFRLQLKSLGFSYDWDRELSTTEPDYYKWTQWIFLQLYKKGLAYQAEV PVNWCPALGTVLANEEVVDGVSERGGHPVIRKPMRQWMLKITAYADRLLEDLDELEWPESIKEM QRNWIGRSEGAELNFSILDGEGRETDKEITVYTTRPDTLFGATYMVVAPEHQLLSYFVTAEQKQ QVEEYKDFASRKSDLERTELQKDKTGVFTGCYAKNPANGDAIPIWVADYVLA(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G04350_circ_g.4

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