Plant Circular RNA Database

Detail information of AT5G60410_circ_g.29

			
						 General Information
					
						CircRNA Name
						AT5G60410_circ_g.29
					
						ID in PlantcircBase
						ath_circ_045010
					
						Alias
						At_ciR241, AT5G60410_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 24297871-24298832  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
					
						Parent gene
						
							AT5G60410						
					
						Parent gene annotation
						
							DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and
 SAP domain
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G60410_circ_g.1 AT5G60410_circ_g.2 AT5G60410_circ_g.3 AT5G60410_circ_g.4 AT5G60410_circ_g.5 AT5G60410_circ_g.6 AT5G60410_circ_g.7 AT5G60410_circ_g.8 AT5G60410_circ_g.9 AT5G60410_circ_g.10 AT5G60410_circ_g.11 AT5G60410_circ_g.12 AT5G60410_circ_g.13 AT5G60410_circ_g.14 AT5G60410_circ_g.15 AT5G60410_circ_g.16 AT5G60410_circ_g.17 AT5G60410_circ_g.18 AT5G60410_circ_g.19 AT5G60410_circ_g.20 AT5G60410_circ_g.21 AT5G60410_circ_g.22 AT5G60410_circ_g.23 AT5G60410_circ_g.24 AT5G60410_circ_g.25 AT5G60410_circ_g.26 AT5G60410_circ_g.27 AT5G60410_circ_g.28 AT5G60410_circ_g.30 AT5G60410_circ_g.31 						
					
						Support reads
						122/4/3
					
						Tissues
						leaf/root, leaf, whole_plant/seedlings
					
						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
						AT5G60410.3:3
AT5G60410.2:3
AT5G60410.4:3
AT5G60410.6:3
AT5G60410.1:3
AT5G60410.5:3

General Information
CircRNA Name	AT5G60410_circ_g.29
ID in PlantcircBase	ath_circ_045010
Alias	At_ciR241, AT5G60410_C2
Organism	Arabidpsis thaliana
Position	chr5: 24297871-24298832 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
Parent gene	AT5G60410
Parent gene annotation	DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain
Parent gene strand	+
Alternative splicing	AT5G60410_circ_g.1 AT5G60410_circ_g.2 AT5G60410_circ_g.3 AT5G60410_circ_g.4 AT5G60410_circ_g.5 AT5G60410_circ_g.6 AT5G60410_circ_g.7 AT5G60410_circ_g.8 AT5G60410_circ_g.9 AT5G60410_circ_g.10 AT5G60410_circ_g.11 AT5G60410_circ_g.12 AT5G60410_circ_g.13 AT5G60410_circ_g.14 AT5G60410_circ_g.15 AT5G60410_circ_g.16 AT5G60410_circ_g.17 AT5G60410_circ_g.18 AT5G60410_circ_g.19 AT5G60410_circ_g.20 AT5G60410_circ_g.21 AT5G60410_circ_g.22 AT5G60410_circ_g.23 AT5G60410_circ_g.24 AT5G60410_circ_g.25 AT5G60410_circ_g.26 AT5G60410_circ_g.27 AT5G60410_circ_g.28 AT5G60410_circ_g.30 AT5G60410_circ_g.31
Support reads	122/4/3
Tissues	leaf/root, leaf, whole_plant/seedlings
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	AT5G60410.3:3 AT5G60410.2:3 AT5G60410.4:3 AT5G60410.6:3 AT5G60410.1:3 AT5G60410.5:3

			
						 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  
						
							CGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTACCCTGTGTGCACATGGGCTGTTTTGACCTT
GATGTGTTTGTGGAGTTGAATCAACGTTCCAGAAAGattacatcttgtattagggatggagtta
acagaatatccttgagtggaggtgacgttcggattttttgttttggggtcagacttgtgaagcg
caggactc

						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: 375
Transcript exons: 24297871-24297978,24298462-24298623,24298728-24298832
ATTACATCTTGTATTAGGGATGGAGTTAACAGAATATCCTTGAGTGGAGGTGACGTTCGGATTT
TTTGTTTTGGGGTCAGACTTGTGAAGCGCAGGACTCTACAACAGGTTCTAAATTTGATTCCAGA
AGAGGGTAAAGGGGAGACTTTTGAAGATGCTCTTGCACGTGTCCGCCGATGCATTGGAGGTGGA
GGTGGAGATGATAATGCCGACAGTGATAGTGACATTGAAGTTGTTGCTGATTTCTTCGGTGTCA
ATCTTCGGTGTCCTATGAGCGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTACCCTGTGTGCA
CATGGGCTGTTTTGACCTTGATGTGTTTGTGGAGTTGAATCAACGTTCCAGAAAG
						
						Genomic sequence
						
							ATTACATCTTGTATTAGGGATGGAGTTAACAGAATATCCTTGAGTGGAGGTGACGTTCGGATTT
TTTGTTTTGGGGTCAGACTTGTGAAGCGCAGGACTCTACAACAGGTACTGATAACATATATGCA
TAAGAAACATTCAAAGATTTGGTCGTATATGTGGTCAATGAAGAGTCCAAACATAAATGTTCAA
AAAGGAACGAAATTAATATTCTGAATACAAAAAGAAAGAATAAATTATGTTGGCGTACCCAAGA
AAGTAATTTTGTGGAAGTTACCTGTGGTTACACACTTACGTTAAACTATTCCCATGTTATTTCC
CACTCCCACTAAATCTAGAAAAGTTAGTCAGATTTCAAATTTCACAGTCCTATTCTTCTTCCTA
TATTTCACGTATATGAGCCACTGAGCCTGGCCTTGTATGAGATTTGGTTACGGAAGTGTAGTCT
GTCCTTGTGCTGCAACATTTATCCCTTTAATCAATATATTTATCACTTTTGTTGGTGTTCTTGT
ATACAGAGGAATTCATATTGTACGTTAATGATCTAATGATCTCCAAGTTGCTTATATATATACT
CATTTTTGCATCTAGGTTCTAAATTTGATTCCAGAAGAGGGTAAAGGGGAGACTTTTGAAGATG
CTCTTGCACGTGTCCGCCGATGCATTGGAGGTGGAGGTGGAGATGATAATGCCGACAGTGATAG
TGACATTGAAGTTGTTGCTGATTTCTTCGGTGTCAATCTTCGGTGTCCTGTAAGTTACTAATAG
CTCGTAGCCCAGTTTTTATACTTATCCTCTTCCTAGGGCTATCTTGCAGACTGAATTTTTTTTA
TTGTCTTTTCTGTTTGCGTCATTAGATGAGCGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTA
CCCTGTGTGCACATGGGCTGTTTTGACCTTGATGTGTTTGTGGAGTTGAATCAACGTTCCAGAA
AG

Sequences
Splice junction sequence	CGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTACCCTGTGTGCACATGGGCTGTTTTGACCTT GATGTGTTTGTGGAGTTGAATCAACGTTCCAGAAAGattacatcttgtattagggatggagtta acagaatatccttgagtggaggtgacgttcggattttttgttttggggtcagacttgtgaagcg caggactc
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: 375 Transcript exons: 24297871-24297978,24298462-24298623,24298728-24298832 ATTACATCTTGTATTAGGGATGGAGTTAACAGAATATCCTTGAGTGGAGGTGACGTTCGGATTT TTTGTTTTGGGGTCAGACTTGTGAAGCGCAGGACTCTACAACAGGTTCTAAATTTGATTCCAGA AGAGGGTAAAGGGGAGACTTTTGAAGATGCTCTTGCACGTGTCCGCCGATGCATTGGAGGTGGA GGTGGAGATGATAATGCCGACAGTGATAGTGACATTGAAGTTGTTGCTGATTTCTTCGGTGTCA ATCTTCGGTGTCCTATGAGCGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTACCCTGTGTGCA CATGGGCTGTTTTGACCTTGATGTGTTTGTGGAGTTGAATCAACGTTCCAGAAAG
Genomic sequence	ATTACATCTTGTATTAGGGATGGAGTTAACAGAATATCCTTGAGTGGAGGTGACGTTCGGATTT TTTGTTTTGGGGTCAGACTTGTGAAGCGCAGGACTCTACAACAGGTACTGATAACATATATGCA TAAGAAACATTCAAAGATTTGGTCGTATATGTGGTCAATGAAGAGTCCAAACATAAATGTTCAA AAAGGAACGAAATTAATATTCTGAATACAAAAAGAAAGAATAAATTATGTTGGCGTACCCAAGA AAGTAATTTTGTGGAAGTTACCTGTGGTTACACACTTACGTTAAACTATTCCCATGTTATTTCC CACTCCCACTAAATCTAGAAAAGTTAGTCAGATTTCAAATTTCACAGTCCTATTCTTCTTCCTA TATTTCACGTATATGAGCCACTGAGCCTGGCCTTGTATGAGATTTGGTTACGGAAGTGTAGTCT GTCCTTGTGCTGCAACATTTATCCCTTTAATCAATATATTTATCACTTTTGTTGGTGTTCTTGT ATACAGAGGAATTCATATTGTACGTTAATGATCTAATGATCTCCAAGTTGCTTATATATATACT CATTTTTGCATCTAGGTTCTAAATTTGATTCCAGAAGAGGGTAAAGGGGAGACTTTTGAAGATG CTCTTGCACGTGTCCGCCGATGCATTGGAGGTGGAGGTGGAGATGATAATGCCGACAGTGATAG TGACATTGAAGTTGTTGCTGATTTCTTCGGTGTCAATCTTCGGTGTCCTGTAAGTTACTAATAG CTCGTAGCCCAGTTTTTATACTTATCCTCTTCCTAGGGCTATCTTGCAGACTGAATTTTTTTTA TTGTCTTTTCTGTTTGCGTCATTAGATGAGCGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTA CCCTGTGTGCACATGGGCTGTTTTGACCTTGATGTGTTTGTGGAGTTGAATCAACGTTCCAGAA AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.397470275

Conservation Information
Conserved circRNAs	NA
PMCS	0.397470275

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24298728-24298829(+)
						
						Potential amino acid sequence
						
							MSGSRIKVAGRFLPCVHMGCFDLDVFVELNQRSRKITSCIRDGVNRISLSGGDVRIFCFGVRLV
KRRTLQQVLNLIPEEGKGETFEDALARVRRCIGGGGGDDNADSDSDIEVVADFFGVNLRCPMSG
SRIKVAGRFLPCVHMGCFDLDVFVELNQRSRKITSCIRDGVNRISLSGGDVRIFCFGVRLVKRR
TLQQVLNLIPEEGKGETFEDALARVRRCIGGGGGDDNADSDSDIEVVADFFGVNLRCPMSGSRI
KVAGRFLPCVHMGCFDLDVFVELNQRSRKITSCIRDGVNRISLSGGDVRIFCFGVRLVKRRTLQ
QVLNLIPEEGKGETFEDALARVRRCIGGGGGDDNADSDSDIEVVADFFGVNLRCPMSGSRIKVA
GRFLPCVHMGCFDLDVFVELNQRSRK(+)
						
						Sponge-miRNAs
						
							ath-miR394a 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24298728-24298829(+)
Potential amino acid sequence	MSGSRIKVAGRFLPCVHMGCFDLDVFVELNQRSRKITSCIRDGVNRISLSGGDVRIFCFGVRLV KRRTLQQVLNLIPEEGKGETFEDALARVRRCIGGGGGDDNADSDSDIEVVADFFGVNLRCPMSG SRIKVAGRFLPCVHMGCFDLDVFVELNQRSRKITSCIRDGVNRISLSGGDVRIFCFGVRLVKRR TLQQVLNLIPEEGKGETFEDALARVRRCIGGGGGDDNADSDSDIEVVADFFGVNLRCPMSGSRI KVAGRFLPCVHMGCFDLDVFVELNQRSRKITSCIRDGVNRISLSGGDVRIFCFGVRLVKRRTLQ QVLNLIPEEGKGETFEDALARVRRCIGGGGGDDNADSDSDIEVVADFFGVNLRCPMSGSRIKVA GRFLPCVHMGCFDLDVFVELNQRSRK(+)
Sponge-miRNAs	ath-miR394a
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT5G60410_circ_g.29

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