Plant Circular RNA Database

Detail information of AT2G39800_circ_g.14

			
						 General Information
					
						CircRNA Name
						AT2G39800_circ_g.14
					
						ID in PlantcircBase
						ath_circ_017528
					
						Alias
						Ath_circ_FC1588, Ath_circ_FC1589, AT2G39800_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16601323-16602049  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, CIRI2
					
						Parent gene
						
							AT2G39800						
					
						Parent gene annotation
						
							Delta-1-pyrroline-5-carboxylate synthase A
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G39800_circ_g.1 AT2G39800_circ_g.2 AT2G39800_circ_g.3 AT2G39800_circ_g.4 AT2G39800_circ_g.5 AT2G39800_circ_g.6 AT2G39800_circ_g.7 AT2G39800_circ_g.8 AT2G39800_circ_g.9 AT2G39800_circ_g.10 AT2G39800_circ_g.11 AT2G39800_circ_g.12 AT2G39800_circ_g.13 AT2G39800_circ_g.15 AT2G39800_circ_g.16 AT2G39800_circ_g.17 						
					
						Support reads
						3
					
						Tissues
						leaf, aerial
					
						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
						AT2G39800.3:3
AT2G39800.4:3
AT2G39800.2:3
AT2G39800.1:3

General Information
CircRNA Name	AT2G39800_circ_g.14
ID in PlantcircBase	ath_circ_017528
Alias	Ath_circ_FC1588, Ath_circ_FC1589, AT2G39800_C1
Organism	Arabidpsis thaliana
Position	chr2: 16601323-16602049 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, CIRI2
Parent gene	AT2G39800
Parent gene annotation	Delta-1-pyrroline-5-carboxylate synthase A
Parent gene strand	-
Alternative splicing	AT2G39800_circ_g.1 AT2G39800_circ_g.2 AT2G39800_circ_g.3 AT2G39800_circ_g.4 AT2G39800_circ_g.5 AT2G39800_circ_g.6 AT2G39800_circ_g.7 AT2G39800_circ_g.8 AT2G39800_circ_g.9 AT2G39800_circ_g.10 AT2G39800_circ_g.11 AT2G39800_circ_g.12 AT2G39800_circ_g.13 AT2G39800_circ_g.15 AT2G39800_circ_g.16 AT2G39800_circ_g.17
Support reads	3
Tissues	leaf, aerial
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	AT2G39800.3:3 AT2G39800.4:3 AT2G39800.2:3 AT2G39800.1:3

			
						 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  
						
							GTCAAACATAGTCTCATAGTAAGCCATAAGACTGCTTTGTCCAACACCAGCACAAGCCTTCCCA
TCAAGTTCAGTCTGAGGCTTCTGAAGATCCGCAAAGctggttatgatgacaggaatcccagcat
aagctgcattgactgcagctttgacttttgcagtcataccccctctccctaatcttgatttgtc
gccgaatg

						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: 543
Transcript exons: 16601323-16601600,16601705-16601866,16601947-16602049
CTGGTTATGATGACAGGAATCCCAGCATAAGCTGCATTGACTGCAGCTTTGACTTTTGCAGTCA
TACCCCCTCTCCCTAATCTTGATTTGTCGCCGAATGTAATCTCATCTTGATGTTTTTCTTTAAC
AAAAGTGTGGATCAACTTTGAGTTAGGATCACTTGGAGGGCCTGTGTAAAGACCTTCAACATCG
CTCAGAAGAATCAGAAGATCAGCTTTCAGTTCCAACGCCAGTAGAGCAGCTAAGCTATCGTTAT
CCCAGAAAATACCAGAAGAATCCTGATATGGGGCTCTTCGGGTGCTAATAGCATCATTCTCATT
GAAAATTGGAATAACCCTCAAATCAAGCATAGACTTGACAGTTTCATTAAGTTGCTTCCTGAAA
TCCTTGTCTCTAAAACTACTGTCATTCACCAGAAGTTGAGCTGCCGTCACATCAAGCTGGTCAA
ACATAGTCTCATAGTAAGCCATAAGACTGCTTTGTCCAACACCAGCACAAGCCTTCCCATCAAG
TTCAGTCTGAGGCTTCTGAAGATCCGCAAAG
						
						Genomic sequence
						
							CTGGTTATGATGACAGGAATCCCAGCATAAGCTGCATTGACTGCAGCTTTGACTTTTGCAGTCA
TACCCCCTCTCCCTAATCTTGATTTGTCGCCGAATGTAATCTCATCTTGATGTTTTTCTTTAAC
AAAAGTGTGGATCAACTTTGAGTTAGGATCACTTGGAGGGCCTGTGTAAAGACCTTCAACATCG
CTCAGAAGAATCAGAAGATCAGCTTTCAGTTCCAACGCCAGTAGAGCAGCTAAGCTATCGTTAT
CCCAGAAAATACCAGAAGAATCCTGCATATATCAAGATCCAGTGAAGCTGAACATTAGACTACG
AGATTCAAAGAATCCCTCACATCTCAGAGTGTGTAGAAAAGTTCATGTCAAAAGGGACAAACCT
GATATGGGGCTCTTCGGGTGCTAATAGCATCATTCTCATTGAAAATTGGAATAACCCTCAAATC
AAGCATAGACTTGACAGTTTCATTAAGTTGCTTCCTGAAATCCTTGTCTCTAAAACTACTGTCA
TTCACCAGAAGTTGAGCTGCCGTCACATCAAGCTAACCAAAGAAAAACAACAGCATCAATATTT
GGATGTCTTACACAATAATCTAGAATTCGATAACAAAGGAAAAATCACCTGGTCAAACATAGTC
TCATAGTAAGCCATAAGACTGCTTTGTCCAACACCAGCACAAGCCTTCCCATCAAGTTCAGTCT
GAGGCTTCTGAAGATCCGCAAAG

Sequences
Splice junction sequence	GTCAAACATAGTCTCATAGTAAGCCATAAGACTGCTTTGTCCAACACCAGCACAAGCCTTCCCA TCAAGTTCAGTCTGAGGCTTCTGAAGATCCGCAAAGctggttatgatgacaggaatcccagcat aagctgcattgactgcagctttgacttttgcagtcataccccctctccctaatcttgatttgtc gccgaatg
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: 543 Transcript exons: 16601323-16601600,16601705-16601866,16601947-16602049 CTGGTTATGATGACAGGAATCCCAGCATAAGCTGCATTGACTGCAGCTTTGACTTTTGCAGTCA TACCCCCTCTCCCTAATCTTGATTTGTCGCCGAATGTAATCTCATCTTGATGTTTTTCTTTAAC AAAAGTGTGGATCAACTTTGAGTTAGGATCACTTGGAGGGCCTGTGTAAAGACCTTCAACATCG CTCAGAAGAATCAGAAGATCAGCTTTCAGTTCCAACGCCAGTAGAGCAGCTAAGCTATCGTTAT CCCAGAAAATACCAGAAGAATCCTGATATGGGGCTCTTCGGGTGCTAATAGCATCATTCTCATT GAAAATTGGAATAACCCTCAAATCAAGCATAGACTTGACAGTTTCATTAAGTTGCTTCCTGAAA TCCTTGTCTCTAAAACTACTGTCATTCACCAGAAGTTGAGCTGCCGTCACATCAAGCTGGTCAA ACATAGTCTCATAGTAAGCCATAAGACTGCTTTGTCCAACACCAGCACAAGCCTTCCCATCAAG TTCAGTCTGAGGCTTCTGAAGATCCGCAAAG
Genomic sequence	CTGGTTATGATGACAGGAATCCCAGCATAAGCTGCATTGACTGCAGCTTTGACTTTTGCAGTCA TACCCCCTCTCCCTAATCTTGATTTGTCGCCGAATGTAATCTCATCTTGATGTTTTTCTTTAAC AAAAGTGTGGATCAACTTTGAGTTAGGATCACTTGGAGGGCCTGTGTAAAGACCTTCAACATCG CTCAGAAGAATCAGAAGATCAGCTTTCAGTTCCAACGCCAGTAGAGCAGCTAAGCTATCGTTAT CCCAGAAAATACCAGAAGAATCCTGCATATATCAAGATCCAGTGAAGCTGAACATTAGACTACG AGATTCAAAGAATCCCTCACATCTCAGAGTGTGTAGAAAAGTTCATGTCAAAAGGGACAAACCT GATATGGGGCTCTTCGGGTGCTAATAGCATCATTCTCATTGAAAATTGGAATAACCCTCAAATC AAGCATAGACTTGACAGTTTCATTAAGTTGCTTCCTGAAATCCTTGTCTCTAAAACTACTGTCA TTCACCAGAAGTTGAGCTGCCGTCACATCAAGCTAACCAAAGAAAAACAACAGCATCAATATTT GGATGTCTTACACAATAATCTAGAATTCGATAACAAAGGAAAAATCACCTGGTCAAACATAGTC TCATAGTAAGCCATAAGACTGCTTTGTCCAACACCAGCACAAGCCTTCCCATCAAGTTCAGTCT GAGGCTTCTGAAGATCCGCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.515843527

Conservation Information
Conserved circRNAs	NA
PMCS	0.515843527

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16601977-16601325(-)
						
						Potential amino acid sequence
						
							MAYYETMFDQLDVTAAQLLVNDSSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQ
DSSGIFWDNDSLAALLALELKADLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEITFGDK
SRLGRGGMTAKVKAAVNAAYAGIPVIITSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQL
DVTAAQLLVNDSSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDS
LAALLALELKADLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEITFGDKSRLGRGGMTAK
VKAAVNAAYAGIPVIITSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVND
SSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALELKA
DLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEITFGDKSRLGRGGMTAKVKAAVNAAYAG
IPVIITSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVNDSSFRDKDFRKQ
LNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALELKADLLILLSDVEG
LYTGPPSDPNSKLIHTFVKEKHQDEITFGDKSRLGRGGMTAKVKAAVNAAYAGIPVIIT(-)
						
						Sponge-miRNAs
						
							ath-miR172d-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	16601977-16601325(-)
Potential amino acid sequence	MAYYETMFDQLDVTAAQLLVNDSSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQ DSSGIFWDNDSLAALLALELKADLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEITFGDK SRLGRGGMTAKVKAAVNAAYAGIPVIITSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQL DVTAAQLLVNDSSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDS LAALLALELKADLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEITFGDKSRLGRGGMTAK VKAAVNAAYAGIPVIITSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVND SSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALELKA DLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEITFGDKSRLGRGGMTAKVKAAVNAAYAG IPVIITSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVNDSSFRDKDFRKQ LNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALELKADLLILLSDVEG LYTGPPSDPNSKLIHTFVKEKHQDEITFGDKSRLGRGGMTAKVKAAVNAAYAGIPVIIT(-)
Sponge-miRNAs	ath-miR172d-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of AT2G39800_circ_g.14

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