Plant Circular RNA Database

Detail information of 4_circ_ig.4

			
						 General Information
					
						CircRNA Name
						4_circ_ig.4
					
						ID in PlantcircBase
						ath_circ_029911
					
						Alias
						AtciR54
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 5059540-5060151  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							4_circ_ig.3 4_circ_ig.5 						
					
						Support reads
						14
					
						Tissues
						root, inflorescences, whole_plant, leaf
					
						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	4_circ_ig.4
ID in PlantcircBase	ath_circ_029911
Alias	AtciR54
Organism	Arabidpsis thaliana
Position	chr4: 5059540-5060151 JBrowse»
Reference genome	TAIR10.38
Type	ig-circRNA
Identification method	circRNA_finder, find_circ, CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	4_circ_ig.3 4_circ_ig.5
Support reads	14
Tissues	root, inflorescences, whole_plant, leaf
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  
						
							TTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGT
TGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTCctcagtagaatgttctggagatgtagtc
atccatatctgcttgagtgtactcagcaagcatgaccggttcttgatgtggctccgccatctcc
tcgtcatt

									
								

					

						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: 166
Transcript exons: 5059540-5059674,5060121-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACCCCTGCTGTTACTCCAGCTGTTATTCATTTC
Transcript length: 194
Transcript exons: 5059540-5059690,5060109-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTCACCGGTTGCATCCCTGCTGTTACTCCAGCTGTTATTCATT
TC
Transcript length: 211
Transcript exons: 5059540-5059619,5060021-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGA
TCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTAC
TCCAGCTGTTATTCATTTC
Transcript length: 220
Transcript exons: 5059540-5059628,5060021-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTC
ATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCC
TGCTGTTACTCCAGCTGTTATTCATTTC
Transcript length: 273
Transcript exons: 5059540-5059681,5060021-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATC
GAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTC
CAGCTGTTATTCATTTC
Transcript length: 273
Transcript exons: 5059540-5059682,5060022-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCACCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATC
GAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTC
CAGCTGTTATTCATTTC
Transcript length: 317
Transcript exons: 5059540-5059710,5060006-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACTGAGAAAGATGTTGTCCCAAA
ACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAAT
TGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTC
Transcript length: 322
Transcript exons: 5059540-5059730,5060021-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAC
CCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATCGAGTAATTCATAAAA
AAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTCCAGCTGTTATTCATT
TC
Transcript length: 335
Transcript exons: 5059540-5059744,5060022-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG
TTCTAGCACTCTTCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATCGA
GTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTCCA
GCTGTTATTCATTTC
Transcript length: 341
Transcript exons: 5059540-5059737,5060009-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG
TTCTAGGAAAGATGTTGTCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGC
GATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTT
ACTCCAGCTGTTATTCATTTC
Transcript length: 351
Transcript exons: 5059540-5059756,5060018-5060151
CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG
TTCTAGCACTCTTCCTCCTCTTGTGTGTCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACT
CTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCAT
CCCTGCTGTTACTCCAGCTGTTATTCATTTC
						
					

						Genomic sequence
						
							CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC
CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT
GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG
TTCTAGCACTCTTCCTCCTCTTGTGTTCCATTGGCTCATGAGACGAGTGCCTTGCGGAAACTTG
TGGAACGGTGTGGTCCCTTTGTTGATAGGTGGATTGCCTTGGTGGGAGAAAGTCGTGGCAGCTG
GATGGCATGTCTTCAGGCGGGTTGTCATTGAAGTCCTGTCGGGCATTTTCACTTCTCCTTGCGA
TTGAGTGGTTTGGGCAATTCCACTAAGAGACCACTCGATCACACCACTTCCATGTTGCGATCGA
GTAGTTTGACATTTTTGTTGAGAAAGATGTTGTCCCAAAACCAGTAGATCGCACTCTCGAGCTT
TTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGT
TGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTC
						
					

			
		

Sequences
Splice junction sequence	TTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGT TGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTCctcagtagaatgttctggagatgtagtc atccatatctgcttgagtgtactcagcaagcatgaccggttcttgatgtggctccgccatctcc tcgtcatt
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: 166 Transcript exons: 5059540-5059674,5060121-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACCCCTGCTGTTACTCCAGCTGTTATTCATTTC Transcript length: 194 Transcript exons: 5059540-5059690,5060109-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTCACCGGTTGCATCCCTGCTGTTACTCCAGCTGTTATTCATT TC Transcript length: 211 Transcript exons: 5059540-5059619,5060021-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGA TCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTAC TCCAGCTGTTATTCATTTC Transcript length: 220 Transcript exons: 5059540-5059628,5060021-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTC ATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCC TGCTGTTACTCCAGCTGTTATTCATTTC Transcript length: 273 Transcript exons: 5059540-5059681,5060021-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATC GAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTC CAGCTGTTATTCATTTC Transcript length: 273 Transcript exons: 5059540-5059682,5060022-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCACCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATC GAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTC CAGCTGTTATTCATTTC Transcript length: 317 Transcript exons: 5059540-5059710,5060006-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACTGAGAAAGATGTTGTCCCAAA ACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAAT TGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTC Transcript length: 322 Transcript exons: 5059540-5059730,5060021-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAC CCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATCGAGTAATTCATAAAA AAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTCCAGCTGTTATTCATT TC Transcript length: 335 Transcript exons: 5059540-5059744,5060022-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG TTCTAGCACTCTTCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGCGATCGA GTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTTACTCCA GCTGTTATTCATTTC Transcript length: 341 Transcript exons: 5059540-5059737,5060009-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG TTCTAGGAAAGATGTTGTCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACTCTCATCATGC GATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCATCCCTGCTGTT ACTCCAGCTGTTATTCATTTC Transcript length: 351 Transcript exons: 5059540-5059756,5060018-5060151 CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG TTCTAGCACTCTTCCTCCTCTTGTGTGTCCCAAAACCAGTAGATCGCACTCTCGAGCTTTTACT CTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGTTGCAT CCCTGCTGTTACTCCAGCTGTTATTCATTTC
Genomic sequence	CTCAGTAGAATGTTCTGGAGATGTAGTCATCCATATCTGCTTGAGTGTACTCAGCAAGCATGAC CGGTTCTTGATGTGGCTCCGCCATCTCCTCGTCATTATGCTCGATCGCAACCCCAGCAGGTTGT GAAGCACGTCGCTCATGTGTTCTACGACCCGACATTATTCGACCCTTAATTGATGAATGTACAG TTCTAGCACTCTTCCTCCTCTTGTGTTCCATTGGCTCATGAGACGAGTGCCTTGCGGAAACTTG TGGAACGGTGTGGTCCCTTTGTTGATAGGTGGATTGCCTTGGTGGGAGAAAGTCGTGGCAGCTG GATGGCATGTCTTCAGGCGGGTTGTCATTGAAGTCCTGTCGGGCATTTTCACTTCTCCTTGCGA TTGAGTGGTTTGGGCAATTCCACTAAGAGACCACTCGATCACACCACTTCCATGTTGCGATCGA GTAGTTTGACATTTTTGTTGAGAAAGATGTTGTCCCAAAACCAGTAGATCGCACTCTCGAGCTT TTACTCTCATCATGCGATCGAGTAATTCATAAAAAAAATTGATTTTTTTTATTTGAACACCGGT TGCATCCCTGCTGTTACTCCAGCTGTTATTCATTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.736721103

Conservation Information
Conserved circRNAs	NA
PMCS	0.736721103

			
						 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
						Chu et al., 2017;Zhang et al., 2019

circRNA

Detail information of 4_circ_ig.4

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