Plant Circular RNA Database

Detail information of scaffold3516_A13_circ_ig.2

			
						 General Information
					
						CircRNA Name
						scaffold3516_A13_circ_ig.2
					
						ID in PlantcircBase
						ghi_circ_003756
					
						Alias
						ghr_circ_0002646
					
						Organism
						
							Gossypium hirsutum						
					
						Position
						
							chrscaffold3516_A13: 4274-4839  JBrowse»						
					
						Reference genome
						
							v1.1						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						find_circ; CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							scaffold3516_A13_circ_ig.1 scaffold3516_A13_circ_ig.3 scaffold3516_A13_circ_ig.4 scaffold3516_A13_circ_ig.5 scaffold3516_A13_circ_ig.6 scaffold3516_A13_circ_ig.7 scaffold3516_A13_circ_ig.8 scaffold3516_A13_circ_ig.9 scaffold3516_A13_circ_ig.10 scaffold3516_A13_circ_ig.11 scaffold3516_A13_circ_ig.12 scaffold3516_A13_circ_ig.13 scaffold3516_A13_circ_ig.14 scaffold3516_A13_circ_ig.15 scaffold3516_A13_circ_ig.16 scaffold3516_A13_circ_ig.17 scaffold3516_A13_circ_ig.18 scaffold3516_A13_circ_ig.19 scaffold3516_A13_circ_ig.20 scaffold3516_A13_circ_ig.21 scaffold3516_A13_circ_ig.22 scaffold3516_A13_circ_ig.23 scaffold3516_A13_circ_ig.24 scaffold3516_A13_circ_ig.25 scaffold3516_A13_circ_ig.26 						
					
						Support reads
						NA
					
						Tissues
						fiber/ stem
					
						Exon boundary  
						
							NA-NA							"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-CA							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	scaffold3516_A13_circ_ig.2
ID in PlantcircBase	ghi_circ_003756
Alias	ghr_circ_0002646
Organism	Gossypium hirsutum
Position	chrscaffold3516_A13: 4274-4839 JBrowse»
Reference genome	v1.1
Type	ig-circRNA
Identification method	find_circ; CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	scaffold3516_A13_circ_ig.1 scaffold3516_A13_circ_ig.3 scaffold3516_A13_circ_ig.4 scaffold3516_A13_circ_ig.5 scaffold3516_A13_circ_ig.6 scaffold3516_A13_circ_ig.7 scaffold3516_A13_circ_ig.8 scaffold3516_A13_circ_ig.9 scaffold3516_A13_circ_ig.10 scaffold3516_A13_circ_ig.11 scaffold3516_A13_circ_ig.12 scaffold3516_A13_circ_ig.13 scaffold3516_A13_circ_ig.14 scaffold3516_A13_circ_ig.15 scaffold3516_A13_circ_ig.16 scaffold3516_A13_circ_ig.17 scaffold3516_A13_circ_ig.18 scaffold3516_A13_circ_ig.19 scaffold3516_A13_circ_ig.20 scaffold3516_A13_circ_ig.21 scaffold3516_A13_circ_ig.22 scaffold3516_A13_circ_ig.23 scaffold3516_A13_circ_ig.24 scaffold3516_A13_circ_ig.25 scaffold3516_A13_circ_ig.26
Support reads	NA
Tissues	fiber/ stem
Exon boundary	NA-NA "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-CA 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  
						
							CCGATCGGAGATCCATGGATCACAGACGGTATCTCCCCATGGCCTTTCGCCTCTGAAAGCGTCC
TTCCTTCTCAATGCCCGGGCATCCATCCAATGCATTcggtacttgtacgctatcggtcattgag
gaatacttaggcttagagggtggtccccctttctcgcgtaaaagcgatcagaattcgaacacgc
cgcgtttt

						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
						
							CGGTACTTGTACGCTATCGGTCATTGAGGAATACTTAGGCTTAGAGGGTGGTCCCCCTTTCTCG
CGTAAAAGCGATCAGAATTCGAACACGCCGCGTTTTACTGGGAAGGATCGAACCATGGGAACGA
ATCTACAGGGCTATCACCTTCTTTGGCCAGATCTTCCAACCTTTTCACAATTACAGTTCACTGC
GCCCTTTACTAAATAGAAAGTCAAGGGGCTTGCTGGTTTTTCCATCATCCAATCCACAACAAAT
CGAATGAAACCTGGCGAAAAAGAAGTGAACACTTTGCTGAGGAACGAAGCTTCGTGTTTGTTTT
TCTTCAAACCCCCAATCCGCTCTCGCTCGCCGCTACTAACGGGGTCTCGGTTGATTTCCCTTCC
TTTAGCTATTCAGATGTTTCAGTTCGCTAAGTTTTAAAAGTCCAAAGAGCGCAGACTAGCCACG
GAGCTTGGATACGGTTTCCCGATCGGAGATCCATGGATCACAGACGGTATCTCCCCATGGCCTT
TCGCCTCTGAAAGCGTCCTTCCTTCTCAATGCCCGGGCATCCATCCAATGCATT

Sequences
Splice junction sequence	CCGATCGGAGATCCATGGATCACAGACGGTATCTCCCCATGGCCTTTCGCCTCTGAAAGCGTCC TTCCTTCTCAATGCCCGGGCATCCATCCAATGCATTcggtacttgtacgctatcggtcattgag gaatacttaggcttagagggtggtccccctttctcgcgtaaaagcgatcagaattcgaacacgc cgcgtttt
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	CGGTACTTGTACGCTATCGGTCATTGAGGAATACTTAGGCTTAGAGGGTGGTCCCCCTTTCTCG CGTAAAAGCGATCAGAATTCGAACACGCCGCGTTTTACTGGGAAGGATCGAACCATGGGAACGA ATCTACAGGGCTATCACCTTCTTTGGCCAGATCTTCCAACCTTTTCACAATTACAGTTCACTGC GCCCTTTACTAAATAGAAAGTCAAGGGGCTTGCTGGTTTTTCCATCATCCAATCCACAACAAAT CGAATGAAACCTGGCGAAAAAGAAGTGAACACTTTGCTGAGGAACGAAGCTTCGTGTTTGTTTT TCTTCAAACCCCCAATCCGCTCTCGCTCGCCGCTACTAACGGGGTCTCGGTTGATTTCCCTTCC TTTAGCTATTCAGATGTTTCAGTTCGCTAAGTTTTAAAAGTCCAAAGAGCGCAGACTAGCCACG GAGCTTGGATACGGTTTCCCGATCGGAGATCCATGGATCACAGACGGTATCTCCCCATGGCCTT TCGCCTCTGAAAGCGTCCTTCCTTCTCAATGCCCGGGCATCCATCCAATGCATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							ath_circ_035761 ghi_circ_000476 						
					
						PMCS

Conservation Information
Conserved circRNAs	ath_circ_035761 ghi_circ_000476
PMCS

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Salih et al., 2020

circRNA

Detail information of scaffold3516_A13_circ_ig.2

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