Plant Circular RNA Database

Detail information of Zm00001d003655_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d003655_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007176
					
						Alias
						Zm02circ00049, zma_circ_0000729, GRMZM2G013283_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 52527804-52528811  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d003655						
					
						Parent gene annotation
						
							DExH-box ATP-dependent RNA helicase DExH7 chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d003655_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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  
						
							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
						Zm00001d003655_T025:2
Zm00001d003655_T003:2
Zm00001d003655_T028:2
Zm00001d003655_T027:2
Zm00001d003655_T026:2
Zm00001d003655_T006:2
Zm00001d003655_T005:2
Zm00001d003655_T014:2
Zm00001d003655_T004:2
Zm00001d003655_T012:2
Zm00001d003655_T010:2
Zm00001d003655_T016:2
Zm00001d003655_T024:2
Zm00001d003655_T009:2
Zm00001d003655_T018:2
Zm00001d003655_T019:2

General Information
CircRNA Name	Zm00001d003655_circ_g.3
ID in PlantcircBase	zma_circ_007176
Alias	Zm02circ00049, zma_circ_0000729, GRMZM2G013283_C2
Organism	Zea mays
Position	chr2: 52527804-52528811 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d003655
Parent gene annotation	DExH-box ATP-dependent RNA helicase DExH7 chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d003655_circ_g.2
Support reads	NA
Tissues	leaf, endosperm, 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	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	Zm00001d003655_T025:2 Zm00001d003655_T003:2 Zm00001d003655_T028:2 Zm00001d003655_T027:2 Zm00001d003655_T026:2 Zm00001d003655_T006:2 Zm00001d003655_T005:2 Zm00001d003655_T014:2 Zm00001d003655_T004:2 Zm00001d003655_T012:2 Zm00001d003655_T010:2 Zm00001d003655_T016:2 Zm00001d003655_T024:2 Zm00001d003655_T009:2 Zm00001d003655_T018:2 Zm00001d003655_T019:2

			
						 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  
						
							GAGGCACAAGGTGGGCAGTAGAAAAAATAATCTCGAGAGCTGGTTTTCTAATATGTCTCTTCCA
TTCAATGCCTATGCTCGCTGCACCTCGGTTATTAAGggacatgcgtcttcagtttggtaccttg
ttagcagacattggacttatagatcttcctaaagatactctggtatgtctgtttaagagaattg
atctagat

						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: 169
Transcript exons: 52527804-52527873,52528713-52528811
GGACATGCGTCTTCAGTTTGGTACCTTGTTAGCAGACATTGGACTTATAGATCTTCCTAAAGAT
ACTCTGAGGCACAAGGTGGGCAGTAGAAAAAATAATCTCGAGAGCTGGTTTTCTAATATGTCTC
TTCCATTCAATGCCTATGCTCGCTGCACCTCGGTTATTAAG
						
						Genomic sequence
						
							GGACATGCGTCTTCAGTTTGGTACCTTGTTAGCAGACATTGGACTTATAGATCTTCCTAAAGAT
ACTCTGGTATGTCTGTTTAAGAGAATTGATCTAGATTCTAGAAACCCCTTAACATGTAAAGTAC
CTCTCTGCCCTCTAGCAGGACTCTTGAAATGAAAGGTGTGTCACTTAGGTCATTTGTGTCATTA
TTGGGATGGGTTAAGAGCAAGTCTGTCCTCTCCCTTCCTCTTCTTCTCAGATAGAAAACATAAC
AAAGAAACTTTTAGAAGATTAATATCTGTACTGATTAACTTATTTGTCATGAATCACTTAGGCC
CCGTTTGTTTCGTTGGAATTGAATTCCATTTTAATAATATAATTTAGACAAAACTAATTAAGTT
CATATATTTATATATGTAATATATTTGTATATTATCTTAAATTATATGAGAGAGATAGTTATAT
ACTACATTAATGTTATAACGAAGCAAGTAGAAGAGTGTGCTATAAGTTGTATATTGGAAAAATA
GCATGTAAATCAATAGAATTAATTTCCATCTCTCACCCATGAATTTGAGATAGGCTTATATGAT
AACTTTGGAAAGTGGTGGAATGTCACATTCTAAAAAAATAGCCTATTCCAATAGTAAGATTCAA
TTCCTTAAAATGAAAGGAAACAAACGGGGCCTTATAGATGTTAAGTTCAATATACTTCTTCCAC
AATTCTCTACACTACCTTAGGGACTATAACTTATTAAAAGAAACTGGCAGGTTTGTAGTCAACG
ATGTGCTAAGCTACTTCAGTTCTATTAATATACCATATACCTCTTTGTAACTATTTTAACAAAT
ACTTTTTTCTTAATCTGAATGGAAACACATCAAAATTAATCTTCTGAGAAAGTGAGAATTGGTT
TTCCTATTTCCAGAGGCACAAGGTGGGCAGTAGAAAAAATAATCTCGAGAGCTGGTTTTCTAAT
ATGTCTCTTCCATTCAATGCCTATGCTCGCTGCACCTCGGTTATTAAG

Sequences
Splice junction sequence	GAGGCACAAGGTGGGCAGTAGAAAAAATAATCTCGAGAGCTGGTTTTCTAATATGTCTCTTCCA TTCAATGCCTATGCTCGCTGCACCTCGGTTATTAAGggacatgcgtcttcagtttggtaccttg ttagcagacattggacttatagatcttcctaaagatactctggtatgtctgtttaagagaattg atctagat
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: 169 Transcript exons: 52527804-52527873,52528713-52528811 GGACATGCGTCTTCAGTTTGGTACCTTGTTAGCAGACATTGGACTTATAGATCTTCCTAAAGAT ACTCTGAGGCACAAGGTGGGCAGTAGAAAAAATAATCTCGAGAGCTGGTTTTCTAATATGTCTC TTCCATTCAATGCCTATGCTCGCTGCACCTCGGTTATTAAG
Genomic sequence	GGACATGCGTCTTCAGTTTGGTACCTTGTTAGCAGACATTGGACTTATAGATCTTCCTAAAGAT ACTCTGGTATGTCTGTTTAAGAGAATTGATCTAGATTCTAGAAACCCCTTAACATGTAAAGTAC CTCTCTGCCCTCTAGCAGGACTCTTGAAATGAAAGGTGTGTCACTTAGGTCATTTGTGTCATTA TTGGGATGGGTTAAGAGCAAGTCTGTCCTCTCCCTTCCTCTTCTTCTCAGATAGAAAACATAAC AAAGAAACTTTTAGAAGATTAATATCTGTACTGATTAACTTATTTGTCATGAATCACTTAGGCC CCGTTTGTTTCGTTGGAATTGAATTCCATTTTAATAATATAATTTAGACAAAACTAATTAAGTT CATATATTTATATATGTAATATATTTGTATATTATCTTAAATTATATGAGAGAGATAGTTATAT ACTACATTAATGTTATAACGAAGCAAGTAGAAGAGTGTGCTATAAGTTGTATATTGGAAAAATA GCATGTAAATCAATAGAATTAATTTCCATCTCTCACCCATGAATTTGAGATAGGCTTATATGAT AACTTTGGAAAGTGGTGGAATGTCACATTCTAAAAAAATAGCCTATTCCAATAGTAAGATTCAA TTCCTTAAAATGAAAGGAAACAAACGGGGCCTTATAGATGTTAAGTTCAATATACTTCTTCCAC AATTCTCTACACTACCTTAGGGACTATAACTTATTAAAAGAAACTGGCAGGTTTGTAGTCAACG ATGTGCTAAGCTACTTCAGTTCTATTAATATACCATATACCTCTTTGTAACTATTTTAACAAAT ACTTTTTTCTTAATCTGAATGGAAACACATCAAAATTAATCTTCTGAGAAAGTGAGAATTGGTT TTCCTATTTCCAGAGGCACAAGGTGGGCAGTAGAAAAAATAATCTCGAGAGCTGGTTTTCTAAT ATGTCTCTTCCATTCAATGCCTATGCTCGCTGCACCTCGGTTATTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.096796412

Conservation Information
Conserved circRNAs	NA
PMCS	0.096796412

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							52527809-52527860(+)
52528781-52527860(+)
52527811-52527834(-)
						
						Potential amino acid sequence
						
							MRLQFGTLLADIGLIDLPKDTLRHKVGSRKNNLESWFSNMSLPFNAYARCTSVIKGHASSVWYL
VSRHWTYRSS*(+)
MPMLAAPRLLRDMRLQFGTLLADIGLIDLPKDTLRHKVGSRKNNLESWFSNMSLPFNAYARCTS
VIKGHASSVWYLVSRHWTYRSS*(+)
MSLNNRGAASIGIEWKRHIRKPALEIIFSTAHLVPQSIFRKIYKSNVC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	52527809-52527860(+) 52528781-52527860(+) 52527811-52527834(-)
Potential amino acid sequence	MRLQFGTLLADIGLIDLPKDTLRHKVGSRKNNLESWFSNMSLPFNAYARCTSVIKGHASSVWYL VSRHWTYRSS(+) MPMLAAPRLLRDMRLQFGTLLADIGLIDLPKDTLRHKVGSRKNNLESWFSNMSLPFNAYARCTS VIKGHASSVWYLVSRHWTYRSS(+) MSLNNRGAASIGIEWKRHIRKPALEIIFSTAHLVPQSIFRKIYKSNVC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d003655_circ_g.3

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