Plant Circular RNA Database

Detail information of AT3G48110_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G48110_circ_g.1
					
						ID in PlantcircBase
						ath_circ_026491
					
						Alias
						At_ciR4985, Ath_circ_FC2290
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 17763948-17765278  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, MapSplice, find_circ
					
						Parent gene
						
							AT3G48110						
					
						Parent gene annotation
						
							Glycine--tRNA ligase, chloroplastic/mitochondrial 2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G48110_circ_g.2 						
					
						Support reads
						2/3
					
						Tissues
						leaf/seedlings
					
						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
						AT3G48110.1:7

General Information
CircRNA Name	AT3G48110_circ_g.1
ID in PlantcircBase	ath_circ_026491
Alias	At_ciR4985, Ath_circ_FC2290
Organism	Arabidpsis thaliana
Position	chr3: 17763948-17765278 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, MapSplice, find_circ
Parent gene	AT3G48110
Parent gene annotation	Glycine--tRNA ligase, chloroplastic/mitochondrial 2
Parent gene strand	+
Alternative splicing	AT3G48110_circ_g.2
Support reads	2/3
Tissues	leaf/seedlings
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	AT3G48110.1:7

			
						 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  
						
							GTTAGCGACACGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAACCAGTTCCTCCCGTT
TGTCACAGAGCTGCTCTGGAAAAAGTGGCTGAAAAGgtattgatgtgactgcacacgatatacg
gtttgtagaagacaactgggagagcccggtaatgtgtgaacccatgttttatgcgttttccatc
tcttttag

									
								

					

						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: 154
Transcript exons: 17763948-17764005,17765183-17765278
GTATTGATGTGACTGCACACGATATACGGTTTGTAGAAGACAACTGGGAGAGCCCGGTGCGACA
CGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAACCAGTTCCTCCCGTTTGTCACAGAG
CTGCTCTGGAAAAAGTGGCTGAAAAG
Transcript length: 626
Transcript exons: 17763948-17764003,17764121-17764198,17764354-17764428,17
764523-17764593,17764685-17764801,17764898-17764999,1776
5152-17765278
GTATTGATGTGACTGCACACGATATACGGTTTGTAGAAGACAACTGGGAGAGCCCGGTGCTTGG
TGCTTGGGGGTTGGGCTGGGAGATTTGGATGGATGGTATGGAAATCACACAATTTACTTACTTC
CAGCAGGCTGGAAGTCTTCCGTTGTCTCCAGTATCTGTTGAAATAACTTATGGGCTTGAGCGCA
TCATCATGTTACTTCAGGAAGTTGACCATTTCAAAAAGATCTTATATGCTGATGGAATCACCTA
TGGGGAGCTTTTCTTGGAAAATGAGAAGGAAATGAGCTCATATTATTTAGAGCATGCTAGTGTG
GATCGCCTTCAAAAGCATTTCGATTATTTTGATGAAGAAGCACGTTCCTTGCTTGCCTTAGGAC
TTCCAATCCCTGCGTATGACCAGCTTCTGAAGACATCTCACGCTTTTAACATTTTAGACGCTAG
AGGTTTCATTGGCGTAACTGAACGTGCTCGTTATTTCGGTCGAATGCGTAGCTTGGCTCGCCAA
TGTGCCCAACTGTGGTTAGCGACACGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAAC
CAGTTCCTCCCGTTTGTCACAGAGCTGCTCTGGAAAAAGTGGCTGAAAAG
						
					

						Genomic sequence
						
							GTATTGATGTGACTGCACACGATATACGGTTTGTAGAAGACAACTGGGAGAGCCCGGTAATGTG
TGAACCCATGTTTTATGCGTTTTCCATCTCTTTTAGTTTCTCATTATACTCTCAGCGTGCAAGT
GTCTGATCATGTGAATGACTGCACACGATATACGGTTTCTTACAGGTGCTTGGTGCTTGGGGGT
TGGGCTGGGAGATTTGGATGGATGGTATGGAAATCACACAATTTACTTACTTCCAGCAGGTAAT
TTTCATTTTATGTAAACATTTCTAGAAATTAACTATAGACTACGGTTTGCATTTTGGTTTCTTA
GGGTAGATTTTATCTTTTGTTCTGTAGTATATTTTCTGCGTCGGTTGTTAGAAAACAATATAAT
TGTGAAGTTTGCTTCTTTCTAGGCTGGAAGTCTTCCGTTGTCTCCAGTATCTGTTGAAATAACT
TATGGGCTTGAGCGCATCATCATGTTACTTCAGGTCAGTCTTATACTCCCTTATTGTTGATGTA
CACATTTTTCCGTTATAGGTCCGTTATGTTTGGGTTAAGTTAGCCTTTCGTTTTAACCTACAGG
AAGTTGACCATTTCAAAAAGATCTTATATGCTGATGGAATCACCTATGGGGAGCTTTTCTTGGA
AAATGAGTAAAAGCCTGATATACTTTTATGGATTTTTAATCAAACATTATCGAACTTATTCTGT
GTTTTGAGACTGATAGTTGGGTGGATATTACAGGAAGGAAATGAGCTCATATTATTTAGAGCAT
GCTAGTGTGGATCGCCTTCAAAAGCATTTCGATTATTTTGATGAAGAAGCACGTTCCTTGCTTG
CCTTAGGACTTCCAATCCCTGCGTATGTTTATCACAATGCTCACGATCGTCAATTTTCTTGTCC
ATATTTAACCACTGCCTCTTGAATTTAACAAATTGCTGCTTGGGGGCATGCTAGGTATGACCAG
CTTCTGAAGACATCTCACGCTTTTAACATTTTAGACGCTAGAGGTTTCATTGGCGTAACTGAAC
GTGCTCGTTATTTCGGTCGAATGCGTAGGTAAGATCTGTTCCAGTTTTTTTAGAGTGTATTATT
GAGCAATCCAACGAGCTTGATTAACCAGAGAGGAAATGCTTTTAAACAAGTCGTTACTTGTAAA
AATATTTATGATGTGCATTTTTTGCTTCTGTGCATCCTCTTTGAAAGAATAGCTTGGCTCGCCA
ATGTGCCCAACTGTGGTTAGCGACACGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAA
CCAGTTCCTCCCGTTTGTCACAGAGCTGCTCTGGAAAAAGTGGCTGAAAAG
						
					

			
		

Sequences
Splice junction sequence	GTTAGCGACACGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAACCAGTTCCTCCCGTT TGTCACAGAGCTGCTCTGGAAAAAGTGGCTGAAAAGgtattgatgtgactgcacacgatatacg gtttgtagaagacaactgggagagcccggtaatgtgtgaacccatgttttatgcgttttccatc tcttttag
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: 154 Transcript exons: 17763948-17764005,17765183-17765278 GTATTGATGTGACTGCACACGATATACGGTTTGTAGAAGACAACTGGGAGAGCCCGGTGCGACA CGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAACCAGTTCCTCCCGTTTGTCACAGAG CTGCTCTGGAAAAAGTGGCTGAAAAG Transcript length: 626 Transcript exons: 17763948-17764003,17764121-17764198,17764354-17764428,17 764523-17764593,17764685-17764801,17764898-17764999,1776 5152-17765278 GTATTGATGTGACTGCACACGATATACGGTTTGTAGAAGACAACTGGGAGAGCCCGGTGCTTGG TGCTTGGGGGTTGGGCTGGGAGATTTGGATGGATGGTATGGAAATCACACAATTTACTTACTTC CAGCAGGCTGGAAGTCTTCCGTTGTCTCCAGTATCTGTTGAAATAACTTATGGGCTTGAGCGCA TCATCATGTTACTTCAGGAAGTTGACCATTTCAAAAAGATCTTATATGCTGATGGAATCACCTA TGGGGAGCTTTTCTTGGAAAATGAGAAGGAAATGAGCTCATATTATTTAGAGCATGCTAGTGTG GATCGCCTTCAAAAGCATTTCGATTATTTTGATGAAGAAGCACGTTCCTTGCTTGCCTTAGGAC TTCCAATCCCTGCGTATGACCAGCTTCTGAAGACATCTCACGCTTTTAACATTTTAGACGCTAG AGGTTTCATTGGCGTAACTGAACGTGCTCGTTATTTCGGTCGAATGCGTAGCTTGGCTCGCCAA TGTGCCCAACTGTGGTTAGCGACACGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAAC CAGTTCCTCCCGTTTGTCACAGAGCTGCTCTGGAAAAAGTGGCTGAAAAG
Genomic sequence	GTATTGATGTGACTGCACACGATATACGGTTTGTAGAAGACAACTGGGAGAGCCCGGTAATGTG TGAACCCATGTTTTATGCGTTTTCCATCTCTTTTAGTTTCTCATTATACTCTCAGCGTGCAAGT GTCTGATCATGTGAATGACTGCACACGATATACGGTTTCTTACAGGTGCTTGGTGCTTGGGGGT TGGGCTGGGAGATTTGGATGGATGGTATGGAAATCACACAATTTACTTACTTCCAGCAGGTAAT TTTCATTTTATGTAAACATTTCTAGAAATTAACTATAGACTACGGTTTGCATTTTGGTTTCTTA GGGTAGATTTTATCTTTTGTTCTGTAGTATATTTTCTGCGTCGGTTGTTAGAAAACAATATAAT TGTGAAGTTTGCTTCTTTCTAGGCTGGAAGTCTTCCGTTGTCTCCAGTATCTGTTGAAATAACT TATGGGCTTGAGCGCATCATCATGTTACTTCAGGTCAGTCTTATACTCCCTTATTGTTGATGTA CACATTTTTCCGTTATAGGTCCGTTATGTTTGGGTTAAGTTAGCCTTTCGTTTTAACCTACAGG AAGTTGACCATTTCAAAAAGATCTTATATGCTGATGGAATCACCTATGGGGAGCTTTTCTTGGA AAATGAGTAAAAGCCTGATATACTTTTATGGATTTTTAATCAAACATTATCGAACTTATTCTGT GTTTTGAGACTGATAGTTGGGTGGATATTACAGGAAGGAAATGAGCTCATATTATTTAGAGCAT GCTAGTGTGGATCGCCTTCAAAAGCATTTCGATTATTTTGATGAAGAAGCACGTTCCTTGCTTG CCTTAGGACTTCCAATCCCTGCGTATGTTTATCACAATGCTCACGATCGTCAATTTTCTTGTCC ATATTTAACCACTGCCTCTTGAATTTAACAAATTGCTGCTTGGGGGCATGCTAGGTATGACCAG CTTCTGAAGACATCTCACGCTTTTAACATTTTAGACGCTAGAGGTTTCATTGGCGTAACTGAAC GTGCTCGTTATTTCGGTCGAATGCGTAGGTAAGATCTGTTCCAGTTTTTTTAGAGTGTATTATT GAGCAATCCAACGAGCTTGATTAACCAGAGAGGAAATGCTTTTAAACAAGTCGTTACTTGTAAA AATATTTATGATGTGCATTTTTTGCTTCTGTGCATCCTCTTTGAAAGAATAGCTTGGCTCGCCA ATGTGCCCAACTGTGGTTAGCGACACGTGAGTCTCTTGGACATCCTCTTGGTGTTGCCTCCGAA CCAGTTCCTCCCGTTTGTCACAGAGCTGCTCTGGAAAAAGTGGCTGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.216022137

Conservation Information
Conserved circRNAs	NA
PMCS	0.216022137

			
						 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;Pan et al., 2017;Chen et al., 2017a;Liu et al., 2017

circRNA

Detail information of AT3G48110_circ_g.1

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