Plant Circular RNA Database

Detail information of 1_circ_ig.28

			
						 General Information
					
						CircRNA Name
						1_circ_ig.28
					
						ID in PlantcircBase
						ath_circ_005588
					
						Alias
						At_ciR2663, Ath_circ_FC0616, Ath_circ_FC0617, AtciR89
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 12197021-12199193  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRI, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT1G33615_circ_g.1 1_circ_igg.2 AT1G33615_circ_g.3 AT1G33615_circ_g.4 AT1G33615_circ_g.5 AT1G33615_circ_g.6 AT1G33615_circ_g.7 AT1G33615_circ_g.8 AT1G33615_circ_g.9 AT1G33615_circ_g.10 AT1G33615_circ_g.11 1_circ_igg.12 1_circ_ag.13 AT1G33615_circ_g.14 AT1G33615_circ_g.15 AT1G33615_circ_g.16 1_circ_igg.17 AT1G33615_circ_g.18 1_circ_igg.19 1_circ_igg.20 1_circ_ig.21 1_circ_ig.22 1_circ_ig.23 1_circ_ig.24 1_circ_ig.25 1_circ_ig.26 1_circ_ig.27 1_circ_ig.29 1_circ_igg.30 AT1G33680_circ_g.1 AT1G33680_circ_g.2 AT1G33680_circ_g.3 AT1G33680_circ_g.4 AT1G33680_circ_g.5 AT1G33680_circ_g.6 AT1G33680_circ_g.7 AT1G33680_circ_g.8 AT1G33680_circ_g.9 AT1G33700_circ_g.1 AT1G33700_circ_g.2 AT1G33700_circ_g.3 AT1G33700_circ_g.4 AT1G33700_circ_g.5 AT1G33790_circ_g.1 AT1G33810_circ_g.1 AT1G33930_circ_g.1 AT1G33960_circ_g.1 AT1G33970_circ_g.1 AT1G33970_circ_g.2 AT1G33970_circ_g.3 AT1G33970_circ_g.4 AT1G33970_circ_g.5 AT1G33980_circ_g.1 AT1G33980_circ_g.2 AT1G33980_circ_g.3 AT1G33980_circ_g.4 AT1G33980_circ_g.5 AT1G33980_circ_g.6 AT1G33980_circ_g.7 AT1G33980_circ_g.8 AT1G33980_circ_g.9 AT1G33990_circ_g.1 AT1G33990_circ_g.2 AT1G34020_circ_g.1 AT1G34020_circ_g.2 AT1G34020_circ_g.3 1_circ_ig.4 1_circ_ig.5 1_circ_ig.6 1_circ_ig.7 1_circ_igg.8 1_circ_igg.9 1_circ_igg.10 1_circ_ig.11 1_circ_igg.12 1_circ_igg.13 1_circ_igg.14 1_circ_igg.15 1_circ_ig.16 						
					
						Support reads
						3/11
					
						Tissues
						leaf/root, inflorescences, whole_plant
					
						Exon boundary  
						
							No-No							"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
						NA

General Information
CircRNA Name	1_circ_ig.28
ID in PlantcircBase	ath_circ_005588
Alias	At_ciR2663, Ath_circ_FC0616, Ath_circ_FC0617, AtciR89
Organism	Arabidpsis thaliana
Position	chr1: 12197021-12199193 JBrowse»
Reference genome	TAIR10.38
Type	ig-circRNA
Identification method	CIRI, circRNA_finder, find_circ, CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT1G33615_circ_g.1 1_circ_igg.2 AT1G33615_circ_g.3 AT1G33615_circ_g.4 AT1G33615_circ_g.5 AT1G33615_circ_g.6 AT1G33615_circ_g.7 AT1G33615_circ_g.8 AT1G33615_circ_g.9 AT1G33615_circ_g.10 AT1G33615_circ_g.11 1_circ_igg.12 1_circ_ag.13 AT1G33615_circ_g.14 AT1G33615_circ_g.15 AT1G33615_circ_g.16 1_circ_igg.17 AT1G33615_circ_g.18 1_circ_igg.19 1_circ_igg.20 1_circ_ig.21 1_circ_ig.22 1_circ_ig.23 1_circ_ig.24 1_circ_ig.25 1_circ_ig.26 1_circ_ig.27 1_circ_ig.29 1_circ_igg.30 AT1G33680_circ_g.1 AT1G33680_circ_g.2 AT1G33680_circ_g.3 AT1G33680_circ_g.4 AT1G33680_circ_g.5 AT1G33680_circ_g.6 AT1G33680_circ_g.7 AT1G33680_circ_g.8 AT1G33680_circ_g.9 AT1G33700_circ_g.1 AT1G33700_circ_g.2 AT1G33700_circ_g.3 AT1G33700_circ_g.4 AT1G33700_circ_g.5 AT1G33790_circ_g.1 AT1G33810_circ_g.1 AT1G33930_circ_g.1 AT1G33960_circ_g.1 AT1G33970_circ_g.1 AT1G33970_circ_g.2 AT1G33970_circ_g.3 AT1G33970_circ_g.4 AT1G33970_circ_g.5 AT1G33980_circ_g.1 AT1G33980_circ_g.2 AT1G33980_circ_g.3 AT1G33980_circ_g.4 AT1G33980_circ_g.5 AT1G33980_circ_g.6 AT1G33980_circ_g.7 AT1G33980_circ_g.8 AT1G33980_circ_g.9 AT1G33990_circ_g.1 AT1G33990_circ_g.2 AT1G34020_circ_g.1 AT1G34020_circ_g.2 AT1G34020_circ_g.3 1_circ_ig.4 1_circ_ig.5 1_circ_ig.6 1_circ_ig.7 1_circ_igg.8 1_circ_igg.9 1_circ_igg.10 1_circ_ig.11 1_circ_igg.12 1_circ_igg.13 1_circ_igg.14 1_circ_igg.15 1_circ_ig.16
Support reads	3/11
Tissues	leaf/root, inflorescences, whole_plant
Exon boundary	No-No "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	NA

			
						 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  
						
							AACAAGATTACCTTGTCAGTCATGAGTATATTAAAGCTCATCTGAAACTTTTGCTCTTTCTTCA
TAAAACCTGTTTTAAACTGCAAACAATGCTCGTGTActttgttggctactgaactgtcttcaaa
acttccttaaagctaaataatccttcatcttgaggacctttgtcaaaaattccatttcaactga
agaaagct

									
								

					

						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: 239
Transcript exons: 12197021-12197076,12197091-12197191,12199112-12199193
CTTTGTTGGCTACTGAACTGTCTTCAAAACTTCCTTAAAGCTAAATAATCCTTCATTCAAAAAT
TCCATTTCAACTGAAGAAAGCTCTTGAAACCAAAGAAACCTTGTTAATAACACGCAGCTTAAAC
ATAGAACGAATAACTTAAATTCAGAAAATGTCATGAGTATATTAAAGCTCATCTGAAACTTTTG
CTCTTTCTTCATAAAACCTGTTTTAAACTGCAAACAATGCTCGTGTA
						
					

						Genomic sequence
						
							CTTTGTTGGCTACTGAACTGTCTTCAAAACTTCCTTAAAGCTAAATAATCCTTCATCTTGAGGA
CCTTTGTCAAAAATTCCATTTCAACTGAAGAAAGCTCTTGAAACCAAAGAAACCTTGTTAATAA
CACGCAGCTTAAACATAGAACGAATAACTTAAATTCAGAAAATCATAAAACCAAAAATGACAAA
CTTACAAAATACTCCCTGTTGACATTTGGTTGCTTCCTCAGCTCATATTATCTTAACGGTAATA
TACATTGTTGGAAGCTGCTGGAAATTTCAAGTCAGCTTTATCTTCTCTAGTTCACCTTATCTAG
TTCTTATTCAAAGATAAAAAATAAACCCGACAAAAGTTTTTTAAGATATAGAATGGTACGGAAG
TAAACTTTTTTGGGATAGTGCAAGCCTCTATATCCTTCGTATCTAATTGCGGTAAAGGAGAGAG
AGGAAGATACTTGACCTTAACATTTGTATGTCCTTGCTAGCGAATAGTCTCCCTTTTGTTCTTT
GCAACTTAAGGATCTCTTCACTTGTGAGGAATGATCTTTATTACTAAGTCAGCAACAAAATAGA
GTAACATAGAGCAAATAAAATGCAAAAGGCTGAACTAAACCAGTAAAAAATTACGGAATTGTAA
AGTTTAACTACATCTTACGTGACCCTTTTCACAAGGGTTGTTAGCTCTGAGATGGAGAAATAGG
AGTGTGGGATCCAGATAAAGCGACAATGTCCTTGTCAGACAAGCCCATCCGCTTAGCAAATACA
TCTCTCAACAGATCAAAACCTTTTGTAGCATCAGGGAGACGACCCTCAGGAGGTGTATGGGGCT
TGTCCTGAAAGCAAGATATGCATGTTAGAAACAGACAATCAAGTCCCACAGCGTTTCAGTATTA
CAAGTATTGAGAGAATGTCTAAATTATCAATCAGCCATGTCAACAAAGAAAGCAGAACACACAC
TCTCAGGAATGATTAACCTCTCTTCAAGGGTGGAAATGAATTTTAGGGCCACCAGTAACTTCAA
CGGCCACAGCACCTGAAAGATCAATTTCTCACCAAAAAGACATTGTAAGTTAGAATCCAAACCC
TAAAGTTATCACCGTCAACAAATTAGAACTTTTCAAAAATCTAAAATCAATCAGCAAGAGAGAT
AGTAGGGAATGCTACCTGATGGGGTCCAGCAACCTAAGAGCAATTTGAATACCATAGTTGGCTC
CATTAACTTGCTCTGCATCAAACCTCATTGTTCTGAATGGACCTCCAGTTCTTGACTGACAATC
GTAAGTTCCAGTAGAGTGCCATCTGCAGAAGAAATCAGATCAGCCATGAGAACCTAAATATTAG
AAACCAACCACACACTGATATAGTTAGTTATTTACGCATGATGCATATCACAACCAATAAAAAT
TAGCAATAAACGGAGACAAATGTGCTTACTTATTTTTGTTTCCTTTCGAATTATGCATATCACA
ACTAAGGCACAATGAGAACGATCACTAATGTGACAAATGTCTTGGTCATCGACTCTGGAATCAG
AGAGGACATTAAAAAGCCTCAGAAATTGGTAGAGACACACATTGTCTTAAAAAGATGACTACGG
TTCAGGGGTTTTGACAAGAAAGTGTACCTCTCAGTGCAAGTCCACCAGCCATTATTCAAGGATC
ATTAGTTCAAACCTTATTCCCTTTATACGTTGAATTTGTGCTTTATATGGCGAGAACTGCATTG
ATATGGATAACTGTGAATTTCAGTATAAATCAAGGTTACGAAACTAGAAAATGATTTACCAATT
CGTCACGAAAGCTTACCTTATTCAAGTCTCTTTATCAACTCCTACATCCGCACACTCACACAAA
ATATTCCAGCAAGAAACACATCAATTAAGGAACAATATCTACATCAAACAGACAGAACCACACA
ACTTAAATATGAGAAAACACACAATGCTATAAAGCACTAACCTTTTTCTCAAATTTTGATACCC
GGTCGGAGCTATCTTCTGAGATTAAAGTGGTTTTACATAAACTCCCATTGGTTCTAATAGAAAA
GAGTTTAAAACGATGAAAAAGATTTAACAAGATTACCTTGTCAGTCATGAGTATATTAAAGCTC
ATCTGAAACTTTTGCTCTTTCTTCATAAAACCTGTTTTAAACTGCAAACAATGCTCGTGTA
						
					

			
		

Sequences
Splice junction sequence	AACAAGATTACCTTGTCAGTCATGAGTATATTAAAGCTCATCTGAAACTTTTGCTCTTTCTTCA TAAAACCTGTTTTAAACTGCAAACAATGCTCGTGTActttgttggctactgaactgtcttcaaa acttccttaaagctaaataatccttcatcttgaggacctttgtcaaaaattccatttcaactga agaaagct
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: 239 Transcript exons: 12197021-12197076,12197091-12197191,12199112-12199193 CTTTGTTGGCTACTGAACTGTCTTCAAAACTTCCTTAAAGCTAAATAATCCTTCATTCAAAAAT TCCATTTCAACTGAAGAAAGCTCTTGAAACCAAAGAAACCTTGTTAATAACACGCAGCTTAAAC ATAGAACGAATAACTTAAATTCAGAAAATGTCATGAGTATATTAAAGCTCATCTGAAACTTTTG CTCTTTCTTCATAAAACCTGTTTTAAACTGCAAACAATGCTCGTGTA
Genomic sequence	CTTTGTTGGCTACTGAACTGTCTTCAAAACTTCCTTAAAGCTAAATAATCCTTCATCTTGAGGA CCTTTGTCAAAAATTCCATTTCAACTGAAGAAAGCTCTTGAAACCAAAGAAACCTTGTTAATAA CACGCAGCTTAAACATAGAACGAATAACTTAAATTCAGAAAATCATAAAACCAAAAATGACAAA CTTACAAAATACTCCCTGTTGACATTTGGTTGCTTCCTCAGCTCATATTATCTTAACGGTAATA TACATTGTTGGAAGCTGCTGGAAATTTCAAGTCAGCTTTATCTTCTCTAGTTCACCTTATCTAG TTCTTATTCAAAGATAAAAAATAAACCCGACAAAAGTTTTTTAAGATATAGAATGGTACGGAAG TAAACTTTTTTGGGATAGTGCAAGCCTCTATATCCTTCGTATCTAATTGCGGTAAAGGAGAGAG AGGAAGATACTTGACCTTAACATTTGTATGTCCTTGCTAGCGAATAGTCTCCCTTTTGTTCTTT GCAACTTAAGGATCTCTTCACTTGTGAGGAATGATCTTTATTACTAAGTCAGCAACAAAATAGA GTAACATAGAGCAAATAAAATGCAAAAGGCTGAACTAAACCAGTAAAAAATTACGGAATTGTAA AGTTTAACTACATCTTACGTGACCCTTTTCACAAGGGTTGTTAGCTCTGAGATGGAGAAATAGG AGTGTGGGATCCAGATAAAGCGACAATGTCCTTGTCAGACAAGCCCATCCGCTTAGCAAATACA TCTCTCAACAGATCAAAACCTTTTGTAGCATCAGGGAGACGACCCTCAGGAGGTGTATGGGGCT TGTCCTGAAAGCAAGATATGCATGTTAGAAACAGACAATCAAGTCCCACAGCGTTTCAGTATTA CAAGTATTGAGAGAATGTCTAAATTATCAATCAGCCATGTCAACAAAGAAAGCAGAACACACAC TCTCAGGAATGATTAACCTCTCTTCAAGGGTGGAAATGAATTTTAGGGCCACCAGTAACTTCAA CGGCCACAGCACCTGAAAGATCAATTTCTCACCAAAAAGACATTGTAAGTTAGAATCCAAACCC TAAAGTTATCACCGTCAACAAATTAGAACTTTTCAAAAATCTAAAATCAATCAGCAAGAGAGAT AGTAGGGAATGCTACCTGATGGGGTCCAGCAACCTAAGAGCAATTTGAATACCATAGTTGGCTC CATTAACTTGCTCTGCATCAAACCTCATTGTTCTGAATGGACCTCCAGTTCTTGACTGACAATC GTAAGTTCCAGTAGAGTGCCATCTGCAGAAGAAATCAGATCAGCCATGAGAACCTAAATATTAG AAACCAACCACACACTGATATAGTTAGTTATTTACGCATGATGCATATCACAACCAATAAAAAT TAGCAATAAACGGAGACAAATGTGCTTACTTATTTTTGTTTCCTTTCGAATTATGCATATCACA ACTAAGGCACAATGAGAACGATCACTAATGTGACAAATGTCTTGGTCATCGACTCTGGAATCAG AGAGGACATTAAAAAGCCTCAGAAATTGGTAGAGACACACATTGTCTTAAAAAGATGACTACGG TTCAGGGGTTTTGACAAGAAAGTGTACCTCTCAGTGCAAGTCCACCAGCCATTATTCAAGGATC ATTAGTTCAAACCTTATTCCCTTTATACGTTGAATTTGTGCTTTATATGGCGAGAACTGCATTG ATATGGATAACTGTGAATTTCAGTATAAATCAAGGTTACGAAACTAGAAAATGATTTACCAATT CGTCACGAAAGCTTACCTTATTCAAGTCTCTTTATCAACTCCTACATCCGCACACTCACACAAA ATATTCCAGCAAGAAACACATCAATTAAGGAACAATATCTACATCAAACAGACAGAACCACACA ACTTAAATATGAGAAAACACACAATGCTATAAAGCACTAACCTTTTTCTCAAATTTTGATACCC GGTCGGAGCTATCTTCTGAGATTAAAGTGGTTTTACATAAACTCCCATTGGTTCTAATAGAAAA GAGTTTAAAACGATGAAAAAGATTTAACAAGATTACCTTGTCAGTCATGAGTATATTAAAGCTC ATCTGAAACTTTTGCTCTTTCTTCATAAAACCTGTTTTAAACTGCAAACAATGCTCGTGTA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.378016512

Conservation Information
Conserved circRNAs	NA
PMCS	0.378016512

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to methyl jasmonate

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to methyl jasmonate

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of 1_circ_ig.28

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