Plant Circular RNA Database

Detail information of AT4G24840_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT4G24840_circ_g.5
					
						ID in PlantcircBase
						ath_circ_032670
					
						Alias
						4:12798063-12800118
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 12798063-12800118  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G24840						
					
						Parent gene annotation
						
							COG complex component, COG2 (InterP /.../009316)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G24840_circ_g.1 AT4G24840_circ_g.2 AT4G24840_circ_g.3 AT4G24840_circ_g.4 AT4G24840_circ_g.6 AT4G24840_circ_g.7 AT4G24840_circ_g.8 AT4G24840_circ_g.9 AT4G24840_circ_g.10 						
					
						Support reads
						3
					
						Tissues
						leaf
					
						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
						AT4G24840.1:6

General Information
CircRNA Name	AT4G24840_circ_g.5
ID in PlantcircBase	ath_circ_032670
Alias	4:12798063-12800118
Organism	Arabidpsis thaliana
Position	chr4: 12798063-12800118 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G24840
Parent gene annotation	COG complex component, COG2 (InterP /.../009316)
Parent gene strand	-
Alternative splicing	AT4G24840_circ_g.1 AT4G24840_circ_g.2 AT4G24840_circ_g.3 AT4G24840_circ_g.4 AT4G24840_circ_g.6 AT4G24840_circ_g.7 AT4G24840_circ_g.8 AT4G24840_circ_g.9 AT4G24840_circ_g.10
Support reads	3
Tissues	leaf
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	AT4G24840.1:6

			
						 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  
						
							TTGAATTCTCATCATTCATAGAACTCCTTCCCATGGAATTTGCATCCTCGTTTTGCCAATCAGA
AGGAGTACTTGGTAGAACTTTAATAAGTTTTTCAACatatacaaagtcttctgcagttgctgaa
acagcccattcacatccaggactcgggctggcattactctttctattattcaacgcagatgaca
cccaaaag

									
								

					

						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: 1116
Transcript exons: 12798063-12798168,12798248-12798457,12798579-12798678,12
798840-12799001,12799198-12799534,12799918-12800118
ATATACAAAGTCTTCTGCAGTTGCTGAAACAGCCCATTCACATCCAGGACTCGGGCTGGCATTA
CTCTTTCTATTATTCAACGCAGATGACACCCAAAAGCTATATCTCGAAAGAAGCTGCAAGGTCA
AGCGAAGAAATTTATCAGCAGCCGAGAAAACAAGAACATCTTCTTTCCAGCACGATCGTAAGCA
CTCCAAAAGAGTATCACTCTGTCTGAGAATTAAGTTGAGCGAACTCTCTTTATCTGAATCCTGA
ATGAAAACCAGAGAAGGAGAAGTAAGAGCAGAATCCAAGGCTCCAGCTATCTCCTGAAACCTCA
GTGAAAAATATACTCCCACATTCCATTGCTTCATGAATTCGACGCATATAGCTTCAGCTCGAAA
CTTAGTTACAGCAGATCTTGACGGACAATAACCTTCAAGATATGCCAGGAAATCCAAGCTTGCC
TTGTAATTCTTTAAGAACTCAGTAGGCCTTCCAGGAGAAAACGCTCCTGGTTTGACTTTCTGGA
TTGCCCAAAGAACTTCTTTCAGGATTGAATTTGCCAAGAAGTCGAAGACATGTAAACCCGATTT
GTCAGTTGAAGATATTTCTAGCAGCATTTTACAGTCCTTAGCAATAAAATGCTTGATCTGCTTG
TAATCGTTTTCAAGTTCATCTTCCGATGTTCCAGCAGCATTCGTTGTTGTTTCATGTGTAATAA
TTTTCTGAATAAATGGAGCTACAATCGTTGTACGGAAAATTTCTTCTGCAGCGTTGGTGTTATC
AATGGCAGCATATGCACGTAAGCAGTTGTAAAGGACACTTGTATCGCTGTTGTTTAGCCCATCA
ATGAAGCAATGACCTAGGCTAGCATCCAATAACACACTAGCGCTCTGAATCCTCTTCTCCATGT
TCTCAATGAAAGGCAGGTTCTGTGCATGAGCCATATAGAACTTGAGCCGATTCATTTCACTAGC
TATTCTTTCCAATAGCATGCTCTGGGTTTCTCTCATGGTTGTGCCATCTTGCTGCGTTGAATTC
TCATCATTCATAGAACTCCTTCCCATGGAATTTGCATCCTCGTTTTGCCAATCAGAAGGAGTAC
TTGGTAGAACTTTAATAAGTTTTTCAAC
						
					

						Genomic sequence
						
							ATATACAAAGTCTTCTGCAGTTGCTGAAACAGCCCATTCACATCCAGGACTCGGGCTGGCATTA
CTCTTTCTATTATTCAACGCAGATGACACCCAAAAGCTATATCTACATGCCATTAACACATAAT
CAAAATTAGAATTGAAACTAGTAAACGTGGATAATATTACAGTCAAATTTTACAAACCTCGAAA
GAAGCTGCAAGGTCAAGCGAAGAAATTTATCAGCAGCCGAGAAAACAAGAACATCTTCTTTCCA
GCACGATCGTAAGCACTCCAAAAGAGTATCACTCTGTCTGAGAATTAAGTTGAGCGAACTCTCT
TTATCTGAATCCTGAATGAAAACCAGAGAAGGAGAAGTAAGAGCAGAATCCAAGGCTCCAGCTA
TCTCCTGAAACCTGAAATTATGTATTTTTGAGTTAGAGAAGCTGAGAAACCACTAATCTAATGG
TAAGCCGACAGTCCCGACCAAAAAAAAAATTGGCAAGTCGACAGTCATCTATGATATTACTCAC
GTACCTCAGTGAAAAATATACTCCCACATTCCATTGCTTCATGAATTCGACGCATATAGCTTCA
GCTCGAAACTTAGTTACAGCAGATCTTGACGGACAATAACCTTCATAAGAAGTATATGGTATGA
GCCAAATGAAAAATATCCAGATCATTTCATCACCTAGTACTAAATTAAAATTTATGCTTACGTA
CGACACATGAAAATCAGTTCACAATGCATCTAATAAGCCATGTGATCAAGCTCAGAGGAAGATA
TACATCTACCTTCAAGATATGCCAGGAAATCCAAGCTTGCCTTGTAATTCTTTAAGAACTCAGT
AGGCCTTCCAGGAGAAAACGCTCCTGGTTTGACTTTCTGGATTGCCCAAAGAACTTCTTTCAGG
ATTGAATTTGCCAAGAAGTCGAAGACATGTAAACCCGATTTGTCTGTTTTAGCACAAGATAACA
AGCACAGAGTACGATGAGTAAAATATAAGCCATGAAATCTAGGTTACTGTGTTAGTTGGAGAAT
TTTTTCTTAGAATGTTTCAGGAAAACGAATTTTCCAGAGAAACATGGAACTTAAAAAAGGCGAT
TGGATATCTGCAACATATATGATCAGACAGCGATTTGCATGAATTACCAGTTGAAGATATTTCT
AGCAGCATTTTACAGTCCTTAGCAATAAAATGCTTGATCTGCTTGTAATCGTTTTCAAGTTCAT
CTTCCGATGTTCCAGCAGCATTCGTTGTTGTTTCATGTGTAATAATTTTCTGAATAAATGGAGC
TACAATCGTTGTACGGAAAATTTCTTCTGCAGCGTTGGTGTTATCAATGGCAGCATATGCACGT
AAGCAGTTGTAAAGGACACTTGTATCGCTGTTGTTTAGCCCATCAATGAAGCAATGACCTAGGC
TAGCATCCAATAACACACTAGCGCTCTGAATCCTCTTCTCCATGTTCTCAATGAAAGGCAGGTT
CTGTACTGGCAATGGCATAACATAAAAAGTAGTGAGCATCAGTCATAAGACCTTCTATTGTCTT
CTGAGGCTAACAAGTATACTGTAGTTTTTGGAAAACACCAGAGATTTCACAAGATTTAACTATG
TAGCATCTGATGTAACCTATTTTTTTGTCAGCAATCTTCTCAAAGGCAATAAATTCTCCTAGCA
GCACAGCAATATCTCAAACCCTATACCATAGCTAGTTTTGATCCCCAATTTACTACTTTTAAGC
AATATACTCAAAGCTTCTTGTACGAGGAAAGAGAGGAGCATTTCTAATGTAATCTATATTTTGA
GATGGACAAGGAATTGTGACTTTGCAAAAAGAAAAAAAGAAGAAGTAAATGCATGATGGAGACC
TGTGCATGAGCCATATAGAACTTGAGCCGATTCATTTCACTAGCTATTCTTTCCAATAGCATGC
TCTGGGTTTCTCTCATGGTTGTGCCATCTTGCTGCGTTGAATTCTCATCATTCATAGAACTCCT
TCCCATGGAATTTGCATCCTCGTTTTGCCAATCAGAAGGAGTACTTGGTAGAACTTTAATAAGT
TTTTCAAC
						
					

			
		

Sequences
Splice junction sequence	TTGAATTCTCATCATTCATAGAACTCCTTCCCATGGAATTTGCATCCTCGTTTTGCCAATCAGA AGGAGTACTTGGTAGAACTTTAATAAGTTTTTCAACatatacaaagtcttctgcagttgctgaa acagcccattcacatccaggactcgggctggcattactctttctattattcaacgcagatgaca cccaaaag
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: 1116 Transcript exons: 12798063-12798168,12798248-12798457,12798579-12798678,12 798840-12799001,12799198-12799534,12799918-12800118 ATATACAAAGTCTTCTGCAGTTGCTGAAACAGCCCATTCACATCCAGGACTCGGGCTGGCATTA CTCTTTCTATTATTCAACGCAGATGACACCCAAAAGCTATATCTCGAAAGAAGCTGCAAGGTCA AGCGAAGAAATTTATCAGCAGCCGAGAAAACAAGAACATCTTCTTTCCAGCACGATCGTAAGCA CTCCAAAAGAGTATCACTCTGTCTGAGAATTAAGTTGAGCGAACTCTCTTTATCTGAATCCTGA ATGAAAACCAGAGAAGGAGAAGTAAGAGCAGAATCCAAGGCTCCAGCTATCTCCTGAAACCTCA GTGAAAAATATACTCCCACATTCCATTGCTTCATGAATTCGACGCATATAGCTTCAGCTCGAAA CTTAGTTACAGCAGATCTTGACGGACAATAACCTTCAAGATATGCCAGGAAATCCAAGCTTGCC TTGTAATTCTTTAAGAACTCAGTAGGCCTTCCAGGAGAAAACGCTCCTGGTTTGACTTTCTGGA TTGCCCAAAGAACTTCTTTCAGGATTGAATTTGCCAAGAAGTCGAAGACATGTAAACCCGATTT GTCAGTTGAAGATATTTCTAGCAGCATTTTACAGTCCTTAGCAATAAAATGCTTGATCTGCTTG TAATCGTTTTCAAGTTCATCTTCCGATGTTCCAGCAGCATTCGTTGTTGTTTCATGTGTAATAA TTTTCTGAATAAATGGAGCTACAATCGTTGTACGGAAAATTTCTTCTGCAGCGTTGGTGTTATC AATGGCAGCATATGCACGTAAGCAGTTGTAAAGGACACTTGTATCGCTGTTGTTTAGCCCATCA ATGAAGCAATGACCTAGGCTAGCATCCAATAACACACTAGCGCTCTGAATCCTCTTCTCCATGT TCTCAATGAAAGGCAGGTTCTGTGCATGAGCCATATAGAACTTGAGCCGATTCATTTCACTAGC TATTCTTTCCAATAGCATGCTCTGGGTTTCTCTCATGGTTGTGCCATCTTGCTGCGTTGAATTC TCATCATTCATAGAACTCCTTCCCATGGAATTTGCATCCTCGTTTTGCCAATCAGAAGGAGTAC TTGGTAGAACTTTAATAAGTTTTTCAAC
Genomic sequence	ATATACAAAGTCTTCTGCAGTTGCTGAAACAGCCCATTCACATCCAGGACTCGGGCTGGCATTA CTCTTTCTATTATTCAACGCAGATGACACCCAAAAGCTATATCTACATGCCATTAACACATAAT CAAAATTAGAATTGAAACTAGTAAACGTGGATAATATTACAGTCAAATTTTACAAACCTCGAAA GAAGCTGCAAGGTCAAGCGAAGAAATTTATCAGCAGCCGAGAAAACAAGAACATCTTCTTTCCA GCACGATCGTAAGCACTCCAAAAGAGTATCACTCTGTCTGAGAATTAAGTTGAGCGAACTCTCT TTATCTGAATCCTGAATGAAAACCAGAGAAGGAGAAGTAAGAGCAGAATCCAAGGCTCCAGCTA TCTCCTGAAACCTGAAATTATGTATTTTTGAGTTAGAGAAGCTGAGAAACCACTAATCTAATGG TAAGCCGACAGTCCCGACCAAAAAAAAAATTGGCAAGTCGACAGTCATCTATGATATTACTCAC GTACCTCAGTGAAAAATATACTCCCACATTCCATTGCTTCATGAATTCGACGCATATAGCTTCA GCTCGAAACTTAGTTACAGCAGATCTTGACGGACAATAACCTTCATAAGAAGTATATGGTATGA GCCAAATGAAAAATATCCAGATCATTTCATCACCTAGTACTAAATTAAAATTTATGCTTACGTA CGACACATGAAAATCAGTTCACAATGCATCTAATAAGCCATGTGATCAAGCTCAGAGGAAGATA TACATCTACCTTCAAGATATGCCAGGAAATCCAAGCTTGCCTTGTAATTCTTTAAGAACTCAGT AGGCCTTCCAGGAGAAAACGCTCCTGGTTTGACTTTCTGGATTGCCCAAAGAACTTCTTTCAGG ATTGAATTTGCCAAGAAGTCGAAGACATGTAAACCCGATTTGTCTGTTTTAGCACAAGATAACA AGCACAGAGTACGATGAGTAAAATATAAGCCATGAAATCTAGGTTACTGTGTTAGTTGGAGAAT TTTTTCTTAGAATGTTTCAGGAAAACGAATTTTCCAGAGAAACATGGAACTTAAAAAAGGCGAT TGGATATCTGCAACATATATGATCAGACAGCGATTTGCATGAATTACCAGTTGAAGATATTTCT AGCAGCATTTTACAGTCCTTAGCAATAAAATGCTTGATCTGCTTGTAATCGTTTTCAAGTTCAT CTTCCGATGTTCCAGCAGCATTCGTTGTTGTTTCATGTGTAATAATTTTCTGAATAAATGGAGC TACAATCGTTGTACGGAAAATTTCTTCTGCAGCGTTGGTGTTATCAATGGCAGCATATGCACGT AAGCAGTTGTAAAGGACACTTGTATCGCTGTTGTTTAGCCCATCAATGAAGCAATGACCTAGGC TAGCATCCAATAACACACTAGCGCTCTGAATCCTCTTCTCCATGTTCTCAATGAAAGGCAGGTT CTGTACTGGCAATGGCATAACATAAAAAGTAGTGAGCATCAGTCATAAGACCTTCTATTGTCTT CTGAGGCTAACAAGTATACTGTAGTTTTTGGAAAACACCAGAGATTTCACAAGATTTAACTATG TAGCATCTGATGTAACCTATTTTTTTGTCAGCAATCTTCTCAAAGGCAATAAATTCTCCTAGCA GCACAGCAATATCTCAAACCCTATACCATAGCTAGTTTTGATCCCCAATTTACTACTTTTAAGC AATATACTCAAAGCTTCTTGTACGAGGAAAGAGAGGAGCATTTCTAATGTAATCTATATTTTGA GATGGACAAGGAATTGTGACTTTGCAAAAAGAAAAAAAGAAGAAGTAAATGCATGATGGAGACC TGTGCATGAGCCATATAGAACTTGAGCCGATTCATTTCACTAGCTATTCTTTCCAATAGCATGC TCTGGGTTTCTCTCATGGTTGTGCCATCTTGCTGCGTTGAATTCTCATCATTCATAGAACTCCT TCCCATGGAATTTGCATCCTCGTTTTGCCAATCAGAAGGAGTACTTGGTAGAACTTTAATAAGT TTTTCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.198462492

Conservation Information
Conserved circRNAs	NA
PMCS	0.198462492

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT4G24840_circ_g.5

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