Plant Circular RNA Database

Detail information of AT5G12230_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT5G12230_circ_g.7
					
						ID in PlantcircBase
						ath_circ_037769
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 3954126-3955343  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						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.3 AT5G12230_circ_g.4 AT5G12230_circ_g.5 AT5G12230_circ_g.6 AT5G12230_circ_g.8 AT5G12230_circ_g.9 AT5G12230_circ_g.10 						
					
						Support reads
						14
					
						Tissues
						root, inflorescences, 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
						AT5G12230.1:4

General Information
CircRNA Name	AT5G12230_circ_g.7
ID in PlantcircBase	ath_circ_037769
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 3954126-3955343 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
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.3 AT5G12230_circ_g.4 AT5G12230_circ_g.5 AT5G12230_circ_g.6 AT5G12230_circ_g.8 AT5G12230_circ_g.9 AT5G12230_circ_g.10
Support reads	14
Tissues	root, inflorescences, 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	AT5G12230.1:4

			
						 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  
						
							CGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATT
TCTTTTGCATGATCACTGGCTCACTGCATATATATCcttgttttttttgtgcctctgaacgtca
ttaagatcttcatctccatcgtgtttccttttctgaaatataagtgaaaaggctccataaaaac
tcaataaa

									
								

					

						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: 673
Transcript exons: 3954126-3954185,3954375-3954611,3954846-3955135,3955258-
3955343
CTTGTTTTTTTTGTGCCTCTGAACGTCATTAAGATCTTCATCTCCATCGTGTTTCCTTTTCTTA
TCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTGTCTC
GGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTATGCTC
TCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGACTCA
CTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCTGGGGGTAATTCAACAGGAGTCA
TATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATATCAAAAGGCTGGATGCGAATATTAGT
CTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCTGATC
TCTGTGTCCCCAACCACATTATGAAGATAATGGGAATCTGATAAAGAAACAGGAAGAGATTTCT
TGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGAGATATAAGATCCGCAGCACCGCACAA
CTCTCTTGGACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATTTCT
TTTGCATGATCACTGGCTCACTGCATATATATC
						
					

						Genomic sequence
						
							CTTGTTTTTTTTGTGCCTCTGAACGTCATTAAGATCTTCATCTCCATCGTGTTTCCTTTTCTGA
AATATAAGTGAAAAGGCTCCATAAAAACTCAATAAAATGTTCTAGAGCAGTCTCTAGATCTGCT
AATTTCATGCCAAGCAGGTCAAAAAAGCAGCCTAACTCAAGAGCAACAAATACAAAACTTTCCA
TTAAGCTATTCTTCTTTGGAAAGACAGACACCTTCAACAAACAGACATGTTCTTTACCTTATCA
TGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTGTCTCGGT
CCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTATGCTCTCT
ATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGACTCACTT
TTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCCTGAAAGAAGAATAGTACCAAGGTCA
ATCATCTCCATAGGACACCCAGATGTAATTCACATTACTAGGGAAAGATTCTCAATTAACCAAA
GAACTTGATGTTACAGGAAATAGGACATTCATTACTGAGCCAGTTTTTAAGTTCAATGTAATGG
CAAATACTGTTACTCTTATGAAAAGAAGGACATTTAAAACTCAAAACACCAAGAGAGAGTGAGA
AAGATCAGATTCTTACTGGGGGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAGACTCCTG
AAGCTCATCTATATCAAAAGGCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATATGCTCTCA
ATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACATTATGAA
GATAATGGGAATCTGATAAAGAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGTGTTGCAC
TAGTTTGAATTGAGATATAAGATCCGCAGCACCGCACAACTCTCTTGGACCTGCACTTGAAACA
AACAACACATTGACCTCAAGGTGAGCCAAAGGGGAAAACAAAGGACAACGAGCTACAAAAAAAA
TAACTTCACGAACTGAAGAAGCTCCAAATTCGAAACCAATGTACCTCCAAATTTTAAACGTTCA
GGCTCCATCTTCTCTATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGCATATATA
TC
						
					

			
		

Sequences
Splice junction sequence	CGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATT TCTTTTGCATGATCACTGGCTCACTGCATATATATCcttgttttttttgtgcctctgaacgtca ttaagatcttcatctccatcgtgtttccttttctgaaatataagtgaaaaggctccataaaaac tcaataaa
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: 673 Transcript exons: 3954126-3954185,3954375-3954611,3954846-3955135,3955258- 3955343 CTTGTTTTTTTTGTGCCTCTGAACGTCATTAAGATCTTCATCTCCATCGTGTTTCCTTTTCTTA TCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTGTCTC GGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTATGCTC TCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGACTCA CTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCTGGGGGTAATTCAACAGGAGTCA TATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATATCAAAAGGCTGGATGCGAATATTAGT CTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCTGATC TCTGTGTCCCCAACCACATTATGAAGATAATGGGAATCTGATAAAGAAACAGGAAGAGATTTCT TGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGAGATATAAGATCCGCAGCACCGCACAA CTCTCTTGGACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATTTCT TTTGCATGATCACTGGCTCACTGCATATATATC
Genomic sequence	CTTGTTTTTTTTGTGCCTCTGAACGTCATTAAGATCTTCATCTCCATCGTGTTTCCTTTTCTGA AATATAAGTGAAAAGGCTCCATAAAAACTCAATAAAATGTTCTAGAGCAGTCTCTAGATCTGCT AATTTCATGCCAAGCAGGTCAAAAAAGCAGCCTAACTCAAGAGCAACAAATACAAAACTTTCCA TTAAGCTATTCTTCTTTGGAAAGACAGACACCTTCAACAAACAGACATGTTCTTTACCTTATCA TGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTGTCTCGGT CCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTATGCTCTCT ATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGACTCACTT TTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCCTGAAAGAAGAATAGTACCAAGGTCA ATCATCTCCATAGGACACCCAGATGTAATTCACATTACTAGGGAAAGATTCTCAATTAACCAAA GAACTTGATGTTACAGGAAATAGGACATTCATTACTGAGCCAGTTTTTAAGTTCAATGTAATGG CAAATACTGTTACTCTTATGAAAAGAAGGACATTTAAAACTCAAAACACCAAGAGAGAGTGAGA AAGATCAGATTCTTACTGGGGGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAGACTCCTG AAGCTCATCTATATCAAAAGGCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATATGCTCTCA ATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACATTATGAA GATAATGGGAATCTGATAAAGAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGTGTTGCAC TAGTTTGAATTGAGATATAAGATCCGCAGCACCGCACAACTCTCTTGGACCTGCACTTGAAACA AACAACACATTGACCTCAAGGTGAGCCAAAGGGGAAAACAAAGGACAACGAGCTACAAAAAAAA TAACTTCACGAACTGAAGAAGCTCCAAATTCGAAACCAATGTACCTCCAAATTTTAAACGTTCA GGCTCCATCTTCTCTATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGCATATATA TC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211888524

Conservation Information
Conserved circRNAs	NA
PMCS	0.211888524

			
						 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
						responsive to methyl jasmonate

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	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G12230_circ_g.7

Address

Any questions?

Supported by