Plant Circular RNA Database

Detail information of Zm00001d011713_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d011713_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009756
					
						Alias
						zma_circ_0002873
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 159550355-159551404  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d011713						
					
						Parent gene annotation
						
							Myosin family protein with Dil domain
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d011713_circ_g.2 Zm00001d011713_circ_g.3 Zm00001d011713_circ_g.5 						
					
						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
						Zm00001d011713_T010:3
Zm00001d011713_T016:3
Zm00001d011713_T013:3
Zm00001d011713_T008:3
Zm00001d011713_T006:3
Zm00001d011713_T004:3
Zm00001d011713_T003:3
Zm00001d011713_T007:3
Zm00001d011713_T005:3
Zm00001d011713_T009:3
Zm00001d011713_T015:3
Zm00001d011713_T012:3
Zm00001d011713_T014:3

General Information
CircRNA Name	Zm00001d011713_circ_g.4
ID in PlantcircBase	zma_circ_009756
Alias	zma_circ_0002873
Organism	Zea mays
Position	chr8: 159550355-159551404 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d011713
Parent gene annotation	Myosin family protein with Dil domain
Parent gene strand	-
Alternative splicing	Zm00001d011713_circ_g.2 Zm00001d011713_circ_g.3 Zm00001d011713_circ_g.5
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	Zm00001d011713_T010:3 Zm00001d011713_T016:3 Zm00001d011713_T013:3 Zm00001d011713_T008:3 Zm00001d011713_T006:3 Zm00001d011713_T004:3 Zm00001d011713_T003:3 Zm00001d011713_T007:3 Zm00001d011713_T005:3 Zm00001d011713_T009:3 Zm00001d011713_T015:3 Zm00001d011713_T012:3 Zm00001d011713_T014:3

			
						 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  
						
							ACTTCTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGC
AAAAGGGCCTCATATTCACTTACAGTCCCTTCTAGTctttggacagtttcttggaagtgagcaa
tgtctttctcagcaacttcaattttcattagtaagtccttgtttctatcctcagattcattgag
cgatttct

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 504
Transcript exons: 159550355-159550522,159550853-159551020,159551237-159551
404
CTTTGGACAGTTTCTTGGAAGTGAGCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGT
CCTTGTTTCTATCCTCAGATTCATTGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGT
TGTCAATAGAGCATCCTTCTCTCCTAACCTTTCTTCAAGGCTTTGTATACTAGTCTGAAGCAGG
GTGGATTTTTCATCAGTGTCCCCAACTTCTCTTTGAAGTTCTTCAATCTTTTCTCGCGCTTCAT
CTAATTCTATCAAATTTGCCTGATGCCGTTGCTTCTCAAATGTTAGTGAAGATTCCAAATTTTT
TGTAGCTTCTTCAAATCTTTGAGCAGCTTCATGGAGGAGATCATTTTGTTTCACAGCATCTTCG
AGCTTGCTTACCAATGCTTCACTTCTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCAT
TTTGTTGTCTTTCTGTTAGCAAAAGGGCCTCATATTCACTTACAGTCCCTTCTAGT
						
					

						Genomic sequence
						
							CTTTGGACAGTTTCTTGGAAGTGAGCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGT
CCTTGTTTCTATCCTCAGATTCATTGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGT
TGTCAATAGAGCATCCTTCTCTCCTAACCTTTCTTCAAGGCTATGTCCACCCATCAAAGAAAGA
AATAACTATTAGTCTAACAAAAAGTGAGGGGTTAATCCTTCCCCCTTATCCATGCAAATAGATC
CATACATTGTACTTTTATAGTTTATTGACTCAAAGTATATTTTGTATTTTCTTGATAATATATT
CTTACAGCATGCTCTCTCTTGATGCATCCCCACAAAGAAAAAAGGAATTAACAGAGTTTTTATT
AAAATATTAAATATATAGTTTCAAAGGAAACATCACATAACAAATTTGCTCAAAAAAATGCAAT
GCATTATCACACGAAGTTAGAACTCTTGAAAAGGGGAAGAAAAGAAAAACCTTTGTATACTAGT
CTGAAGCAGGGTGGATTTTTCATCAGTGTCCCCAACTTCTCTTTGAAGTTCTTCAATCTTTTCT
CGCGCTTCATCTAATTCTATCAAATTTGCCTGATGCCGTTGCTTCTCAAATGTTAGTGAAGATT
CCAAATTTTTTGTAGCTTCTTCAAATCTGCATTCAACCACAAGATACAAACTATGTGGAACACA
TATAGAAATATGAAAAGATTAAAACTGTACAGCTCACAATAATTAATGCCACTGTGTTATTGGG
CCATTATTTGCTCTTAAAGAGTAGCTATGACCTTATAAATATGCAAATTAGGGATTATTGATGA
CACTACAATTTGCAGAGTTGGCCACATTACTTTCTGGAATAAACACTAACCTTTGAGCAGCTTC
ATGGAGGAGATCATTTTGTTTCACAGCATCTTCGAGCTTGCTTACCAATGCTTCACTTCTTGCT
TGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGCAAAAGGGCCT
CATATTCACTTACAGTCCCTTCTAGT
						
					

			
		

Sequences
Splice junction sequence	ACTTCTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGC AAAAGGGCCTCATATTCACTTACAGTCCCTTCTAGTctttggacagtttcttggaagtgagcaa tgtctttctcagcaacttcaattttcattagtaagtccttgtttctatcctcagattcattgag cgatttct
Assembled circRNA sequence	Yes 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	Transcript length: 504 Transcript exons: 159550355-159550522,159550853-159551020,159551237-159551 404 CTTTGGACAGTTTCTTGGAAGTGAGCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGT CCTTGTTTCTATCCTCAGATTCATTGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGT TGTCAATAGAGCATCCTTCTCTCCTAACCTTTCTTCAAGGCTTTGTATACTAGTCTGAAGCAGG GTGGATTTTTCATCAGTGTCCCCAACTTCTCTTTGAAGTTCTTCAATCTTTTCTCGCGCTTCAT CTAATTCTATCAAATTTGCCTGATGCCGTTGCTTCTCAAATGTTAGTGAAGATTCCAAATTTTT TGTAGCTTCTTCAAATCTTTGAGCAGCTTCATGGAGGAGATCATTTTGTTTCACAGCATCTTCG AGCTTGCTTACCAATGCTTCACTTCTTGCTTGAGATTCAGCAACTGCAGCATTAGCTGCTTCAT TTTGTTGTCTTTCTGTTAGCAAAAGGGCCTCATATTCACTTACAGTCCCTTCTAGT
Genomic sequence	CTTTGGACAGTTTCTTGGAAGTGAGCAATGTCTTTCTCAGCAACTTCAATTTTCATTAGTAAGT CCTTGTTTCTATCCTCAGATTCATTGAGCGATTTCTTAGTTGCTTCACTTTCTAGCCTTTCTGT TGTCAATAGAGCATCCTTCTCTCCTAACCTTTCTTCAAGGCTATGTCCACCCATCAAAGAAAGA AATAACTATTAGTCTAACAAAAAGTGAGGGGTTAATCCTTCCCCCTTATCCATGCAAATAGATC CATACATTGTACTTTTATAGTTTATTGACTCAAAGTATATTTTGTATTTTCTTGATAATATATT CTTACAGCATGCTCTCTCTTGATGCATCCCCACAAAGAAAAAAGGAATTAACAGAGTTTTTATT AAAATATTAAATATATAGTTTCAAAGGAAACATCACATAACAAATTTGCTCAAAAAAATGCAAT GCATTATCACACGAAGTTAGAACTCTTGAAAAGGGGAAGAAAAGAAAAACCTTTGTATACTAGT CTGAAGCAGGGTGGATTTTTCATCAGTGTCCCCAACTTCTCTTTGAAGTTCTTCAATCTTTTCT CGCGCTTCATCTAATTCTATCAAATTTGCCTGATGCCGTTGCTTCTCAAATGTTAGTGAAGATT CCAAATTTTTTGTAGCTTCTTCAAATCTGCATTCAACCACAAGATACAAACTATGTGGAACACA TATAGAAATATGAAAAGATTAAAACTGTACAGCTCACAATAATTAATGCCACTGTGTTATTGGG CCATTATTTGCTCTTAAAGAGTAGCTATGACCTTATAAATATGCAAATTAGGGATTATTGATGA CACTACAATTTGCAGAGTTGGCCACATTACTTTCTGGAATAAACACTAACCTTTGAGCAGCTTC ATGGAGGAGATCATTTTGTTTCACAGCATCTTCGAGCTTGCTTACCAATGCTTCACTTCTTGCT TGAGATTCAGCAACTGCAGCATTAGCTGCTTCATTTTGTTGTCTTTCTGTTAGCAAAAGGGCCT CATATTCACTTACAGTCCCTTCTAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.184642412

Conservation Information
Conserved circRNAs	NA
PMCS	0.184642412

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							159550412-159550357(-)
						
						Potential amino acid sequence
						
							MKIEVAEKDIAHFQETVQRLEGTVSEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVK
QNDLLHEAAQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTS
IQSLEERLGEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRLEGTV
SEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVKQNDLLHEAAQRFEEATKNLESSLT
FEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTSIQSLEERLGEKDALLTTERLESEA
TKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRLEGTVSEYEALLLTERQQNEAANAAVAES
QARSEALVSKLEDAVKQNDLLHEAAQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQ
REVGDTDEKSTLLQTSIQSLEERLGEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEK
DIAHFQETVQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	159550412-159550357(-)
Potential amino acid sequence	MKIEVAEKDIAHFQETVQRLEGTVSEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVK QNDLLHEAAQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTS IQSLEERLGEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRLEGTV SEYEALLLTERQQNEAANAAVAESQARSEALVSKLEDAVKQNDLLHEAAQRFEEATKNLESSLT FEKQRHQANLIELDEAREKIEELQREVGDTDEKSTLLQTSIQSLEERLGEKDALLTTERLESEA TKKSLNESEDRNKDLLMKIEVAEKDIAHFQETVQRLEGTVSEYEALLLTERQQNEAANAAVAES QARSEALVSKLEDAVKQNDLLHEAAQRFEEATKNLESSLTFEKQRHQANLIELDEAREKIEELQ REVGDTDEKSTLLQTSIQSLEERLGEKDALLTTERLESEATKKSLNESEDRNKDLLMKIEVAEK DIAHFQETVQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d011713_circ_g.4

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