Plant Circular RNA Database

Detail information of AT4G13040_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G13040_circ_g.3
					
						ID in PlantcircBase
						ath_circ_030638
					
						Alias
						4:7614220-7615142
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7614220-7615142  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G13040						
					
						Parent gene annotation
						
							Integrase-type DNA-binding superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G13040_circ_g.1 AT4G13040_circ_g.2 AT4G13040_circ_g.4 AT4G13040_circ_g.5 AT4G13040_circ_g.6 						
					
						Support reads
						1/1
					
						Tissues
						root;flower
					
						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  
						
							GT-AG							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
						AT4G13040.4:4
AT4G13040.1:4
AT4G13040.8:4
AT4G13040.5:4
AT4G13040.3:4
AT4G13040.7:4
AT4G13040.6:4
AT4G13040.2:4

General Information
CircRNA Name	AT4G13040_circ_g.3
ID in PlantcircBase	ath_circ_030638
Alias	4:7614220-7615142
Organism	Arabidpsis thaliana
Position	chr4: 7614220-7615142 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G13040
Parent gene annotation	Integrase-type DNA-binding superfamily protein
Parent gene strand	+
Alternative splicing	AT4G13040_circ_g.1 AT4G13040_circ_g.2 AT4G13040_circ_g.4 AT4G13040_circ_g.5 AT4G13040_circ_g.6
Support reads	1/1
Tissues	root;flower
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	GT-AG 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	AT4G13040.4:4 AT4G13040.1:4 AT4G13040.8:4 AT4G13040.5:4 AT4G13040.3:4 AT4G13040.7:4 AT4G13040.6:4 AT4G13040.2:4

			
						 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  
						
							GAACCGAACTTTGAGCTCTCGGAAGAAGTTATACGAGAACTCAAACAGCAAAGCTGGGAAGAGT
TCTTGAATTGCACACGCCGAACAATTACGAACAAAAgaccaaatggttatgtgacaccacttcc
atttttaactgctgaggagatgatcactgggattccaaatcctaatgccagagcagcttataat
cccgggcc

									
								

					

						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: 7614220-7614350,7614560-7614668,7614768-7614948,7615021-
7615142
GACCAAATGGTTATGTGACACCACTTCCATTTTTAACTGCTGAGGAGATGATCACTGGGATTCC
AAATCCTAATGCCAGAGCAGCTTATAATCCCGGGCCAGCAGAAACGGTTACAACGGTTATCGTG
GAGAAAAAGGCTATTGAAGAAAGAAGCCGAAGAACTCGGTCAAAACATATGCATTTCAGGTCTG
ATTATTCAGATATCTCACCGGTTAATTCTGATTCCATCTCACCAAAATACCAGCCGCCGAAACG
AAGAAAGCAGCATAGAAGAAAGCGAGTACATAACCAAGAACCATGTTTGATGAGAGGAGTCTAC
TACAAAAACATGAAATGGCAAGCCGCCATTAAAGTCGAGAAGAAACAAATCCACTTAGGCACTT
TCTCTTCTCAAGAAGAGGCTGCTCGCTTATACGATAGGGCTGCTTTCATGTGTGGGAGGGAACC
GAACTTTGAGCTCTCGGAAGAAGTTATACGAGAACTCAAACAGCAAAGCTGGGAAGAGTTCTTG
AATTGCACACGCCGAACAATTACGAACAAAA
						
					

						Genomic sequence
						
							GACCAAATGGTTATGTGACACCACTTCCATTTTTAACTGCTGAGGAGATGATCACTGGGATTCC
AAATCCTAATGCCAGAGCAGCTTATAATCCCGGGCCAGCAGAAACGGTTACAACGGTTATCGTG
GAGGTACGGAAAAATGTTTTGATTTATATGGTTTTGCTAATTGTTTATCGAGGTTACTCTAACA
AATGTCTAAGGGCTAGTGCAATATGTAATATGTAGTGTTACTTATGTGATATGTAGTGTTACTT
ATGTGATACATTTCGCTTTAGTGTTTCTTATTTATACGGCTTTAGTCATTCTAACAATTGAGCC
TTCATTCTTTTGGTTTGCAGAAAAAGGCTATTGAAGAAAGAAGCCGAAGAACTCGGTCAAAACA
TATGCATTTCAGGTCTGATTATTCAGATATCTCACCGGTTAATTCTGATTCCATCTCACCAAAA
TGTGAGTAGTAGAACATATGTGAGAGAGGACCAATTTCTCATTTGCTTACTAATTGATTGAGAC
GAGTGAGAATTATATTATATTATCTCCCATTTATAGACCAGCCGCCGAAACGAAGAAAGCAGCA
TAGAAGAAAGCGAGTACATAACCAAGAACCATGTTTGATGAGAGGAGTCTACTACAAAAACATG
AAATGGCAAGCCGCCATTAAAGTCGAGAAGAAACAAATCCACTTAGGCACTTTCTCTTCTCAAG
AAGAGGCTGCTCGCTTATACGATAGGTAAAACTCTTTCGGGTTTTTTTTTTGCAATTCAAGTAA
TTCATTACCATTGACAATTATCACCTCTATTAGGGCTGCTTTCATGTGTGGGAGGGAACCGAAC
TTTGAGCTCTCGGAAGAAGTTATACGAGAACTCAAACAGCAAAGCTGGGAAGAGTTCTTGAATT
GCACACGCCGAACAATTACGAACAAAA
						
					

			
		

Sequences
Splice junction sequence	GAACCGAACTTTGAGCTCTCGGAAGAAGTTATACGAGAACTCAAACAGCAAAGCTGGGAAGAGT TCTTGAATTGCACACGCCGAACAATTACGAACAAAAgaccaaatggttatgtgacaccacttcc atttttaactgctgaggagatgatcactgggattccaaatcctaatgccagagcagcttataat cccgggcc
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: 7614220-7614350,7614560-7614668,7614768-7614948,7615021- 7615142 GACCAAATGGTTATGTGACACCACTTCCATTTTTAACTGCTGAGGAGATGATCACTGGGATTCC AAATCCTAATGCCAGAGCAGCTTATAATCCCGGGCCAGCAGAAACGGTTACAACGGTTATCGTG GAGAAAAAGGCTATTGAAGAAAGAAGCCGAAGAACTCGGTCAAAACATATGCATTTCAGGTCTG ATTATTCAGATATCTCACCGGTTAATTCTGATTCCATCTCACCAAAATACCAGCCGCCGAAACG AAGAAAGCAGCATAGAAGAAAGCGAGTACATAACCAAGAACCATGTTTGATGAGAGGAGTCTAC TACAAAAACATGAAATGGCAAGCCGCCATTAAAGTCGAGAAGAAACAAATCCACTTAGGCACTT TCTCTTCTCAAGAAGAGGCTGCTCGCTTATACGATAGGGCTGCTTTCATGTGTGGGAGGGAACC GAACTTTGAGCTCTCGGAAGAAGTTATACGAGAACTCAAACAGCAAAGCTGGGAAGAGTTCTTG AATTGCACACGCCGAACAATTACGAACAAAA
Genomic sequence	GACCAAATGGTTATGTGACACCACTTCCATTTTTAACTGCTGAGGAGATGATCACTGGGATTCC AAATCCTAATGCCAGAGCAGCTTATAATCCCGGGCCAGCAGAAACGGTTACAACGGTTATCGTG GAGGTACGGAAAAATGTTTTGATTTATATGGTTTTGCTAATTGTTTATCGAGGTTACTCTAACA AATGTCTAAGGGCTAGTGCAATATGTAATATGTAGTGTTACTTATGTGATATGTAGTGTTACTT ATGTGATACATTTCGCTTTAGTGTTTCTTATTTATACGGCTTTAGTCATTCTAACAATTGAGCC TTCATTCTTTTGGTTTGCAGAAAAAGGCTATTGAAGAAAGAAGCCGAAGAACTCGGTCAAAACA TATGCATTTCAGGTCTGATTATTCAGATATCTCACCGGTTAATTCTGATTCCATCTCACCAAAA TGTGAGTAGTAGAACATATGTGAGAGAGGACCAATTTCTCATTTGCTTACTAATTGATTGAGAC GAGTGAGAATTATATTATATTATCTCCCATTTATAGACCAGCCGCCGAAACGAAGAAAGCAGCA TAGAAGAAAGCGAGTACATAACCAAGAACCATGTTTGATGAGAGGAGTCTACTACAAAAACATG AAATGGCAAGCCGCCATTAAAGTCGAGAAGAAACAAATCCACTTAGGCACTTTCTCTTCTCAAG AAGAGGCTGCTCGCTTATACGATAGGTAAAACTCTTTCGGGTTTTTTTTTTGCAATTCAAGTAA TTCATTACCATTGACAATTATCACCTCTATTAGGGCTGCTTTCATGTGTGGGAGGGAACCGAAC TTTGAGCTCTCGGAAGAAGTTATACGAGAACTCAAACAGCAAAGCTGGGAAGAGTTCTTGAATT GCACACGCCGAACAATTACGAACAAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.215790351

Conservation Information
Conserved circRNAs	NA
PMCS	0.215790351

			
						 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 AT4G13040_circ_g.3

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