Plant Circular RNA Database

Detail information of AT5G18830_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT5G18830_circ_g.5
					
						ID in PlantcircBase
						ath_circ_039084
					
						Alias
						At_ciR2647
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6277063-6278657  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, find_circ
					
						Parent gene
						
							AT5G18830						
					
						Parent gene annotation
						
							Squamosa promoter binding protein-like 7
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G18830_circ_g.2 AT5G18830_circ_g.3 AT5G18830_circ_g.4 AT5G18830_circ_g.6 AT5G18830_circ_g.7 AT5G18830_circ_g.8 AT5G18830_circ_g.9 AT5G18830_circ_g.10 AT5G18830_circ_g.11 						
					
						Support reads
						3/1
					
						Tissues
						leaf/inflorescences
					
						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
						AT5G18830.2:6
AT5G18830.3:6
AT5G18830.1:6

General Information
CircRNA Name	AT5G18830_circ_g.5
ID in PlantcircBase	ath_circ_039084
Alias	At_ciR2647
Organism	Arabidpsis thaliana
Position	chr5: 6277063-6278657 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, find_circ
Parent gene	AT5G18830
Parent gene annotation	Squamosa promoter binding protein-like 7
Parent gene strand	+
Alternative splicing	AT5G18830_circ_g.2 AT5G18830_circ_g.3 AT5G18830_circ_g.4 AT5G18830_circ_g.6 AT5G18830_circ_g.7 AT5G18830_circ_g.8 AT5G18830_circ_g.9 AT5G18830_circ_g.10 AT5G18830_circ_g.11
Support reads	3/1
Tissues	leaf/inflorescences
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	AT5G18830.2:6 AT5G18830.3:6 AT5G18830.1:6

			
						 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  
						
							AGTCGCCGAAACTTCAGTTTGTGTATCCTACATGTTTTGAAGCTGGAAAACCAATTGAACTCGT
TGTATGTGGACAAAACCTTCTGCAACCTAAATGCCGgtttcatttgctcccggactttgatgaa
ggaaaacgcagctgtcggagaaagctagagcgtcacaacaacagacggaaaaggaaacctgtag
ataaagga

									
								

					

						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: 837
Transcript exons: 6277063-6277235,6277387-6277613,6277687-6277761,6277864-
6277971,6278288-6278405,6278522-6278657
GTTTCATTTGCTCCCGGACTTTGATGAAGGAAAACGCAGCTGTCGGAGAAAGCTAGAGCGTCAC
AACAACAGACGGAAAAGGAAACCTGTAGATAAAGGAGGTGTTGCTGCAGAACAACAGCAAGTGC
TTTCACAGAATGATAACAGCGTCATTGATGTTGAGGATGGAAAAGATATCACATGCTCTAGTGA
CCAGAGAGCTGAAGAAGAGCCTTCATTGATTTTTGAAGATCGGCATATTACCACTCAGGGTTCT
GTACCTTTTACCCGAAGCATCAACGCAGACAACTTTGTCTCTGTTACAGGTTCGGGTGAAGCTC
AACCAGATGAAGGAATGAATGACACAAAATTTGAACGTTCACCTTCTAATGGCGACAACAAAAG
TGCTTACTCAACTGTGTGTCCAACTGGTCGGATCTCTTTTAAGCTCTACGATTGGAATCCAGCG
GAGTTCCCACGGAGACTACGTCATCAAATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGG
AGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGTG
GGCGAAGTTATCTAAAGATCCTGTGGCATATCTGGATGAATTTATTCTTAAACCTGGAAAGATG
CTGTTTGGAAGAGGCTCGATGACTGTCTATTTGAACAACATGATTTTCCGTCTTATTAAAGGTG
GAACAACTTTAAAGAGAGTCGATGTAAAATTAGAGTCGCCGAAACTTCAGTTTGTGTATCCTAC
ATGTTTTGAAGCTGGAAAACCAATTGAACTCGTTGTATGTGGACAAAACCTTCTGCAACCTAAA
TGCCG
						
					

						Genomic sequence
						
							GTTTCATTTGCTCCCGGACTTTGATGAAGGAAAACGCAGCTGTCGGAGAAAGCTAGAGCGTCAC
AACAACAGACGGAAAAGGAAACCTGTAGATAAAGGAGGTGTTGCTGCAGAACAACAGCAAGTGC
TTTCACAGAATGATAACAGCGTCATTGATGTTGAGGATGGAAAAGGTATAAGTGAACTGCGCAA
ATCTCAAATCATATCACCATGTGGTTTCTTTGTTTTAGTTGTTTGCTTTGCATATTTTGCTAGT
TACCAACGTTTAGAGTTCTCTTGGAAATTCAAGCTGATTCGATTGTCAATGCTATCATTTTGAA
GCAGATATCACATGCTCTAGTGACCAGAGAGCTGAAGAAGAGCCTTCATTGATTTTTGAAGATC
GGCATATTACCACTCAGGGTTCTGTACCTTTTACCCGAAGCATCAACGCAGACAACTTTGTCTC
TGTTACAGGTTCGGGTGAAGCTCAACCAGATGAAGGAATGAATGACACAAAATTTGAACGTTCA
CCTTCTAATGGCGACAACAAAAGTGCTTACTCAACTGTGGTGAGTTTCTCTTCAGCCTCTAACA
TCAAAAACATCGGTGCACTTAATGAACTAATTTCCCATTTCATTGCAGTGTCCAACTGGTCGGA
TCTCTTTTAAGCTCTACGATTGGAATCCAGCGGAGTTCCCACGGAGACTACGTCATCAAGTATT
CTCAAGAATTATATATTACAGTTTAGTGTTCAAAGACTATGTTTACCTTCTCAGAATCTCAAAG
AACTAATATCTTGCGATTAATTTGAATTTGCAGATATTTCAATGGTTGGCCAACATGCCTGTTG
AGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGAT
TATGTGGGCGAAGGTACATCCTGTTATCTTTTACTCATCATTTTCATGTTCATGATGCCGCGAC
ACAACATAAGAAATTGTTTATTTTCAGTAGGTTGTAGTCTCGAGATATGCTCTATTTCTCTATG
CACCTTACCCTCTTAAGTACCATATACACATTAAAGCTCTTACGTTTTTGTGTGACCTGAAGTT
CTTTTGTTACTAAAAATTGTCCATTATTTGGAAGCTTTTGCCCTGGAGGGAGAAAATGCAAACT
TAGTATCTCTTCCCGTGAACTCTCTTTTGACTTTGCACTGTAATAAACTTTTCCAATTTGTTCC
TGTAAACAGTTATCTAAAGATCCTGTGGCATATCTGGATGAATTTATTCTTAAACCTGGAAAGA
TGCTGTTTGGAAGAGGCTCGATGACTGTCTATTTGAACAACATGATTTTCCGTCTTATTAAAGG
CAAGTTGGTGTGCTTTACTTGTTTTCTCTGGATTTTTTCACTCTATCATATTGGATAACCATAA
TGTCGTGAGCTATTAATGTGAACTAATACTTATTTGTCTTGGTTTTGACAGGTGGAACAACTTT
AAAGAGAGTCGATGTAAAATTAGAGTCGCCGAAACTTCAGTTTGTGTATCCTACATGTTTTGAA
GCTGGAAAACCAATTGAACTCGTTGTATGTGGACAAAACCTTCTGCAACCTAAATGCCG
						
					

			
		

Sequences
Splice junction sequence	AGTCGCCGAAACTTCAGTTTGTGTATCCTACATGTTTTGAAGCTGGAAAACCAATTGAACTCGT TGTATGTGGACAAAACCTTCTGCAACCTAAATGCCGgtttcatttgctcccggactttgatgaa ggaaaacgcagctgtcggagaaagctagagcgtcacaacaacagacggaaaaggaaacctgtag ataaagga
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: 837 Transcript exons: 6277063-6277235,6277387-6277613,6277687-6277761,6277864- 6277971,6278288-6278405,6278522-6278657 GTTTCATTTGCTCCCGGACTTTGATGAAGGAAAACGCAGCTGTCGGAGAAAGCTAGAGCGTCAC AACAACAGACGGAAAAGGAAACCTGTAGATAAAGGAGGTGTTGCTGCAGAACAACAGCAAGTGC TTTCACAGAATGATAACAGCGTCATTGATGTTGAGGATGGAAAAGATATCACATGCTCTAGTGA CCAGAGAGCTGAAGAAGAGCCTTCATTGATTTTTGAAGATCGGCATATTACCACTCAGGGTTCT GTACCTTTTACCCGAAGCATCAACGCAGACAACTTTGTCTCTGTTACAGGTTCGGGTGAAGCTC AACCAGATGAAGGAATGAATGACACAAAATTTGAACGTTCACCTTCTAATGGCGACAACAAAAG TGCTTACTCAACTGTGTGTCCAACTGGTCGGATCTCTTTTAAGCTCTACGATTGGAATCCAGCG GAGTTCCCACGGAGACTACGTCATCAAATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGG AGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGTG GGCGAAGTTATCTAAAGATCCTGTGGCATATCTGGATGAATTTATTCTTAAACCTGGAAAGATG CTGTTTGGAAGAGGCTCGATGACTGTCTATTTGAACAACATGATTTTCCGTCTTATTAAAGGTG GAACAACTTTAAAGAGAGTCGATGTAAAATTAGAGTCGCCGAAACTTCAGTTTGTGTATCCTAC ATGTTTTGAAGCTGGAAAACCAATTGAACTCGTTGTATGTGGACAAAACCTTCTGCAACCTAAA TGCCG
Genomic sequence	GTTTCATTTGCTCCCGGACTTTGATGAAGGAAAACGCAGCTGTCGGAGAAAGCTAGAGCGTCAC AACAACAGACGGAAAAGGAAACCTGTAGATAAAGGAGGTGTTGCTGCAGAACAACAGCAAGTGC TTTCACAGAATGATAACAGCGTCATTGATGTTGAGGATGGAAAAGGTATAAGTGAACTGCGCAA ATCTCAAATCATATCACCATGTGGTTTCTTTGTTTTAGTTGTTTGCTTTGCATATTTTGCTAGT TACCAACGTTTAGAGTTCTCTTGGAAATTCAAGCTGATTCGATTGTCAATGCTATCATTTTGAA GCAGATATCACATGCTCTAGTGACCAGAGAGCTGAAGAAGAGCCTTCATTGATTTTTGAAGATC GGCATATTACCACTCAGGGTTCTGTACCTTTTACCCGAAGCATCAACGCAGACAACTTTGTCTC TGTTACAGGTTCGGGTGAAGCTCAACCAGATGAAGGAATGAATGACACAAAATTTGAACGTTCA CCTTCTAATGGCGACAACAAAAGTGCTTACTCAACTGTGGTGAGTTTCTCTTCAGCCTCTAACA TCAAAAACATCGGTGCACTTAATGAACTAATTTCCCATTTCATTGCAGTGTCCAACTGGTCGGA TCTCTTTTAAGCTCTACGATTGGAATCCAGCGGAGTTCCCACGGAGACTACGTCATCAAGTATT CTCAAGAATTATATATTACAGTTTAGTGTTCAAAGACTATGTTTACCTTCTCAGAATCTCAAAG AACTAATATCTTGCGATTAATTTGAATTTGCAGATATTTCAATGGTTGGCCAACATGCCTGTTG AGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGAT TATGTGGGCGAAGGTACATCCTGTTATCTTTTACTCATCATTTTCATGTTCATGATGCCGCGAC ACAACATAAGAAATTGTTTATTTTCAGTAGGTTGTAGTCTCGAGATATGCTCTATTTCTCTATG CACCTTACCCTCTTAAGTACCATATACACATTAAAGCTCTTACGTTTTTGTGTGACCTGAAGTT CTTTTGTTACTAAAAATTGTCCATTATTTGGAAGCTTTTGCCCTGGAGGGAGAAAATGCAAACT TAGTATCTCTTCCCGTGAACTCTCTTTTGACTTTGCACTGTAATAAACTTTTCCAATTTGTTCC TGTAAACAGTTATCTAAAGATCCTGTGGCATATCTGGATGAATTTATTCTTAAACCTGGAAAGA TGCTGTTTGGAAGAGGCTCGATGACTGTCTATTTGAACAACATGATTTTCCGTCTTATTAAAGG CAAGTTGGTGTGCTTTACTTGTTTTCTCTGGATTTTTTCACTCTATCATATTGGATAACCATAA TGTCGTGAGCTATTAATGTGAACTAATACTTATTTGTCTTGGTTTTGACAGGTGGAACAACTTT AAAGAGAGTCGATGTAAAATTAGAGTCGCCGAAACTTCAGTTTGTGTATCCTACATGTTTTGAA GCTGGAAAACCAATTGAACTCGTTGTATGTGGACAAAACCTTCTGCAACCTAAATGCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.286387313

Conservation Information
Conserved circRNAs	NA
PMCS	0.286387313

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6277548-6278654(+)
						
						Potential amino acid sequence
						
							MNDTKFERSPSNGDNKSAYSTVCPTGRISFKLYDWNPAEFPRRLRHQIFQWLANMPVELEGYIR
PGCTILTVFIAMPEIMWAKLSKDPVAYLDEFILKPGKMLFGRGSMTVYLNNMIFRLIKGGTTLK
RVDVKLESPKLQFVYPTCFEAGKPIELVVCGQNLLQPKCRFHLLPDFDEGKRSCRRKLERHNNR
RKRKPVDKGGVAAEQQQVLSQNDNSVIDVEDGKDITCSSDQRAEEEPSLIFEDRHITTQGSVPF
TRSINADNFVSVTGSGEAQPDEGMNDTKFERSPSNGDNKSAYSTVCPTGRISFKLYDWNPAEFP
RRLRHQIFQWLANMPVELEGYIRPGCTILTVFIAMPEIMWAKLSKDPVAYLDEFILKPGKMLFG
RGSMTVYLNNMIFRLIKGGTTLKRVDVKLESPKLQFVYPTCFEAGKPIELVVCGQNLLQPKCRF
HLLPDFDEGKRSCRRKLERHNNRRKRKPVDKGGVAAEQQQVLSQNDNSVIDVEDGKDITCSSDQ
RAEEEPSLIFEDRHITTQGSVPFTRSINADNFVSVTGSGEAQPDEGMNDTKFERSPSNGDNKSA
YSTVCPTGRISFKLYDWNPAEFPRRLRHQIFQWLANMPVELEGYIRPGCTILTVFIAMPEIMWA
KLSKDPVAYLDEFILKPGKMLFGRGSMTVYLNNMIFRLIKGGTTLKRVDVKLESPKLQFVYPTC
FEAGKPIELVVCGQNLLQPKCRFHLLPDFDEGKRSCRRKLERHNNRRKRKPVDKGGVAAEQQQV
LSQNDNSVIDVEDGKDITCSSDQRAEEEPSLIFEDRHITTQGSVPFTRSINADNFVSVTGSGEA
QPDEGMNDTKFERSPSNGDNKSAYSTVCPTGRISFKLYDWNPAEFPRRLRHQIFQWLANMPVEL
EGYIRPGCTILTVFIAMPEIMWAKLSKDPVAYLDEFILKPGKMLFGRGSMTVYLNNMIFRLIKG
GTTLKRVDVKLESPKLQFVYPTCFEAGKPIELVVCGQNLLQPKC(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6277548-6278654(+)
Potential amino acid sequence	MNDTKFERSPSNGDNKSAYSTVCPTGRISFKLYDWNPAEFPRRLRHQIFQWLANMPVELEGYIR PGCTILTVFIAMPEIMWAKLSKDPVAYLDEFILKPGKMLFGRGSMTVYLNNMIFRLIKGGTTLK RVDVKLESPKLQFVYPTCFEAGKPIELVVCGQNLLQPKCRFHLLPDFDEGKRSCRRKLERHNNR RKRKPVDKGGVAAEQQQVLSQNDNSVIDVEDGKDITCSSDQRAEEEPSLIFEDRHITTQGSVPF TRSINADNFVSVTGSGEAQPDEGMNDTKFERSPSNGDNKSAYSTVCPTGRISFKLYDWNPAEFP RRLRHQIFQWLANMPVELEGYIRPGCTILTVFIAMPEIMWAKLSKDPVAYLDEFILKPGKMLFG RGSMTVYLNNMIFRLIKGGTTLKRVDVKLESPKLQFVYPTCFEAGKPIELVVCGQNLLQPKCRF HLLPDFDEGKRSCRRKLERHNNRRKRKPVDKGGVAAEQQQVLSQNDNSVIDVEDGKDITCSSDQ RAEEEPSLIFEDRHITTQGSVPFTRSINADNFVSVTGSGEAQPDEGMNDTKFERSPSNGDNKSA YSTVCPTGRISFKLYDWNPAEFPRRLRHQIFQWLANMPVELEGYIRPGCTILTVFIAMPEIMWA KLSKDPVAYLDEFILKPGKMLFGRGSMTVYLNNMIFRLIKGGTTLKRVDVKLESPKLQFVYPTC FEAGKPIELVVCGQNLLQPKCRFHLLPDFDEGKRSCRRKLERHNNRRKRKPVDKGGVAAEQQQV LSQNDNSVIDVEDGKDITCSSDQRAEEEPSLIFEDRHITTQGSVPFTRSINADNFVSVTGSGEA QPDEGMNDTKFERSPSNGDNKSAYSTVCPTGRISFKLYDWNPAEFPRRLRHQIFQWLANMPVEL EGYIRPGCTILTVFIAMPEIMWAKLSKDPVAYLDEFILKPGKMLFGRGSMTVYLNNMIFRLIKG GTTLKRVDVKLESPKLQFVYPTCFEAGKPIELVVCGQNLLQPKC(+)
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 AT5G18830_circ_g.5

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