Plant Circular RNA Database

Detail information of AT1G49970_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G49970_circ_g.3
					
						ID in PlantcircBase
						ath_circ_006527
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 18502110-18503132  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						MapSplice
					
						Parent gene
						
							AT1G49970						
					
						Parent gene annotation
						
							ATP-dependent Clp protease proteolytic subunit-related protein 1
, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G49970_circ_g.1 AT1G49970_circ_g.2 AT1G49970_circ_g.4 AT1G49970_circ_g.5 AT1G49970_circ_g.6 AT1G49970_circ_g.7 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						AT1G49970.1:5

General Information
CircRNA Name	AT1G49970_circ_g.3
ID in PlantcircBase	ath_circ_006527
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 18502110-18503132 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	MapSplice
Parent gene	AT1G49970
Parent gene annotation	ATP-dependent Clp protease proteolytic subunit-related protein 1 , chloroplastic
Parent gene strand	-
Alternative splicing	AT1G49970_circ_g.1 AT1G49970_circ_g.2 AT1G49970_circ_g.4 AT1G49970_circ_g.5 AT1G49970_circ_g.6 AT1G49970_circ_g.7
Support reads	NA
Tissues	leaf
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	AT1G49970.1:5

			
						 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  
						
							TCCCGGGTGAATTTATATATAAGTAGATGGGCTTTGTTGGGTTATCATAGTCTAACCACATAAA
TTGAGCAACGAGTAACTCAGTAACTGCAGGTACGATccgtttctcgaaagaactgtcctgcgag
tcagctatcttgtctgcaattccatagtcaatggctgcttgagcttggagatatttaggtcgct
tgatgtcc

									
								

					

						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: 525
Transcript exons: 18502110-18502292,18502374-18502435,18502554-18502665,18
502839-18502901,18503028-18503132
CCGTTTCTCGAAAGAACTGTCCTGCGAGTCAGCTATCTTGTCTGCAATTCCATAGTCAATGGCT
GCTTGAGCTTGGAGATATTTAGGTCGCTTGATGTCCTCGTTGATCTGCTCTTTGGATTTCCCTG
TTCCCTTAGCTAACAGCTCGATGTAGTACTCGGTATTTGCATCAAGTTCCTTGGCCTTTATCCA
CATGTCTATGGCAGCTCCACTCGATCTGTTTACTTTTGGCAGATATAATTTTGTTGATGAATGT
GGTTGTACGGCACGATAACCTTTTTTCCCGAGAGAAAGAAGCATTGCTGCTTGACCAAAAGCCA
TGCCACAATTGATAGTGTATACATCTGATTTGCAATAAGAAATAGTATCGGCTATGGCATAAGC
CTCTGTTTCTGATCCAACAGTTTCCATCTTCTCATTCTGGGTCCCGGGTGAATTTATATATAAG
TAGATGGGCTTTGTTGGGTTATCATAGTCTAACCACATAAATTGAGCAACGAGTAACTCAGTAA
CTGCAGGTACGAT
						
					

						Genomic sequence
						
							CCGTTTCTCGAAAGAACTGTCCTGCGAGTCAGCTATCTTGTCTGCAATTCCATAGTCAATGGCT
GCTTGAGCTTGGAGATATTTAGGTCGCTTGATGTCCTCGTTGATCTGCTCTTTGGATTTCCCTG
TTCCCTTAGCTAACAGCTCGATGTAGTACTCGGTATTTGCATCAAGTTCCTTGGCCTGCCAGAG
GATTATTCATTACAGTAGAGGTAAAGAAACTTGAGGGAATTACACAGAAGGGTATAAGAATGTG
AGCACCACCTTTATCCACATGTCTATGGCAGCTCCACTCGATCTGTTTACTTTTGGCAGATATA
ATTTTGCTGCACCATTAACCATCAAAACTTAGAAGCTTACACAAGTGGGCAAGAGGTATTGCAT
TTGTTTATTATGATCAAAATGCAAAGTTAGAGTTCAAATATTTTAGAGAAGAGTACATACTTGA
TGAATGTGGTTGTACGGCACGATAACCTTTTTTCCCGAGAGAAAGAAGCATTGCTGCTTGACCA
AAAGCCATGCCACAATTGATAGTGTATACATCTGATTTGCAATACTAATACGCCACATAAAAAT
AAAAAACAGTGAGGCGATGAGAATCAAAGCTGCTACATAGGTTATTTGCATACCATCTATCGAA
ACAATAATCAGTGACAAACATCAGCAAAAGGAACTTCGTGTTTGTACAATCAGAAGAAAAATGT
AGATAGTTTCAGTAAAATCACTTACAGAAATAGTATCGGCTATGGCATAAGCCTCTGTTTCTGA
TCCAACAGTTTCCATCTTCTCATTCTACATGGCATAAGCAAAAGGAAACAAAAGAATAGATAGC
TTGTTAAAAGTAACAAGTGGGTTATCTAAATAAATCCAGAAAACTACCACCAACAAACAATATA
TAATCAAACTTCTTCTACTGACCTGGGTCCCGGGTGAATTTATATATAAGTAGATGGGCTTTGT
TGGGTTATCATAGTCTAACCACATAAATTGAGCAACGAGTAACTCAGTAACTGCAGGTACGAT
						
					

			
		

Sequences
Splice junction sequence	TCCCGGGTGAATTTATATATAAGTAGATGGGCTTTGTTGGGTTATCATAGTCTAACCACATAAA TTGAGCAACGAGTAACTCAGTAACTGCAGGTACGATccgtttctcgaaagaactgtcctgcgag tcagctatcttgtctgcaattccatagtcaatggctgcttgagcttggagatatttaggtcgct tgatgtcc
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: 525 Transcript exons: 18502110-18502292,18502374-18502435,18502554-18502665,18 502839-18502901,18503028-18503132 CCGTTTCTCGAAAGAACTGTCCTGCGAGTCAGCTATCTTGTCTGCAATTCCATAGTCAATGGCT GCTTGAGCTTGGAGATATTTAGGTCGCTTGATGTCCTCGTTGATCTGCTCTTTGGATTTCCCTG TTCCCTTAGCTAACAGCTCGATGTAGTACTCGGTATTTGCATCAAGTTCCTTGGCCTTTATCCA CATGTCTATGGCAGCTCCACTCGATCTGTTTACTTTTGGCAGATATAATTTTGTTGATGAATGT GGTTGTACGGCACGATAACCTTTTTTCCCGAGAGAAAGAAGCATTGCTGCTTGACCAAAAGCCA TGCCACAATTGATAGTGTATACATCTGATTTGCAATAAGAAATAGTATCGGCTATGGCATAAGC CTCTGTTTCTGATCCAACAGTTTCCATCTTCTCATTCTGGGTCCCGGGTGAATTTATATATAAG TAGATGGGCTTTGTTGGGTTATCATAGTCTAACCACATAAATTGAGCAACGAGTAACTCAGTAA CTGCAGGTACGAT
Genomic sequence	CCGTTTCTCGAAAGAACTGTCCTGCGAGTCAGCTATCTTGTCTGCAATTCCATAGTCAATGGCT GCTTGAGCTTGGAGATATTTAGGTCGCTTGATGTCCTCGTTGATCTGCTCTTTGGATTTCCCTG TTCCCTTAGCTAACAGCTCGATGTAGTACTCGGTATTTGCATCAAGTTCCTTGGCCTGCCAGAG GATTATTCATTACAGTAGAGGTAAAGAAACTTGAGGGAATTACACAGAAGGGTATAAGAATGTG AGCACCACCTTTATCCACATGTCTATGGCAGCTCCACTCGATCTGTTTACTTTTGGCAGATATA ATTTTGCTGCACCATTAACCATCAAAACTTAGAAGCTTACACAAGTGGGCAAGAGGTATTGCAT TTGTTTATTATGATCAAAATGCAAAGTTAGAGTTCAAATATTTTAGAGAAGAGTACATACTTGA TGAATGTGGTTGTACGGCACGATAACCTTTTTTCCCGAGAGAAAGAAGCATTGCTGCTTGACCA AAAGCCATGCCACAATTGATAGTGTATACATCTGATTTGCAATACTAATACGCCACATAAAAAT AAAAAACAGTGAGGCGATGAGAATCAAAGCTGCTACATAGGTTATTTGCATACCATCTATCGAA ACAATAATCAGTGACAAACATCAGCAAAAGGAACTTCGTGTTTGTACAATCAGAAGAAAAATGT AGATAGTTTCAGTAAAATCACTTACAGAAATAGTATCGGCTATGGCATAAGCCTCTGTTTCTGA TCCAACAGTTTCCATCTTCTCATTCTACATGGCATAAGCAAAAGGAAACAAAAGAATAGATAGC TTGTTAAAAGTAACAAGTGGGTTATCTAAATAAATCCAGAAAACTACCACCAACAAACAATATA TAATCAAACTTCTTCTACTGACCTGGGTCCCGGGTGAATTTATATATAAGTAGATGGGCTTTGT TGGGTTATCATAGTCTAACCACATAAATTGAGCAACGAGTAACTCAGTAACTGCAGGTACGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.218981641

Conservation Information
Conserved circRNAs	NA
PMCS	0.218981641

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18503094-18502112(-)
						
						Potential amino acid sequence
						
							MWLDYDNPTKPIYLYINSPGTQNEKMETVGSETEAYAIADTISYCKSDVYTINCGMAFGQAAML
LSLGKKGYRAVQPHSSTKLYLPKVNRSSGAAIDMWIKAKELDANTEYYIELLAKGTGKSKEQIN
EDIKRPKYLQAQAAIDYGIADKIADSQDSSFEKRIVPAVTELLVAQFMWLDYDNPTKPIYLYIN
SPGTQNEKMETVGSETEAYAIADTISYCKSDVYTINCGMAFGQAAMLLSLGKKGYRAVQPHSST
KLYLPKVNRSSGAAIDMWIKAKELDANTEYYIELLAKGTGKSKEQINEDIKRPKYLQAQAAIDY
GIADKIADSQDSSFEKRIVPAVTELLVAQFMWLDYDNPTKPIYLYINSPGTQNEKMETVGSETE
AYAIADTISYCKSDVYTINCGMAFGQAAMLLSLGKKGYRAVQPHSSTKLYLPKVNRSSGAAIDM
WIKAKELDANTEYYIELLAKGTGKSKEQINEDIKRPKYLQAQAAIDYGIADKIADSQDSSFEKR
IVPAVTELLVAQFMWLDYDNPTKPIYLYINSPGTQNEKMETVGSETEAYAIADTISYCKSDVYT
INCGMAFGQAAMLLSLGKKGYRAVQPHSSTKLYLPKVNRSSGAAIDMWIKAKELDANTEYYIEL
LAKGTGKSKEQINEDIKRPKYLQAQAAIDYGIADKIADSQDSSFEKR(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18503094-18502112(-)
Potential amino acid sequence	MWLDYDNPTKPIYLYINSPGTQNEKMETVGSETEAYAIADTISYCKSDVYTINCGMAFGQAAML LSLGKKGYRAVQPHSSTKLYLPKVNRSSGAAIDMWIKAKELDANTEYYIELLAKGTGKSKEQIN EDIKRPKYLQAQAAIDYGIADKIADSQDSSFEKRIVPAVTELLVAQFMWLDYDNPTKPIYLYIN SPGTQNEKMETVGSETEAYAIADTISYCKSDVYTINCGMAFGQAAMLLSLGKKGYRAVQPHSST KLYLPKVNRSSGAAIDMWIKAKELDANTEYYIELLAKGTGKSKEQINEDIKRPKYLQAQAAIDY GIADKIADSQDSSFEKRIVPAVTELLVAQFMWLDYDNPTKPIYLYINSPGTQNEKMETVGSETE AYAIADTISYCKSDVYTINCGMAFGQAAMLLSLGKKGYRAVQPHSSTKLYLPKVNRSSGAAIDM WIKAKELDANTEYYIELLAKGTGKSKEQINEDIKRPKYLQAQAAIDYGIADKIADSQDSSFEKR IVPAVTELLVAQFMWLDYDNPTKPIYLYINSPGTQNEKMETVGSETEAYAIADTISYCKSDVYT INCGMAFGQAAMLLSLGKKGYRAVQPHSSTKLYLPKVNRSSGAAIDMWIKAKELDANTEYYIEL LAKGTGKSKEQINEDIKRPKYLQAQAAIDYGIADKIADSQDSSFEKR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2017

circRNA

Detail information of AT1G49970_circ_g.3

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