Plant Circular RNA Database

Detail information of Zm00001d006438_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d006438_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007363
					
						Alias
						zma_circ_0000906
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 208172909-208174337  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d006438						
					
						Parent gene annotation
						
							Regulator of nonsense transcripts 1 homolog
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d006438_circ_g.2 						
					
						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  
						
							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
						Zm00001d006438_T032:7
Zm00001d006438_T041:7
Zm00001d006438_T068:7
Zm00001d006438_T016:7
Zm00001d006438_T076:6
Zm00001d006438_T013:7
Zm00001d006438_T036:7
Zm00001d006438_T065:6
Zm00001d006438_T024:7
Zm00001d006438_T042:7
Zm00001d006438_T063:7
Zm00001d006438_T055:7
Zm00001d006438_T018:7
Zm00001d006438_T019:7
Zm00001d006438_T022:7
Zm00001d006438_T049:7
Zm00001d006438_T070:7
Zm00001d006438_T020:7
Zm00001d006438_T025:7
Zm00001d006438_T028:7
Zm00001d006438_T010:7
Zm00001d006438_T039:7
Zm00001d006438_T062:7
Zm00001d006438_T023:7
Zm00001d006438_T001:7
Zm00001d006438_T006:7
Zm00001d006438_T030:7
Zm00001d006438_T017:7
Zm00001d006438_T031:7
Zm00001d006438_T007:7
Zm00001d006438_T058:7
Zm00001d006438_T073:7
Zm00001d006438_T072:7
Zm00001d006438_T009:7
Zm00001d006438_T035:7
Zm00001d006438_T026:7
Zm00001d006438_T004:7
Zm00001d006438_T067:7
Zm00001d006438_T005:7
Zm00001d006438_T059:7
Zm00001d006438_T047:7
Zm00001d006438_T051:7
Zm00001d006438_T027:7
Zm00001d006438_T053:7
Zm00001d006438_T033:7

General Information
CircRNA Name	Zm00001d006438_circ_g.1
ID in PlantcircBase	zma_circ_007363
Alias	zma_circ_0000906
Organism	Zea mays
Position	chr2: 208172909-208174337 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d006438
Parent gene annotation	Regulator of nonsense transcripts 1 homolog
Parent gene strand	+
Alternative splicing	Zm00001d006438_circ_g.2
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	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	Zm00001d006438_T032:7 Zm00001d006438_T041:7 Zm00001d006438_T068:7 Zm00001d006438_T016:7 Zm00001d006438_T076:6 Zm00001d006438_T013:7 Zm00001d006438_T036:7 Zm00001d006438_T065:6 Zm00001d006438_T024:7 Zm00001d006438_T042:7 Zm00001d006438_T063:7 Zm00001d006438_T055:7 Zm00001d006438_T018:7 Zm00001d006438_T019:7 Zm00001d006438_T022:7 Zm00001d006438_T049:7 Zm00001d006438_T070:7 Zm00001d006438_T020:7 Zm00001d006438_T025:7 Zm00001d006438_T028:7 Zm00001d006438_T010:7 Zm00001d006438_T039:7 Zm00001d006438_T062:7 Zm00001d006438_T023:7 Zm00001d006438_T001:7 Zm00001d006438_T006:7 Zm00001d006438_T030:7 Zm00001d006438_T017:7 Zm00001d006438_T031:7 Zm00001d006438_T007:7 Zm00001d006438_T058:7 Zm00001d006438_T073:7 Zm00001d006438_T072:7 Zm00001d006438_T009:7 Zm00001d006438_T035:7 Zm00001d006438_T026:7 Zm00001d006438_T004:7 Zm00001d006438_T067:7 Zm00001d006438_T005:7 Zm00001d006438_T059:7 Zm00001d006438_T047:7 Zm00001d006438_T051:7 Zm00001d006438_T027:7 Zm00001d006438_T053:7 Zm00001d006438_T033:7

			
						 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  
						
							ATGTTGGATTCAGTGTGGATTTTGTTTGGAAGAGTACCAGTTTTGATAGGATGCAAGGAGCGAT
GAAAACTTTTGCTGTGGACGAGACAAGTGTCAGTGGgttagggcaaagcataaggaagtatgcc
ttcacaaggatagccctttaggagaaacaattctcgaatgctacaactgtggttgtcggaatgt
atttcttc

						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
						
							GTTAGGGCAAAGCATAAGGAAGTATGCCTTCACAAGGATAGCCCTTTAGGAGAAACAATTCTCG
AATGCTACAACTGTGGTTGTCGGAATGTATTTCTTCTTGGGTTTATCTCAGCAAAGGCGGAGAA
TGTTGTCGTTCTTTTATGCAGAGAACCATGTTTAAGTGTTAATGCACTGAAGGATATGAATTGG
GATCTCAGTCAGTGGTGCCCTCTTATCGACGACAGGTGTTTTTTGTCGTGGCTTGTAAAGGCAA
GTGTTTCCTCATGATGATTTGTTAGGTTGTTCTGTCATGCATTTGTGCTTAGCTAGTAACTTTC
TGATGGTTGAACAATTTACTTTATACCAGGTACCTTCAGAGCAGGAGCAGCTAAGAGCTCGCCA
AATTAGTGCTCAACAAATCAACAAAGTGGAAGAGCTCTGGAAGACAAATCCTGATGCATCTCTT
GAAGATCTTGAAAAGCCCGGTGTAGATGATGAACCTCAGCCAGTTGTTTTGAAGTATGAAGATG
CTTACCAGGTTAAAACTCTGTTTTGTATTCTATCACTTGGGCTTACTTTTTGCGGGTGCTTTAC
TTCTACTCTCAATCTGTCAAAGCTCATATTTTGACCTTGCATTCTGATTAGCATATCCTGCCCT
TCTTTTTGCCAGTACCAAAATGTTTTTGCACCACTGATAAAGCTTGAGGCTGATTATGACAAGG
TACTGTGTTCTGATTACGAGACCATGTTTCTTATCTTTTCCATAACATAATTGAATTGTGTTGC
TGTTTTATATGTTGCTGTAGATGATGAAAGAGTCACAGAGCAAGGATAATGTAACTGTCCGGTG
GGATATTGGGTTGAACAAGAAGCGTGTAGCTTACTTTGTCTTTCCAAAGGTTTGTTTAAGATCT
GAAATATATGGGATTAGTGAATTAATATCATCATTATATAGTGATTTGTTGTAGACTATGTTGG
TATTGCTTTGTGATACTCTTTTGCATAACATGGGAAACAATTGTGTATTTTAGGAAGACAATGA
GTTGAGGCTTGTGCCTGGAGATGAACTACGCCTGAGATATCCTGGTGATAGCTCACATCCCACA
TGGCAATCTGTCGGACATGTGGTAATTAGAAACATGTTGATAATCTATAAATTGGGCCAGCTTG
ATCTTTGTGCCTGTGCTAAGTATATTGTTCTTTCAGATTAAGCTCACTGCACAAGAGGAGGTGG
CACTTGAGCTTCGCGCTAGTCAGGTATAAGGTGTTTTTTTGTCATGTTTTTTTAGCATCTGCTC
AGCCTACTGTAACGTTTCCTTGGATTTCAGGGGGTGCCTACTGAGCTAAATGTTGGATTCAGTG
TGGATTTTGTTTGGAAGAGTACCAGTTTTGATAGGATGCAAGGAGCGATGAAAACTTTTGCTGT
GGACGAGACAAGTGTCAGTGG

Sequences
Splice junction sequence	ATGTTGGATTCAGTGTGGATTTTGTTTGGAAGAGTACCAGTTTTGATAGGATGCAAGGAGCGAT GAAAACTTTTGCTGTGGACGAGACAAGTGTCAGTGGgttagggcaaagcataaggaagtatgcc ttcacaaggatagccctttaggagaaacaattctcgaatgctacaactgtggttgtcggaatgt atttcttc
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	GTTAGGGCAAAGCATAAGGAAGTATGCCTTCACAAGGATAGCCCTTTAGGAGAAACAATTCTCG AATGCTACAACTGTGGTTGTCGGAATGTATTTCTTCTTGGGTTTATCTCAGCAAAGGCGGAGAA TGTTGTCGTTCTTTTATGCAGAGAACCATGTTTAAGTGTTAATGCACTGAAGGATATGAATTGG GATCTCAGTCAGTGGTGCCCTCTTATCGACGACAGGTGTTTTTTGTCGTGGCTTGTAAAGGCAA GTGTTTCCTCATGATGATTTGTTAGGTTGTTCTGTCATGCATTTGTGCTTAGCTAGTAACTTTC TGATGGTTGAACAATTTACTTTATACCAGGTACCTTCAGAGCAGGAGCAGCTAAGAGCTCGCCA AATTAGTGCTCAACAAATCAACAAAGTGGAAGAGCTCTGGAAGACAAATCCTGATGCATCTCTT GAAGATCTTGAAAAGCCCGGTGTAGATGATGAACCTCAGCCAGTTGTTTTGAAGTATGAAGATG CTTACCAGGTTAAAACTCTGTTTTGTATTCTATCACTTGGGCTTACTTTTTGCGGGTGCTTTAC TTCTACTCTCAATCTGTCAAAGCTCATATTTTGACCTTGCATTCTGATTAGCATATCCTGCCCT TCTTTTTGCCAGTACCAAAATGTTTTTGCACCACTGATAAAGCTTGAGGCTGATTATGACAAGG TACTGTGTTCTGATTACGAGACCATGTTTCTTATCTTTTCCATAACATAATTGAATTGTGTTGC TGTTTTATATGTTGCTGTAGATGATGAAAGAGTCACAGAGCAAGGATAATGTAACTGTCCGGTG GGATATTGGGTTGAACAAGAAGCGTGTAGCTTACTTTGTCTTTCCAAAGGTTTGTTTAAGATCT GAAATATATGGGATTAGTGAATTAATATCATCATTATATAGTGATTTGTTGTAGACTATGTTGG TATTGCTTTGTGATACTCTTTTGCATAACATGGGAAACAATTGTGTATTTTAGGAAGACAATGA GTTGAGGCTTGTGCCTGGAGATGAACTACGCCTGAGATATCCTGGTGATAGCTCACATCCCACA TGGCAATCTGTCGGACATGTGGTAATTAGAAACATGTTGATAATCTATAAATTGGGCCAGCTTG ATCTTTGTGCCTGTGCTAAGTATATTGTTCTTTCAGATTAAGCTCACTGCACAAGAGGAGGTGG CACTTGAGCTTCGCGCTAGTCAGGTATAAGGTGTTTTTTTGTCATGTTTTTTTAGCATCTGCTC AGCCTACTGTAACGTTTCCTTGGATTTCAGGGGGTGCCTACTGAGCTAAATGTTGGATTCAGTG TGGATTTTGTTTGGAAGAGTACCAGTTTTGATAGGATGCAAGGAGCGATGAAAACTTTTGCTGT GGACGAGACAAGTGTCAGTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.281460393

Conservation Information
Conserved circRNAs	NA
PMCS	0.281460393

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							208173093-208172954(+)
208172925-208174146(-)
						
						Potential amino acid sequence
						
							MNWDLSQWCPLIDDRCFLSWLVKASVPSEQEQLRARQISAQQINKVEELWKTNPDASLEDLEKP
GVDDEPQPVVLKYEDAYQYQNVFAPLIKLEADYDKMMKESQSKDNVTVRWDIGLNKKRVAYFVF
PKEDNELRLVPGDELRLRYPGDSSHPTWQSVGHVIKLTAQEEVALELRASQGVPTELNVGFSVD
FVWKSTSFDRMQGAMKTFAVDETSVSGLGQSIRKYAFTRIAL*(+)
MLCPNPLTLVSSTAKVFIAPCILSKLVLFQTKSTLNPTFSSVGTP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	208173093-208172954(+) 208172925-208174146(-)
Potential amino acid sequence	MNWDLSQWCPLIDDRCFLSWLVKASVPSEQEQLRARQISAQQINKVEELWKTNPDASLEDLEKP GVDDEPQPVVLKYEDAYQYQNVFAPLIKLEADYDKMMKESQSKDNVTVRWDIGLNKKRVAYFVF PKEDNELRLVPGDELRLRYPGDSSHPTWQSVGHVIKLTAQEEVALELRASQGVPTELNVGFSVD FVWKSTSFDRMQGAMKTFAVDETSVSGLGQSIRKYAFTRIAL(+) MLCPNPLTLVSSTAKVFIAPCILSKLVLFQTKSTLNPTFSSVGTP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d006438_circ_g.1

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