Plant Circular RNA Database

Detail information of AT5G37240_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G37240_circ_g.3
					
						ID in PlantcircBase
						ath_circ_041306
					
						Alias
						AtciR121
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 14738507-14739306  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI, CIRI-full, circRNA_finder, find_circ, circseq_cup, CIRI2
					
						Parent gene
						
							AT5G37240						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G37240_circ_g.1 AT5G37240_circ_g.2 AT5G37240_circ_g.4 5_circ_igg.5 5_circ_ag.6 5_circ_ag.7 5_circ_ig.8 5_circ_igg.9 5_circ_ig.10 5_circ_ig.11 5_circ_ig.12 5_circ_ig.13 5_circ_ig.14 5_circ_igg.15 5_circ_igg.16 5_circ_ag.17 5_circ_ag.18 5_circ_ig.19 5_circ_ig.20 5_circ_igg.21 5_circ_igg.22 AT5G37247_circ_g.1 AT5G37247_circ_g.2 AT5G37247_circ_g.3 						
					
						Support reads
						9
					
						Tissues
						root, inflorescences, whole_plant, leaf
					
						Exon boundary  
						
							Yes-No							"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
						AT5G37240.2:4
AT5G37240.3:4
AT5G37240.5:4
AT5G37240.4:4
AT5G37240.1:4

General Information
CircRNA Name	AT5G37240_circ_g.3
ID in PlantcircBase	ath_circ_041306
Alias	AtciR121
Organism	Arabidpsis thaliana
Position	chr5: 14738507-14739306 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRI, CIRI-full, circRNA_finder, find_circ, circseq_cup, CIRI2
Parent gene	AT5G37240
Parent gene annotation	unknown protein
Parent gene strand	-
Alternative splicing	AT5G37240_circ_g.1 AT5G37240_circ_g.2 AT5G37240_circ_g.4 5_circ_igg.5 5_circ_ag.6 5_circ_ag.7 5_circ_ig.8 5_circ_igg.9 5_circ_ig.10 5_circ_ig.11 5_circ_ig.12 5_circ_ig.13 5_circ_ig.14 5_circ_igg.15 5_circ_igg.16 5_circ_ag.17 5_circ_ag.18 5_circ_ig.19 5_circ_ig.20 5_circ_igg.21 5_circ_igg.22 AT5G37247_circ_g.1 AT5G37247_circ_g.2 AT5G37247_circ_g.3
Support reads	9
Tissues	root, inflorescences, whole_plant, leaf
Exon boundary	Yes-No "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	AT5G37240.2:4 AT5G37240.3:4 AT5G37240.5:4 AT5G37240.4:4 AT5G37240.1:4

			
						 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  
						
							TGTACCTTGACACCTTTAGGTGATTCAACTCTCATTCCATACAAATCCATCTTTATTTGCCTCC
ACTTGGTTTCCCAGTCTCAACCATCTTGCTTACAAGcttaaccttcgggttctcttggctaccc
aatcgtctccccagtgagttgtctctatagtataagaatccattctcctgaaaccgaaacattt
aattagca

						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: 339
Transcript exons: 14738507-14739306
TTGTCTCTATAGTATAAGAATCCATTCTCCTTTCCAGCATCTCCTCAAATAAATCTAGAGAAAA
GCGTACATTACATTACACCTCCAGTGATGAAGAGAGCAATCTTTCAAGTCTTTATTTCCATGCA
GAGAGCTCAAGTTTCTGGTTTTACATGAGAACCTACTGTTTTCAATCTCTTTATGACCCATTTC
TGCATTCTTGACACCTTTAGGTGATTCAACTCTCATTCCATACAAATCCATCTTTATTTGCCTC
CACTTGGTTTCCCAGTCTCAACCATCTTGCTTACAAGCTTAACCTTCGGGTTCTCTTGGCTACC
CAATCGTCTCCCCAGTGAG
						
						Genomic sequence
						
							CTTAACCTTCGGGTTCTCTTGGCTACCCAATCGTCTCCCCAGTGAGTTGTCTCTATAGTATAAG
AATCCATTCTCCTGAAACCGAAACATTTAATTAGCAACATTTTTGGCTTTCGCATGTACAGAAA
ACGAGTATATATGCCTTATGGAAACTAGTTACATTATCATGCAACCAAAAAAGGTCTACCTTTC
CAGCATCTCCTCAAATAAATCTAGAGAAAAGCGTACATTACATTACACCTCCTGTAAGTTAAAA
TTTAGCAATTTAAGAGCTCATTTCAAAAAGAAGACAAAGCCACGAAAACATAAAGTAAAAGCGA
GAAATAGAGAATCAAATTAGCTCATGTGAATTACATAACTTGTCTATATGGTACTTCATAACCA
ACAAAATCTTTAAGTGGAATGCAAATGAAGGACCACTTAAAATGATGAAGAACCACTTAAAATG
AACTAATCACTAAAGTAAAACGAAAAATGTGAAAAAACTTAGAAAGAGGTAAGAACCAGTGATG
AAGAGAGCAATCTTTCAAGTCTTTATTTCCATGCAGAGAGCTCAAGTTTCTGGTTTTACATGAG
AACCTACTGTTTTCAATCTCTTTATGACCCATTTCTGCATTCTAAAAATGAAAAGATGAATAAG
ATATTAATACCACAAAGGTATGAAAGAAGGACATAGTCAAATTACATAAACGATTATAAGTGTA
CCTTGACACCTTTAGGTGATTCAACTCTCATTCCATACAAATCCATCTTTATTTGCCTCCACTT
GGTTTCCCAGTCTCAACCATCTTGCTTACAAG

Sequences
Splice junction sequence	TGTACCTTGACACCTTTAGGTGATTCAACTCTCATTCCATACAAATCCATCTTTATTTGCCTCC ACTTGGTTTCCCAGTCTCAACCATCTTGCTTACAAGcttaaccttcgggttctcttggctaccc aatcgtctccccagtgagttgtctctatagtataagaatccattctcctgaaaccgaaacattt aattagca
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: 339 Transcript exons: 14738507-14739306 TTGTCTCTATAGTATAAGAATCCATTCTCCTTTCCAGCATCTCCTCAAATAAATCTAGAGAAAA GCGTACATTACATTACACCTCCAGTGATGAAGAGAGCAATCTTTCAAGTCTTTATTTCCATGCA GAGAGCTCAAGTTTCTGGTTTTACATGAGAACCTACTGTTTTCAATCTCTTTATGACCCATTTC TGCATTCTTGACACCTTTAGGTGATTCAACTCTCATTCCATACAAATCCATCTTTATTTGCCTC CACTTGGTTTCCCAGTCTCAACCATCTTGCTTACAAGCTTAACCTTCGGGTTCTCTTGGCTACC CAATCGTCTCCCCAGTGAG
Genomic sequence	CTTAACCTTCGGGTTCTCTTGGCTACCCAATCGTCTCCCCAGTGAGTTGTCTCTATAGTATAAG AATCCATTCTCCTGAAACCGAAACATTTAATTAGCAACATTTTTGGCTTTCGCATGTACAGAAA ACGAGTATATATGCCTTATGGAAACTAGTTACATTATCATGCAACCAAAAAAGGTCTACCTTTC CAGCATCTCCTCAAATAAATCTAGAGAAAAGCGTACATTACATTACACCTCCTGTAAGTTAAAA TTTAGCAATTTAAGAGCTCATTTCAAAAAGAAGACAAAGCCACGAAAACATAAAGTAAAAGCGA GAAATAGAGAATCAAATTAGCTCATGTGAATTACATAACTTGTCTATATGGTACTTCATAACCA ACAAAATCTTTAAGTGGAATGCAAATGAAGGACCACTTAAAATGATGAAGAACCACTTAAAATG AACTAATCACTAAAGTAAAACGAAAAATGTGAAAAAACTTAGAAAGAGGTAAGAACCAGTGATG AAGAGAGCAATCTTTCAAGTCTTTATTTCCATGCAGAGAGCTCAAGTTTCTGGTTTTACATGAG AACCTACTGTTTTCAATCTCTTTATGACCCATTTCTGCATTCTAAAAATGAAAAGATGAATAAG ATATTAATACCACAAAGGTATGAAAGAAGGACATAGTCAAATTACATAAACGATTATAAGTGTA CCTTGACACCTTTAGGTGATTCAACTCTCATTCCATACAAATCCATCTTTATTTGCCTCCACTT GGTTTCCCAGTCTCAACCATCTTGCTTACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.292386692

Conservation Information
Conserved circRNAs	NA
PMCS	0.292386692

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to methyl jasmonate

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to methyl jasmonate

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

circRNA

Detail information of AT5G37240_circ_g.3

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