Plant Circular RNA Database

Detail information of AT5G46400_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G46400_circ_g.4
					
						ID in PlantcircBase
						ath_circ_042696
					
						Alias
						At_ciR5966
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 18822920-18824368  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT5G46400						
					
						Parent gene annotation
						
							Tetratricopeptide repeat (TPR)-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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  
						
							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
						AT5G46400.1:1
AT5G46400.2:1
AT5G46400.3:1

General Information
CircRNA Name	AT5G46400_circ_g.4
ID in PlantcircBase	ath_circ_042696
Alias	At_ciR5966
Organism	Arabidpsis thaliana
Position	chr5: 18822920-18824368 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT5G46400
Parent gene annotation	Tetratricopeptide repeat (TPR)-like superfamily protein
Parent gene strand	+
Alternative splicing	NA
Support reads	2
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	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	AT5G46400.1:1 AT5G46400.2:1 AT5G46400.3:1

			
						 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  
						
							TCTCTATATTCAGCAACAGCAGTTGCAAGGAGAAGCAAAAGGCGATGAACAAAGACTCTCTATG
CCGCAGGGTTCCACAACAAACAGTGATATTCAAAAGtttattgatctctctggaaccatccatg
atgtgaggaaggctttgggtcgacacataaaattattcccacattctgctagagccaagttacg
tgggtccc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TTTATTGATCTCTCTGGAACCATCCATGATGTGAGGAAGGCTTTGGGTCGACACATAAAATTAT
TCCCACATTCTGCTAGAGCCAAGTTACGTGGGTCCCGTCCTTCAGGAAATTTATTTAGAGAGTT
GATTCAGAGAAGAGAGAAGACTCGAGAGCGCTTGAATCAGGACCTATTAACAAACAAAGGCATT
AGCAGTATAGTCGATTCACCACCAAAAGAAAAGAAAGAGTCATCTCTAGACTCTTATGGTACCC
AATCTAAAGATGCTGTACGGGCTGACTATGTAAACACTGAGCCTAATCAGGGCTGTCTGACTTC
TGGACATCTAGTTGAAGGAAACGATAATGTTATTGAGAGGGAGACTTTGTGTGAGTCACAGAGC
GATCTGTCCATGGGATTAAAAGCCAATGAAGGTGGTAAACGCTCTCATGAAGTTAGCCTACCGA
TCCAAGCCTCACCAGAACATGGTTTTGTCACTAAACAAGCTCACTTCTCGTCCAATTCAGTAGA
TACTGTGAAGTCAGATGCTATAGTGATCCAACCTAGTGGCTCACAGAGTCCCCAAAGTTACCAA
AGTCAAGAGTCTCTCAGGCAAACTGGTCGGAACAGGTACCACAGAAGAGATTTAAACCAGATGC
ACAGAGATTCAAAACCTCGTTCTCAAGAGAGACCTCCTCAGATGCCATATTCTCCAGTCGGAAC
TGGTCGTGAAATTCTTGGTCAGCACATGGCTTTTACTCATCAAGACAATCGAGTAGCGCTACAA
AGCTCAACCTCTCAGAATCCGCAAAACCAATTTCAGAACTCTGCACTTCAGATGCATCCTGTGG
TTCAAACATCCAATGCTTATCCTCAATCTCAGATACATGGTCAGCACATGATTGTATCCCCTCC
AGAGTCACAGAATCCGCAGAACCAATGTCAAAACTCTACATCTCAGGTTCAAACATCCTTTGCT
TATCCTCAAACTCAGATTCCTCAGAATCCAGTGCAGAGTAACTACCAACAAGAAGGTCAGATGC
AGAGTCATGAAGCTTATAACCAGATGTGGCAACAGTATTATTATAGCTATTATTACTATCAGCA
ACAGCAACAGCTTATGTCTGAACAGCCTCAACCAAATCAGAACCCTCAGCCACAACTAGATCAG
AATCTTGTGCAACTTCTCTCCAAACAGTACCAGTCTCAAGCCAAAACTCAGTATCTACAACCAC
AACAGGTGGAACAGGTCAATACACAGCAACAGAGTCAAGAACCACAAAATCAGCAGCAAATTCA
GTTCCAGCAACAACAACAACAACAAGAGTGGTTCCAACAGCAACAGCAATGGCAACAACAGCAG
TATCTTCTCTATATTCAGCAACAGCAGTTGCAAGGAGAAGCAAAAGGCGATGAACAAAGACTCT
CTATGCCGCAGGGTTCCACAACAAACAGTGATATTCAAAAG

Sequences
Splice junction sequence	TCTCTATATTCAGCAACAGCAGTTGCAAGGAGAAGCAAAAGGCGATGAACAAAGACTCTCTATG CCGCAGGGTTCCACAACAAACAGTGATATTCAAAAGtttattgatctctctggaaccatccatg atgtgaggaaggctttgggtcgacacataaaattattcccacattctgctagagccaagttacg tgggtccc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTTATTGATCTCTCTGGAACCATCCATGATGTGAGGAAGGCTTTGGGTCGACACATAAAATTAT TCCCACATTCTGCTAGAGCCAAGTTACGTGGGTCCCGTCCTTCAGGAAATTTATTTAGAGAGTT GATTCAGAGAAGAGAGAAGACTCGAGAGCGCTTGAATCAGGACCTATTAACAAACAAAGGCATT AGCAGTATAGTCGATTCACCACCAAAAGAAAAGAAAGAGTCATCTCTAGACTCTTATGGTACCC AATCTAAAGATGCTGTACGGGCTGACTATGTAAACACTGAGCCTAATCAGGGCTGTCTGACTTC TGGACATCTAGTTGAAGGAAACGATAATGTTATTGAGAGGGAGACTTTGTGTGAGTCACAGAGC GATCTGTCCATGGGATTAAAAGCCAATGAAGGTGGTAAACGCTCTCATGAAGTTAGCCTACCGA TCCAAGCCTCACCAGAACATGGTTTTGTCACTAAACAAGCTCACTTCTCGTCCAATTCAGTAGA TACTGTGAAGTCAGATGCTATAGTGATCCAACCTAGTGGCTCACAGAGTCCCCAAAGTTACCAA AGTCAAGAGTCTCTCAGGCAAACTGGTCGGAACAGGTACCACAGAAGAGATTTAAACCAGATGC ACAGAGATTCAAAACCTCGTTCTCAAGAGAGACCTCCTCAGATGCCATATTCTCCAGTCGGAAC TGGTCGTGAAATTCTTGGTCAGCACATGGCTTTTACTCATCAAGACAATCGAGTAGCGCTACAA AGCTCAACCTCTCAGAATCCGCAAAACCAATTTCAGAACTCTGCACTTCAGATGCATCCTGTGG TTCAAACATCCAATGCTTATCCTCAATCTCAGATACATGGTCAGCACATGATTGTATCCCCTCC AGAGTCACAGAATCCGCAGAACCAATGTCAAAACTCTACATCTCAGGTTCAAACATCCTTTGCT TATCCTCAAACTCAGATTCCTCAGAATCCAGTGCAGAGTAACTACCAACAAGAAGGTCAGATGC AGAGTCATGAAGCTTATAACCAGATGTGGCAACAGTATTATTATAGCTATTATTACTATCAGCA ACAGCAACAGCTTATGTCTGAACAGCCTCAACCAAATCAGAACCCTCAGCCACAACTAGATCAG AATCTTGTGCAACTTCTCTCCAAACAGTACCAGTCTCAAGCCAAAACTCAGTATCTACAACCAC AACAGGTGGAACAGGTCAATACACAGCAACAGAGTCAAGAACCACAAAATCAGCAGCAAATTCA GTTCCAGCAACAACAACAACAACAAGAGTGGTTCCAACAGCAACAGCAATGGCAACAACAGCAG TATCTTCTCTATATTCAGCAACAGCAGTTGCAAGGAGAAGCAAAAGGCGATGAACAAAGACTCT CTATGCCGCAGGGTTCCACAACAAACAGTGATATTCAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.115552392

Conservation Information
Conserved circRNAs	NA
PMCS	0.115552392

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							18823313-18824365(+)
						
					

						Potential amino acid sequence
						
							MGLKANEGGKRSHEVSLPIQASPEHGFVTKQAHFSSNSVDTVKSDAIVIQPSGSQSPQSYQSQE
SLRQTGRNRYHRRDLNQMHRDSKPRSQERPPQMPYSPVGTGREILGQHMAFTHQDNRVALQSST
SQNPQNQFQNSALQMHPVVQTSNAYPQSQIHGQHMIVSPPESQNPQNQCQNSTSQVQTSFAYPQ
TQIPQNPVQSNYQQEGQMQSHEAYNQMWQQYYYSYYYYQQQQQLMSEQPQPNQNPQPQLDQNLV
QLLSKQYQSQAKTQYLQPQQVEQVNTQQQSQEPQNQQQIQFQQQQQQQEWFQQQQQWQQQQYLL
YIQQQQLQGEAKGDEQRLSMPQGSTTNSDIQKFIDLSGTIHDVRKALGRHIKLFPHSARAKLRG
SRPSGNLFRELIQRREKTRERLNQDLLTNKGISSIVDSPPKEKKESSLDSYGTQSKDAVRADYV
NTEPNQGCLTSGHLVEGNDNVIERETLCESQSDLSMGLKANEGGKRSHEVSLPIQASPEHGFVT
KQAHFSSNSVDTVKSDAIVIQPSGSQSPQSYQSQESLRQTGRNRYHRRDLNQMHRDSKPRSQER
PPQMPYSPVGTGREILGQHMAFTHQDNRVALQSSTSQNPQNQFQNSALQMHPVVQTSNAYPQSQ
IHGQHMIVSPPESQNPQNQCQNSTSQVQTSFAYPQTQIPQNPVQSNYQQEGQMQSHEAYNQMWQ
QYYYSYYYYQQQQQLMSEQPQPNQNPQPQLDQNLVQLLSKQYQSQAKTQYLQPQQVEQVNTQQQ
SQEPQNQQQIQFQQQQQQQEWFQQQQQWQQQQYLLYIQQQQLQGEAKGDEQRLSMPQGSTTNSD
IQKFIDLSGTIHDVRKALGRHIKLFPHSARAKLRGSRPSGNLFRELIQRREKTRERLNQDLLTN
KGISSIVDSPPKEKKESSLDSYGTQSKDAVRADYVNTEPNQGCLTSGHLVEGNDNVIERETLCE
SQSDLSMGLKANEGGKRSHEVSLPIQASPEHGFVTKQAHFSSNSVDTVKSDAIVIQPSGSQSPQ
SYQSQESLRQTGRNRYHRRDLNQMHRDSKPRSQERPPQMPYSPVGTGREILGQHMAFTHQDNRV
ALQSSTSQNPQNQFQNSALQMHPVVQTSNAYPQSQIHGQHMIVSPPESQNPQNQCQNSTSQVQT
SFAYPQTQIPQNPVQSNYQQEGQMQSHEAYNQMWQQYYYSYYYYQQQQQLMSEQPQPNQNPQPQ
LDQNLVQLLSKQYQSQAKTQYLQPQQVEQVNTQQQSQEPQNQQQIQFQQQQQQQEWFQQQQQWQ
QQQYLLYIQQQQLQGEAKGDEQRLSMPQGSTTNSDIQKFIDLSGTIHDVRKALGRHIKLFPHSA
RAKLRGSRPSGNLFRELIQRREKTRERLNQDLLTNKGISSIVDSPPKEKKESSLDSYGTQSKDA
VRADYVNTEPNQGCLTSGHLVEGNDNVIERETLCESQSDLSMGLKANEGGKRSHEVSLPIQASP
EHGFVTKQAHFSSNSVDTVKSDAIVIQPSGSQSPQSYQSQESLRQTGRNRYHRRDLNQMHRDSK
PRSQERPPQMPYSPVGTGREILGQHMAFTHQDNRVALQSSTSQNPQNQFQNSALQMHPVVQTSN
AYPQSQIHGQHMIVSPPESQNPQNQCQNSTSQVQTSFAYPQTQIPQNPVQSNYQQEGQMQSHEA
YNQMWQQYYYSYYYYQQQQQLMSEQPQPNQNPQPQLDQNLVQLLSKQYQSQAKTQYLQPQQVEQ
VNTQQQSQEPQNQQQIQFQQQQQQQEWFQQQQQWQQQQYLLYIQQQQLQGEAKGDEQRLSMPQG
STTNSDIQK(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	18823313-18824365(+)
Potential amino acid sequence	MGLKANEGGKRSHEVSLPIQASPEHGFVTKQAHFSSNSVDTVKSDAIVIQPSGSQSPQSYQSQE SLRQTGRNRYHRRDLNQMHRDSKPRSQERPPQMPYSPVGTGREILGQHMAFTHQDNRVALQSST SQNPQNQFQNSALQMHPVVQTSNAYPQSQIHGQHMIVSPPESQNPQNQCQNSTSQVQTSFAYPQ TQIPQNPVQSNYQQEGQMQSHEAYNQMWQQYYYSYYYYQQQQQLMSEQPQPNQNPQPQLDQNLV QLLSKQYQSQAKTQYLQPQQVEQVNTQQQSQEPQNQQQIQFQQQQQQQEWFQQQQQWQQQQYLL YIQQQQLQGEAKGDEQRLSMPQGSTTNSDIQKFIDLSGTIHDVRKALGRHIKLFPHSARAKLRG SRPSGNLFRELIQRREKTRERLNQDLLTNKGISSIVDSPPKEKKESSLDSYGTQSKDAVRADYV NTEPNQGCLTSGHLVEGNDNVIERETLCESQSDLSMGLKANEGGKRSHEVSLPIQASPEHGFVT KQAHFSSNSVDTVKSDAIVIQPSGSQSPQSYQSQESLRQTGRNRYHRRDLNQMHRDSKPRSQER PPQMPYSPVGTGREILGQHMAFTHQDNRVALQSSTSQNPQNQFQNSALQMHPVVQTSNAYPQSQ IHGQHMIVSPPESQNPQNQCQNSTSQVQTSFAYPQTQIPQNPVQSNYQQEGQMQSHEAYNQMWQ QYYYSYYYYQQQQQLMSEQPQPNQNPQPQLDQNLVQLLSKQYQSQAKTQYLQPQQVEQVNTQQQ SQEPQNQQQIQFQQQQQQQEWFQQQQQWQQQQYLLYIQQQQLQGEAKGDEQRLSMPQGSTTNSD IQKFIDLSGTIHDVRKALGRHIKLFPHSARAKLRGSRPSGNLFRELIQRREKTRERLNQDLLTN KGISSIVDSPPKEKKESSLDSYGTQSKDAVRADYVNTEPNQGCLTSGHLVEGNDNVIERETLCE SQSDLSMGLKANEGGKRSHEVSLPIQASPEHGFVTKQAHFSSNSVDTVKSDAIVIQPSGSQSPQ SYQSQESLRQTGRNRYHRRDLNQMHRDSKPRSQERPPQMPYSPVGTGREILGQHMAFTHQDNRV ALQSSTSQNPQNQFQNSALQMHPVVQTSNAYPQSQIHGQHMIVSPPESQNPQNQCQNSTSQVQT SFAYPQTQIPQNPVQSNYQQEGQMQSHEAYNQMWQQYYYSYYYYQQQQQLMSEQPQPNQNPQPQ LDQNLVQLLSKQYQSQAKTQYLQPQQVEQVNTQQQSQEPQNQQQIQFQQQQQQQEWFQQQQQWQ QQQYLLYIQQQQLQGEAKGDEQRLSMPQGSTTNSDIQKFIDLSGTIHDVRKALGRHIKLFPHSA RAKLRGSRPSGNLFRELIQRREKTRERLNQDLLTNKGISSIVDSPPKEKKESSLDSYGTQSKDA VRADYVNTEPNQGCLTSGHLVEGNDNVIERETLCESQSDLSMGLKANEGGKRSHEVSLPIQASP EHGFVTKQAHFSSNSVDTVKSDAIVIQPSGSQSPQSYQSQESLRQTGRNRYHRRDLNQMHRDSK PRSQERPPQMPYSPVGTGREILGQHMAFTHQDNRVALQSSTSQNPQNQFQNSALQMHPVVQTSN AYPQSQIHGQHMIVSPPESQNPQNQCQNSTSQVQTSFAYPQTQIPQNPVQSNYQQEGQMQSHEA YNQMWQQYYYSYYYYQQQQQLMSEQPQPNQNPQPQLDQNLVQLLSKQYQSQAKTQYLQPQQVEQ VNTQQQSQEPQNQQQIQFQQQQQQQEWFQQQQQWQQQQYLLYIQQQQLQGEAKGDEQRLSMPQG STTNSDIQK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT5G46400_circ_g.4

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