Plant Circular RNA Database

Detail information of AT2G41700_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT2G41700_circ_g.9
					
						ID in PlantcircBase
						ath_circ_017856
					
						Alias
						2:17389781-17392091
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 17389781-17392091  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G41700						
					
						Parent gene annotation
						
							ABC transporter A family member 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G41700_circ_g.8 AT2G41700_circ_g.10 AT2G41700_circ_g.11 AT2G41700_circ_g.12 AT2G41700_circ_g.13 AT2G41700_circ_g.14 						
					
						Support reads
						1/1
					
						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
						AT2G41700.2:7
AT2G41700.1:7

General Information
CircRNA Name	AT2G41700_circ_g.9
ID in PlantcircBase	ath_circ_017856
Alias	2:17389781-17392091
Organism	Arabidpsis thaliana
Position	chr2: 17389781-17392091 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G41700
Parent gene annotation	ABC transporter A family member 1
Parent gene strand	-
Alternative splicing	AT2G41700_circ_g.8 AT2G41700_circ_g.10 AT2G41700_circ_g.11 AT2G41700_circ_g.12 AT2G41700_circ_g.13 AT2G41700_circ_g.14
Support reads	1/1
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	AT2G41700.2:7 AT2G41700.1:7

			
						 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  
						
							GTTATAATACTGTTTCCAAGTATCAGGGCATCTCCAGACGTTGGGGGAAGAAGGCCAACAAGCA
TTGATATTGTTGTGCTTTTACCAGCTCCATTATGTCctcactcacacaggttgctgatggaatg
tgacgatgaactatatgtgcggcaacagagacagttggagaagtctacaacataaaggaccacc
agttattg

									
								

					

						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: 668
Transcript exons: 17389781-17389852,17389938-17389992,17390448-17390632,17
390711-17390809,17391109-17391195,17391731-17391793,1739
1985-17392091
CTCACTCACACAGGTTGCTGATGGAATGTGACGATGAACTATATGTGCGGCAACAGAGACAGTT
GGAGAAGTCTTAACTAGCGTAAGAGTGTAACCAACCCCATAGTGATGCTTCAGGAAAATCGAAC
TGCCACAACACTTAAGAGACCCATTAGCCATGATTCCTATCCGATCTCCAAGTTCTTCAGCTTC
ATCCATGGAATGTGTTGTCAACAATATTATTCTACCCTTTTTAATTTTCTTAATTAACTGCCAT
GTAAGACGCATTGAGTAAGGATCCATTCCACTGGTTGGTTCATCGAGAATGATCACCTTACTGT
TACCTATCAATGCGATTCCAAGTGACAATTTCCTCTTCATCCCTCCAGAAAGTGCCCGTACAAG
TGTATTAATTTTATCAGACAATCCCACTTCCTCCGCCATATCAACAACTGTGCTCTTCAAGGAA
CCTTCTTCAACACCTTTAAGAACCGCAAACATCTCCAAGTGTTCTCTAACTGTCAGTTCTGGAA
AGAGGATGTCATGCTGAGGGCAAACACCTAGTTCTTTCCGTATCTCATCCATGTTTGTTATAAT
ACTGTTTCCAAGTATCAGGGCATCTCCAGACGTTGGGGGAAGAAGGCCAACAAGCATTGATATT
GTTGTGCTTTTACCAGCTCCATTATGTC
						
					

						Genomic sequence
						
							CTCACTCACACAGGTTGCTGATGGAATGTGACGATGAACTATATGTGCGGCAACAGAGACAGTT
GGAGAAGTCTACAACATAAAGGACCACCAGTTATTGATGTCCTAAATAGAAACATTAACAACAT
AGACGAAAATGAAAAGAATACAAACAAACCTTAACTAGCGTAAGAGTGTAACCAACCCCATAGT
GATGCTTCAGGAAAATCGAACTGCTTAGCCATAAAAACCCCAAAATAATTGGTAAAATGTTAAA
TGGTTAACTAAAGTCTAGAAAACTATAAATGAATAATTCCTATGGGTCAGAAAAAGAAAGATTT
TTTTTTATTTGTGAAGCACTTTCACATGTCTAGTTAGATAGCGTAAGCTTGGGGAATCTTTTGT
TTTCTTTATTTGAAATTATCACAGCACCAACACCAAATCAAAACACCTTCTACGAGTCATGAGC
AACCAATTGAAAAATCCAACCTAATCATATCACTTCATAGTAACTAACTCATGTTAAGCAATCC
CATGGTGTGAATGCTTTGTATAATTTGTGTTATTAGCATGCCTTCAACATATGCATCGTTGTTC
TTCCTAACTTGGAATGAAATAACTTTCTTTTTTAAAAAAAATGGGAAGGACAAGCAACAGAAAA
AGCCAGAGTAGTCTAAAAACACTTAACCTGCCACAACACTTAAGAGACCCATTAGCCATGATTC
CTATCCGATCTCCAAGTTCTTCAGCTTCATCCATGGAATGTGTTGTCAACAATATTATTCTACC
CTTTTTAATTTTCTTAATTAACTGCCATGTAAGACGCATTGAGTAAGGATCCATTCCACTGGTT
GGTTCATCGAGAATGATCACCTGAAATATAAAGCATATTCAACGACAACCGATTAAGAGAAACA
CAAGAAATAAGATGTCTTTGTGTTTCTTTCTCACCTTACTGTTACCTATCAATGCGATTCCAAG
TGACAATTTCCTCTTCATCCCTCCAGAAAGTGCCCGTACAAGTGTATTAATTTTATCAGACAAT
CCCACCTGGAAAAAAATCAATACCCAAGATCAGACAGTCTGTGACCTATACCCAAAATTGGCAG
GAAAGACAACTACAGCTTTCCACCCCAAACGGCAGCATCAAACAACAAAATGAATTCATCTGCT
GTTCTCCAAACTATGTTACATACTCAAACTTATGCAGTCTGAAGTTTTAATGCTTTTAGGCCAT
AATTGAATTAGCAACCAGATGCTATGAAATCAAATTTCAGAAATCCAAGTGTGTGAATATAGAT
TGTAGGAGAGGGAAAATCTACAAAGCTTGAATTTCACTACATACTTACTTCCTCCGCCATATCA
ACAACTGTGCTCTTCAAGGAACCTTCTTCAACACCTTTAAGAACCGCAAACATCTCCAAGTGTT
CTCTAACCTACAGTAGATATAAATCATTTCGAAATCATATTATATATCATCATTCGGATGGAAA
ACATCTAATCTGTCATAAGACTGAAACTTTTGCATAGAAAGAAACGATATAACAACAAAAGAAG
CAGATAAATGTTTCATTGTACAACACATATATGGTACATGTTCCTATCCTACGCTTGAAACAAG
CATGACCCTAGCAGTGGTTTTACTTCTGGTATAGAAAATGTATGAACTATATAGCATAAATTGA
CAATTGACTATAGAAGATAATTGGACAAAAACCAGTAACAGTAAAAGAATAAAAAACAAAAACA
TCTGAGGAATGAGCCCTGTGAATTTAAAGAAAATAAGAAAACCAACCAAATCTGCCTAAATGAA
AAAAGAATGCCGTGTTTTTTTTCCTGGCCTTTTTCACATTTTATGTTCTCTTTCTTTGATCAAG
ATAATATTACCATGTTATTGGATCCGAATTGCAAGCATCTCATCCGTCACTTAGAATAAAACAA
GAGGCAAAAGAAGGGATTTTTTTCACTTACTGTCAGTTCTGGAAAGAGGATGTCATGCTGAGGG
CAAACACCTAGTTCTTTCCGTATCTCATCCTACCAAAAGAGAGTCGTATAGTCAGAAACAAAAA
TGCAAGAATAGGGGAATTAACAGCATAAAAAACATACAGATGGTATTCAACTGATGCTAGAAAA
CAAAAATGCATATCTTAGTAGCTTATAGGTCAGAGTTTTTTGGTTATGCAAGAAAATTAGAGAT
TCAAGTAATAGCAACAGAAAAAATTTACCATGTTTGTTATAATACTGTTTCCAAGTATCAGGGC
ATCTCCAGACGTTGGGGGAAGAAGGCCAACAAGCATTGATATTGTTGTGCTTTTACCAGCTCCA
TTATGTC
						
					

			
		

Sequences
Splice junction sequence	GTTATAATACTGTTTCCAAGTATCAGGGCATCTCCAGACGTTGGGGGAAGAAGGCCAACAAGCA TTGATATTGTTGTGCTTTTACCAGCTCCATTATGTCctcactcacacaggttgctgatggaatg tgacgatgaactatatgtgcggcaacagagacagttggagaagtctacaacataaaggaccacc agttattg
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: 668 Transcript exons: 17389781-17389852,17389938-17389992,17390448-17390632,17 390711-17390809,17391109-17391195,17391731-17391793,1739 1985-17392091 CTCACTCACACAGGTTGCTGATGGAATGTGACGATGAACTATATGTGCGGCAACAGAGACAGTT GGAGAAGTCTTAACTAGCGTAAGAGTGTAACCAACCCCATAGTGATGCTTCAGGAAAATCGAAC TGCCACAACACTTAAGAGACCCATTAGCCATGATTCCTATCCGATCTCCAAGTTCTTCAGCTTC ATCCATGGAATGTGTTGTCAACAATATTATTCTACCCTTTTTAATTTTCTTAATTAACTGCCAT GTAAGACGCATTGAGTAAGGATCCATTCCACTGGTTGGTTCATCGAGAATGATCACCTTACTGT TACCTATCAATGCGATTCCAAGTGACAATTTCCTCTTCATCCCTCCAGAAAGTGCCCGTACAAG TGTATTAATTTTATCAGACAATCCCACTTCCTCCGCCATATCAACAACTGTGCTCTTCAAGGAA CCTTCTTCAACACCTTTAAGAACCGCAAACATCTCCAAGTGTTCTCTAACTGTCAGTTCTGGAA AGAGGATGTCATGCTGAGGGCAAACACCTAGTTCTTTCCGTATCTCATCCATGTTTGTTATAAT ACTGTTTCCAAGTATCAGGGCATCTCCAGACGTTGGGGGAAGAAGGCCAACAAGCATTGATATT GTTGTGCTTTTACCAGCTCCATTATGTC
Genomic sequence	CTCACTCACACAGGTTGCTGATGGAATGTGACGATGAACTATATGTGCGGCAACAGAGACAGTT GGAGAAGTCTACAACATAAAGGACCACCAGTTATTGATGTCCTAAATAGAAACATTAACAACAT AGACGAAAATGAAAAGAATACAAACAAACCTTAACTAGCGTAAGAGTGTAACCAACCCCATAGT GATGCTTCAGGAAAATCGAACTGCTTAGCCATAAAAACCCCAAAATAATTGGTAAAATGTTAAA TGGTTAACTAAAGTCTAGAAAACTATAAATGAATAATTCCTATGGGTCAGAAAAAGAAAGATTT TTTTTTATTTGTGAAGCACTTTCACATGTCTAGTTAGATAGCGTAAGCTTGGGGAATCTTTTGT TTTCTTTATTTGAAATTATCACAGCACCAACACCAAATCAAAACACCTTCTACGAGTCATGAGC AACCAATTGAAAAATCCAACCTAATCATATCACTTCATAGTAACTAACTCATGTTAAGCAATCC CATGGTGTGAATGCTTTGTATAATTTGTGTTATTAGCATGCCTTCAACATATGCATCGTTGTTC TTCCTAACTTGGAATGAAATAACTTTCTTTTTTAAAAAAAATGGGAAGGACAAGCAACAGAAAA AGCCAGAGTAGTCTAAAAACACTTAACCTGCCACAACACTTAAGAGACCCATTAGCCATGATTC CTATCCGATCTCCAAGTTCTTCAGCTTCATCCATGGAATGTGTTGTCAACAATATTATTCTACC CTTTTTAATTTTCTTAATTAACTGCCATGTAAGACGCATTGAGTAAGGATCCATTCCACTGGTT GGTTCATCGAGAATGATCACCTGAAATATAAAGCATATTCAACGACAACCGATTAAGAGAAACA CAAGAAATAAGATGTCTTTGTGTTTCTTTCTCACCTTACTGTTACCTATCAATGCGATTCCAAG TGACAATTTCCTCTTCATCCCTCCAGAAAGTGCCCGTACAAGTGTATTAATTTTATCAGACAAT CCCACCTGGAAAAAAATCAATACCCAAGATCAGACAGTCTGTGACCTATACCCAAAATTGGCAG GAAAGACAACTACAGCTTTCCACCCCAAACGGCAGCATCAAACAACAAAATGAATTCATCTGCT GTTCTCCAAACTATGTTACATACTCAAACTTATGCAGTCTGAAGTTTTAATGCTTTTAGGCCAT AATTGAATTAGCAACCAGATGCTATGAAATCAAATTTCAGAAATCCAAGTGTGTGAATATAGAT TGTAGGAGAGGGAAAATCTACAAAGCTTGAATTTCACTACATACTTACTTCCTCCGCCATATCA ACAACTGTGCTCTTCAAGGAACCTTCTTCAACACCTTTAAGAACCGCAAACATCTCCAAGTGTT CTCTAACCTACAGTAGATATAAATCATTTCGAAATCATATTATATATCATCATTCGGATGGAAA ACATCTAATCTGTCATAAGACTGAAACTTTTGCATAGAAAGAAACGATATAACAACAAAAGAAG CAGATAAATGTTTCATTGTACAACACATATATGGTACATGTTCCTATCCTACGCTTGAAACAAG CATGACCCTAGCAGTGGTTTTACTTCTGGTATAGAAAATGTATGAACTATATAGCATAAATTGA CAATTGACTATAGAAGATAATTGGACAAAAACCAGTAACAGTAAAAGAATAAAAAACAAAAACA TCTGAGGAATGAGCCCTGTGAATTTAAAGAAAATAAGAAAACCAACCAAATCTGCCTAAATGAA AAAAGAATGCCGTGTTTTTTTTCCTGGCCTTTTTCACATTTTATGTTCTCTTTCTTTGATCAAG ATAATATTACCATGTTATTGGATCCGAATTGCAAGCATCTCATCCGTCACTTAGAATAAAACAA GAGGCAAAAGAAGGGATTTTTTTCACTTACTGTCAGTTCTGGAAAGAGGATGTCATGCTGAGGG CAAACACCTAGTTCTTTCCGTATCTCATCCTACCAAAAGAGAGTCGTATAGTCAGAAACAAAAA TGCAAGAATAGGGGAATTAACAGCATAAAAAACATACAGATGGTATTCAACTGATGCTAGAAAA CAAAAATGCATATCTTAGTAGCTTATAGGTCAGAGTTTTTTGGTTATGCAAGAAAATTAGAGAT TCAAGTAATAGCAACAGAAAAAATTTACCATGTTTGTTATAATACTGTTTCCAAGTATCAGGGC ATCTCCAGACGTTGGGGGAAGAAGGCCAACAAGCATTGATATTGTTGTGCTTTTACCAGCTCCA TTATGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.186998328

Conservation Information
Conserved circRNAs	NA
PMCS	0.186998328

			
						 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 AT2G41700_circ_g.9

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