Plant Circular RNA Database

Detail information of POPTR_0001s26030_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0001s26030_circ_g.2
					
						ID in PlantcircBase
						pop_circ_000270
					
						Alias
						Chr01:26318377-26321428
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr1: 25128922-25131973  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0001s26030						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						stem xylem
					
						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  
						
							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
						POPTR_0001s26030.1:7

General Information
CircRNA Name	POPTR_0001s26030_circ_g.2
ID in PlantcircBase	pop_circ_000270
Alias	Chr01:26318377-26321428
Organism	Populus trichocarpa
Position	chr1: 25128922-25131973 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0001s26030
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	stem xylem
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	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	POPTR_0001s26030.1:7

			
						 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  
						
							TCTTTGTGTAATAAGAATCGTCATCGTCATCACCATCTGAGATGACCAAATCATCACTGTTATT
ATCTTCATCTGAATCTTTACCCTCCCAGTCTTTATCcttttcctttcttacgctgtagatccac
cattttcccctgtacagcaattgcagcctcacgtgcctgcaaaagaaatgatgaatacaaaaaa
tctctgca

									
								

					

						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
						
							CTTTTCCTTTCTTACGCTGTAGATCCACCATTTTCCCCTGTACAGCAATTGCAGCCTCACGTGC
CTGCAAAAGAAATGATGAATACAAAAAATCTCTGCATGTAAATTGCCAGGGCAAAAATTTCTTG
TAAAAATCAAGACCAAAAACACAATTTGTTTGCACCAAACCTTGTACTCATCAATAGCATCTTG
TGCAAAAGAAATGTCTACATCCTTTTCCCTGTACCACACATCATTAACTATTAAATGTCAGAGC
AACTATCACAAACACCTACTCATACATCACTACTTCATCAGTGGATAGTCAAGAAGCTAATTTC
ATAAGCATGGTGTTGGACCCCATAACCCAGGCAAAAAAGACCACATCTATGATGTAATTATGCA
TAAAAAAGGTATATAAGATTTTCAGAAGTACCACTCAAAATAATAAGACTAGTATAGTTTAGAA
TACCAAGTAGCTTCAGCATAAGAGAGTCCTTGCCACTTGACTAAATACTCCGGCACAACATTTC
CAGAGCTATCTTTATTGATTCGATCAGCAATAATTCTCTCCACCTACAAAAACATATAAACAAG
AATTGGAGTGAAAGAGATTTTAAAAACAGTGTAAGATTATAAAAAAGAAAAGGAAAAAAGACCA
CAATAAAGTAATGCTAAAAAGATAAACCTGACTATTTTGCTTGATTAGATCCAAATCCATTTCC
TTGCTCACATCATTCACCTCGATCTGATAGATGAAAACCAAACGTTATCCCAAATAACCAATTT
GTCAGGCAACTTTAATTTGTATTTAAGTAAACTATGTAAAACCAGAAAGATAATTTGGATCGGG
GAATATAATGTTGAAAAGACAAGCATTTGTGCATTTCTATAATTACAAGTATCTAAGTATCAAC
ATGCCAAGTTGGACTACCATCTTGGAAAAATAAACATCTGACTTGCAAGACAACTAAATTCCAA
TTATATCACCTATTCATTCTGGGTCCTTGTAAATAATATACTAGTACAACATATGAAGCTATTT
CATTGTTGTAGAAACAATGTTTGTGTATTTCTATACAAATATCTCACATCCACAGCAGGTAACA
AAGTAAACTCATATCAAGAGTTTTTTTATCATATCTAACCATGCACATCCCAGCATTTCTCCCT
CTTCTTCTCACATACTATTATGAAAAGAAAAGTTATACCTCCTCGCGTGTAAATTTTCTCCTGT
ACCTCACATCTTCCATCACTTTTTTAGTGTAGTTCAGTACCTTCTTAAAACCACTCAGCTGGTG
ACACAAAAAACAGGCAGAAAATCAGGCAACGTAAATAGCAGATAAAAAAAATCAAAGCAGAGTA
AATCAAAACCAAAAAATGCATCTAAAATTAGAGCTTAAATTGCATGCATAAGGAACAGAATTAT
AGCAATCAAAAATGCATCTAAAAAATAGAGCTTAAATTGCATGCATAAGCAACAGAAATACAGC
AATCATACATTTTGTAATTCAGAGAATGATTTCCATTGGCAGTGCAAATGTGACTGGCCTTTCC
ACTTTATCAAGAACTCCATTTCTTTCCAATCAAGAGCAGAATCAAACAGGTGGCTTAAGAGAAT
AGGTGCTGTTGATCTATTGTTCCTCACTGCATCTTCAGCCATGCCCCTTGGCTGATGCCACAGT
ACCCTTTCAATGGAGTCACCATCTTCTTCTTCAACTTCTTCCTATTTTGGGGAAGACAAAAATA
AGGAAATGTAATAAGAGCAGACATAGTAATGAGAGGATCCATTAAAGCACTGAAGCCTGTGAAG
ACTAGTATAATAAAATCCAAAGCACTACCACAATTGCAAAAACAAGAACAAAGTTAAGATAAAA
TAATCTTTAAGAGCAGACATAGTAATGAGAGGATCCATTAAACTACTGAAGCCTGTGAAGTCTA
GTATAATCCAATCCAAAGTACAACCACAATTGCAGAAACAAGAACAATGTTAGGATATAATAAT
CTTTAAGTACAATTACATATAAAATAAGAACAAGAAGATTAGGAATTCCAAATGATTTCCAGTC
ATCATTCACCTCTACCACAAAAAAAAAAAAAATTGAGACCTACCTAGAATCCTCCAACCATACA
CCACAAGGACTGATCTGACCTCATTGATAGGATTTTGGACAAAAAAATTAAAATATCAAAAATT
TGGCTAAACATAGAAATGCATGGATTCTACAAGAATATCCCAGTGTAAATTTCCCCTAGAGAGC
ATAAATCATACACGTTGCAAAACCCGGCTTACCAGCTAGGCTGGGGAAAAAGAGAGGCCTGACA
TAGTTAAACAAACAAACATGCGCATGCAAAAAAAAAATGGAGTTGAGACCAACGACCCTGATTA
TTTTGGGCACAAGACCAATTTACTTTCACTTTCATTGCAAAAACTCATGCACCTTCAGTTTTAA
AAACTTGAAGAAAAGAAAGATAAAAGGCAAATTTAAAAAAGAACATCATACAAACATGCCCTGA
TCTGTAAGATGATAATTTCTAACCAAACCAGCTAGATCATAACATTTTTTCATGCAGATAAAAC
AATAAAGAAAGTTAGGTTTGTGGTAAAATATAGTACGGTAGACTGCACCTTTTGGGCCTTCTTC
TTTTTCCCTTCATCAATTTCTTCGCTTTCATCACTTTCAACATATGACACCTTACGAACCGACC
TGCTAGAAGTTCGAACCTCATTGTTTCTTCCACCAATGTTTGTTGACATAGCCGACCGGGCATT
AGATTTACGAAAATGTGCACCTCTCTTGGTCATGTTCTTTGAAACAGCATCACTATCACTGTCA
GAATCCTCTGCTGAATACTCATCTTCTTCAAACGATGGTTTCCCTCTCTTTTGTCGTCCAGAAG
CATGCAATGACTTGTTCTCTTTGGCAGATTTTGTATTCCGCCCACTTTTACCATGTTGCCTACT
CTTAGGTTTCTTTGTGTAATAAGAATCGTCATCGTCATCACCATCTGAGATGACCAAATCATCA
CTGTTATTATCTTCATCTGAATCTTTACCCTCCCAGTCTTTATC
						
					

			
		

Sequences
Splice junction sequence	TCTTTGTGTAATAAGAATCGTCATCGTCATCACCATCTGAGATGACCAAATCATCACTGTTATT ATCTTCATCTGAATCTTTACCCTCCCAGTCTTTATCcttttcctttcttacgctgtagatccac cattttcccctgtacagcaattgcagcctcacgtgcctgcaaaagaaatgatgaatacaaaaaa tctctgca
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	CTTTTCCTTTCTTACGCTGTAGATCCACCATTTTCCCCTGTACAGCAATTGCAGCCTCACGTGC CTGCAAAAGAAATGATGAATACAAAAAATCTCTGCATGTAAATTGCCAGGGCAAAAATTTCTTG TAAAAATCAAGACCAAAAACACAATTTGTTTGCACCAAACCTTGTACTCATCAATAGCATCTTG TGCAAAAGAAATGTCTACATCCTTTTCCCTGTACCACACATCATTAACTATTAAATGTCAGAGC AACTATCACAAACACCTACTCATACATCACTACTTCATCAGTGGATAGTCAAGAAGCTAATTTC ATAAGCATGGTGTTGGACCCCATAACCCAGGCAAAAAAGACCACATCTATGATGTAATTATGCA TAAAAAAGGTATATAAGATTTTCAGAAGTACCACTCAAAATAATAAGACTAGTATAGTTTAGAA TACCAAGTAGCTTCAGCATAAGAGAGTCCTTGCCACTTGACTAAATACTCCGGCACAACATTTC CAGAGCTATCTTTATTGATTCGATCAGCAATAATTCTCTCCACCTACAAAAACATATAAACAAG AATTGGAGTGAAAGAGATTTTAAAAACAGTGTAAGATTATAAAAAAGAAAAGGAAAAAAGACCA CAATAAAGTAATGCTAAAAAGATAAACCTGACTATTTTGCTTGATTAGATCCAAATCCATTTCC TTGCTCACATCATTCACCTCGATCTGATAGATGAAAACCAAACGTTATCCCAAATAACCAATTT GTCAGGCAACTTTAATTTGTATTTAAGTAAACTATGTAAAACCAGAAAGATAATTTGGATCGGG GAATATAATGTTGAAAAGACAAGCATTTGTGCATTTCTATAATTACAAGTATCTAAGTATCAAC ATGCCAAGTTGGACTACCATCTTGGAAAAATAAACATCTGACTTGCAAGACAACTAAATTCCAA TTATATCACCTATTCATTCTGGGTCCTTGTAAATAATATACTAGTACAACATATGAAGCTATTT CATTGTTGTAGAAACAATGTTTGTGTATTTCTATACAAATATCTCACATCCACAGCAGGTAACA AAGTAAACTCATATCAAGAGTTTTTTTATCATATCTAACCATGCACATCCCAGCATTTCTCCCT CTTCTTCTCACATACTATTATGAAAAGAAAAGTTATACCTCCTCGCGTGTAAATTTTCTCCTGT ACCTCACATCTTCCATCACTTTTTTAGTGTAGTTCAGTACCTTCTTAAAACCACTCAGCTGGTG ACACAAAAAACAGGCAGAAAATCAGGCAACGTAAATAGCAGATAAAAAAAATCAAAGCAGAGTA AATCAAAACCAAAAAATGCATCTAAAATTAGAGCTTAAATTGCATGCATAAGGAACAGAATTAT AGCAATCAAAAATGCATCTAAAAAATAGAGCTTAAATTGCATGCATAAGCAACAGAAATACAGC AATCATACATTTTGTAATTCAGAGAATGATTTCCATTGGCAGTGCAAATGTGACTGGCCTTTCC ACTTTATCAAGAACTCCATTTCTTTCCAATCAAGAGCAGAATCAAACAGGTGGCTTAAGAGAAT AGGTGCTGTTGATCTATTGTTCCTCACTGCATCTTCAGCCATGCCCCTTGGCTGATGCCACAGT ACCCTTTCAATGGAGTCACCATCTTCTTCTTCAACTTCTTCCTATTTTGGGGAAGACAAAAATA AGGAAATGTAATAAGAGCAGACATAGTAATGAGAGGATCCATTAAAGCACTGAAGCCTGTGAAG ACTAGTATAATAAAATCCAAAGCACTACCACAATTGCAAAAACAAGAACAAAGTTAAGATAAAA TAATCTTTAAGAGCAGACATAGTAATGAGAGGATCCATTAAACTACTGAAGCCTGTGAAGTCTA GTATAATCCAATCCAAAGTACAACCACAATTGCAGAAACAAGAACAATGTTAGGATATAATAAT CTTTAAGTACAATTACATATAAAATAAGAACAAGAAGATTAGGAATTCCAAATGATTTCCAGTC ATCATTCACCTCTACCACAAAAAAAAAAAAAATTGAGACCTACCTAGAATCCTCCAACCATACA CCACAAGGACTGATCTGACCTCATTGATAGGATTTTGGACAAAAAAATTAAAATATCAAAAATT TGGCTAAACATAGAAATGCATGGATTCTACAAGAATATCCCAGTGTAAATTTCCCCTAGAGAGC ATAAATCATACACGTTGCAAAACCCGGCTTACCAGCTAGGCTGGGGAAAAAGAGAGGCCTGACA TAGTTAAACAAACAAACATGCGCATGCAAAAAAAAAATGGAGTTGAGACCAACGACCCTGATTA TTTTGGGCACAAGACCAATTTACTTTCACTTTCATTGCAAAAACTCATGCACCTTCAGTTTTAA AAACTTGAAGAAAAGAAAGATAAAAGGCAAATTTAAAAAAGAACATCATACAAACATGCCCTGA TCTGTAAGATGATAATTTCTAACCAAACCAGCTAGATCATAACATTTTTTCATGCAGATAAAAC AATAAAGAAAGTTAGGTTTGTGGTAAAATATAGTACGGTAGACTGCACCTTTTGGGCCTTCTTC TTTTTCCCTTCATCAATTTCTTCGCTTTCATCACTTTCAACATATGACACCTTACGAACCGACC TGCTAGAAGTTCGAACCTCATTGTTTCTTCCACCAATGTTTGTTGACATAGCCGACCGGGCATT AGATTTACGAAAATGTGCACCTCTCTTGGTCATGTTCTTTGAAACAGCATCACTATCACTGTCA GAATCCTCTGCTGAATACTCATCTTCTTCAAACGATGGTTTCCCTCTCTTTTGTCGTCCAGAAG CATGCAATGACTTGTTCTCTTTGGCAGATTTTGTATTCCGCCCACTTTTACCATGTTGCCTACT CTTAGGTTTCTTTGTGTAATAAGAATCGTCATCGTCATCACCATCTGAGATGACCAAATCATCA CTGTTATTATCTTCATCTGAATCTTTACCCTCCCAGTCTTTATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.09826564

Conservation Information
Conserved circRNAs	NA
PMCS	0.09826564

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25131916-25128940(+)
25131708-25131971(-)
25129111-25131971(-)
						
						Potential amino acid sequence
						
							MTKSSLLLSSSESLPSQSLSFSFLTL*(+)
MTKRGAHFRKSNARSAMSTNIGGRNNEVRTSSRSVRKVSYVESDESEEIDEGKKKKAQKEEVEE
EDGDSIERVLWHQPRGMAEDAVRNNRSTAPILLSHLFDSALDWKEMEFLIKWKGQSHLHCQWKS
FSELQNLSGFKKVLNYTKKVMEDVRYRRKFTREEIEVNDVSKEMDLDLIKQNSQVERIIADRIN
KDSSGNVVPEYLVKWQGLSYAEATWEKDVDISFAQDAIDEYKAREAAIAVQGKMVDLQRKKGKG
*(-)
MLLMSTRHVRLQLLYRGKWWIYSVRKEKDKDWEGKDSDEDNNSDDLVISDGDDDDDSYYTKKPK
SRQHGKSGRNTKSAKENKSLHASGRQKRGKPSFEEDEYSAEDSDSDSDAVSKNMTKRGAHFRKS
NARSAMSTNIGGRNNEVRTSSRSVRKVSYVESDESEEIDEGKKKKAQKEEVEEEDGDSIERVLW
HQPRGMAEDAVRNNRSTAPILLSHLFDSALDWKEMEFLIKWKGQSHLHCQWKSFSELQNLSGFK
KVLNYTKKVMEDVRYRRKFTREEIEVNDVSKEMDLDLIKQNSQVERIIADRINKDSSGNVVPEY
LVKWQGLSYAEATWEKDVDISFAQDAIDEYKAREAAIAVQGKMVDLQRKKGKG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25131916-25128940(+) 25131708-25131971(-) 25129111-25131971(-)
Potential amino acid sequence	MTKSSLLLSSSESLPSQSLSFSFLTL(+) MTKRGAHFRKSNARSAMSTNIGGRNNEVRTSSRSVRKVSYVESDESEEIDEGKKKKAQKEEVEE EDGDSIERVLWHQPRGMAEDAVRNNRSTAPILLSHLFDSALDWKEMEFLIKWKGQSHLHCQWKS FSELQNLSGFKKVLNYTKKVMEDVRYRRKFTREEIEVNDVSKEMDLDLIKQNSQVERIIADRIN KDSSGNVVPEYLVKWQGLSYAEATWEKDVDISFAQDAIDEYKAREAAIAVQGKMVDLQRKKGKG (-) MLLMSTRHVRLQLLYRGKWWIYSVRKEKDKDWEGKDSDEDNNSDDLVISDGDDDDDSYYTKKPK SRQHGKSGRNTKSAKENKSLHASGRQKRGKPSFEEDEYSAEDSDSDSDAVSKNMTKRGAHFRKS NARSAMSTNIGGRNNEVRTSSRSVRKVSYVESDESEEIDEGKKKKAQKEEVEEEDGDSIERVLW HQPRGMAEDAVRNNRSTAPILLSHLFDSALDWKEMEFLIKWKGQSHLHCQWKSFSELQNLSGFK KVLNYTKKVMEDVRYRRKFTREEIEVNDVSKEMDLDLIKQNSQVERIIADRINKDSSGNVVPEY LVKWQGLSYAEATWEKDVDISFAQDAIDEYKAREAAIAVQGKMVDLQRKKGKG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0001s26030_circ_g.2

Address

Any questions?

Supported by