Plant Circular RNA Database

Detail information of AT1G08520_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G08520_circ_g.3
					
						ID in PlantcircBase
						ath_circ_001403
					
						Alias
						At_ciR5767
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 2697015-2698722  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, MapSplice, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT1G08520						
					
						Parent gene annotation
						
							Mg-protoporphyrin IX chelatase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G08520_circ_g.1 AT1G08520_circ_g.2 AT1G08520_circ_g.4 AT1G08520_circ_g.5 AT1G08520_circ_g.6 AT1G08520_circ_g.7 AT1G08520_circ_g.8 AT1G08520_circ_g.9 AT1G08520_circ_g.10 AT1G08520_circ_g.11 AT1G08520_circ_g.12 AT1G08520_circ_g.13 AT1G08520_circ_g.14 						
					
						Support reads
						2/34
					
						Tissues
						leaf/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
						AT1G08520.1:6

General Information
CircRNA Name	AT1G08520_circ_g.3
ID in PlantcircBase	ath_circ_001403
Alias	At_ciR5767
Organism	Arabidpsis thaliana
Position	chr1: 2697015-2698722 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, MapSplice, PcircRNA_finder, find_circ
Parent gene	AT1G08520
Parent gene annotation	Mg-protoporphyrin IX chelatase
Parent gene strand	+
Alternative splicing	AT1G08520_circ_g.1 AT1G08520_circ_g.2 AT1G08520_circ_g.4 AT1G08520_circ_g.5 AT1G08520_circ_g.6 AT1G08520_circ_g.7 AT1G08520_circ_g.8 AT1G08520_circ_g.9 AT1G08520_circ_g.10 AT1G08520_circ_g.11 AT1G08520_circ_g.12 AT1G08520_circ_g.13 AT1G08520_circ_g.14
Support reads	2/34
Tissues	leaf/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	AT1G08520.1:6

			
						 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  
						
							ACAGGGACACCGCGCCGAATTGTATGCAGCTCGTGTGGCGAAGTGTTTAGCTGCAATTGAAGGA
CGAGAAAAAGTCACAATCGATGACCTCAGAAAGGCCgaaggcataaaaactgctcttttacttg
gcgcggttgatcgtgaaatcggagggattgccatttcaggtcgtagaggcactgcaaaaacagt
catggcgc

									
								

					

						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: 204
Transcript exons: 2697015-2697135,2698640-2698722
GAAGGCATAAAAACTGCTCTTTTACTTGGCGCGGTTGATCGTGAAATCGGAGGGATTGCCATTT
CAGGTCGTAGAGGCACTGCAAAAACAGTCATGGCGCGAGGGCTTCATGAAATCCTCCAATTGTA
TGCAGCTCGTGTGGCGAAGTGTTTAGCTGCAATTGAAGGACGAGAAAAAGTCACAATCGATGAC
CTCAGAAAGGCC
Transcript length: 894
Transcript exons: 2697015-2697193,2697283-2697367,2697453-2697769,2697872-
2697995,2698111-2698203,2698627-2698722
GAAGGCATAAAAACTGCTCTTTTACTTGGCGCGGTTGATCGTGAAATCGGAGGGATTGCCATTT
CAGGTCGTAGAGGCACTGCAAAAACAGTCATGGCGCGAGGGCTTCATGAAATCCTCCCTCCTAT
TGAAGTTGTTGTAGGCTCAATATCAAATGCTGACCCAGCTTGTCCAGATGAGTGGGAAGATGAC
TTAGATGAGCGCATAGAGTACAATGCTGACAATACCATTAAGACTGAGATTGTCAAATCTCCTT
TCATTCAGATTCCACTAGGAGTTACAGAAGACAGACTCATTGGGTCTGTTGATGTTGAGGAGTC
TGTGAAAAGGGGGACAACTGTTTTCCAACCTGGTCTTTTGGCTGAAGCCCATAGAGGAGTGTTG
TATGTTGATGAAATAAATCTCTTAGATGAGGGAATTAGTAATTTGCTTCTCAATGTATTGACGG
ATGGTGTTAATATAGTTGAAAGAGAAGGAATCAGCTTTAGGCACCCGTGCAAACCACTTTTAAT
TGCAACCTATAACCCTGAAGAAGGTGCTGTTCGAGAGCACTTGCTAGACCGTGTTGCCATTAAT
TTAAGTGCAGACCTACCTATGAGTTTTGAAGATCGTGTCGCAGCAGTTGGAATTGCCACACAGT
TTCAGGAACGCTGTAATGAGGTTTTTAGAATGGTAAATGAAGAGACAGAAACAGCAAAGACGCA
GATTATATTGGCTAGAGAATATTTGAAAGATGTCAAGATAAGTAGAGAGCAATTGAAGTATCTG
GTTTTGGAAGCTGTCCGAGGTGGTGTCCAGGGACACCGCGCCGAATTGTATGCAGCTCGTGTGG
CGAAGTGTTTAGCTGCAATTGAAGGACGAGAAAAAGTCACAATCGATGACCTCAGAAAGGCC
						
					

						Genomic sequence
						
							GAAGGCATAAAAACTGCTCTTTTACTTGGCGCGGTTGATCGTGAAATCGGAGGGATTGCCATTT
CAGGTCGTAGAGGCACTGCAAAAACAGTCATGGCGCGAGGGCTTCATGAAATCCTCCCTCCTAT
TGAAGTTGTTGTAGGCTCAATATCAAATGCTGACCCAGCTTGTCCAGATGAGTAAGATTCTTAC
AATCTGAGAAAGAAATTGCTTTTCTTCTTCTTTTAATTCTTACACTGTTGGCTTGTACCTTTTG
TGATATATGTAGGTGGGAAGATGACTTAGATGAGCGCATAGAGTACAATGCTGACAATACCATT
AAGACTGAGATTGTCAAATCTCCTTTCATTCAGGTACATTTAGTTTTAGGAGGCATTACAATTT
TTCTGAAATTGTTTTTCTTTTTACTTAGGTTTTCCTGTCGTTTATGTCACACAGATTCCACTAG
GAGTTACAGAAGACAGACTCATTGGGTCTGTTGATGTTGAGGAGTCTGTGAAAAGGGGGACAAC
TGTTTTCCAACCTGGTCTTTTGGCTGAAGCCCATAGAGGAGTGTTGTATGTTGATGAAATAAAT
CTCTTAGATGAGGGAATTAGTAATTTGCTTCTCAATGTATTGACGGATGGTGTTAATATAGTTG
AAAGAGAAGGAATCAGCTTTAGGCACCCGTGCAAACCACTTTTAATTGCAACCTATAACCCTGA
AGAAGGTGCTGTTCGAGAGCACTTGCTAGACCGTGTTGCCATTAATTTAAGGTACTACTGGAGT
TTATAAATCAAGTGTGATAAATATTGCCTGTTTCTTTTGGGTAATTCCCATTTCTTTCTCTTTT
TACATCACGATGTTAACCTTTGCAGTGCAGACCTACCTATGAGTTTTGAAGATCGTGTCGCAGC
AGTTGGAATTGCCACACAGTTTCAGGAACGCTGTAATGAGGTTTTTAGAATGGTAAATGAAGAG
ACAGAAACAGCAAAGACGCAGGTATCTTCAAATGAATTAAGAAAAAAAGGGCCTCATTAGTAAA
AATTTGATGGGATGCTATGCTTCTCATCCCACTTTTCTCGATCATAATCCAGTGCATTTTCTCT
GACTTTAGATTATATTGGCTAGAGAATATTTGAAAGATGTCAAGATAAGTAGAGAGCAATTGAA
GTATCTGGTTTTGGAAGCTGTCCGAGGTGGTGTCCAGGTATTGAGCAAAAATTCTGAAGTAATT
TTTTGTTAATGGAAGAAATACACTTAGTAACATATTCCTGGAAGAAAAAGGATAAACACGAAAA
GAAAGGACAAGATGCATGCAATGATGCAACATAATGTCACGATTATAGACTTCAACTAGTATAG
GGCTCAAGAAATGGCTCACCACAGGCAGAAAGATACATCTAGATAGAGTTGTTTTGATTTAGAA
ACAACGCTGGAAAAAGAAGGGCCTGGCATCAAATGCTTTTGTTGCGCTGTTGATTGTAATATTT
CACCAAGTTATGATCATATCACTATAGTTATATTTCTGCGTTTGGTTTACTTGGTAGTTACTTC
TCATGGCGTATCTTTTGTCGATGATTACCTGGAATCGTTTAATACTCCTTTCCCAAATAACAAA
TTTATGATACAGGGACACCGCGCCGAATTGTATGCAGCTCGTGTGGCGAAGTGTTTAGCTGCAA
TTGAAGGACGAGAAAAAGTCACAATCGATGACCTCAGAAAGGCC
						
					

			
		

Sequences
Splice junction sequence	ACAGGGACACCGCGCCGAATTGTATGCAGCTCGTGTGGCGAAGTGTTTAGCTGCAATTGAAGGA CGAGAAAAAGTCACAATCGATGACCTCAGAAAGGCCgaaggcataaaaactgctcttttacttg gcgcggttgatcgtgaaatcggagggattgccatttcaggtcgtagaggcactgcaaaaacagt catggcgc
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: 204 Transcript exons: 2697015-2697135,2698640-2698722 GAAGGCATAAAAACTGCTCTTTTACTTGGCGCGGTTGATCGTGAAATCGGAGGGATTGCCATTT CAGGTCGTAGAGGCACTGCAAAAACAGTCATGGCGCGAGGGCTTCATGAAATCCTCCAATTGTA TGCAGCTCGTGTGGCGAAGTGTTTAGCTGCAATTGAAGGACGAGAAAAAGTCACAATCGATGAC CTCAGAAAGGCC Transcript length: 894 Transcript exons: 2697015-2697193,2697283-2697367,2697453-2697769,2697872- 2697995,2698111-2698203,2698627-2698722 GAAGGCATAAAAACTGCTCTTTTACTTGGCGCGGTTGATCGTGAAATCGGAGGGATTGCCATTT CAGGTCGTAGAGGCACTGCAAAAACAGTCATGGCGCGAGGGCTTCATGAAATCCTCCCTCCTAT TGAAGTTGTTGTAGGCTCAATATCAAATGCTGACCCAGCTTGTCCAGATGAGTGGGAAGATGAC TTAGATGAGCGCATAGAGTACAATGCTGACAATACCATTAAGACTGAGATTGTCAAATCTCCTT TCATTCAGATTCCACTAGGAGTTACAGAAGACAGACTCATTGGGTCTGTTGATGTTGAGGAGTC TGTGAAAAGGGGGACAACTGTTTTCCAACCTGGTCTTTTGGCTGAAGCCCATAGAGGAGTGTTG TATGTTGATGAAATAAATCTCTTAGATGAGGGAATTAGTAATTTGCTTCTCAATGTATTGACGG ATGGTGTTAATATAGTTGAAAGAGAAGGAATCAGCTTTAGGCACCCGTGCAAACCACTTTTAAT TGCAACCTATAACCCTGAAGAAGGTGCTGTTCGAGAGCACTTGCTAGACCGTGTTGCCATTAAT TTAAGTGCAGACCTACCTATGAGTTTTGAAGATCGTGTCGCAGCAGTTGGAATTGCCACACAGT TTCAGGAACGCTGTAATGAGGTTTTTAGAATGGTAAATGAAGAGACAGAAACAGCAAAGACGCA GATTATATTGGCTAGAGAATATTTGAAAGATGTCAAGATAAGTAGAGAGCAATTGAAGTATCTG GTTTTGGAAGCTGTCCGAGGTGGTGTCCAGGGACACCGCGCCGAATTGTATGCAGCTCGTGTGG CGAAGTGTTTAGCTGCAATTGAAGGACGAGAAAAAGTCACAATCGATGACCTCAGAAAGGCC
Genomic sequence	GAAGGCATAAAAACTGCTCTTTTACTTGGCGCGGTTGATCGTGAAATCGGAGGGATTGCCATTT CAGGTCGTAGAGGCACTGCAAAAACAGTCATGGCGCGAGGGCTTCATGAAATCCTCCCTCCTAT TGAAGTTGTTGTAGGCTCAATATCAAATGCTGACCCAGCTTGTCCAGATGAGTAAGATTCTTAC AATCTGAGAAAGAAATTGCTTTTCTTCTTCTTTTAATTCTTACACTGTTGGCTTGTACCTTTTG TGATATATGTAGGTGGGAAGATGACTTAGATGAGCGCATAGAGTACAATGCTGACAATACCATT AAGACTGAGATTGTCAAATCTCCTTTCATTCAGGTACATTTAGTTTTAGGAGGCATTACAATTT TTCTGAAATTGTTTTTCTTTTTACTTAGGTTTTCCTGTCGTTTATGTCACACAGATTCCACTAG GAGTTACAGAAGACAGACTCATTGGGTCTGTTGATGTTGAGGAGTCTGTGAAAAGGGGGACAAC TGTTTTCCAACCTGGTCTTTTGGCTGAAGCCCATAGAGGAGTGTTGTATGTTGATGAAATAAAT CTCTTAGATGAGGGAATTAGTAATTTGCTTCTCAATGTATTGACGGATGGTGTTAATATAGTTG AAAGAGAAGGAATCAGCTTTAGGCACCCGTGCAAACCACTTTTAATTGCAACCTATAACCCTGA AGAAGGTGCTGTTCGAGAGCACTTGCTAGACCGTGTTGCCATTAATTTAAGGTACTACTGGAGT TTATAAATCAAGTGTGATAAATATTGCCTGTTTCTTTTGGGTAATTCCCATTTCTTTCTCTTTT TACATCACGATGTTAACCTTTGCAGTGCAGACCTACCTATGAGTTTTGAAGATCGTGTCGCAGC AGTTGGAATTGCCACACAGTTTCAGGAACGCTGTAATGAGGTTTTTAGAATGGTAAATGAAGAG ACAGAAACAGCAAAGACGCAGGTATCTTCAAATGAATTAAGAAAAAAAGGGCCTCATTAGTAAA AATTTGATGGGATGCTATGCTTCTCATCCCACTTTTCTCGATCATAATCCAGTGCATTTTCTCT GACTTTAGATTATATTGGCTAGAGAATATTTGAAAGATGTCAAGATAAGTAGAGAGCAATTGAA GTATCTGGTTTTGGAAGCTGTCCGAGGTGGTGTCCAGGTATTGAGCAAAAATTCTGAAGTAATT TTTTGTTAATGGAAGAAATACACTTAGTAACATATTCCTGGAAGAAAAAGGATAAACACGAAAA GAAAGGACAAGATGCATGCAATGATGCAACATAATGTCACGATTATAGACTTCAACTAGTATAG GGCTCAAGAAATGGCTCACCACAGGCAGAAAGATACATCTAGATAGAGTTGTTTTGATTTAGAA ACAACGCTGGAAAAAGAAGGGCCTGGCATCAAATGCTTTTGTTGCGCTGTTGATTGTAATATTT CACCAAGTTATGATCATATCACTATAGTTATATTTCTGCGTTTGGTTTACTTGGTAGTTACTTC TCATGGCGTATCTTTTGTCGATGATTACCTGGAATCGTTTAATACTCCTTTCCCAAATAACAAA TTTATGATACAGGGACACCGCGCCGAATTGTATGCAGCTCGTGTGGCGAAGTGTTTAGCTGCAA TTGAAGGACGAGAAAAAGTCACAATCGATGACCTCAGAAAGGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.416801757

Conservation Information
Conserved circRNAs	NA
PMCS	0.416801757

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2697108-2698719(+)
						
						Potential amino acid sequence
						
							MARGLHEILPPIEVVVGSISNADPACPDEWEDDLDERIEYNADNTIKTEIVKSPFIQIPLGVTE
DRLIGSVDVEESVKRGTTVFQPGLLAEAHRGVLYVDEINLLDEGISNLLLNVLTDGVNIVEREG
ISFRHPCKPLLIATYNPEEGAVREHLLDRVAINLSADLPMSFEDRVAAVGIATQFQERCNEVFR
MVNEETETAKTQIILAREYLKDVKISREQLKYLVLEAVRGGVQGHRAELYAARVAKCLAAIEGR
EKVTIDDLRKAEGIKTALLLGAVDREIGGIAISGRRGTAKTVMARGLHEILPPIEVVVGSISNA
DPACPDEWEDDLDERIEYNADNTIKTEIVKSPFIQIPLGVTEDRLIGSVDVEESVKRGTTVFQP
GLLAEAHRGVLYVDEINLLDEGISNLLLNVLTDGVNIVEREGISFRHPCKPLLIATYNPEEGAV
REHLLDRVAINLSADLPMSFEDRVAAVGIATQFQERCNEVFRMVNEETETAKTQIILAREYLKD
VKISREQLKYLVLEAVRGGVQGHRAELYAARVAKCLAAIEGREKVTIDDLRKAEGIKTALLLGA
VDREIGGIAISGRRGTAKTVMARGLHEILPPIEVVVGSISNADPACPDEWEDDLDERIEYNADN
TIKTEIVKSPFIQIPLGVTEDRLIGSVDVEESVKRGTTVFQPGLLAEAHRGVLYVDEINLLDEG
ISNLLLNVLTDGVNIVEREGISFRHPCKPLLIATYNPEEGAVREHLLDRVAINLSADLPMSFED
RVAAVGIATQFQERCNEVFRMVNEETETAKTQIILAREYLKDVKISREQLKYLVLEAVRGGVQG
HRAELYAARVAKCLAAIEGREKVTIDDLRKAEGIKTALLLGAVDREIGGIAISGRRGTAKTVMA
RGLHEILPPIEVVVGSISNADPACPDEWEDDLDERIEYNADNTIKTEIVKSPFIQIPLGVTEDR
LIGSVDVEESVKRGTTVFQPGLLAEAHRGVLYVDEINLLDEGISNLLLNVLTDGVNIVEREGIS
FRHPCKPLLIATYNPEEGAVREHLLDRVAINLSADLPMSFEDRVAAVGIATQFQERCNEVFRMV
NEETETAKTQIILAREYLKDVKISREQLKYLVLEAVRGGVQGHRAELYAARVAKCLAAIEGREK
VTIDDLRKA(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2697108-2698719(+)
Potential amino acid sequence	MARGLHEILPPIEVVVGSISNADPACPDEWEDDLDERIEYNADNTIKTEIVKSPFIQIPLGVTE DRLIGSVDVEESVKRGTTVFQPGLLAEAHRGVLYVDEINLLDEGISNLLLNVLTDGVNIVEREG ISFRHPCKPLLIATYNPEEGAVREHLLDRVAINLSADLPMSFEDRVAAVGIATQFQERCNEVFR MVNEETETAKTQIILAREYLKDVKISREQLKYLVLEAVRGGVQGHRAELYAARVAKCLAAIEGR EKVTIDDLRKAEGIKTALLLGAVDREIGGIAISGRRGTAKTVMARGLHEILPPIEVVVGSISNA DPACPDEWEDDLDERIEYNADNTIKTEIVKSPFIQIPLGVTEDRLIGSVDVEESVKRGTTVFQP GLLAEAHRGVLYVDEINLLDEGISNLLLNVLTDGVNIVEREGISFRHPCKPLLIATYNPEEGAV REHLLDRVAINLSADLPMSFEDRVAAVGIATQFQERCNEVFRMVNEETETAKTQIILAREYLKD VKISREQLKYLVLEAVRGGVQGHRAELYAARVAKCLAAIEGREKVTIDDLRKAEGIKTALLLGA VDREIGGIAISGRRGTAKTVMARGLHEILPPIEVVVGSISNADPACPDEWEDDLDERIEYNADN TIKTEIVKSPFIQIPLGVTEDRLIGSVDVEESVKRGTTVFQPGLLAEAHRGVLYVDEINLLDEG ISNLLLNVLTDGVNIVEREGISFRHPCKPLLIATYNPEEGAVREHLLDRVAINLSADLPMSFED RVAAVGIATQFQERCNEVFRMVNEETETAKTQIILAREYLKDVKISREQLKYLVLEAVRGGVQG HRAELYAARVAKCLAAIEGREKVTIDDLRKAEGIKTALLLGAVDREIGGIAISGRRGTAKTVMA RGLHEILPPIEVVVGSISNADPACPDEWEDDLDERIEYNADNTIKTEIVKSPFIQIPLGVTEDR LIGSVDVEESVKRGTTVFQPGLLAEAHRGVLYVDEINLLDEGISNLLLNVLTDGVNIVEREGIS FRHPCKPLLIATYNPEEGAVREHLLDRVAINLSADLPMSFEDRVAAVGIATQFQERCNEVFRMV NEETETAKTQIILAREYLKDVKISREQLKYLVLEAVRGGVQGHRAELYAARVAKCLAAIEGREK VTIDDLRKA(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Liu et al., 2017

circRNA

Detail information of AT1G08520_circ_g.3

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