Plant Circular RNA Database

Detail information of AT2G29050_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT2G29050_circ_g.6
					
						ID in PlantcircBase
						ath_circ_015472
					
						Alias
						At_ciR3325, Ath_circ_FC0765, Ath_circ_FC1387
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 12478852-12479830  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder, find_circ
					
						Parent gene
						
							AT2G29050						
					
						Parent gene annotation
						
							RHOMBOID-like protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G29050_circ_g.2 AT2G29050_circ_g.3 AT2G29050_circ_g.4 AT2G29050_circ_g.5 						
					
						Support reads
						2/1
					
						Tissues
						leaf/aerial
					
						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
						AT2G29050.1:4
AT2G29050.2:2

General Information
CircRNA Name	AT2G29050_circ_g.6
ID in PlantcircBase	ath_circ_015472
Alias	At_ciR3325, Ath_circ_FC0765, Ath_circ_FC1387
Organism	Arabidpsis thaliana
Position	chr2: 12478852-12479830 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder, find_circ
Parent gene	AT2G29050
Parent gene annotation	RHOMBOID-like protein 1
Parent gene strand	+
Alternative splicing	AT2G29050_circ_g.2 AT2G29050_circ_g.3 AT2G29050_circ_g.4 AT2G29050_circ_g.5
Support reads	2/1
Tissues	leaf/aerial
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	AT2G29050.1:4 AT2G29050.2:2

			
						 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  
						
							TCGAGGAACGGATCTAAACAAGCATTGTTCATGGTGCCATTATCTCAGCTGTATTCCTACGTCG
CTTTGGAGCTGTAAATCTCAAAATGTCTACTGTGAGattggagaagatgggggctttagatgta
tcaatggtggttcataagcacgaggtgtggcgcttgttcacttgtatatggctacatgctgggg
tttttcat

									
								

					

						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: 180
Transcript exons: 12478852-12478942,12479742-12479830
ATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTG
TTCACTTGTATATGGCTACATGCTGGGATCTAAACAAGCATTGTTCATGGTGCCATTATCTCAG
CTGTATTCCTACGTCGCTTTGGAGCTGTAAATCTCAAAATGTCTACTGTGAG
Transcript length: 715
Transcript exons: 12478852-12479015,12479109-12479272,12479357-12479616,12
479704-12479830
ATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTG
TTCACTTGTATATGGCTACATGCTGGGGTTTTTCATGTTCTTGCCAACATGTTGAGCCTTATCT
TCATTGGCATTCGACTTGAGCAAGAATTTGGATTTGTACGCATTGGATTGCTTTATATGATATC
TGGATTTGGTGGAAGTTTGTTATCTTCTCTATTTAACCGGGCTGGTATATCCGTTGGTGCCTCT
GGAGCATTATTCGGCTTGCTTGGTGCTATGCTTTCAGAGCTTCTCACTAATTGGACTATTTACG
CTAATAAGTTTGCAGCTCTTTTGACACTCATCTTCATCATAGCCATTAATTTAGCAGTAGGTAT
TCTTCCACATGTAGACAACTTTGCCCATCTTGGAGGATTCACATCAGGGTTTCTTCTAGGCTTT
GTTTTCTTGATACGTCCTCAGTATGGATACTTCAACCAGCGGAACAATCCTCGGGGTTATGCTG
CACCGTCTGCTAAATCCAAACACAAGCCATACCAATACGTTCTTTGGATCACCTCTTTAGTGCT
TTTAATAGCAGGATATACCGCTGGACTCGTAGTGCTTCTTCGAGGAACGGATCTAAACAAGCAT
TGTTCATGGTGCCATTATCTCAGCTGTATTCCTACGTCGCTTTGGAGCTGTAAATCTCAAAATG
TCTACTGTGAG
						
					

						Genomic sequence
						
							ATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTG
TTCACTTGTATATGGCTACATGCTGGGGTTTTTCATGTTCTTGCCAACATGTTGAGCCTTATCT
TCATTGGCATTCGACTTGAGCAAGAATTTGGATTTGGTATGCATCATGAGTTGGTTTATGTGCC
AAAATGTGTATGGCTGATGCTGAAAGACTTGCTTTTTATTTACTAATTCTCATTTTCTTTGACA
GTACGCATTGGATTGCTTTATATGATATCTGGATTTGGTGGAAGTTTGTTATCTTCTCTATTTA
ACCGGGCTGGTATATCCGTTGGTGCCTCTGGAGCATTATTCGGCTTGCTTGGTGCTATGCTTTC
AGAGCTTCTCACTAATTGGACTATTTACGCTAATAAGGTAGCCAAATCTTCCCTTGTTAAACAA
GCCGCACTTTCGATGAATGATGTGTCAATAATGTCATTGGTTTTTCTACATTTGCAGTTTGCAG
CTCTTTTGACACTCATCTTCATCATAGCCATTAATTTAGCAGTAGGTATTCTTCCACATGTAGA
CAACTTTGCCCATCTTGGAGGATTCACATCAGGGTTTCTTCTAGGCTTTGTTTTCTTGATACGT
CCTCAGTATGGATACTTCAACCAGCGGAACAATCCTCGGGGTTATGCTGCACCGTCTGCTAAAT
CCAAACACAAGCCATACCAATACGTTCTTTGGATCACCTCTTTAGTGCTTTTAATAGCAGGGTA
TACTTCTTTTTCTTTCATCATGATTACAAAATGAAACAGATTCAGTCAATTCTTTAATGCAAAT
TTTTGAAAATTTGGTGTTAGATATACCGCTGGACTCGTAGTGCTTCTTCGAGGAACGGATCTAA
ACAAGCATTGTTCATGGTGCCATTATCTCAGCTGTATTCCTACGTCGCTTTGGAGCTGTAAATC
TCAAAATGTCTACTGTGAG
						
					

			
		

Sequences
Splice junction sequence	TCGAGGAACGGATCTAAACAAGCATTGTTCATGGTGCCATTATCTCAGCTGTATTCCTACGTCG CTTTGGAGCTGTAAATCTCAAAATGTCTACTGTGAGattggagaagatgggggctttagatgta tcaatggtggttcataagcacgaggtgtggcgcttgttcacttgtatatggctacatgctgggg tttttcat
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: 180 Transcript exons: 12478852-12478942,12479742-12479830 ATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTG TTCACTTGTATATGGCTACATGCTGGGATCTAAACAAGCATTGTTCATGGTGCCATTATCTCAG CTGTATTCCTACGTCGCTTTGGAGCTGTAAATCTCAAAATGTCTACTGTGAG Transcript length: 715 Transcript exons: 12478852-12479015,12479109-12479272,12479357-12479616,12 479704-12479830 ATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTG TTCACTTGTATATGGCTACATGCTGGGGTTTTTCATGTTCTTGCCAACATGTTGAGCCTTATCT TCATTGGCATTCGACTTGAGCAAGAATTTGGATTTGTACGCATTGGATTGCTTTATATGATATC TGGATTTGGTGGAAGTTTGTTATCTTCTCTATTTAACCGGGCTGGTATATCCGTTGGTGCCTCT GGAGCATTATTCGGCTTGCTTGGTGCTATGCTTTCAGAGCTTCTCACTAATTGGACTATTTACG CTAATAAGTTTGCAGCTCTTTTGACACTCATCTTCATCATAGCCATTAATTTAGCAGTAGGTAT TCTTCCACATGTAGACAACTTTGCCCATCTTGGAGGATTCACATCAGGGTTTCTTCTAGGCTTT GTTTTCTTGATACGTCCTCAGTATGGATACTTCAACCAGCGGAACAATCCTCGGGGTTATGCTG CACCGTCTGCTAAATCCAAACACAAGCCATACCAATACGTTCTTTGGATCACCTCTTTAGTGCT TTTAATAGCAGGATATACCGCTGGACTCGTAGTGCTTCTTCGAGGAACGGATCTAAACAAGCAT TGTTCATGGTGCCATTATCTCAGCTGTATTCCTACGTCGCTTTGGAGCTGTAAATCTCAAAATG TCTACTGTGAG
Genomic sequence	ATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTG TTCACTTGTATATGGCTACATGCTGGGGTTTTTCATGTTCTTGCCAACATGTTGAGCCTTATCT TCATTGGCATTCGACTTGAGCAAGAATTTGGATTTGGTATGCATCATGAGTTGGTTTATGTGCC AAAATGTGTATGGCTGATGCTGAAAGACTTGCTTTTTATTTACTAATTCTCATTTTCTTTGACA GTACGCATTGGATTGCTTTATATGATATCTGGATTTGGTGGAAGTTTGTTATCTTCTCTATTTA ACCGGGCTGGTATATCCGTTGGTGCCTCTGGAGCATTATTCGGCTTGCTTGGTGCTATGCTTTC AGAGCTTCTCACTAATTGGACTATTTACGCTAATAAGGTAGCCAAATCTTCCCTTGTTAAACAA GCCGCACTTTCGATGAATGATGTGTCAATAATGTCATTGGTTTTTCTACATTTGCAGTTTGCAG CTCTTTTGACACTCATCTTCATCATAGCCATTAATTTAGCAGTAGGTATTCTTCCACATGTAGA CAACTTTGCCCATCTTGGAGGATTCACATCAGGGTTTCTTCTAGGCTTTGTTTTCTTGATACGT CCTCAGTATGGATACTTCAACCAGCGGAACAATCCTCGGGGTTATGCTGCACCGTCTGCTAAAT CCAAACACAAGCCATACCAATACGTTCTTTGGATCACCTCTTTAGTGCTTTTAATAGCAGGGTA TACTTCTTTTTCTTTCATCATGATTACAAAATGAAACAGATTCAGTCAATTCTTTAATGCAAAT TTTTGAAAATTTGGTGTTAGATATACCGCTGGACTCGTAGTGCTTCTTCGAGGAACGGATCTAA ACAAGCATTGTTCATGGTGCCATTATCTCAGCTGTATTCCTACGTCGCTTTGGAGCTGTAAATC TCAAAATGTCTACTGTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.25016295

Conservation Information
Conserved circRNAs	NA
PMCS	0.25016295

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

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

circRNA

Detail information of AT2G29050_circ_g.6

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