Plant Circular RNA Database

Detail information of AT3G56510_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G56510_circ_g.1
					
						ID in PlantcircBase
						ath_circ_027859
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20945193-20946247  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT3G56510						
					
						Parent gene annotation
						
							At3g56510
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G56510_circ_g.2 AT3G56510_circ_g.3 						
					
						Support reads
						15
					
						Tissues
						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
						AT3G56510.5:5
AT3G56510.3:5
AT3G56510.2:5
AT3G56510.1:5
AT3G56510.4:5

General Information
CircRNA Name	AT3G56510_circ_g.1
ID in PlantcircBase	ath_circ_027859
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 20945193-20946247 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT3G56510
Parent gene annotation	At3g56510
Parent gene strand	-
Alternative splicing	AT3G56510_circ_g.2 AT3G56510_circ_g.3
Support reads	15
Tissues	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	AT3G56510.5:5 AT3G56510.3:5 AT3G56510.2:5 AT3G56510.1:5 AT3G56510.4:5

			
						 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  
						
							TATCAGCCTTTTGACTCTTCATCGTTTCCTTGGACTCCTTCTCCTCGGATATTCCATCCGTAAG
CTCGTGAGATTCCTCACTCTGCATCTTCTTCAGCAGcttttccattcgtgcatctatctcggtc
atggcacgagacttctctattttagatagataaaagtctttctccctctttgcagcagaaagaa
ccatattt

									
								

					

						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: 618
Transcript exons: 20945193-20945323,20945413-20945502,20945595-20945662,20
945806-20945869,20945983-20946247
CTTTTCCATTCGTGCATCTATCTCGGTCATGGCACGAGACTTCTCTATTTTAGATAGATAAAAG
TCTTTCTCCCTCTTTGCAGCAGAAAGAACCATATTTAATTTCTGTTCCCGTATTGCACTTTTGT
ATGCGATTTCTTCAGTAAGATCATCCCATTTAAATTTGGTCAAGTATTTGATGTTCCAAATATC
ATAGTATACTGATGACTTCTTTTTCCCCCCGATTTGTTCTCCATTTAGCATATCTGCAACCCGT
TTAGCTACGCTCTTCTTAGCAAACTCCACCCACCCTTCAGAAAACCTTTGGCCACGAAATCCAC
CAGCCCGCTTACGGTGCACTTGTGCTTCAGAATCTTCAGGTGCAAGATAAATCCTTCCGAGTTC
TCCATATTGAGCGAGAATATGGCGAAGTCTAACGTGATCCATGTGTGGTGGGATACGACTTAAG
TAGCAAACACCTCTATTGTCAGCTTTCGAAGCTTCCTTAAGCAATTTCTCTTTCAACTTCTTTT
TCTTTCTATCAGCCTTTTGACTCTTCATCGTTTCCTTGGACTCCTTCTCCTCGGATATTCCATC
CGTAAGCTCGTGAGATTCCTCACTCTGCATCTTCTTCAGCAG
						
					

						Genomic sequence
						
							CTTTTCCATTCGTGCATCTATCTCGGTCATGGCACGAGACTTCTCTATTTTAGATAGATAAAAG
TCTTTCTCCCTCTTTGCAGCAGAAAGAACCATATTTAATTTCTGTTCCCGTATTGCACTTTTGT
ATGCTGCACAAAGCAATCCCTTTGTAGATTAGAGATCATATCATAGAAAATTGTCAAGAATTTC
AGCAGAGATATTGTGCGGTTAACAATACCGATTTCTTCAGTAAGATCATCCCATTTAAATTTGG
TCAAGTATTTGATGTTCCAAATATCATAGTATACTGATGACTTCTTTTTCCCCCCTGAGGAAAG
AAAACAGCAAACATTAACAATCATATAAGCTTATAGATTTAACCTGTCGACTATGCATACTGAT
ATGATTCATTAGGAATACCGATTTGTTCTCCATTTAGCATATCTGCAACCCGTTTAGCTACGCT
CTTCTTAGCAAACTCCACCCACCTGCAGTTAATGAACAGAATAATATATCGAAAACTATTATTA
AAAGAATCCAAATTATCAATGTGGAGAAGTGTTTTGAACACAACAAACAGACAAGGGAAAAGCC
AATAACTAGCGGGGGAAACACATATCCTTAAGCGTACCCTTCAGAAAACCTTTGGCCACGAAAT
CCACCAGCCCGCTTACGGTGCACTTGTGCTTCAGAATCTGAATAGCAATAGACAAATGTATCAG
CTAACTTTTCAATACAGAAACACATTAATATGACCAAGATGTGCTTTTGACATTAAACGAGGAC
TCGATAGGATAAAAAACCTCACCTTCAGGTGCAAGATAAATCCTTCCGAGTTCTCCATATTGAG
CGAGAATATGGCGAAGTCTAACGTGATCCATGTGTGGTGGGATACGACTTAAGTAGCAAACACC
TCTATTGTCAGCTTTCGAAGCTTCCTTAAGCAATTTCTCTTTCAACTTCTTTTTCTTTCTATCA
GCCTTTTGACTCTTCATCGTTTCCTTGGACTCCTTCTCCTCGGATATTCCATCCGTAAGCTCGT
GAGATTCCTCACTCTGCATCTTCTTCAGCAG
						
					

			
		

Sequences
Splice junction sequence	TATCAGCCTTTTGACTCTTCATCGTTTCCTTGGACTCCTTCTCCTCGGATATTCCATCCGTAAG CTCGTGAGATTCCTCACTCTGCATCTTCTTCAGCAGcttttccattcgtgcatctatctcggtc atggcacgagacttctctattttagatagataaaagtctttctccctctttgcagcagaaagaa ccatattt
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: 618 Transcript exons: 20945193-20945323,20945413-20945502,20945595-20945662,20 945806-20945869,20945983-20946247 CTTTTCCATTCGTGCATCTATCTCGGTCATGGCACGAGACTTCTCTATTTTAGATAGATAAAAG TCTTTCTCCCTCTTTGCAGCAGAAAGAACCATATTTAATTTCTGTTCCCGTATTGCACTTTTGT ATGCGATTTCTTCAGTAAGATCATCCCATTTAAATTTGGTCAAGTATTTGATGTTCCAAATATC ATAGTATACTGATGACTTCTTTTTCCCCCCGATTTGTTCTCCATTTAGCATATCTGCAACCCGT TTAGCTACGCTCTTCTTAGCAAACTCCACCCACCCTTCAGAAAACCTTTGGCCACGAAATCCAC CAGCCCGCTTACGGTGCACTTGTGCTTCAGAATCTTCAGGTGCAAGATAAATCCTTCCGAGTTC TCCATATTGAGCGAGAATATGGCGAAGTCTAACGTGATCCATGTGTGGTGGGATACGACTTAAG TAGCAAACACCTCTATTGTCAGCTTTCGAAGCTTCCTTAAGCAATTTCTCTTTCAACTTCTTTT TCTTTCTATCAGCCTTTTGACTCTTCATCGTTTCCTTGGACTCCTTCTCCTCGGATATTCCATC CGTAAGCTCGTGAGATTCCTCACTCTGCATCTTCTTCAGCAG
Genomic sequence	CTTTTCCATTCGTGCATCTATCTCGGTCATGGCACGAGACTTCTCTATTTTAGATAGATAAAAG TCTTTCTCCCTCTTTGCAGCAGAAAGAACCATATTTAATTTCTGTTCCCGTATTGCACTTTTGT ATGCTGCACAAAGCAATCCCTTTGTAGATTAGAGATCATATCATAGAAAATTGTCAAGAATTTC AGCAGAGATATTGTGCGGTTAACAATACCGATTTCTTCAGTAAGATCATCCCATTTAAATTTGG TCAAGTATTTGATGTTCCAAATATCATAGTATACTGATGACTTCTTTTTCCCCCCTGAGGAAAG AAAACAGCAAACATTAACAATCATATAAGCTTATAGATTTAACCTGTCGACTATGCATACTGAT ATGATTCATTAGGAATACCGATTTGTTCTCCATTTAGCATATCTGCAACCCGTTTAGCTACGCT CTTCTTAGCAAACTCCACCCACCTGCAGTTAATGAACAGAATAATATATCGAAAACTATTATTA AAAGAATCCAAATTATCAATGTGGAGAAGTGTTTTGAACACAACAAACAGACAAGGGAAAAGCC AATAACTAGCGGGGGAAACACATATCCTTAAGCGTACCCTTCAGAAAACCTTTGGCCACGAAAT CCACCAGCCCGCTTACGGTGCACTTGTGCTTCAGAATCTGAATAGCAATAGACAAATGTATCAG CTAACTTTTCAATACAGAAACACATTAATATGACCAAGATGTGCTTTTGACATTAAACGAGGAC TCGATAGGATAAAAAACCTCACCTTCAGGTGCAAGATAAATCCTTCCGAGTTCTCCATATTGAG CGAGAATATGGCGAAGTCTAACGTGATCCATGTGTGGTGGGATACGACTTAAGTAGCAAACACC TCTATTGTCAGCTTTCGAAGCTTCCTTAAGCAATTTCTCTTTCAACTTCTTTTTCTTTCTATCA GCCTTTTGACTCTTCATCGTTTCCTTGGACTCCTTCTCCTCGGATATTCCATCCGTAAGCTCGT GAGATTCCTCACTCTGCATCTTCTTCAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.195207778

Conservation Information
Conserved circRNAs	NA
PMCS	0.195207778

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20946236-20945195(-)
						
						Potential amino acid sequence
						
							MQSEESHELTDGISEEKESKETMKSQKADRKKKKLKEKLLKEASKADNRGVCYLSRIPPHMDHV
RLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQI
GGKKKSSVYYDIWNIKYLTKFKWDDLTEEIAYKSAIREQKLNMVLSAAKREKDFYLSKIEKSRA
MTEIDARMEKLLKKMQSEESHELTDGISEEKESKETMKSQKADRKKKKLKEKLLKEASKADNRG
VCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKS
VAKRVADMLNGEQIGGKKKSSVYYDIWNIKYLTKFKWDDLTEEIAYKSAIREQKLNMVLSAAKR
EKDFYLSKIEKSRAMTEIDARMEKLLKKMQSEESHELTDGISEEKESKETMKSQKADRKKKKLK
EKLLKEASKADNRGVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRG
QRFSEGWVEFAKKSVAKRVADMLNGEQIGGKKKSSVYYDIWNIKYLTKFKWDDLTEEIAYKSAI
REQKLNMVLSAAKREKDFYLSKIEKSRAMTEIDARMEKLLKKMQSEESHELTDGISEEKESKET
MKSQKADRKKKKLKEKLLKEASKADNRGVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDS
EAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQIGGKKKSSVYYDIWNIKYLTKFK
WDDLTEEIAYKSAIREQKLNMVLSAAKREKDFYLSKIEKSRAMTEIDARMEK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20946236-20945195(-)
Potential amino acid sequence	MQSEESHELTDGISEEKESKETMKSQKADRKKKKLKEKLLKEASKADNRGVCYLSRIPPHMDHV RLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQI GGKKKSSVYYDIWNIKYLTKFKWDDLTEEIAYKSAIREQKLNMVLSAAKREKDFYLSKIEKSRA MTEIDARMEKLLKKMQSEESHELTDGISEEKESKETMKSQKADRKKKKLKEKLLKEASKADNRG VCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKS VAKRVADMLNGEQIGGKKKSSVYYDIWNIKYLTKFKWDDLTEEIAYKSAIREQKLNMVLSAAKR EKDFYLSKIEKSRAMTEIDARMEKLLKKMQSEESHELTDGISEEKESKETMKSQKADRKKKKLK EKLLKEASKADNRGVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRG QRFSEGWVEFAKKSVAKRVADMLNGEQIGGKKKSSVYYDIWNIKYLTKFKWDDLTEEIAYKSAI REQKLNMVLSAAKREKDFYLSKIEKSRAMTEIDARMEKLLKKMQSEESHELTDGISEEKESKET MKSQKADRKKKKLKEKLLKEASKADNRGVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDS EAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQIGGKKKSSVYYDIWNIKYLTKFK WDDLTEEIAYKSAIREQKLNMVLSAAKREKDFYLSKIEKSRAMTEIDARMEK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G56510_circ_g.1

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