Plant Circular RNA Database

Detail information of AT1G04680_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G04680_circ_g.3
					
						ID in PlantcircBase
						ath_circ_000675
					
						Alias
						At_ciR4993, Ath_circ_FC3919
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1304621-1305465  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder, find_circ
					
						Parent gene
						
							AT1G04680						
					
						Parent gene annotation
						
							Pectate lyase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G04680_circ_g.1 AT1G04680_circ_g.2 AT1G04680_circ_g.4 AT1G04680_circ_g.5 						
					
						Support reads
						2/31
					
						Tissues
						leaf/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
						AT1G04680.1:2

General Information
CircRNA Name	AT1G04680_circ_g.3
ID in PlantcircBase	ath_circ_000675
Alias	At_ciR4993, Ath_circ_FC3919
Organism	Arabidpsis thaliana
Position	chr1: 1304621-1305465 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder, find_circ
Parent gene	AT1G04680
Parent gene annotation	Pectate lyase
Parent gene strand	-
Alternative splicing	AT1G04680_circ_g.1 AT1G04680_circ_g.2 AT1G04680_circ_g.4 AT1G04680_circ_g.5
Support reads	2/31
Tissues	leaf/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	AT1G04680.1:2

			
						 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  
						
							GTGCCAATTGGGGTCACATCGCCAACAATCGTCGATAGGGTTTCCTGTTCCGCAAGTAAAGTAA
CCTAGTTTCCTCCTCTCGGTATGGTTTCTCACACTCctcggcattctttgaataagtccgactc
caaaatgattgtaagcaatggtcacttgcatagctttgtccctcatgtacgagtcactatgtcc
tagcaaca

									
								

					

						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: 747
Transcript exons: 1304621-1304724,1304823-1305465
CTCGGCATTCTTTGAATAAGTCCGACTCCAAAATGATTGTAAGCAATGGTCACTTGCATAGCTT
TGTCCCTCATGTACGAGTCACTATGTCCTAGCAACATAACCTCGTTATGGTGAGTTAAGTGGTT
GTTAGAGATGGTAATCGCGGTTGAGCCCATGACTGCGTCCACAAGCCCATCAGCGCAATGGGAC
AACGAGTTATGATCAATCCATACATGACTCGATCCAAAGATCGAAATCGCGTCACCATCTGCCA
TTGTCCTCCACCCAAAATGCGTCTCTGAGCTTCTCACCATAGCGTTACCAGTTGGTTTACAGTC
ATGAATATGCAATCCGTGAACGATCACATTCGTCACAAACTGAATCGTGATGCAACCACCGTTA
GCAATGTGAACGTTTGCGCCACGTCCATCGATCGTTTTGAAACTGTTAACGATAAGCTCTTGTT
TTAGCTGAATCACCATGTCACGTTTGAAAACGATCCATAGTGGTCGGTCTTGGATCACGGCGTG
ACGTAAAGTCCCCGGTCTAGGGTTAACCGGATTGTCGTCTCTTGGGTCAGTGACTACGTAGAAT
CGTCCATCACGACCACCGATCGCGTTTCTTCCAAATCCGATACCGCAATCCGCTAGGCGTTTAC
GGTTCTTGTGCCAATTGGGGTCACATCGCCAACAATCGTCGATAGGGTTTCCTGTTCCGCAAGT
AAAGTAACCTAGTTTCCTCCTCTCGGTATGGTTTCTCACACTC
						
					

						Genomic sequence
						
							CTCGGCATTCTTTGAATAAGTCCGACTCCAAAATGATTGTAAGCAATGGTCACTTGCATAGCTT
TGTCCCTCATGTACGAGTCACTATGTCCTAGCAACATAACCTGTAAAAAAGTAGATCAAACCAT
ATCATCAAAAACCGAATTCAGCCAAAGAAAAGAAGCAATTATTAACTAATGAAACAACAAGTCT
TGAAAAGAACCTCGTTATGGTGAGTTAAGTGGTTGTTAGAGATGGTAATCGCGGTTGAGCCCAT
GACTGCGTCCACAAGCCCATCAGCGCAATGGGACAACGAGTTATGATCAATCCATACATGACTC
GATCCAAAGATCGAAATCGCGTCACCATCTGCCATTGTCCTCCACCCAAAATGCGTCTCTGAGC
TTCTCACCATAGCGTTACCAGTTGGTTTACAGTCATGAATATGCAATCCGTGAACGATCACATT
CGTCACAAACTGAATCGTGATGCAACCACCGTTAGCAATGTGAACGTTTGCGCCACGTCCATCG
ATCGTTTTGAAACTGTTAACGATAAGCTCTTGTTTTAGCTGAATCACCATGTCACGTTTGAAAA
CGATCCATAGTGGTCGGTCTTGGATCACGGCGTGACGTAAAGTCCCCGGTCTAGGGTTAACCGG
ATTGTCGTCTCTTGGGTCAGTGACTACGTAGAATCGTCCATCACGACCACCGATCGCGTTTCTT
CCAAATCCGATACCGCAATCCGCTAGGCGTTTACGGTTCTTGTGCCAATTGGGGTCACATCGCC
AACAATCGTCGATAGGGTTTCCTGTTCCGCAAGTAAAGTAACCTAGTTTCCTCCTCTCGGTATG
GTTTCTCACACTC
						
					

			
		

Sequences
Splice junction sequence	GTGCCAATTGGGGTCACATCGCCAACAATCGTCGATAGGGTTTCCTGTTCCGCAAGTAAAGTAA CCTAGTTTCCTCCTCTCGGTATGGTTTCTCACACTCctcggcattctttgaataagtccgactc caaaatgattgtaagcaatggtcacttgcatagctttgtccctcatgtacgagtcactatgtcc tagcaaca
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: 747 Transcript exons: 1304621-1304724,1304823-1305465 CTCGGCATTCTTTGAATAAGTCCGACTCCAAAATGATTGTAAGCAATGGTCACTTGCATAGCTT TGTCCCTCATGTACGAGTCACTATGTCCTAGCAACATAACCTCGTTATGGTGAGTTAAGTGGTT GTTAGAGATGGTAATCGCGGTTGAGCCCATGACTGCGTCCACAAGCCCATCAGCGCAATGGGAC AACGAGTTATGATCAATCCATACATGACTCGATCCAAAGATCGAAATCGCGTCACCATCTGCCA TTGTCCTCCACCCAAAATGCGTCTCTGAGCTTCTCACCATAGCGTTACCAGTTGGTTTACAGTC ATGAATATGCAATCCGTGAACGATCACATTCGTCACAAACTGAATCGTGATGCAACCACCGTTA GCAATGTGAACGTTTGCGCCACGTCCATCGATCGTTTTGAAACTGTTAACGATAAGCTCTTGTT TTAGCTGAATCACCATGTCACGTTTGAAAACGATCCATAGTGGTCGGTCTTGGATCACGGCGTG ACGTAAAGTCCCCGGTCTAGGGTTAACCGGATTGTCGTCTCTTGGGTCAGTGACTACGTAGAAT CGTCCATCACGACCACCGATCGCGTTTCTTCCAAATCCGATACCGCAATCCGCTAGGCGTTTAC GGTTCTTGTGCCAATTGGGGTCACATCGCCAACAATCGTCGATAGGGTTTCCTGTTCCGCAAGT AAAGTAACCTAGTTTCCTCCTCTCGGTATGGTTTCTCACACTC
Genomic sequence	CTCGGCATTCTTTGAATAAGTCCGACTCCAAAATGATTGTAAGCAATGGTCACTTGCATAGCTT TGTCCCTCATGTACGAGTCACTATGTCCTAGCAACATAACCTGTAAAAAAGTAGATCAAACCAT ATCATCAAAAACCGAATTCAGCCAAAGAAAAGAAGCAATTATTAACTAATGAAACAACAAGTCT TGAAAAGAACCTCGTTATGGTGAGTTAAGTGGTTGTTAGAGATGGTAATCGCGGTTGAGCCCAT GACTGCGTCCACAAGCCCATCAGCGCAATGGGACAACGAGTTATGATCAATCCATACATGACTC GATCCAAAGATCGAAATCGCGTCACCATCTGCCATTGTCCTCCACCCAAAATGCGTCTCTGAGC TTCTCACCATAGCGTTACCAGTTGGTTTACAGTCATGAATATGCAATCCGTGAACGATCACATT CGTCACAAACTGAATCGTGATGCAACCACCGTTAGCAATGTGAACGTTTGCGCCACGTCCATCG ATCGTTTTGAAACTGTTAACGATAAGCTCTTGTTTTAGCTGAATCACCATGTCACGTTTGAAAA CGATCCATAGTGGTCGGTCTTGGATCACGGCGTGACGTAAAGTCCCCGGTCTAGGGTTAACCGG ATTGTCGTCTCTTGGGTCAGTGACTACGTAGAATCGTCCATCACGACCACCGATCGCGTTTCTT CCAAATCCGATACCGCAATCCGCTAGGCGTTTACGGTTCTTGTGCCAATTGGGGTCACATCGCC AACAATCGTCGATAGGGTTTCCTGTTCCGCAAGTAAAGTAACCTAGTTTCCTCCTCTCGGTATG GTTTCTCACACTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.403937848

Conservation Information
Conserved circRNAs	NA
PMCS	0.403937848

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1305183-1304623(-)
						
						Potential amino acid sequence
						
							MVIQLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETH
FGWRTMADGDAISIFGSSHVWIDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSD
SYMRDKAMQVTIAYNHFGVGLIQRMPRSVRNHTERRKLGYFTCGTGNPIDDCWRCDPNWHKNRK
RLADCGIGFGRNAIGGRDGRFYVVTDPRDDNPVNPRPGTLRHAVIQDRPLWIVFKRDMVIQLKQ
ELIVNSFKTIDGRGANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETHFGWRTMA
DGDAISIFGSSHVWIDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSDSYMRDKA
MQVTIAYNHFGVGLIQRMPRSVRNHTERRKLGYFTCGTGNPIDDCWRCDPNWHKNRKRLADCGI
GFGRNAIGGRDGRFYVVTDPRDDNPVNPRPGTLRHAVIQDRPLWIVFKRDMVIQLKQELIVNSF
KTIDGRGANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETHFGWRTMADGDAISI
FGSSHVWIDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSDSYMRDKAMQVTIAY
NHFGVGLIQRMPRSVRNHTERRKLGYFTCGTGNPIDDCWRCDPNWHKNRKRLADCGIGFGRNAI
GGRDGRFYVVTDPRDDNPVNPRPGTLRHAVIQDRPLWIVFKRDMVIQLKQELIVNSFKTIDGRG
ANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETHFGWRTMADGDAISIFGSSHVW
IDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSDSYMRDKAMQVTIAYNHFGVGL
IQRMP(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1305183-1304623(-)
Potential amino acid sequence	MVIQLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETH FGWRTMADGDAISIFGSSHVWIDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSD SYMRDKAMQVTIAYNHFGVGLIQRMPRSVRNHTERRKLGYFTCGTGNPIDDCWRCDPNWHKNRK RLADCGIGFGRNAIGGRDGRFYVVTDPRDDNPVNPRPGTLRHAVIQDRPLWIVFKRDMVIQLKQ ELIVNSFKTIDGRGANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETHFGWRTMA DGDAISIFGSSHVWIDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSDSYMRDKA MQVTIAYNHFGVGLIQRMPRSVRNHTERRKLGYFTCGTGNPIDDCWRCDPNWHKNRKRLADCGI GFGRNAIGGRDGRFYVVTDPRDDNPVNPRPGTLRHAVIQDRPLWIVFKRDMVIQLKQELIVNSF KTIDGRGANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETHFGWRTMADGDAISI FGSSHVWIDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSDSYMRDKAMQVTIAY NHFGVGLIQRMPRSVRNHTERRKLGYFTCGTGNPIDDCWRCDPNWHKNRKRLADCGIGFGRNAI GGRDGRFYVVTDPRDDNPVNPRPGTLRHAVIQDRPLWIVFKRDMVIQLKQELIVNSFKTIDGRG ANVHIANGGCITIQFVTNVIVHGLHIHDCKPTGNAMVRSSETHFGWRTMADGDAISIFGSSHVW IDHNSLSHCADGLVDAVMGSTAITISNNHLTHHNEVMLLGHSDSYMRDKAMQVTIAYNHFGVGL IQRMP(-)
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 AT1G04680_circ_g.3

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