Plant Circular RNA Database

Detail information of AT5G12230_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G12230_circ_g.3
					
						ID in PlantcircBase
						ath_circ_037765
					
						Alias
						At_ciR1212
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 3953819-3955343  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT5G12230						
					
						Parent gene annotation
						
							Mediator of RNA polymerase II transcription subunit 19a
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G12230_circ_g.1 AT5G12230_circ_g.2 AT5G12230_circ_g.4 AT5G12230_circ_g.5 AT5G12230_circ_g.6 AT5G12230_circ_g.7 AT5G12230_circ_g.8 AT5G12230_circ_g.9 AT5G12230_circ_g.10 						
					
						Support reads
						4/4
					
						Tissues
						leaf/root, inflorescences, seed, 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  
						
							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
						AT5G12230.1:5

General Information
CircRNA Name	AT5G12230_circ_g.3
ID in PlantcircBase	ath_circ_037765
Alias	At_ciR1212
Organism	Arabidpsis thaliana
Position	chr5: 3953819-3955343 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full
Parent gene	AT5G12230
Parent gene annotation	Mediator of RNA polymerase II transcription subunit 19a
Parent gene strand	-
Alternative splicing	AT5G12230_circ_g.1 AT5G12230_circ_g.2 AT5G12230_circ_g.4 AT5G12230_circ_g.5 AT5G12230_circ_g.6 AT5G12230_circ_g.7 AT5G12230_circ_g.8 AT5G12230_circ_g.9 AT5G12230_circ_g.10
Support reads	4/4
Tissues	leaf/root, inflorescences, seed, 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	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	AT5G12230.1:5

			
						 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  
						
							CGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATT
TCTTTTGCATGATCACTGGCTCACTGCATATATATCctaataagctgtctacagtgagttgaaa
agtgcttctaaagtctccatgacacctactcgagtgcagaatacaaaattggaatgtctacaac
ttttttag

									
								

					

						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: 820
Transcript exons: 3953819-3953965,3954126-3954185,3954375-3954611,3954846-
3955135,3955258-3955343
CTAATAAGCTGTCTACAGTGAGTTGAAAAGTGCTTCTAAAGTCTCCATGACACCTACTCGAGTG
CAGAATACAAAATTGGAATGTCTACAACTTTTTTAGCCAGCAACCCTTATTGCACCCACCTCAT
CAAGCTTTGAGCTTTTATGCTTGTTTTTTTTGTGCCTCTGAACGTCATTAAGATCTTCATCTCC
ATCGTGTTTCCTTTTCTTATCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTT
TTGTCCTTCTTTCTGTCTCGGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGT
GCTTGTGCTTCTTATGCTCTCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCT
GTCCCTATCTTTCGACTCACTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCTGGG
GGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATATCAAAAG
GCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTAATTGCAT
TCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACATTATGAAGATAATGGGAATCTGATAAA
GAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGAGATATAA
GATCCGCAGCACCGCACAACTCTCTTGGACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTC
TATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGCATATATATC
Transcript length: 233
Transcript exons: 3953819-3955343
CTAATAAGCTGTCTACAGTGAGTTGAAAAGTGCTTCTAAAGTCTCCATGACACCTACTCGAGTG
CAGAATACAAAATTGGAATGTCTACAACTTTTTTAGCCAGCAACCCTTATTGCACCCACCTCAT
CAAGCTTTGAGCTTTTATGCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCT
GAATTTCTTTTGCATGATCACTGGCTCACTGCATATATATC
						
					

						Genomic sequence
						
							CTAATAAGCTGTCTACAGTGAGTTGAAAAGTGCTTCTAAAGTCTCCATGACACCTACTCGAGTG
CAGAATACAAAATTGGAATGTCTACAACTTTTTTAGCCAGCAACCCTTATTGCACCCACCTCAT
CAAGCTTTGAGCTTTTATGCTGCAACAGGTTCAATCAAGAGCTGAATCAATACAATTTATCAAA
GACATATTACTAGTTCTCTAGCACCTTTGTGCAAAAAAAACATTATGGTGGAAATTTCATGTTG
AGTGTTAATGAAGAACGAGAAAAATTTGAGGCCCCACTTCATTACCATTACCTTGTTTTTTTTG
TGCCTCTGAACGTCATTAAGATCTTCATCTCCATCGTGTTTCCTTTTCTGAAATATAAGTGAAA
AGGCTCCATAAAAACTCAATAAAATGTTCTAGAGCAGTCTCTAGATCTGCTAATTTCATGCCAA
GCAGGTCAAAAAAGCAGCCTAACTCAAGAGCAACAAATACAAAACTTTCCATTAAGCTATTCTT
CTTTGGAAAGACAGACACCTTCAACAAACAGACATGTTCTTTACCTTATCATGATGTTTCTTAG
AATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTGTCTCGGTCCTTGTCTTTATC
TTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTATGCTCTCTATCTTTGTCTTTA
TCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGACTCACTTTTTGACTTAGACG
GAATTGTAGGAGCTCCCTTCTCTGCCTGAAAGAAGAATAGTACCAAGGTCAATCATCTCCATAG
GACACCCAGATGTAATTCACATTACTAGGGAAAGATTCTCAATTAACCAAAGAACTTGATGTTA
CAGGAAATAGGACATTCATTACTGAGCCAGTTTTTAAGTTCAATGTAATGGCAAATACTGTTAC
TCTTATGAAAAGAAGGACATTTAAAACTCAAAACACCAAGAGAGAGTGAGAAAGATCAGATTCT
TACTGGGGGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATA
TCAAAAGGCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTA
ATTGCATTCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACATTATGAAGATAATGGGAATC
TGATAAAGAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGA
GATATAAGATCCGCAGCACCGCACAACTCTCTTGGACCTGCACTTGAAACAAACAACACATTGA
CCTCAAGGTGAGCCAAAGGGGAAAACAAAGGACAACGAGCTACAAAAAAAATAACTTCACGAAC
TGAAGAAGCTCCAAATTCGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCT
CTATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGCATATATATC
						
					

			
		

Sequences
Splice junction sequence	CGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATT TCTTTTGCATGATCACTGGCTCACTGCATATATATCctaataagctgtctacagtgagttgaaa agtgcttctaaagtctccatgacacctactcgagtgcagaatacaaaattggaatgtctacaac ttttttag
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: 820 Transcript exons: 3953819-3953965,3954126-3954185,3954375-3954611,3954846- 3955135,3955258-3955343 CTAATAAGCTGTCTACAGTGAGTTGAAAAGTGCTTCTAAAGTCTCCATGACACCTACTCGAGTG CAGAATACAAAATTGGAATGTCTACAACTTTTTTAGCCAGCAACCCTTATTGCACCCACCTCAT CAAGCTTTGAGCTTTTATGCTTGTTTTTTTTGTGCCTCTGAACGTCATTAAGATCTTCATCTCC ATCGTGTTTCCTTTTCTTATCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTT TTGTCCTTCTTTCTGTCTCGGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGT GCTTGTGCTTCTTATGCTCTCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCT GTCCCTATCTTTCGACTCACTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCTGGG GGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATATCAAAAG GCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTAATTGCAT TCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACATTATGAAGATAATGGGAATCTGATAAA GAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGAGATATAA GATCCGCAGCACCGCACAACTCTCTTGGACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTC TATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGCATATATATC Transcript length: 233 Transcript exons: 3953819-3955343 CTAATAAGCTGTCTACAGTGAGTTGAAAAGTGCTTCTAAAGTCTCCATGACACCTACTCGAGTG CAGAATACAAAATTGGAATGTCTACAACTTTTTTAGCCAGCAACCCTTATTGCACCCACCTCAT CAAGCTTTGAGCTTTTATGCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCT GAATTTCTTTTGCATGATCACTGGCTCACTGCATATATATC
Genomic sequence	CTAATAAGCTGTCTACAGTGAGTTGAAAAGTGCTTCTAAAGTCTCCATGACACCTACTCGAGTG CAGAATACAAAATTGGAATGTCTACAACTTTTTTAGCCAGCAACCCTTATTGCACCCACCTCAT CAAGCTTTGAGCTTTTATGCTGCAACAGGTTCAATCAAGAGCTGAATCAATACAATTTATCAAA GACATATTACTAGTTCTCTAGCACCTTTGTGCAAAAAAAACATTATGGTGGAAATTTCATGTTG AGTGTTAATGAAGAACGAGAAAAATTTGAGGCCCCACTTCATTACCATTACCTTGTTTTTTTTG TGCCTCTGAACGTCATTAAGATCTTCATCTCCATCGTGTTTCCTTTTCTGAAATATAAGTGAAA AGGCTCCATAAAAACTCAATAAAATGTTCTAGAGCAGTCTCTAGATCTGCTAATTTCATGCCAA GCAGGTCAAAAAAGCAGCCTAACTCAAGAGCAACAAATACAAAACTTTCCATTAAGCTATTCTT CTTTGGAAAGACAGACACCTTCAACAAACAGACATGTTCTTTACCTTATCATGATGTTTCTTAG AATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTGTCTCGGTCCTTGTCTTTATC TTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTATGCTCTCTATCTTTGTCTTTA TCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGACTCACTTTTTGACTTAGACG GAATTGTAGGAGCTCCCTTCTCTGCCTGAAAGAAGAATAGTACCAAGGTCAATCATCTCCATAG GACACCCAGATGTAATTCACATTACTAGGGAAAGATTCTCAATTAACCAAAGAACTTGATGTTA CAGGAAATAGGACATTCATTACTGAGCCAGTTTTTAAGTTCAATGTAATGGCAAATACTGTTAC TCTTATGAAAAGAAGGACATTTAAAACTCAAAACACCAAGAGAGAGTGAGAAAGATCAGATTCT TACTGGGGGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATA TCAAAAGGCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTA ATTGCATTCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACATTATGAAGATAATGGGAATC TGATAAAGAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGA GATATAAGATCCGCAGCACCGCACAACTCTCTTGGACCTGCACTTGAAACAAACAACACATTGA CCTCAAGGTGAGCCAAAGGGGAAAACAAAGGACAACGAGCTACAAAAAAAATAACTTCACGAAC TGAAGAAGCTCCAAATTCGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCT CTATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGCATATATATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.264569892

Conservation Information
Conserved circRNAs	NA
PMCS	0.264569892

			
						 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

circRNA

Detail information of AT5G12230_circ_g.3

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