Plant Circular RNA Database

Detail information of AT1G07910_circ_g.13

			
						 General Information
					
						CircRNA Name
						AT1G07910_circ_g.13
					
						ID in PlantcircBase
						ath_circ_001236
					
						Alias
						Ath_circ_FC0240
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 2452807-2453856  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G07910						
					
						Parent gene annotation
						
							RNAligase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G07910_circ_g.3 AT1G07910_circ_g.4 AT1G07910_circ_g.5 AT1G07910_circ_g.6 AT1G07910_circ_g.7 AT1G07910_circ_g.8 AT1G07910_circ_g.9 AT1G07910_circ_g.10 AT1G07910_circ_g.11 AT1G07910_circ_g.12 AT1G07910_circ_g.14 						
					
						Support reads
						1
					
						Tissues
						leaf, whole_plant
					
						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
						AT1G07910.1:4
AT1G07910.2:4

General Information
CircRNA Name	AT1G07910_circ_g.13
ID in PlantcircBase	ath_circ_001236
Alias	Ath_circ_FC0240
Organism	Arabidpsis thaliana
Position	chr1: 2452807-2453856 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT1G07910
Parent gene annotation	RNAligase
Parent gene strand	+
Alternative splicing	AT1G07910_circ_g.3 AT1G07910_circ_g.4 AT1G07910_circ_g.5 AT1G07910_circ_g.6 AT1G07910_circ_g.7 AT1G07910_circ_g.8 AT1G07910_circ_g.9 AT1G07910_circ_g.10 AT1G07910_circ_g.11 AT1G07910_circ_g.12 AT1G07910_circ_g.14
Support reads	1
Tissues	leaf, whole_plant
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	AT1G07910.1:4 AT1G07910.2:4

			
						 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  
						
							TGATTACAAGCCACCAAGTTCGGAGAAAAGAAAACACGGGTCTATTGTTTTCGCTGCCATCAAC
TTGCCTGCTACTCAAGTTCACAGTCTTCTTGAAAAGaaccgtaatgaatttgagagtgaattga
ttgagcgctttggctccctcatcaagatgccactattgaaatcagacaggtatacagttgacat
cacatgcg

									
								

					

						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: 420
Transcript exons: 2452807-2452883,2453003-2453083,2453442-2453544,2453698-
2453856
AACCGTAATGAATTTGAGAGTGAATTGATTGAGCGCTTTGGCTCCCTCATCAAGATGCCACTAT
TGAAATCAGACAGGACTCCTTTACCTGATCCTGTTAAATCAGTTCTTGAGGAGGGCATTGATTT
GTTCAATCTCCATAGTAGAAGACATGGGAGACTCGAGTCAACAAAAGGAACATATGCAGCGGAA
TGGACCAAATGGGAGAAACAACTACGAGATACTCTAGTTGCAAATTCTGAGTATCTCAGTTCTA
TTCAGGTTCCATTTGAGTCTATGGTTCATCAAGTGCGAGAAGAGCTAAAAACAATAGCGAAGGG
TGATTACAAGCCACCAAGTTCGGAGAAAAGAAAACACGGGTCTATTGTTTTCGCTGCCATCAAC
TTGCCTGCTACTCAAGTTCACAGTCTTCTTGAAAAG
						
					

						Genomic sequence
						
							AACCGTAATGAATTTGAGAGTGAATTGATTGAGCGCTTTGGCTCCCTCATCAAGATGCCACTAT
TGAAATCAGACAGGTATACAGTTGACATCACATGCGAGCTAACAAACTCGAACTTAGCACAGCT
ACAAATTGCAACTTCATATTTAATTGGTTCATAAGCAATTTAATTGTCTTCTCTTTGTGCATAT
ACAGGACTCCTTTACCTGATCCTGTTAAATCAGTTCTTGAGGAGGGCATTGATTTGTTCAATCT
CCATAGTAGAAGACATGGGAGGTGGGTACCAACACTACCATTTTAAATGACTTGAAAAGTTGAA
TTTATGTCAAACCGAAGTATTTTGAGCATCGTATGCCAAAACTTGTTCATCGTGTTATATATTA
AACAACACCTTCTGTTCTGACGATAAAAAATGAAAGGCAATAGTAATAATTTAGCAAAAACTAA
CAAGACATCGGATTTATTTATCCTGTGACTAGATGTACTTGGATCATGTAACTGGAGAAATCCT
ACACATGAGTGTGCTCACAGGCGTTTTTATTTCTTGTTCTGGCTGTTCTCTACTTCATTCTTTT
AGCTCTAGCTCCTGTTGGTTGCTTCTGACCTGTTTTCCTTCTGATTTTTCTTGTTGTAGACTCG
AGTCAACAAAAGGAACATATGCAGCGGAATGGACCAAATGGGAGAAACAACTACGAGATACTCT
AGTTGCAAATTCTGAGTATCTCAGTTCTATTCAGGTAAAAAATTCCTTTGTCATTGATGGCTCA
TGAAAAGCAAGAAATCTGCGATTGAATTTTAAACTGCTTCAATGTTCCTTCAGTACATGGTAAA
AGAGTATAAGAAGAAGGATGTACATATGATGTCTTTGTTTTCTGGTTTGCAACTTTCAGGTTCC
ATTTGAGTCTATGGTTCATCAAGTGCGAGAAGAGCTAAAAACAATAGCGAAGGGTGATTACAAG
CCACCAAGTTCGGAGAAAAGAAAACACGGGTCTATTGTTTTCGCTGCCATCAACTTGCCTGCTA
CTCAAGTTCACAGTCTTCTTGAAAAG
						
					

			
		

Sequences
Splice junction sequence	TGATTACAAGCCACCAAGTTCGGAGAAAAGAAAACACGGGTCTATTGTTTTCGCTGCCATCAAC TTGCCTGCTACTCAAGTTCACAGTCTTCTTGAAAAGaaccgtaatgaatttgagagtgaattga ttgagcgctttggctccctcatcaagatgccactattgaaatcagacaggtatacagttgacat cacatgcg
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: 420 Transcript exons: 2452807-2452883,2453003-2453083,2453442-2453544,2453698- 2453856 AACCGTAATGAATTTGAGAGTGAATTGATTGAGCGCTTTGGCTCCCTCATCAAGATGCCACTAT TGAAATCAGACAGGACTCCTTTACCTGATCCTGTTAAATCAGTTCTTGAGGAGGGCATTGATTT GTTCAATCTCCATAGTAGAAGACATGGGAGACTCGAGTCAACAAAAGGAACATATGCAGCGGAA TGGACCAAATGGGAGAAACAACTACGAGATACTCTAGTTGCAAATTCTGAGTATCTCAGTTCTA TTCAGGTTCCATTTGAGTCTATGGTTCATCAAGTGCGAGAAGAGCTAAAAACAATAGCGAAGGG TGATTACAAGCCACCAAGTTCGGAGAAAAGAAAACACGGGTCTATTGTTTTCGCTGCCATCAAC TTGCCTGCTACTCAAGTTCACAGTCTTCTTGAAAAG
Genomic sequence	AACCGTAATGAATTTGAGAGTGAATTGATTGAGCGCTTTGGCTCCCTCATCAAGATGCCACTAT TGAAATCAGACAGGTATACAGTTGACATCACATGCGAGCTAACAAACTCGAACTTAGCACAGCT ACAAATTGCAACTTCATATTTAATTGGTTCATAAGCAATTTAATTGTCTTCTCTTTGTGCATAT ACAGGACTCCTTTACCTGATCCTGTTAAATCAGTTCTTGAGGAGGGCATTGATTTGTTCAATCT CCATAGTAGAAGACATGGGAGGTGGGTACCAACACTACCATTTTAAATGACTTGAAAAGTTGAA TTTATGTCAAACCGAAGTATTTTGAGCATCGTATGCCAAAACTTGTTCATCGTGTTATATATTA AACAACACCTTCTGTTCTGACGATAAAAAATGAAAGGCAATAGTAATAATTTAGCAAAAACTAA CAAGACATCGGATTTATTTATCCTGTGACTAGATGTACTTGGATCATGTAACTGGAGAAATCCT ACACATGAGTGTGCTCACAGGCGTTTTTATTTCTTGTTCTGGCTGTTCTCTACTTCATTCTTTT AGCTCTAGCTCCTGTTGGTTGCTTCTGACCTGTTTTCCTTCTGATTTTTCTTGTTGTAGACTCG AGTCAACAAAAGGAACATATGCAGCGGAATGGACCAAATGGGAGAAACAACTACGAGATACTCT AGTTGCAAATTCTGAGTATCTCAGTTCTATTCAGGTAAAAAATTCCTTTGTCATTGATGGCTCA TGAAAAGCAAGAAATCTGCGATTGAATTTTAAACTGCTTCAATGTTCCTTCAGTACATGGTAAA AGAGTATAAGAAGAAGGATGTACATATGATGTCTTTGTTTTCTGGTTTGCAACTTTCAGGTTCC ATTTGAGTCTATGGTTCATCAAGTGCGAGAAGAGCTAAAAACAATAGCGAAGGGTGATTACAAG CCACCAAGTTCGGAGAAAAGAAAACACGGGTCTATTGTTTTCGCTGCCATCAACTTGCCTGCTA CTCAAGTTCACAGTCTTCTTGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.303266666

Conservation Information
Conserved circRNAs	NA
PMCS	0.303266666

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2452861-2453853(+)
						
						Potential amino acid sequence
						
							MPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTKGTYAAEWTKWEKQLRDTLVANSEY
LSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSIVFAAINLPATQVHSLLEKNRNEFE
SELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTKGTYAAEWTKWEK
QLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSIVFAAINLPATQV
HSLLEKNRNEFESELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTK
GTYAAEWTKWEKQLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSI
VFAAINLPATQVHSLLEKNRNEFESELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNL
HSRRHGRLESTKGTYAAEWTKWEKQLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYK
PPSSEKRKHGSIVFAAINLPATQVHSLLEK(+)
						
						Sponge-miRNAs
						
							ath-miR5645e 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2452861-2453853(+)
Potential amino acid sequence	MPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTKGTYAAEWTKWEKQLRDTLVANSEY LSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSIVFAAINLPATQVHSLLEKNRNEFE SELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTKGTYAAEWTKWEK QLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSIVFAAINLPATQV HSLLEKNRNEFESELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTK GTYAAEWTKWEKQLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSI VFAAINLPATQVHSLLEKNRNEFESELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNL HSRRHGRLESTKGTYAAEWTKWEKQLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYK PPSSEKRKHGSIVFAAINLPATQVHSLLEK(+)
Sponge-miRNAs	ath-miR5645e
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT1G07910_circ_g.13

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