Plant Circular RNA Database

Detail information of Zm00001d025461_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d025461_circ_g.4
					
						ID in PlantcircBase
						zma_circ_010312
					
						Alias
						zma_circ_0000047
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 119224643-119225117  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d025461						
					
						Parent gene annotation
						
							Regulator of nonsense transcripts UPF3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025461_circ_g.1 Zm00001d025461_circ_g.2 Zm00001d025461_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						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
						Zm00001d025461_T005:1
Zm00001d025461_T013:1
Zm00001d025461_T011:1
Zm00001d025461_T008:1
Zm00001d025461_T016:1
Zm00001d025461_T004:1
Zm00001d025461_T010:1
Zm00001d025461_T012:1
Zm00001d025461_T007:1
Zm00001d025461_T006:1
Zm00001d025461_T009:1
Zm00001d025461_T015:1
Zm00001d025461_T017:1
Zm00001d025461_T002:1
Zm00001d025461_T014:1
Zm00001d025461_T003:1
Zm00001d025461_T001:1

General Information
CircRNA Name	Zm00001d025461_circ_g.4
ID in PlantcircBase	zma_circ_010312
Alias	zma_circ_0000047
Organism	Zea mays
Position	chr10: 119224643-119225117 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Zm00001d025461
Parent gene annotation	Regulator of nonsense transcripts UPF3
Parent gene strand	-
Alternative splicing	Zm00001d025461_circ_g.1 Zm00001d025461_circ_g.2 Zm00001d025461_circ_g.3
Support reads	NA
Tissues	leaf, root
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	Zm00001d025461_T005:1 Zm00001d025461_T013:1 Zm00001d025461_T011:1 Zm00001d025461_T008:1 Zm00001d025461_T016:1 Zm00001d025461_T004:1 Zm00001d025461_T010:1 Zm00001d025461_T012:1 Zm00001d025461_T007:1 Zm00001d025461_T006:1 Zm00001d025461_T009:1 Zm00001d025461_T015:1 Zm00001d025461_T017:1 Zm00001d025461_T002:1 Zm00001d025461_T014:1 Zm00001d025461_T003:1 Zm00001d025461_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  
						
							TAATTTTTCCACTGGCTTCAAGTCGCTGGTCTTGTCTAGAACGCGATGGTGGCACATTCTTGAT
AGGGGTTGATGAGTGCTGAGTTGCTCCATTAGGTGTcatctgctagttgcaaaatattatctcc
agaatgtgactgcatttgagggaactctgacgacgaaggatgtgaactacctgcagatgtagat
ttgtcata

						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
						
							CATCTGCTAGTTGCAAAATATTATCTCCAGAATGTGACTGCATTTGAGGGAACTCTGACGACGA
AGGATGTGAACTACCTGCAGATGTAGATTTGTCATAGCGGCGAGCTGCCCATACACCACGATCG
GGTCTATCTCTGTTTCTAGCATGCCTTTCAACCTTCTCACCAATGGGAACGGAGCCATGGAGAT
GATTAGCCTTCTCATCAAAATGGCTCCTCTCAGCATTTTCAACTACCTGATCTTTCACAATGGT
ACGAGGGTTGAAAGCCCGTGGTGGCCGCTTATCCTTCTCAGTATTAAACATGTGACCTTCCTGC
TCATGTTCAGAAGGATTTGAACTGCGGGCTTCCTTGTTTGATAGTATAGTCTTAATAATTTTTC
CACTGGCTTCAAGTCGCTGGTCTTGTCTAGAACGCGATGGTGGCACATTCTTGATAGGGGTTGA
TGAGTGCTGAGTTGCTCCATTAGGTGT

Sequences
Splice junction sequence	TAATTTTTCCACTGGCTTCAAGTCGCTGGTCTTGTCTAGAACGCGATGGTGGCACATTCTTGAT AGGGGTTGATGAGTGCTGAGTTGCTCCATTAGGTGTcatctgctagttgcaaaatattatctcc agaatgtgactgcatttgagggaactctgacgacgaaggatgtgaactacctgcagatgtagat ttgtcata
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	CATCTGCTAGTTGCAAAATATTATCTCCAGAATGTGACTGCATTTGAGGGAACTCTGACGACGA AGGATGTGAACTACCTGCAGATGTAGATTTGTCATAGCGGCGAGCTGCCCATACACCACGATCG GGTCTATCTCTGTTTCTAGCATGCCTTTCAACCTTCTCACCAATGGGAACGGAGCCATGGAGAT GATTAGCCTTCTCATCAAAATGGCTCCTCTCAGCATTTTCAACTACCTGATCTTTCACAATGGT ACGAGGGTTGAAAGCCCGTGGTGGCCGCTTATCCTTCTCAGTATTAAACATGTGACCTTCCTGC TCATGTTCAGAAGGATTTGAACTGCGGGCTTCCTTGTTTGATAGTATAGTCTTAATAATTTTTC CACTGGCTTCAAGTCGCTGGTCTTGTCTAGAACGCGATGGTGGCACATTCTTGATAGGGGTTGA TGAGTGCTGAGTTGCTCCATTAGGTGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.215763649

Conservation Information
Conserved circRNAs	NA
PMCS	0.215763649

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							119224951-119225112(-)
119224647-119225112(-)
						
						Potential amino acid sequence
						
							MFNTEKDKRPPRAFNPRTIVKDQVVENAERSHFDEKANHLHGSVPIGEKVERHARNRDRPDRGV
WAARRYDKSTSAGSSHPSSSEFPQMQSHSGDNILQLADDT*(-)
MTPNGATQHSSTPIKNVPPSRSRQDQRLEASGKIIKTILSNKEARSSNPSEHEQEGHMFNTEKD
KRPPRAFNPRTIVKDQVVENAERSHFDEKANHLHGSVPIGEKVERHARNRDRPDRGVWAARRYD
KSTSAGSSHPSSSEFPQMQSHSGDNILQLADDT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	119224951-119225112(-) 119224647-119225112(-)
Potential amino acid sequence	MFNTEKDKRPPRAFNPRTIVKDQVVENAERSHFDEKANHLHGSVPIGEKVERHARNRDRPDRGV WAARRYDKSTSAGSSHPSSSEFPQMQSHSGDNILQLADDT(-) MTPNGATQHSSTPIKNVPPSRSRQDQRLEASGKIIKTILSNKEARSSNPSEHEQEGHMFNTEKD KRPPRAFNPRTIVKDQVVENAERSHFDEKANHLHGSVPIGEKVERHARNRDRPDRGVWAARRYD KSTSAGSSHPSSSEFPQMQSHSGDNILQLADDT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d025461_circ_g.4

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