Plant Circular RNA Database

Detail information of AT4G29900_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT4G29900_circ_g.9
					
						ID in PlantcircBase
						ath_circ_033549
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 14616256-14618411  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI
					
						Parent gene
						
							AT4G29900						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 10, plasma membrane-type
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G29900_circ_g.1 AT4G29900_circ_g.2 AT4G29900_circ_g.3 AT4G29900_circ_g.4 AT4G29900_circ_g.5 AT4G29900_circ_g.6 AT4G29900_circ_g.7 AT4G29900_circ_g.8 AT4G29900_circ_g.10 AT4G29900_circ_g.11 AT4G29900_circ_g.12 AT4G29900_circ_g.13 AT4G29900_circ_g.14 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						AT4G29900.2:9
AT4G29900.1:9

General Information
CircRNA Name	AT4G29900_circ_g.9
ID in PlantcircBase	ath_circ_033549
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 14616256-14618411 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI
Parent gene	AT4G29900
Parent gene annotation	Calcium-transporting ATPase 10, plasma membrane-type
Parent gene strand	-
Alternative splicing	AT4G29900_circ_g.1 AT4G29900_circ_g.2 AT4G29900_circ_g.3 AT4G29900_circ_g.4 AT4G29900_circ_g.5 AT4G29900_circ_g.6 AT4G29900_circ_g.7 AT4G29900_circ_g.8 AT4G29900_circ_g.10 AT4G29900_circ_g.11 AT4G29900_circ_g.12 AT4G29900_circ_g.13 AT4G29900_circ_g.14
Support reads	2
Tissues	root
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	AT4G29900.2:9 AT4G29900.1:9

			
						 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  
						
							GCGCTCTCATCTTCCTCAGCATCTGTTTCTTATCTTCTTCCCTTTTTAAGTCCAGCGTATATCG
AAATCGACGAGAAGCATTAAGAACAAGCGCAGCTTGaattttgctctctccagtcatgctggac
tcatcaactgcaagggaatgtccagcaactaaaactccatccgcaggtacctatggaaattatt
ggcagatc

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							AATTTTGCTCTCTCCAGTCATGCTGGACTCATCAACTGCAAGGGAATGTCCAGCAACTAAAACT
CCATCCGCAGGTACCTATGGAAATTATTGGCAGATCAAACATAAATTATAGCTATACTGAAATT
CGGAAAAGAGCTAAGAAATACTGCATTGACAAAATCATGAAACTTGCCTGATCACCAATATTGA
GGGGTATGACATCGCCTACTACAATGTCATAAATTGAAATCTCCACTCTTCTCCCATCACGGGT
TACCTGCACATATACACGATGCATTTTTAAAAATTAAACCAACAAAAATGGAATTATCTATGAG
CTGCATGATCAACCAAGCTCTCACCTCTAGACGTATATTTCTTTTCTCTTCATTTAAGTTCTGG
AATTGAAGAGATTGCCGATAATCACTGGTAGCTGCCAAGGGAAGAGGTATACAAATTAGTACAA
TACACGCAGCAGTCACTTGTATGAGTGAAATCAGCAAGGAATATCAATACCTGTCACCACAATG
ACAAGAAGAACGGCAAAAGCAATGCTGATACCATCGTACCATCCCTTTTCGATACCCTAAGAAG
GCAGCCAAAGAGGTACCAAAAGCTCAGGAAGAACAAAGAAAACTGTGAAACTTTGGACAATGGA
GAGAGAACAACTTTCTGCCCTCTTAGAGCAGGAAAGCTTAGAATGAGTACAATGACAAAGTAAA
GGATAGTCAATAGACGTGGTATCGAGCGTCAACGATATGGACACGAGAAAGACATAACTCATTC
AAATACTGAGGTACAGAAACTCTGGAAGTCTTGTTTCTATAATTATTCGTCGATTGTTCTAAAG
CTATGCCACATAGAAAAAGGACTTAAAATTTTCAAGGTAGGCGCTGAGCCAAATATACTGTATT
AGTTCTTAAATTGCATACCTCGGTCTTTATTCCCAATGCCAAAGAAGCAACTGCTGCTACAATC
AGTATGATCAAAGTAAGATCTTGAGAAGCTTCCCATACAAACCTCTATCGGACATGAGGAAAAA
AAAAGGAAGGAACAAAATAGTAATTAGCTGAAAAATCTCACAGTTAATGGAAACTGCTACAAAG
CAAAAATTCTAAAGTATTAATACCCAGAAACTCCTCCCTTTCTTCTGAGGGTATGTGTTTGATC
CAAAAGCAGATTTCCTTTTCAATATGTCATCATCATCCCCGTGTATACCCTTCTCCAAGTTTGT
TTTCAACAGGTCAGATAACCCTCTTACCTAATGAAGTAAACAAGAGGATAAACATAAATGCATA
AGTTTCATGGCTGAGAAACAATTGCTGAAGAAAAAAGTAACAGATCAGCTAAAGCAAAGACATA
CCCCTCCAAGCTCTTGAAGAGCTCCTATATTTTGATCCCTTGATATTGACACAATCTGCTCCTG
TCCGATACCAAAATCACCACCGCCAGGAGTTGGAAGTGGACTTGCAATTCCTAAAAAGAGATAA
ACCTCAGTCAACTACAGCATCAATCAGAAAAATTATGAAAAAAAAATCCTTACAAGGAAAAGTA
ATAACCCAAGCAACTAATGTAAGTGAATAAGATAACTTGAATTGAAACCATCAACTGGTTCTAC
AAAGCTATCCAATAAATATCAAGGTCGCAAATTGACAGTGAGTATACTATTTACACTACATATA
AAAGATAATCAACTCAACCCATTGCAATGCAGATCAATCACATTTTGTAAAATATGAGTCAAAA
CAAAAATCATCCAGAATTTTGACTACACACCTAACCATAGTGTCAGTCAAAATCGTTAATGCAT
ATAAAACAAATGGTATAAAATTAAAAATCACTTAATCTCTATGAAAATGAAAGAGAACATATAC
ATGCTTCACAAAATGGGATGGAGAGAAGAAAATTAAGGAAAAGAACAAGAAAATGAAAGAAATT
ACCAGTCACGCGGCTTGCAGCTGCTTTAAAAAGGTGTGCAGCCTACGAAAGCAAACAGCATTGA
TAAGACACCACTAAGACGTTTATTTAAGTAAAACTTACTAGCGAGGCTTATATACTCTTATTGC
TTGGGCGTGCGCTCTCATCTTCCTCAGCATCTGTTTCTTATCTTCTTCCCTTTTTAAGTCCAGC
GTATATCGAAATCGACGAGAAGCATTAAGAACAAGCGCAGCTTG
						
					

			
		

Sequences
Splice junction sequence	GCGCTCTCATCTTCCTCAGCATCTGTTTCTTATCTTCTTCCCTTTTTAAGTCCAGCGTATATCG AAATCGACGAGAAGCATTAAGAACAAGCGCAGCTTGaattttgctctctccagtcatgctggac tcatcaactgcaagggaatgtccagcaactaaaactccatccgcaggtacctatggaaattatt ggcagatc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AATTTTGCTCTCTCCAGTCATGCTGGACTCATCAACTGCAAGGGAATGTCCAGCAACTAAAACT CCATCCGCAGGTACCTATGGAAATTATTGGCAGATCAAACATAAATTATAGCTATACTGAAATT CGGAAAAGAGCTAAGAAATACTGCATTGACAAAATCATGAAACTTGCCTGATCACCAATATTGA GGGGTATGACATCGCCTACTACAATGTCATAAATTGAAATCTCCACTCTTCTCCCATCACGGGT TACCTGCACATATACACGATGCATTTTTAAAAATTAAACCAACAAAAATGGAATTATCTATGAG CTGCATGATCAACCAAGCTCTCACCTCTAGACGTATATTTCTTTTCTCTTCATTTAAGTTCTGG AATTGAAGAGATTGCCGATAATCACTGGTAGCTGCCAAGGGAAGAGGTATACAAATTAGTACAA TACACGCAGCAGTCACTTGTATGAGTGAAATCAGCAAGGAATATCAATACCTGTCACCACAATG ACAAGAAGAACGGCAAAAGCAATGCTGATACCATCGTACCATCCCTTTTCGATACCCTAAGAAG GCAGCCAAAGAGGTACCAAAAGCTCAGGAAGAACAAAGAAAACTGTGAAACTTTGGACAATGGA GAGAGAACAACTTTCTGCCCTCTTAGAGCAGGAAAGCTTAGAATGAGTACAATGACAAAGTAAA GGATAGTCAATAGACGTGGTATCGAGCGTCAACGATATGGACACGAGAAAGACATAACTCATTC AAATACTGAGGTACAGAAACTCTGGAAGTCTTGTTTCTATAATTATTCGTCGATTGTTCTAAAG CTATGCCACATAGAAAAAGGACTTAAAATTTTCAAGGTAGGCGCTGAGCCAAATATACTGTATT AGTTCTTAAATTGCATACCTCGGTCTTTATTCCCAATGCCAAAGAAGCAACTGCTGCTACAATC AGTATGATCAAAGTAAGATCTTGAGAAGCTTCCCATACAAACCTCTATCGGACATGAGGAAAAA AAAAGGAAGGAACAAAATAGTAATTAGCTGAAAAATCTCACAGTTAATGGAAACTGCTACAAAG CAAAAATTCTAAAGTATTAATACCCAGAAACTCCTCCCTTTCTTCTGAGGGTATGTGTTTGATC CAAAAGCAGATTTCCTTTTCAATATGTCATCATCATCCCCGTGTATACCCTTCTCCAAGTTTGT TTTCAACAGGTCAGATAACCCTCTTACCTAATGAAGTAAACAAGAGGATAAACATAAATGCATA AGTTTCATGGCTGAGAAACAATTGCTGAAGAAAAAAGTAACAGATCAGCTAAAGCAAAGACATA CCCCTCCAAGCTCTTGAAGAGCTCCTATATTTTGATCCCTTGATATTGACACAATCTGCTCCTG TCCGATACCAAAATCACCACCGCCAGGAGTTGGAAGTGGACTTGCAATTCCTAAAAAGAGATAA ACCTCAGTCAACTACAGCATCAATCAGAAAAATTATGAAAAAAAAATCCTTACAAGGAAAAGTA ATAACCCAAGCAACTAATGTAAGTGAATAAGATAACTTGAATTGAAACCATCAACTGGTTCTAC AAAGCTATCCAATAAATATCAAGGTCGCAAATTGACAGTGAGTATACTATTTACACTACATATA AAAGATAATCAACTCAACCCATTGCAATGCAGATCAATCACATTTTGTAAAATATGAGTCAAAA CAAAAATCATCCAGAATTTTGACTACACACCTAACCATAGTGTCAGTCAAAATCGTTAATGCAT ATAAAACAAATGGTATAAAATTAAAAATCACTTAATCTCTATGAAAATGAAAGAGAACATATAC ATGCTTCACAAAATGGGATGGAGAGAAGAAAATTAAGGAAAAGAACAAGAAAATGAAAGAAATT ACCAGTCACGCGGCTTGCAGCTGCTTTAAAAAGGTGTGCAGCCTACGAAAGCAAACAGCATTGA TAAGACACCACTAAGACGTTTATTTAAGTAAAACTTACTAGCGAGGCTTATATACTCTTATTGC TTGGGCGTGCGCTCTCATCTTCCTCAGCATCTGTTTCTTATCTTCTTCCCTTTTTAAGTCCAGC GTATATCGAAATCGACGAGAAGCATTAAGAACAAGCGCAGCTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.150520196

Conservation Information
Conserved circRNAs	NA
PMCS	0.150520196

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14618334-14616258(-)
						
						Potential amino acid sequence
						
							MLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGGGDFGIGQEQIVSISRDQNIGALQELGG
VRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQKKGRSFWRFVWEASQDLTLIILIVAAV
ASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSDYRQSLQFQNLNEEKRNIRLEVTRDGRR
VEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVDESSMTGESKIQAALVLNASRRFRYTLD
LKREEDKKQMLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGGGDFGIGQEQIVSISRDQN
IGALQELGGVRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQKKGRSFWRFVWEASQDLT
LIILIVAAVASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSDYRQSLQFQNLNEEKRNIR
LEVTRDGRRVEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVDESSMTGESKIQAALVLNA
SRRFRYTLDLKREEDKKQMLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGGGDFGIGQEQ
IVSISRDQNIGALQELGGVRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQKKGRSFWRF
VWEASQDLTLIILIVAAVASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSDYRQSLQFQN
LNEEKRNIRLEVTRDGRRVEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVDESSMTGESK
IQAALVLNASRRFRYTLDLKREEDKKQMLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGG
GDFGIGQEQIVSISRDQNIGALQELGGVRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQ
KKGRSFWRFVWEASQDLTLIILIVAAVASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSD
YRQSLQFQNLNEEKRNIRLEVTRDGRRVEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVD
ESSMTGESKI(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	14618334-14616258(-)
Potential amino acid sequence	MLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGGGDFGIGQEQIVSISRDQNIGALQELGG VRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQKKGRSFWRFVWEASQDLTLIILIVAAV ASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSDYRQSLQFQNLNEEKRNIRLEVTRDGRR VEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVDESSMTGESKIQAALVLNASRRFRYTLD LKREEDKKQMLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGGGDFGIGQEQIVSISRDQN IGALQELGGVRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQKKGRSFWRFVWEASQDLT LIILIVAAVASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSDYRQSLQFQNLNEEKRNIR LEVTRDGRRVEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVDESSMTGESKIQAALVLNA SRRFRYTLDLKREEDKKQMLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGGGDFGIGQEQ IVSISRDQNIGALQELGGVRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQKKGRSFWRF VWEASQDLTLIILIVAAVASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSDYRQSLQFQN LNEEKRNIRLEVTRDGRRVEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVDESSMTGESK IQAALVLNASRRFRYTLDLKREEDKKQMLRKMRAHAQAIRAAHLFKAAASRVTGIASPLPTPGG GDFGIGQEQIVSISRDQNIGALQELGGVRGLSDLLKTNLEKGIHGDDDDILKRKSAFGSNTYPQ KKGRSFWRFVWEASQDLTLIILIVAAVASLALGIKTEGIEKGWYDGISIAFAVLLVIVVTATSD YRQSLQFQNLNEEKRNIRLEVTRDGRRVEISIYDIVVGDVIPLNIGDQVPADGVLVAGHSLAVD ESSMTGESKI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G29900_circ_g.9

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