Plant Circular RNA Database

Detail information of AT4G38200_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G38200_circ_g.3
					
						ID in PlantcircBase
						ath_circ_035326
					
						Alias
						At_ciR3307, Ath_circ_FC3049
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 17918231-17919084  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT4G38200						
					
						Parent gene annotation
						
							Brefeldin A-inhibited guanine nucleotide-exchange protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							4_circ_ag.2 AT4G37680_circ_g.3 4_circ_ag.4 4_circ_ag.5 4_circ_ag.6 4_circ_ig.7 AT4G37750_circ_g.1 AT4G37760_circ_g.1 AT4G37800_circ_g.1 AT4G37800_circ_g.2 AT4G37820_circ_g.1 AT4G37870_circ_g.1 AT4G37870_circ_g.2 AT4G37870_circ_g.3 AT4G37870_circ_g.4 AT4G37870_circ_g.5 AT4G37870_circ_g.6 AT4G37870_circ_g.7 AT4G37870_circ_g.8 AT4G37870_circ_g.9 AT4G37870_circ_g.10 AT4G37870_circ_g.11 AT4G37870_circ_g.12 AT4G37870_circ_g.13 AT4G37870_circ_g.14 AT4G37870_circ_g.15 AT4G37870_circ_g.16 AT4G37900_circ_g.1 AT4G37900_circ_g.2 AT4G37900_circ_g.3 AT4G37910_circ_g.1 AT4G37910_circ_g.2 AT4G37910_circ_g.3 AT4G37920_circ_g.1 AT4G37930_circ_g.1 AT4G37930_circ_g.2 AT4G37930_circ_g.3 AT4G37930_circ_g.4 AT4G37930_circ_g.5 AT4G37930_circ_g.6 AT4G37930_circ_g.7 AT4G37930_circ_g.8 AT4G37930_circ_g.9 AT4G37930_circ_g.10 AT4G37930_circ_g.11 AT4G37930_circ_g.12 AT4G37930_circ_g.13 AT4G37930_circ_g.14 AT4G37930_circ_g.15 AT4G37930_circ_g.16 AT4G37930_circ_g.17 AT4G37930_circ_g.18 AT4G37930_circ_g.19 AT4G37930_circ_g.20 AT4G37930_circ_g.21 AT4G37930_circ_g.22 AT4G37930_circ_g.23 AT4G37940_circ_g.1 AT4G37980_circ_g.1 AT4G37980_circ_g.2 AT4G37980_circ_g.3 AT4G37990_circ_g.1 AT4G38040_circ_g.1 AT4G38060_circ_g.1 AT4G38060_circ_g.2 AT4G38100_circ_g.1 AT4G38100_circ_g.2 AT4G38100_circ_g.3 AT4G38100_circ_g.4 AT4G38100_circ_g.5 AT4G38120_circ_g.1 AT4G38120_circ_g.2 AT4G38120_circ_g.3 AT4G38120_circ_g.4 AT4G38120_circ_g.5 AT4G38120_circ_g.6 AT4G38120_circ_g.7 AT4G38120_circ_g.8 AT4G38120_circ_g.9 AT4G38130_circ_g.1 AT4G38130_circ_g.2 AT4G38130_circ_g.3 AT4G38130_circ_g.4 AT4G38130_circ_g.5 AT4G38160_circ_g.1 AT4G38160_circ_g.2 AT4G38180_circ_g.1 AT4G38200_circ_g.1 AT4G38200_circ_g.2 AT4G38200_circ_g.4 AT4G38200_circ_g.5 AT4G38200_circ_g.6 AT4G38200_circ_g.7 AT4G38200_circ_g.8 AT4G38200_circ_g.9 AT4G38200_circ_g.10 AT4G38220_circ_g.1 AT4G38220_circ_g.2 AT4G38220_circ_g.3 AT4G38230_circ_g.1 AT4G38230_circ_g.2 AT4G38240_circ_g.1 AT4G38240_circ_g.2 AT4G38240_circ_g.3 AT4G38240_circ_g.4 AT4G38240_circ_g.5 AT4G38240_circ_g.6 AT4G38240_circ_g.7 AT4G38240_circ_g.8 AT4G38250_circ_g.1 AT4G38260_circ_g.1 AT4G38260_circ_g.2 AT4G38260_circ_g.3 AT4G38270_circ_g.1 AT4G38270_circ_g.2 AT4G38280_circ_g.1 AT4G38280_circ_g.2 4_circ_ag.3 						
					
						Support reads
						2
					
						Tissues
						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
						AT4G38200.2:2
AT4G38200.1:2

General Information
CircRNA Name	AT4G38200_circ_g.3
ID in PlantcircBase	ath_circ_035326
Alias	At_ciR3307, Ath_circ_FC3049
Organism	Arabidpsis thaliana
Position	chr4: 17918231-17919084 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT4G38200
Parent gene annotation	Brefeldin A-inhibited guanine nucleotide-exchange protein 1
Parent gene strand	+
Alternative splicing	4_circ_ag.2 AT4G37680_circ_g.3 4_circ_ag.4 4_circ_ag.5 4_circ_ag.6 4_circ_ig.7 AT4G37750_circ_g.1 AT4G37760_circ_g.1 AT4G37800_circ_g.1 AT4G37800_circ_g.2 AT4G37820_circ_g.1 AT4G37870_circ_g.1 AT4G37870_circ_g.2 AT4G37870_circ_g.3 AT4G37870_circ_g.4 AT4G37870_circ_g.5 AT4G37870_circ_g.6 AT4G37870_circ_g.7 AT4G37870_circ_g.8 AT4G37870_circ_g.9 AT4G37870_circ_g.10 AT4G37870_circ_g.11 AT4G37870_circ_g.12 AT4G37870_circ_g.13 AT4G37870_circ_g.14 AT4G37870_circ_g.15 AT4G37870_circ_g.16 AT4G37900_circ_g.1 AT4G37900_circ_g.2 AT4G37900_circ_g.3 AT4G37910_circ_g.1 AT4G37910_circ_g.2 AT4G37910_circ_g.3 AT4G37920_circ_g.1 AT4G37930_circ_g.1 AT4G37930_circ_g.2 AT4G37930_circ_g.3 AT4G37930_circ_g.4 AT4G37930_circ_g.5 AT4G37930_circ_g.6 AT4G37930_circ_g.7 AT4G37930_circ_g.8 AT4G37930_circ_g.9 AT4G37930_circ_g.10 AT4G37930_circ_g.11 AT4G37930_circ_g.12 AT4G37930_circ_g.13 AT4G37930_circ_g.14 AT4G37930_circ_g.15 AT4G37930_circ_g.16 AT4G37930_circ_g.17 AT4G37930_circ_g.18 AT4G37930_circ_g.19 AT4G37930_circ_g.20 AT4G37930_circ_g.21 AT4G37930_circ_g.22 AT4G37930_circ_g.23 AT4G37940_circ_g.1 AT4G37980_circ_g.1 AT4G37980_circ_g.2 AT4G37980_circ_g.3 AT4G37990_circ_g.1 AT4G38040_circ_g.1 AT4G38060_circ_g.1 AT4G38060_circ_g.2 AT4G38100_circ_g.1 AT4G38100_circ_g.2 AT4G38100_circ_g.3 AT4G38100_circ_g.4 AT4G38100_circ_g.5 AT4G38120_circ_g.1 AT4G38120_circ_g.2 AT4G38120_circ_g.3 AT4G38120_circ_g.4 AT4G38120_circ_g.5 AT4G38120_circ_g.6 AT4G38120_circ_g.7 AT4G38120_circ_g.8 AT4G38120_circ_g.9 AT4G38130_circ_g.1 AT4G38130_circ_g.2 AT4G38130_circ_g.3 AT4G38130_circ_g.4 AT4G38130_circ_g.5 AT4G38160_circ_g.1 AT4G38160_circ_g.2 AT4G38180_circ_g.1 AT4G38200_circ_g.1 AT4G38200_circ_g.2 AT4G38200_circ_g.4 AT4G38200_circ_g.5 AT4G38200_circ_g.6 AT4G38200_circ_g.7 AT4G38200_circ_g.8 AT4G38200_circ_g.9 AT4G38200_circ_g.10 AT4G38220_circ_g.1 AT4G38220_circ_g.2 AT4G38220_circ_g.3 AT4G38230_circ_g.1 AT4G38230_circ_g.2 AT4G38240_circ_g.1 AT4G38240_circ_g.2 AT4G38240_circ_g.3 AT4G38240_circ_g.4 AT4G38240_circ_g.5 AT4G38240_circ_g.6 AT4G38240_circ_g.7 AT4G38240_circ_g.8 AT4G38250_circ_g.1 AT4G38260_circ_g.1 AT4G38260_circ_g.2 AT4G38260_circ_g.3 AT4G38270_circ_g.1 AT4G38270_circ_g.2 AT4G38280_circ_g.1 AT4G38280_circ_g.2 4_circ_ag.3
Support reads	2
Tissues	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	AT4G38200.2:2 AT4G38200.1:2

			
						 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  
						
							TATGCAAACGCAAAGAGATGCATTTGTCACTTCCATGGCCAAGTTCACAAATCTCCATTGCGCA
GGAGATATGAAGCAAAAGAATGTCGATGCTGTTAAAatgaccaaggctgattttatcagaaata
accgaggcattgatgatggcaaagatctcccagaagagtatcttggtgcgctttatgaccaagt
tgtcataa

						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: 567
Transcript exons: 17918231-17918523,17918811-17919084
ATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAAGATCTCCCAGAAG
AGTATCTTGGTGCGCTTTATGACCAAGTTGTCATAAATGAAATAAAGATGAGTTCTGATTCTTC
AGCCCCAGAAAGCAGGCAGTCCAATGGCCTGAATAAACTACTGGGTCTGGACGGTATACTCAAT
CTGGTTTATTGGACACAGACGGAAGAAAAAGCGGTGGGGGCTAATGGTCTTCTTATAAAGGATA
TTCAAGAAAAGTTCAGGTCGAAGTCTGGAAAATCAGAATCAGCTTACCATGTAGTCACAGACGT
TGCAATATTGCGTTTTATGGTTGAAGTTTCCTGGGGACCAATGCTTGCCGCATTCAGCGTGACA
CTTGATCAGAGTGATGACAGGCTTGCTGCAGTTGAATGCTTACGAGGCTTTCGGTATGCAGTTC
ATGTGACAGCAGTTATGGGTATGCAAACGCAAAGAGATGCATTTGTCACTTCCATGGCCAAGTT
CACAAATCTCCATTGCGCAGGAGATATGAAGCAAAAGAATGTCGATGCTGTTAAA
						
						Genomic sequence
						
							ATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAAGATCTCCCAGAAG
AGTATCTTGGTGCGCTTTATGACCAAGTTGTCATAAATGAAATAAAGATGAGTTCTGATTCTTC
AGCCCCAGAAAGCAGGCAGTCCAATGGCCTGAATAAACTACTGGGTCTGGACGGTATACTCAAT
CTGGTTTATTGGACACAGACGGAAGAAAAAGCGGTGGGGGCTAATGGTCTTCTTATAAAGGATA
TTCAAGAAAAGTTCAGGTCGAAGTCTGGAAAATCAGAGTAAGCTCGTTTACCTTAAGGTCTAGT
GTGAAGAGATGCTTATGAGCGAGTCAGGTTACCTGCAACATTAGCGAACTAAGATGAAACCATC
GTTTCCTTATACGTTAATAAACCATACTTCCCCTTAGTTTACCTTGTTCATTGTTTGTCTCTGA
AATTGTGTATTCCTGAGAATTGAGAAACTATCTTTTTAAAAGGATTAATATTGACAAATACCGT
GGACGGATGTTAGGATCTGTAATCATAACATTGATCTAATGAACTGGATTATTTTTTTGGTCTT
GTAGATCAGCTTACCATGTAGTCACAGACGTTGCAATATTGCGTTTTATGGTTGAAGTTTCCTG
GGGACCAATGCTTGCCGCATTCAGCGTGACACTTGATCAGAGTGATGACAGGCTTGCTGCAGTT
GAATGCTTACGAGGCTTTCGGTATGCAGTTCATGTGACAGCAGTTATGGGTATGCAAACGCAAA
GAGATGCATTTGTCACTTCCATGGCCAAGTTCACAAATCTCCATTGCGCAGGAGATATGAAGCA
AAAGAATGTCGATGCTGTTAAA

Sequences
Splice junction sequence	TATGCAAACGCAAAGAGATGCATTTGTCACTTCCATGGCCAAGTTCACAAATCTCCATTGCGCA GGAGATATGAAGCAAAAGAATGTCGATGCTGTTAAAatgaccaaggctgattttatcagaaata accgaggcattgatgatggcaaagatctcccagaagagtatcttggtgcgctttatgaccaagt tgtcataa
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: 567 Transcript exons: 17918231-17918523,17918811-17919084 ATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAAGATCTCCCAGAAG AGTATCTTGGTGCGCTTTATGACCAAGTTGTCATAAATGAAATAAAGATGAGTTCTGATTCTTC AGCCCCAGAAAGCAGGCAGTCCAATGGCCTGAATAAACTACTGGGTCTGGACGGTATACTCAAT CTGGTTTATTGGACACAGACGGAAGAAAAAGCGGTGGGGGCTAATGGTCTTCTTATAAAGGATA TTCAAGAAAAGTTCAGGTCGAAGTCTGGAAAATCAGAATCAGCTTACCATGTAGTCACAGACGT TGCAATATTGCGTTTTATGGTTGAAGTTTCCTGGGGACCAATGCTTGCCGCATTCAGCGTGACA CTTGATCAGAGTGATGACAGGCTTGCTGCAGTTGAATGCTTACGAGGCTTTCGGTATGCAGTTC ATGTGACAGCAGTTATGGGTATGCAAACGCAAAGAGATGCATTTGTCACTTCCATGGCCAAGTT CACAAATCTCCATTGCGCAGGAGATATGAAGCAAAAGAATGTCGATGCTGTTAAA
Genomic sequence	ATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAAGATCTCCCAGAAG AGTATCTTGGTGCGCTTTATGACCAAGTTGTCATAAATGAAATAAAGATGAGTTCTGATTCTTC AGCCCCAGAAAGCAGGCAGTCCAATGGCCTGAATAAACTACTGGGTCTGGACGGTATACTCAAT CTGGTTTATTGGACACAGACGGAAGAAAAAGCGGTGGGGGCTAATGGTCTTCTTATAAAGGATA TTCAAGAAAAGTTCAGGTCGAAGTCTGGAAAATCAGAGTAAGCTCGTTTACCTTAAGGTCTAGT GTGAAGAGATGCTTATGAGCGAGTCAGGTTACCTGCAACATTAGCGAACTAAGATGAAACCATC GTTTCCTTATACGTTAATAAACCATACTTCCCCTTAGTTTACCTTGTTCATTGTTTGTCTCTGA AATTGTGTATTCCTGAGAATTGAGAAACTATCTTTTTAAAAGGATTAATATTGACAAATACCGT GGACGGATGTTAGGATCTGTAATCATAACATTGATCTAATGAACTGGATTATTTTTTTGGTCTT GTAGATCAGCTTACCATGTAGTCACAGACGTTGCAATATTGCGTTTTATGGTTGAAGTTTCCTG GGGACCAATGCTTGCCGCATTCAGCGTGACACTTGATCAGAGTGATGACAGGCTTGCTGCAGTT GAATGCTTACGAGGCTTTCGGTATGCAGTTCATGTGACAGCAGTTATGGGTATGCAAACGCAAA GAGATGCATTTGTCACTTCCATGGCCAAGTTCACAAATCTCCATTGCGCAGGAGATATGAAGCA AAAGAATGTCGATGCTGTTAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.290693258

Conservation Information
Conserved circRNAs	NA
PMCS	0.290693258

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17918231-17919081(+)
						
						Potential amino acid sequence
						
							MTKADFIRNNRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILN
LVYWTQTEEKAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVT
LDQSDDRLAAVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVKMTK
ADFIRNNRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILNLVY
WTQTEEKAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVTLDQ
SDDRLAAVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVKMTKADF
IRNNRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILNLVYWTQ
TEEKAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVTLDQSDD
RLAAVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVKMTKADFIRN
NRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILNLVYWTQTEE
KAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVTLDQSDDRLA
AVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17918231-17919081(+)
Potential amino acid sequence	MTKADFIRNNRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILN LVYWTQTEEKAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVT LDQSDDRLAAVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVKMTK ADFIRNNRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILNLVY WTQTEEKAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVTLDQ SDDRLAAVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVKMTKADF IRNNRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILNLVYWTQ TEEKAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVTLDQSDD RLAAVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVKMTKADFIRN NRGIDDGKDLPEEYLGALYDQVVINEIKMSSDSSAPESRQSNGLNKLLGLDGILNLVYWTQTEE KAVGANGLLIKDIQEKFRSKSGKSESAYHVVTDVAILRFMVEVSWGPMLAAFSVTLDQSDDRLA AVECLRGFRYAVHVTAVMGMQTQRDAFVTSMAKFTNLHCAGDMKQKNVDAVK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT4G38200_circ_g.3

Address

Any questions?

Supported by