Plant Circular RNA Database

Detail information of Zm00001d050551_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d050551_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008078
					
						Alias
						Zm04circ00047, GRMZM2G028766_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 99653627-99654384  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d050551						
					
						Parent gene annotation
						
							ubiquitin-associated (UBA)/TS-N domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d050551_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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  
						
							GT-AG							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
						Zm00001d050551_T002:3
Zm00001d050551_T004:4
Zm00001d050551_T011:3
Zm00001d050551_T013:2
Zm00001d050551_T008:4
Zm00001d050551_T007:4
Zm00001d050551_T003:4
Zm00001d050551_T010:4
Zm00001d050551_T012:2
Zm00001d050551_T001:4

General Information
CircRNA Name	Zm00001d050551_circ_g.2
ID in PlantcircBase	zma_circ_008078
Alias	Zm04circ00047, GRMZM2G028766_C1
Organism	Zea mays
Position	chr4: 99653627-99654384 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d050551
Parent gene annotation	ubiquitin-associated (UBA)/TS-N domain-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d050551_circ_g.1
Support reads	NA
Tissues	leaf, endosperm
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	GT-AG 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	Zm00001d050551_T002:3 Zm00001d050551_T004:4 Zm00001d050551_T011:3 Zm00001d050551_T013:2 Zm00001d050551_T008:4 Zm00001d050551_T007:4 Zm00001d050551_T003:4 Zm00001d050551_T010:4 Zm00001d050551_T012:2 Zm00001d050551_T001:4

			
						 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  
						
							ACTGTGGTATATGAATCTGCAGAGTGCATTGCCTGTCCGGCCAGCTACAAAGGCTGAGAGGATG
AGGGATTGCCTAAGAAATCTTAAGCAACAGAACAAGgaaagaatacgaattggaaaagaacttc
tggaagccaaaagaattgaggagcaaaatgaaaggaaacggttggtcttcttctctgtgatttg
tttctttc

						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
						
							GAAAGAATACGAATTGGAAAAGAACTTCTGGAAGCCAAAAGAATTGAGGAGCAAAATGAAAGGA
AACGGTTGGTCTTCTTCTCTGTGATTTGTTTCTTTCCCTTTCTTTTTGATTTATTTTGATTTAC
TGTACTCACTCCCTGTTGACTAATTTCTTTTCCACCATTTGAAGCATGATAGAACTGCGAAAAC
TTGAGAAAGAGGAGGAGAAAAGAGCTAGAGAAAAAATCCGCCAGAAGTTAGAAGAAGATAAGGT
TTCTAGTTTGTCCACTTCATCAATAACCTTTCTTGCTTTGTCATTCAGTTTTTAACAGATACAG
AAAATACTAGTAATTGAGCCTTAAAATGTTTTCTTGGGTTCTCAGGCTGAAAGGAGAAGGAAAC
TAGGACTGCCACCAGAAGACCCAGCAGCTGCCAAACCAAGTGCACCGCTTCCTGTTGAAGAGAA
GAAGGCATTTTCTTTTGAATCTGGATTCTCCTTTACTATGATGGCTATAGCTATACTTTAAACG
TCACTTTGTTCTATTTTTAAGATCTTGACCTATTGGACCGCTGAGATGAAAATTGTTGAGTGCT
ATACTTCCTAGGAGAACATATTTCATCTATTAGTCTTAGTATAGGTTAATCTTTATTCACTTCT
TGTTTTTTTATTTTACTCACTGTGGTATATGAATCTGCAGAGTGCATTGCCTGTCCGGCCAGCT
ACAAAGGCTGAGAGGATGAGGGATTGCCTAAGAAATCTTAAGCAACAGAACAAG

Sequences
Splice junction sequence	ACTGTGGTATATGAATCTGCAGAGTGCATTGCCTGTCCGGCCAGCTACAAAGGCTGAGAGGATG AGGGATTGCCTAAGAAATCTTAAGCAACAGAACAAGgaaagaatacgaattggaaaagaacttc tggaagccaaaagaattgaggagcaaaatgaaaggaaacggttggtcttcttctctgtgatttg tttctttc
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	GAAAGAATACGAATTGGAAAAGAACTTCTGGAAGCCAAAAGAATTGAGGAGCAAAATGAAAGGA AACGGTTGGTCTTCTTCTCTGTGATTTGTTTCTTTCCCTTTCTTTTTGATTTATTTTGATTTAC TGTACTCACTCCCTGTTGACTAATTTCTTTTCCACCATTTGAAGCATGATAGAACTGCGAAAAC TTGAGAAAGAGGAGGAGAAAAGAGCTAGAGAAAAAATCCGCCAGAAGTTAGAAGAAGATAAGGT TTCTAGTTTGTCCACTTCATCAATAACCTTTCTTGCTTTGTCATTCAGTTTTTAACAGATACAG AAAATACTAGTAATTGAGCCTTAAAATGTTTTCTTGGGTTCTCAGGCTGAAAGGAGAAGGAAAC TAGGACTGCCACCAGAAGACCCAGCAGCTGCCAAACCAAGTGCACCGCTTCCTGTTGAAGAGAA GAAGGCATTTTCTTTTGAATCTGGATTCTCCTTTACTATGATGGCTATAGCTATACTTTAAACG TCACTTTGTTCTATTTTTAAGATCTTGACCTATTGGACCGCTGAGATGAAAATTGTTGAGTGCT ATACTTCCTAGGAGAACATATTTCATCTATTAGTCTTAGTATAGGTTAATCTTTATTCACTTCT TGTTTTTTTATTTTACTCACTGTGGTATATGAATCTGCAGAGTGCATTGCCTGTCCGGCCAGCT ACAAAGGCTGAGAGGATGAGGGATTGCCTAAGAAATCTTAAGCAACAGAACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.081422988

Conservation Information
Conserved circRNAs	NA
PMCS	0.081422988

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							99654347-99654132(+)
99653803-99654141(-)
						
						Potential amino acid sequence
						
							MRDCLRNLKQQNKERIRIGKELLEAKRIEEQNERKRMIELRKLEKEEEKRAREKIRQKLEEDKA
ERRRKLGLPPEDPAAAKPSAPLPVEEKKAFSFESGFSFTMMAIAIL*(+)
MRFLSFCSSILLASRSSFPIRILSLFCCLRFLRQSLILSAFVAGLGSIALNNFHLSGPIGQDLK
NRTK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	99654347-99654132(+) 99653803-99654141(-)
Potential amino acid sequence	MRDCLRNLKQQNKERIRIGKELLEAKRIEEQNERKRMIELRKLEKEEEKRAREKIRQKLEEDKA ERRRKLGLPPEDPAAAKPSAPLPVEEKKAFSFESGFSFTMMAIAIL(+) MRFLSFCSSILLASRSSFPIRILSLFCCLRFLRQSLILSAFVAGLGSIALNNFHLSGPIGQDLK NRTK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d050551_circ_g.2

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