Plant Circular RNA Database

Detail information of POPTR_0005s25550_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0005s25550_circ_g.1
					
						ID in PlantcircBase
						pop_circ_001681
					
						Alias
						Chr05:24186855-24190344
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr5: 23778605-23782094  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0005s25550						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							POPTR_0005s25550_circ_g.2 POPTR_0005s25550_circ_g.3 						
					
						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_0005s25550.1:9

General Information
CircRNA Name	POPTR_0005s25550_circ_g.1
ID in PlantcircBase	pop_circ_001681
Alias	Chr05:24186855-24190344
Organism	Populus trichocarpa
Position	chr5: 23778605-23782094 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0005s25550
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	POPTR_0005s25550_circ_g.2 POPTR_0005s25550_circ_g.3
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_0005s25550.1:9

			
						 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  
						
							ATAATGATCTCTCAACGGATTGTTCAGTAGTGTTATATAATTCAAGTTCACCCTGCTGAGCTGC
AACAATGCTTTGAGCTGAGTGGAAAAGTTCACCAGCcagatgtttatgttatctccaaagaact
ttgcattgaagtagctcattataatcccaagattcatctgggccactccaaataaaattgacat
cttcatct

									
								

					

						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
						
							CAGATGTTTATGTTATCTCCAAAGAACTTTGCATTGAAGTAGCTCATTATAATCCCAAGATTCA
TCTGGGCCACTCCAAATAAAATTGACATCTTCATCTTCATTGAGTTAAGAAAAGGTAACTCGCT
CCGGCTACCATGCCATTTGGGATCCAAACCAAATGGATACGTAGCATGGACCTTAACTAGACCA
GCAGTATAAGCATCCCTACAATGCAAATAAAGCATAAATCATTTACAGGTAAAGTTGAACCACT
CGTGCACATGTAAAGTTGTACTGGTTAATACCTGCAAGACTGGTCACGACAGCCATACGCAGAG
GGCCCAAACAGTTCAAATGGAACCGAAAAGAATTCATTGTATATCAACCCCGTGTAGATTGAAA
AAATTCCCATCATCATTATCACATAACGACCACTGAAAGCCATTTCCATAATGTCTCCAAGCTT
CTGTTGTTTGCAAAAGGAAGTAAGCCAAAGCATGCGACAATTAAGAGGAAGACAGTGCTTGCTA
AGACAAACCAACGAGCTGTATCACAATTACCTGACTGGAAAGTTTCTTTTCCCTGATAATAAGA
TATAATGTTGCCAACAGCAAGCAAATACCATGGCCCCAATCACCAAACATTACAGCAAAAAGGA
AAGGGAATGTGACAATTGTGTATACACTAGGATTTGCTTCCTGGTACTTGGCAACCCTGAAAAA
TTATTTTGTCAGCTAACACCTCTATTTCATCTTTGAAATAGTCAACAAGAACAGTCAATGGGGC
AAATTAAATGATGCATGGATTACAGGTTGTGGAATGGGAGGAATGTCTAAGCCAAATGTATCCA
CTCATTATGCAACATGCAAGGACAAGAGAAGACCTATCCCTAAACTGTTTACACATATAAATTG
ACCAGCATTGAATTATTGGGACTGACATCCTGCAAAGACAGATAATATCAACTAAATATACTTC
GGTCAACCACTACATATCACCTGGAACATACTAACAACAATCAGACACTAGTTTTCTATCTCTC
AAACGCCATAATTTCTGTGTTCGAACAAATAATTTACTTAAAGAAACTGTAAGTTCTGCCAGTG
CCTAACATGGTTGTCACATGCTGGTATTACCAGTCCGATCTTAAAGGCATCTGAAAACTTCTAA
AGTTATGCTAGAACCATATAGCCAATTATCCTCCCAAAAATTACTTTAAAAAATTTCAGACTCT
TTGTATTGTTTGCATGGCATAAGTAACTCACCCGTACGCATCTACAATTTCTTGAAAAGCAGAA
GTAAATTTGTTTGTTTGGAAAAAGGTAGGTGGTGATTCCTTTGTCTGCAAAACATGGAATATGG
CTCCAATTTGTGAGTTGCTGTCTAAAGTCGCTCGCCTTAATCCATTTTGTATCTGCAGAGATAC
AACGATGAGACAATTTAAAAGATATGATTAATGCAAGATTTAACCAAGCACTGAGTATTATAAG
TTAAGGGAACAAACCTGATCTTTTGCAAAAACAGGACACCAACCTTCAGCAACAAGACACTTCT
TTGTCACATCCATGTTGAGCATGTTTAAAATGTGGTAAATCGATTTTTCCTTCTTCACCTATAT
GAGTTGAAAGCGACAAACTTAGTTGACAAAAAAGATTCAGCTCAGCTTAACTCAACTTTTATTA
ATCCAGTGATGATCCAAAATATTAAGTAAAATGACTTGAACAAACCAGAAAATTCCACTGCTCA
AATTCAAAGCCGATGGTTTGTAACAAATTGCTCCGGTGCGCCAATCCAGCATCTATGGTGGTTT
TAAGCTCTGCAAGTCTTCCAGACACCTAGAAATCAGTGAATTTACAAAATTTACATCAGAAAAC
TGGACAGAAAGATGCTAGTGCACCTAAGACAGAGCACTAAACAAAAACTCTAGGTTCATTTCAA
AGTTGGGGAAAATGCAATTTTTTTTATCCTCAGTTTACTACAAGTGAAACACTATATATTAATA
AATTAGGACTTTCGTGCAATTATTTAGTTCTACCTGGGAGTGAGGTTGCTTATGCCTTGATGTG
CTTTTCCCTTAAAAGAAATCAAATTAATGCTTTTTAGTGCTTTTCAATGGTTTTGATGTGTTGA
TGTCAAAAATAAAATAAAAAAAATCTGAAAAAATCATTTTTATGCATTTTCAAGCAAAAAGCAC
TTTAGAAAAGCACCCTGCACCACAATGTCAAACACCCTAAACTAGCTTGGGGATTGATGTTATC
TTCCGGCAATTATGCTCTACTGATTTCTTATTAAAAGCATTATCTAGCTCATGAACTTTTTTTC
CCTTTCTGAAGCATCAAGGGAAAAATACCTTTCCTGTTAAATTTGACACCTTTTCAGTTTTGCC
CCTGAAACTGTTACACATTTATTTATATGCCTATATAAGAACACTCACAAGGCCACAATACCTT
GTACTAACAAAATCATGTCCATTGACATAAAGTAAAAGCAAATTAAATTCCTATGAATCTCAAG
CCACATTGCTTCAAACTCGACATGCTGTACTTGGATCTTCTGTCCCAATAATTGTTGCCAGTTG
ATAGGGAGTGAACTCCGTTCTCTTTCCCAGTAATTGGAGCATGCTTTATGGTTGTCTAGACCAA
ATGACAGTAAAGTACCCGGAAAGCAAGAAAAAGAAAAGGCAATTCATGTTTCTTATGTGTAATC
AAGTATGGCAATGAGCAGATGGTAAAAAAAGATGAAACAGAGAGAAAAATAATCCAAGTCCTCC
AGAATCCTCAAGAAGAGAAATAAAAATAATTGTTTGCTCTCTAAAATTGACCAACTAATCAACT
TTCAATGTGCCGGGCTTCTAACCTACCAGAATCAGAGGTAAGAAACATGAGCAATCATGAATTA
TACCTGTGAAATAATCTGAAACTGTTTGTTTAGGTCCTCCGTAAAAGGGTAGCGGTTTGCTCCA
AAACCTTCACAGAGTTTAAGAATCTTGTTCTTTGCTCTTTCACCAGAATAGAAGACAACAAATA
CATTTTTCTCAACCTGTAAATTGATAAATCATAAGCTTTTCAAAATAAAGCGCGTATATCCAAC
TCTGGAAATGGAGAGCAGATAAACATCATCCAGGAATCAACCTCATCCCCCGACACAGGATCAA
CAACAGCATTTTCAAGCACAGTTTGCTTCAAAAAGACATTGCCCCTAGTTGCTCGAAACAAAAT
CCTTTCAAAAGCCATTGATTTTTCTCTTGCAACAAGACCACTGATATACCCCAGCTTTACTTGC
TTTGATGGATCCATTGTCATTTCCTAAACAATGTTCATTTTTAAGAATCAGTTAGCAGAAAATG
ACAAACTTTCAGCTGTTATAGTAAAGAACAGGAAAAACTGAAAAGCAGTACCTGCTCCAACAAT
AATGATCTCTCAACGGATTGTTCAGTAGTGTTATATAATTCAAGTTCACCCTGCTGAGCTGCAA
CAATGCTTTGAGCTGAGTGGAAAAGTTCACCAGC
						
					

			
		

Sequences
Splice junction sequence	ATAATGATCTCTCAACGGATTGTTCAGTAGTGTTATATAATTCAAGTTCACCCTGCTGAGCTGC AACAATGCTTTGAGCTGAGTGGAAAAGTTCACCAGCcagatgtttatgttatctccaaagaact ttgcattgaagtagctcattataatcccaagattcatctgggccactccaaataaaattgacat cttcatct
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	CAGATGTTTATGTTATCTCCAAAGAACTTTGCATTGAAGTAGCTCATTATAATCCCAAGATTCA TCTGGGCCACTCCAAATAAAATTGACATCTTCATCTTCATTGAGTTAAGAAAAGGTAACTCGCT CCGGCTACCATGCCATTTGGGATCCAAACCAAATGGATACGTAGCATGGACCTTAACTAGACCA GCAGTATAAGCATCCCTACAATGCAAATAAAGCATAAATCATTTACAGGTAAAGTTGAACCACT CGTGCACATGTAAAGTTGTACTGGTTAATACCTGCAAGACTGGTCACGACAGCCATACGCAGAG GGCCCAAACAGTTCAAATGGAACCGAAAAGAATTCATTGTATATCAACCCCGTGTAGATTGAAA AAATTCCCATCATCATTATCACATAACGACCACTGAAAGCCATTTCCATAATGTCTCCAAGCTT CTGTTGTTTGCAAAAGGAAGTAAGCCAAAGCATGCGACAATTAAGAGGAAGACAGTGCTTGCTA AGACAAACCAACGAGCTGTATCACAATTACCTGACTGGAAAGTTTCTTTTCCCTGATAATAAGA TATAATGTTGCCAACAGCAAGCAAATACCATGGCCCCAATCACCAAACATTACAGCAAAAAGGA AAGGGAATGTGACAATTGTGTATACACTAGGATTTGCTTCCTGGTACTTGGCAACCCTGAAAAA TTATTTTGTCAGCTAACACCTCTATTTCATCTTTGAAATAGTCAACAAGAACAGTCAATGGGGC AAATTAAATGATGCATGGATTACAGGTTGTGGAATGGGAGGAATGTCTAAGCCAAATGTATCCA CTCATTATGCAACATGCAAGGACAAGAGAAGACCTATCCCTAAACTGTTTACACATATAAATTG ACCAGCATTGAATTATTGGGACTGACATCCTGCAAAGACAGATAATATCAACTAAATATACTTC GGTCAACCACTACATATCACCTGGAACATACTAACAACAATCAGACACTAGTTTTCTATCTCTC AAACGCCATAATTTCTGTGTTCGAACAAATAATTTACTTAAAGAAACTGTAAGTTCTGCCAGTG CCTAACATGGTTGTCACATGCTGGTATTACCAGTCCGATCTTAAAGGCATCTGAAAACTTCTAA AGTTATGCTAGAACCATATAGCCAATTATCCTCCCAAAAATTACTTTAAAAAATTTCAGACTCT TTGTATTGTTTGCATGGCATAAGTAACTCACCCGTACGCATCTACAATTTCTTGAAAAGCAGAA GTAAATTTGTTTGTTTGGAAAAAGGTAGGTGGTGATTCCTTTGTCTGCAAAACATGGAATATGG CTCCAATTTGTGAGTTGCTGTCTAAAGTCGCTCGCCTTAATCCATTTTGTATCTGCAGAGATAC AACGATGAGACAATTTAAAAGATATGATTAATGCAAGATTTAACCAAGCACTGAGTATTATAAG TTAAGGGAACAAACCTGATCTTTTGCAAAAACAGGACACCAACCTTCAGCAACAAGACACTTCT TTGTCACATCCATGTTGAGCATGTTTAAAATGTGGTAAATCGATTTTTCCTTCTTCACCTATAT GAGTTGAAAGCGACAAACTTAGTTGACAAAAAAGATTCAGCTCAGCTTAACTCAACTTTTATTA ATCCAGTGATGATCCAAAATATTAAGTAAAATGACTTGAACAAACCAGAAAATTCCACTGCTCA AATTCAAAGCCGATGGTTTGTAACAAATTGCTCCGGTGCGCCAATCCAGCATCTATGGTGGTTT TAAGCTCTGCAAGTCTTCCAGACACCTAGAAATCAGTGAATTTACAAAATTTACATCAGAAAAC TGGACAGAAAGATGCTAGTGCACCTAAGACAGAGCACTAAACAAAAACTCTAGGTTCATTTCAA AGTTGGGGAAAATGCAATTTTTTTTATCCTCAGTTTACTACAAGTGAAACACTATATATTAATA AATTAGGACTTTCGTGCAATTATTTAGTTCTACCTGGGAGTGAGGTTGCTTATGCCTTGATGTG CTTTTCCCTTAAAAGAAATCAAATTAATGCTTTTTAGTGCTTTTCAATGGTTTTGATGTGTTGA TGTCAAAAATAAAATAAAAAAAATCTGAAAAAATCATTTTTATGCATTTTCAAGCAAAAAGCAC TTTAGAAAAGCACCCTGCACCACAATGTCAAACACCCTAAACTAGCTTGGGGATTGATGTTATC TTCCGGCAATTATGCTCTACTGATTTCTTATTAAAAGCATTATCTAGCTCATGAACTTTTTTTC CCTTTCTGAAGCATCAAGGGAAAAATACCTTTCCTGTTAAATTTGACACCTTTTCAGTTTTGCC CCTGAAACTGTTACACATTTATTTATATGCCTATATAAGAACACTCACAAGGCCACAATACCTT GTACTAACAAAATCATGTCCATTGACATAAAGTAAAAGCAAATTAAATTCCTATGAATCTCAAG CCACATTGCTTCAAACTCGACATGCTGTACTTGGATCTTCTGTCCCAATAATTGTTGCCAGTTG ATAGGGAGTGAACTCCGTTCTCTTTCCCAGTAATTGGAGCATGCTTTATGGTTGTCTAGACCAA ATGACAGTAAAGTACCCGGAAAGCAAGAAAAAGAAAAGGCAATTCATGTTTCTTATGTGTAATC AAGTATGGCAATGAGCAGATGGTAAAAAAAGATGAAACAGAGAGAAAAATAATCCAAGTCCTCC AGAATCCTCAAGAAGAGAAATAAAAATAATTGTTTGCTCTCTAAAATTGACCAACTAATCAACT TTCAATGTGCCGGGCTTCTAACCTACCAGAATCAGAGGTAAGAAACATGAGCAATCATGAATTA TACCTGTGAAATAATCTGAAACTGTTTGTTTAGGTCCTCCGTAAAAGGGTAGCGGTTTGCTCCA AAACCTTCACAGAGTTTAAGAATCTTGTTCTTTGCTCTTTCACCAGAATAGAAGACAACAAATA CATTTTTCTCAACCTGTAAATTGATAAATCATAAGCTTTTCAAAATAAAGCGCGTATATCCAAC TCTGGAAATGGAGAGCAGATAAACATCATCCAGGAATCAACCTCATCCCCCGACACAGGATCAA CAACAGCATTTTCAAGCACAGTTTGCTTCAAAAAGACATTGCCCCTAGTTGCTCGAAACAAAAT CCTTTCAAAAGCCATTGATTTTTCTCTTGCAACAAGACCACTGATATACCCCAGCTTTACTTGC TTTGATGGATCCATTGTCATTTCCTAAACAATGTTCATTTTTAAGAATCAGTTAGCAGAAAATG ACAAACTTTCAGCTGTTATAGTAAAGAACAGGAAAAACTGAAAAGCAGTACCTGCTCCAACAAT AATGATCTCTCAACGGATTGTTCAGTAGTGTTATATAATTCAAGTTCACCCTGCTGAGCTGCAA CAATGCTTTGAGCTGAGTGGAAAAGTTCACCAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.120421882

Conservation Information
Conserved circRNAs	NA
PMCS	0.120421882

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23781890-23781887(-)
						
						Potential amino acid sequence
						
							MTMDPSKQVKLGYISGLVAREKSMAFERILFRATRGNVFLKQTVLENAVVDPVSGDEVEKNVFV
VFYSGERAKNKILKLCEGFGANRYPFTEDLNKQFQIISQVSGRLAELKTTIDAGLAHRSNLLQT
IGFEFEQWNFLVKKEKSIYHILNMLNMDVTKKCLVAEGWCPVFAKDQIQNGLRRATLDSNSQIG
AIFHVLQTKESPPTFFQTNKFTSAFQEIVDAYGVAKYQEANPSVYTIVTFPFLFAVMFGDWGHG
ICLLLATLYLIIREKKLSSQKLGDIMEMAFSGRYVIMMMGIFSIYTGLIYNEFFSVPFELFGPS
AYGCRDQSCRDAYTAGLVKVHATYPFGLDPKWHGSRSELPFLNSMKMKMSILFGVAQMNLGIIM
SYFNAKFFGDNINIWLVNFSTQLKALLQLSRVNLNYITLLNNPLRDHYCWSRK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23781890-23781887(-)
Potential amino acid sequence	MTMDPSKQVKLGYISGLVAREKSMAFERILFRATRGNVFLKQTVLENAVVDPVSGDEVEKNVFV VFYSGERAKNKILKLCEGFGANRYPFTEDLNKQFQIISQVSGRLAELKTTIDAGLAHRSNLLQT IGFEFEQWNFLVKKEKSIYHILNMLNMDVTKKCLVAEGWCPVFAKDQIQNGLRRATLDSNSQIG AIFHVLQTKESPPTFFQTNKFTSAFQEIVDAYGVAKYQEANPSVYTIVTFPFLFAVMFGDWGHG ICLLLATLYLIIREKKLSSQKLGDIMEMAFSGRYVIMMMGIFSIYTGLIYNEFFSVPFELFGPS AYGCRDQSCRDAYTAGLVKVHATYPFGLDPKWHGSRSELPFLNSMKMKMSILFGVAQMNLGIIM SYFNAKFFGDNINIWLVNFSTQLKALLQLSRVNLNYITLLNNPLRDHYCWSRK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0005s25550_circ_g.1

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