Plant Circular RNA Database

Detail information of Zm00001d053834_circ_g.40

			
						 General Information
					
						CircRNA Name
						Zm00001d053834_circ_g.40
					
						ID in PlantcircBase
						zma_circ_004689
					
						Alias
						seedling_test_circ_001465
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 242113173-242113629  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d053834						
					
						Parent gene annotation
						
							Putative ubiquitin family protein; Ubiquitin2  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d053834_circ_ag.1 Zm00001d053834_circ_g.1 Zm00001d053834_circ_g.2 Zm00001d053834_circ_ag.3 Zm00001d053834_circ_g.4 Zm00001d053834_circ_g.5 Zm00001d053834_circ_ag.6 Zm00001d053834_circ_ag.7 Zm00001d053834_circ_ag.8 Zm00001d053834_circ_ag.9 Zm00001d053834_circ_ag.10 Zm00001d053834_circ_ag.11 Zm00001d053834_circ_g.12 Zm00001d053834_circ_g.13 Zm00001d053834_circ_g.14 Zm00001d053834_circ_ag.15 Zm00001d053834_circ_g.16 Zm00001d053834_circ_g.17 Zm00001d053834_circ_g.18 Zm00001d053834_circ_ag.19 Zm00001d053834_circ_g.20 Zm00001d053834_circ_g.21 Zm00001d053834_circ_g.22 Zm00001d053834_circ_g.23 Zm00001d053834_circ_g.24 Zm00001d053834_circ_g.25 Zm00001d053834_circ_g.26 Zm00001d053834_circ_ag.27 Zm00001d053834_circ_ag.28 Zm00001d053834_circ_ag.29 Zm00001d053834_circ_ag.30 Zm00001d053834_circ_ag.31 Zm00001d053834_circ_ag.32 Zm00001d053834_circ_ag.33 Zm00001d053834_circ_g.34 Zm00001d053834_circ_g.35 Zm00001d053834_circ_g.36 Zm00001d053834_circ_ag.37 Zm00001d053834_circ_ag.38 Zm00001d053834_circ_ag.39 Zm00001d053834_circ_ag.41 Zm00001d053834_circ_g.42 Zm00001d053834_circ_ag.43 Zm00001d053834_circ_g.44 Zm00001d053834_circ_g.45 Zm00001d053834_circ_ag.46 Zm00001d053834_circ_ag.47 Zm00001d053834_circ_g.48 Zm00001d053834_circ_g.49 Zm00001d053834_circ_g.50 Zm00001d053834_circ_ag.51 Zm00001d053834_circ_ag.52 Zm00001d053834_circ_ag.53 Zm00001d053834_circ_g.54 Zm00001d053834_circ_ag.55 Zm00001d053834_circ_g.56 Zm00001d053834_circ_g.57 Zm00001d053834_circ_ag.58 Zm00001d053834_circ_g.59 Zm00001d053834_circ_ag.60 Zm00001d053834_circ_ag.61 Zm00001d053834_circ_g.62 Zm00001d053834_circ_ag.63 Zm00001d053834_circ_ag.64 Zm00001d053834_circ_ag.65 Zm00001d053834_circ_ag.66 Zm00001d053834_circ_ag.67 Zm00001d053834_circ_g.68 Zm00001d053834_circ_ag.69 Zm00001d053834_circ_ag.70 Zm00001d053834_circ_ag.71 Zm00001d053834_circ_ag.72 Zm00001d053834_circ_ag.73 Zm00001d053834_circ_ag.74 Zm00001d053834_circ_ag.75 Zm00001d053834_circ_ag.76 Zm00001d053834_circ_ag.77 Zm00001d053834_circ_ag.78 Zm00001d053834_circ_ag.79 Zm00001d053834_circ_ag.80 Zm00001d053838_circ_g.1 Zm00001d053838_circ_g.2 Zm00001d053838_circ_g.3 Zm00001d053838_circ_g.4 Zm00001d053838_circ_g.5 Zm00001d053838_circ_g.6 Zm00001d053838_circ_g.7 Zm00001d053838_circ_g.8 Zm00001d053838_circ_g.9 Zm00001d053838_circ_g.10 Zm00001d053838_circ_g.11 Zm00001d053838_circ_g.12 Zm00001d053838_circ_g.13 Zm00001d053838_circ_g.14 Zm00001d053838_circ_g.15 Zm00001d053838_circ_g.16 Zm00001d053838_circ_g.17 Zm00001d053838_circ_g.18 Zm00001d053838_circ_g.19 Zm00001d053838_circ_g.20 Zm00001d053838_circ_g.21 Zm00001d053838_circ_g.22 Zm00001d053838_circ_g.23 Zm00001d053838_circ_g.24 Zm00001d053838_circ_g.25 Zm00001d053838_circ_g.26 Zm00001d053838_circ_g.27 Zm00001d053838_circ_g.28 Zm00001d053838_circ_g.29 Zm00001d053838_circ_g.30 Zm00001d053838_circ_g.31 Zm00001d053838_circ_g.32 Zm00001d053838_circ_g.33 						
					
						Support reads
						NA
					
						Tissues
						seedling
					
						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-AA							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
						Zm00001d053834_T004:1
Zm00001d053834_T005:1
Zm00001d053834_T003:2
Zm00001d053834_T002:1
Zm00001d053834_T001:1

General Information
CircRNA Name	Zm00001d053834_circ_g.40
ID in PlantcircBase	zma_circ_004689
Alias	seedling_test_circ_001465
Organism	Zea mays
Position	chr4: 242113173-242113629 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Zm00001d053834
Parent gene annotation	Putative ubiquitin family protein; Ubiquitin2
Parent gene strand	+
Alternative splicing	Zm00001d053834_circ_ag.1 Zm00001d053834_circ_g.1 Zm00001d053834_circ_g.2 Zm00001d053834_circ_ag.3 Zm00001d053834_circ_g.4 Zm00001d053834_circ_g.5 Zm00001d053834_circ_ag.6 Zm00001d053834_circ_ag.7 Zm00001d053834_circ_ag.8 Zm00001d053834_circ_ag.9 Zm00001d053834_circ_ag.10 Zm00001d053834_circ_ag.11 Zm00001d053834_circ_g.12 Zm00001d053834_circ_g.13 Zm00001d053834_circ_g.14 Zm00001d053834_circ_ag.15 Zm00001d053834_circ_g.16 Zm00001d053834_circ_g.17 Zm00001d053834_circ_g.18 Zm00001d053834_circ_ag.19 Zm00001d053834_circ_g.20 Zm00001d053834_circ_g.21 Zm00001d053834_circ_g.22 Zm00001d053834_circ_g.23 Zm00001d053834_circ_g.24 Zm00001d053834_circ_g.25 Zm00001d053834_circ_g.26 Zm00001d053834_circ_ag.27 Zm00001d053834_circ_ag.28 Zm00001d053834_circ_ag.29 Zm00001d053834_circ_ag.30 Zm00001d053834_circ_ag.31 Zm00001d053834_circ_ag.32 Zm00001d053834_circ_ag.33 Zm00001d053834_circ_g.34 Zm00001d053834_circ_g.35 Zm00001d053834_circ_g.36 Zm00001d053834_circ_ag.37 Zm00001d053834_circ_ag.38 Zm00001d053834_circ_ag.39 Zm00001d053834_circ_ag.41 Zm00001d053834_circ_g.42 Zm00001d053834_circ_ag.43 Zm00001d053834_circ_g.44 Zm00001d053834_circ_g.45 Zm00001d053834_circ_ag.46 Zm00001d053834_circ_ag.47 Zm00001d053834_circ_g.48 Zm00001d053834_circ_g.49 Zm00001d053834_circ_g.50 Zm00001d053834_circ_ag.51 Zm00001d053834_circ_ag.52 Zm00001d053834_circ_ag.53 Zm00001d053834_circ_g.54 Zm00001d053834_circ_ag.55 Zm00001d053834_circ_g.56 Zm00001d053834_circ_g.57 Zm00001d053834_circ_ag.58 Zm00001d053834_circ_g.59 Zm00001d053834_circ_ag.60 Zm00001d053834_circ_ag.61 Zm00001d053834_circ_g.62 Zm00001d053834_circ_ag.63 Zm00001d053834_circ_ag.64 Zm00001d053834_circ_ag.65 Zm00001d053834_circ_ag.66 Zm00001d053834_circ_ag.67 Zm00001d053834_circ_g.68 Zm00001d053834_circ_ag.69 Zm00001d053834_circ_ag.70 Zm00001d053834_circ_ag.71 Zm00001d053834_circ_ag.72 Zm00001d053834_circ_ag.73 Zm00001d053834_circ_ag.74 Zm00001d053834_circ_ag.75 Zm00001d053834_circ_ag.76 Zm00001d053834_circ_ag.77 Zm00001d053834_circ_ag.78 Zm00001d053834_circ_ag.79 Zm00001d053834_circ_ag.80 Zm00001d053838_circ_g.1 Zm00001d053838_circ_g.2 Zm00001d053838_circ_g.3 Zm00001d053838_circ_g.4 Zm00001d053838_circ_g.5 Zm00001d053838_circ_g.6 Zm00001d053838_circ_g.7 Zm00001d053838_circ_g.8 Zm00001d053838_circ_g.9 Zm00001d053838_circ_g.10 Zm00001d053838_circ_g.11 Zm00001d053838_circ_g.12 Zm00001d053838_circ_g.13 Zm00001d053838_circ_g.14 Zm00001d053838_circ_g.15 Zm00001d053838_circ_g.16 Zm00001d053838_circ_g.17 Zm00001d053838_circ_g.18 Zm00001d053838_circ_g.19 Zm00001d053838_circ_g.20 Zm00001d053838_circ_g.21 Zm00001d053838_circ_g.22 Zm00001d053838_circ_g.23 Zm00001d053838_circ_g.24 Zm00001d053838_circ_g.25 Zm00001d053838_circ_g.26 Zm00001d053838_circ_g.27 Zm00001d053838_circ_g.28 Zm00001d053838_circ_g.29 Zm00001d053838_circ_g.30 Zm00001d053838_circ_g.31 Zm00001d053838_circ_g.32 Zm00001d053838_circ_g.33
Support reads	NA
Tissues	seedling
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-AA 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	Zm00001d053834_T004:1 Zm00001d053834_T005:1 Zm00001d053834_T003:2 Zm00001d053834_T002:1 Zm00001d053834_T001:1

			
						 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  
						
							TGGAGGATGGTCGCACCTTGGCTGACTACAACATCCAGAAGGAGAGCACCCTCCATCTGGTGCT
CCGCCTGAGGGGCGGTATGCAGATCTTTGTGAAGACcccttactggcaagaccatcactcttga
ggtggagtcttcagataccattgacaatgtcaaggccaagatccaggacaaggagggcatcccg
ccggacca

						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
						
							CCCTTACTGGCAAGACCATCACTCTTGAGGTGGAGTCTTCAGATACCATTGACAATGTCAAGGC
CAAGATCCAGGACAAGGAGGGCATCCCGCCGGACCAGCAGCGTCTTATCTTTGCCGGCAAGCAG
CTGGAGGATGGACGCACCCTTGCGGATTACAACATTCAGAAGGAGAGCACCCTCCACCTGGTGC
TGCGCCTCAGGGGAGGAATGCAGATCTTCGTGAAGACATTGACTGGCAAGACCATCACCTTGGA
GGTTGAGAGCTCCGACACCATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGTATCCCC
CCGGACCAGCAGCGGCTGATCTTCGCCGGCAAGCAGCTGGAGGATGGTCGCACCTTGGCTGACT
ACAACATCCAGAAGGAGAGCACCCTCCATCTGGTGCTCCGCCTGAGGGGCGGTATGCAGATCTT
TGTGAAGAC

Sequences
Splice junction sequence	TGGAGGATGGTCGCACCTTGGCTGACTACAACATCCAGAAGGAGAGCACCCTCCATCTGGTGCT CCGCCTGAGGGGCGGTATGCAGATCTTTGTGAAGACcccttactggcaagaccatcactcttga ggtggagtcttcagataccattgacaatgtcaaggccaagatccaggacaaggagggcatcccg ccggacca
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	CCCTTACTGGCAAGACCATCACTCTTGAGGTGGAGTCTTCAGATACCATTGACAATGTCAAGGC CAAGATCCAGGACAAGGAGGGCATCCCGCCGGACCAGCAGCGTCTTATCTTTGCCGGCAAGCAG CTGGAGGATGGACGCACCCTTGCGGATTACAACATTCAGAAGGAGAGCACCCTCCACCTGGTGC TGCGCCTCAGGGGAGGAATGCAGATCTTCGTGAAGACATTGACTGGCAAGACCATCACCTTGGA GGTTGAGAGCTCCGACACCATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGTATCCCC CCGGACCAGCAGCGGCTGATCTTCGCCGGCAAGCAGCTGGAGGATGGTCGCACCTTGGCTGACT ACAACATCCAGAAGGAGAGCACCCTCCATCTGGTGCTCCGCCTGAGGGGCGGTATGCAGATCTT TGTGAAGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_013230 osa_circ_013234 osa_circ_013232 osi_circ_003673 
pop_circ_000493 osa_circ_013229 pop_circ_000492 osa_circ_025430 
osa_circ_025432 osa_circ_032068 osa_circ_013247 osa_circ_013227 
osi_circ_003676 osi_circ_012542 osi_circ_012543 osa_circ_032067 
osa_circ_025433 gma_circ_008846 osa_circ_013245 						
					
						PMCS
						0.069790907

Conservation Information
Conserved circRNAs	osa_circ_013230 osa_circ_013234 osa_circ_013232 osi_circ_003673 pop_circ_000493 osa_circ_013229 pop_circ_000492 osa_circ_025430 osa_circ_025432 osa_circ_032068 osa_circ_013247 osa_circ_013227 osi_circ_003676 osi_circ_012542 osi_circ_012543 osa_circ_032067 osa_circ_025433 gma_circ_008846 osa_circ_013245
PMCS	0.069790907

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Tang et al., 2018

circRNA

Detail information of Zm00001d053834_circ_g.40

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