Plant Circular RNA Database

Detail information of AT4G24190_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT4G24190_circ_g.5
					
						ID in PlantcircBase
						ath_circ_032472
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 12552752-12553414  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT4G24190						
					
						Parent gene annotation
						
							Endoplasmin homolog
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G24190_circ_g.1 AT4G24190_circ_g.2 AT4G24190_circ_g.3 AT4G24190_circ_g.4 AT4G24190_circ_g.6 AT4G24190_circ_g.7 AT4G24190_circ_g.8 AT4G24190_circ_g.9 AT4G24190_circ_g.10 AT4G24190_circ_g.11 AT4G24190_circ_g.12 AT4G24190_circ_g.13 AT4G24190_circ_g.14 AT4G24190_circ_g.15 AT4G24190_circ_g.16 AT4G24190_circ_g.17 AT4G24190_circ_g.18 						
					
						Support reads
						1/2
					
						Tissues
						root/seedlings
					
						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
						AT4G24190.1:3
AT4G24190.2:3

General Information
CircRNA Name	AT4G24190_circ_g.5
ID in PlantcircBase	ath_circ_032472
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 12552752-12553414 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT4G24190
Parent gene annotation	Endoplasmin homolog
Parent gene strand	-
Alternative splicing	AT4G24190_circ_g.1 AT4G24190_circ_g.2 AT4G24190_circ_g.3 AT4G24190_circ_g.4 AT4G24190_circ_g.6 AT4G24190_circ_g.7 AT4G24190_circ_g.8 AT4G24190_circ_g.9 AT4G24190_circ_g.10 AT4G24190_circ_g.11 AT4G24190_circ_g.12 AT4G24190_circ_g.13 AT4G24190_circ_g.14 AT4G24190_circ_g.15 AT4G24190_circ_g.16 AT4G24190_circ_g.17 AT4G24190_circ_g.18
Support reads	1/2
Tissues	root/seedlings
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	AT4G24190.1:3 AT4G24190.2:3

			
						 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  
						
							CCTTTCGGATAAGCTTCTTCTTAATTGTCTTTAAGCTGCTGTGTTGTTGAAGCATTTCTCTTGA
TACATTTAGAGGCAATGTGTCAGAGTCAACAAGACCctcatagcccttcttgatgagcctctcc
aggaatggagatttctctagctgttccttgctgcttcctgtgatgtaaaatatgtccttttggc
tctttttc

						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: 459
Transcript exons: 12552752-12552902,12552987-12553128,12553249-12553414
CTCATAGCCCTTCTTGATGAGCCTCTCCAGGAATGGAGATTTCTCTAGCTGTTCCTTGCTGCTT
CCTGTGATGTAAAATATGTCCTTTTGGCTCTTTTTCATTCTCTTAATGTACTGATCCAGGGAAG
TCAATTTTCCATCGGACTTTGTTGTCTCAAAACGAAGAAGTTTTGCCAAGCGGTTCCTGTTAGC
AGCATCCTCAATGATACCTAGTTTGACAGACTTGCCAAACTCGTTCCAGAATTTTGTGTATTGA
CCCTTCTTCTCATCGTTCTCACCAGACTTCTCCACATCTTTTTTCTCATCATCATGGATTTCAT
CAGGATCTTCTTCAGCAAGCTTGCGGATCATATCAAGCGCCTTTCGGATAAGCTTCTTCTTAAT
TGTCTTTAAGCTGCTGTGTTGTTGAAGCATTTCTCTTGATACATTTAGAGGCAATGTGTCAGAG
TCAACAAGACC
						
						Genomic sequence
						
							CTCATAGCCCTTCTTGATGAGCCTCTCCAGGAATGGAGATTTCTCTAGCTGTTCCTTGCTGCTT
CCTGTGATGTAAAATATGTCCTTTTGGCTCTTTTTCATTCTCTTAATGTACTGATCCAGGGAAG
TCAATTTTCCATCGGACTTTGTTCTGAAATAGCAAAATACAAATCTTTAGCCTGCTGGTGCTAA
TGAATGGACAGACGTGTATTAAAAAAAAAGTAACAGAGCTTACGTCTCAAAACGAAGAAGTTTT
GCCAAGCGGTTCCTGTTAGCAGCATCCTCAATGATACCTAGTTTGACAGACTTGCCAAACTCGT
TCCAGAATTTTGTGTATTGACCCTTCTTCTCATCGTTCTCACCAGACTTCTCCACATCTGCGTG
CCAACAAGTCAATAAGCTTAGACCATGTTTCAGAAAGATGAAGCTACCAAATGGTAAAAAAAAG
TGGAACGGTCAAAGTGGATTGATACCAAGAAACTTGTTTTATGGAATACCTTTTTTCTCATCAT
CATGGATTTCATCAGGATCTTCTTCAGCAAGCTTGCGGATCATATCAAGCGCCTTTCGGATAAG
CTTCTTCTTAATTGTCTTTAAGCTGCTGTGTTGTTGAAGCATTTCTCTTGATACATTTAGAGGC
AATGTGTCAGAGTCAACAAGACC

Sequences
Splice junction sequence	CCTTTCGGATAAGCTTCTTCTTAATTGTCTTTAAGCTGCTGTGTTGTTGAAGCATTTCTCTTGA TACATTTAGAGGCAATGTGTCAGAGTCAACAAGACCctcatagcccttcttgatgagcctctcc aggaatggagatttctctagctgttccttgctgcttcctgtgatgtaaaatatgtccttttggc tctttttc
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: 459 Transcript exons: 12552752-12552902,12552987-12553128,12553249-12553414 CTCATAGCCCTTCTTGATGAGCCTCTCCAGGAATGGAGATTTCTCTAGCTGTTCCTTGCTGCTT CCTGTGATGTAAAATATGTCCTTTTGGCTCTTTTTCATTCTCTTAATGTACTGATCCAGGGAAG TCAATTTTCCATCGGACTTTGTTGTCTCAAAACGAAGAAGTTTTGCCAAGCGGTTCCTGTTAGC AGCATCCTCAATGATACCTAGTTTGACAGACTTGCCAAACTCGTTCCAGAATTTTGTGTATTGA CCCTTCTTCTCATCGTTCTCACCAGACTTCTCCACATCTTTTTTCTCATCATCATGGATTTCAT CAGGATCTTCTTCAGCAAGCTTGCGGATCATATCAAGCGCCTTTCGGATAAGCTTCTTCTTAAT TGTCTTTAAGCTGCTGTGTTGTTGAAGCATTTCTCTTGATACATTTAGAGGCAATGTGTCAGAG TCAACAAGACC
Genomic sequence	CTCATAGCCCTTCTTGATGAGCCTCTCCAGGAATGGAGATTTCTCTAGCTGTTCCTTGCTGCTT CCTGTGATGTAAAATATGTCCTTTTGGCTCTTTTTCATTCTCTTAATGTACTGATCCAGGGAAG TCAATTTTCCATCGGACTTTGTTCTGAAATAGCAAAATACAAATCTTTAGCCTGCTGGTGCTAA TGAATGGACAGACGTGTATTAAAAAAAAAGTAACAGAGCTTACGTCTCAAAACGAAGAAGTTTT GCCAAGCGGTTCCTGTTAGCAGCATCCTCAATGATACCTAGTTTGACAGACTTGCCAAACTCGT TCCAGAATTTTGTGTATTGACCCTTCTTCTCATCGTTCTCACCAGACTTCTCCACATCTGCGTG CCAACAAGTCAATAAGCTTAGACCATGTTTCAGAAAGATGAAGCTACCAAATGGTAAAAAAAAG TGGAACGGTCAAAGTGGATTGATACCAAGAAACTTGTTTTATGGAATACCTTTTTTCTCATCAT CATGGATTTCATCAGGATCTTCTTCAGCAAGCTTGCGGATCATATCAAGCGCCTTTCGGATAAG CTTCTTCTTAATTGTCTTTAAGCTGCTGTGTTGTTGAAGCATTTCTCTTGATACATTTAGAGGC AATGTGTCAGAGTCAACAAGACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.317313136

Conservation Information
Conserved circRNAs	NA
PMCS	0.317313136

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12553370-12552754(-)
						
						Potential amino acid sequence
						
							MLQQHSSLKTIKKKLIRKALDMIRKLAEEDPDEIHDDEKKDVEKSGENDEKKGQYTKFWNEFGK
SVKLGIIEDAANRNRLAKLLRFETTKSDGKLTSLDQYIKRMKKSQKDIFYITGSSKEQLEKSPF
LERLIKKGYEGLVDSDTLPLNVSREMLQQHSSLKTIKKKLIRKALDMIRKLAEEDPDEIHDDEK
KDVEKSGENDEKKGQYTKFWNEFGKSVKLGIIEDAANRNRLAKLLRFETTKSDGKLTSLDQYIK
RMKKSQKDIFYITGSSKEQLEKSPFLERLIKKGYEGLVDSDTLPLNVSREMLQQHSSLKTIKKK
LIRKALDMIRKLAEEDPDEIHDDEKKDVEKSGENDEKKGQYTKFWNEFGKSVKLGIIEDAANRN
RLAKLLRFETTKSDGKLTSLDQYIKRMKKSQKDIFYITGSSKEQLEKSPFLERLIKKGYEGLVD
SDTLPLNVSREMLQQHSSLKTIKKKLIRKALDMIRKLAEEDPDEIHDDEKKDVEKSGENDEKKG
QYTKFWNEFGKSVKLGIIEDAANRNRLAKLLRFETTKSDGKLTSLDQYIKRMKKSQKDIFYITG
SSKEQLEKSPFLERLIKKGYE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12553370-12552754(-)
Potential amino acid sequence	MLQQHSSLKTIKKKLIRKALDMIRKLAEEDPDEIHDDEKKDVEKSGENDEKKGQYTKFWNEFGK SVKLGIIEDAANRNRLAKLLRFETTKSDGKLTSLDQYIKRMKKSQKDIFYITGSSKEQLEKSPF LERLIKKGYEGLVDSDTLPLNVSREMLQQHSSLKTIKKKLIRKALDMIRKLAEEDPDEIHDDEK KDVEKSGENDEKKGQYTKFWNEFGKSVKLGIIEDAANRNRLAKLLRFETTKSDGKLTSLDQYIK RMKKSQKDIFYITGSSKEQLEKSPFLERLIKKGYEGLVDSDTLPLNVSREMLQQHSSLKTIKKK LIRKALDMIRKLAEEDPDEIHDDEKKDVEKSGENDEKKGQYTKFWNEFGKSVKLGIIEDAANRN RLAKLLRFETTKSDGKLTSLDQYIKRMKKSQKDIFYITGSSKEQLEKSPFLERLIKKGYEGLVD SDTLPLNVSREMLQQHSSLKTIKKKLIRKALDMIRKLAEEDPDEIHDDEKKDVEKSGENDEKKG QYTKFWNEFGKSVKLGIIEDAANRNRLAKLLRFETTKSDGKLTSLDQYIKRMKKSQKDIFYITG SSKEQLEKSPFLERLIKKGYE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Pan et al., 2017

circRNA

Detail information of AT4G24190_circ_g.5

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