Plant Circular RNA Database

Detail information of Zm00001d030340_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d030340_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006620
					
						Alias
						zma_circ_0000250
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 123401298-123402041  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d030340						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d030340_circ_g.1 Zm00001d030340_circ_g.2 Zm00001d030340_circ_g.4 						
					
						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
						Zm00001d030340_T028:3
Zm00001d030340_T057:3
Zm00001d030340_T046:3
Zm00001d030340_T005:3
Zm00001d030340_T003:3
Zm00001d030340_T051:3
Zm00001d030340_T054:3
Zm00001d030340_T058:3
Zm00001d030340_T043:3
Zm00001d030340_T037:3
Zm00001d030340_T010:3
Zm00001d030340_T006:3
Zm00001d030340_T034:3
Zm00001d030340_T007:3
Zm00001d030340_T023:3
Zm00001d030340_T002:3
Zm00001d030340_T040:3
Zm00001d030340_T059:3
Zm00001d030340_T026:3
Zm00001d030340_T015:3
Zm00001d030340_T050:3
Zm00001d030340_T053:3
Zm00001d030340_T039:3
Zm00001d030340_T048:3
Zm00001d030340_T033:3
Zm00001d030340_T001:3
Zm00001d030340_T014:3
Zm00001d030340_T021:3
Zm00001d030340_T009:3
Zm00001d030340_T030:3
Zm00001d030340_T041:3
Zm00001d030340_T013:3
Zm00001d030340_T049:3

General Information
CircRNA Name	Zm00001d030340_circ_g.3
ID in PlantcircBase	zma_circ_006620
Alias	zma_circ_0000250
Organism	Zea mays
Position	chr1: 123401298-123402041 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d030340
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Zm00001d030340_circ_g.1 Zm00001d030340_circ_g.2 Zm00001d030340_circ_g.4
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	Zm00001d030340_T028:3 Zm00001d030340_T057:3 Zm00001d030340_T046:3 Zm00001d030340_T005:3 Zm00001d030340_T003:3 Zm00001d030340_T051:3 Zm00001d030340_T054:3 Zm00001d030340_T058:3 Zm00001d030340_T043:3 Zm00001d030340_T037:3 Zm00001d030340_T010:3 Zm00001d030340_T006:3 Zm00001d030340_T034:3 Zm00001d030340_T007:3 Zm00001d030340_T023:3 Zm00001d030340_T002:3 Zm00001d030340_T040:3 Zm00001d030340_T059:3 Zm00001d030340_T026:3 Zm00001d030340_T015:3 Zm00001d030340_T050:3 Zm00001d030340_T053:3 Zm00001d030340_T039:3 Zm00001d030340_T048:3 Zm00001d030340_T033:3 Zm00001d030340_T001:3 Zm00001d030340_T014:3 Zm00001d030340_T021:3 Zm00001d030340_T009:3 Zm00001d030340_T030:3 Zm00001d030340_T041:3 Zm00001d030340_T013:3 Zm00001d030340_T049:3

			
						 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  
						
							TGATTAATCATGATGTATTTAATTGAGAAAACAATTAAAGGTGATATTATATCATCAGCATCTG
CTCCTTTCCGAAGAACCTGAGTGGTAAAGTCAAGCActctggtaaattggacaggatgtgatat
ataatatcaagtccattgcaaaggacaagctggatatcttcaatatccttaagaccatgataat
tgctccta

						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: 401
Transcript exons: 123401298-123401405,123401485-123401628,123401893-123402
041
CTCTGGTAAATTGGACAGGATGTGATATATAATATCAAGTCCATTGCAAAGGACAAGCTGGATA
TCTTCAATATCCTTAAGACCATGATAATTGCTCCTATATGAGTCATGCAGTAATCGTGTTAGTA
CAGATAATATGCTCCAGAGTACACCGTGGACAGATGAATCATATAGTAGAATTTCCCAAATGAT
GCCACCAAGCTTTGATGAGAATGGTTTTACTTGAAGACAGCTTTTCACCAATTCAAACACCCGT
AGGGTTGTCTTCCAACGACTACATTCCTTGTGTTTCCAGTTCACATGATTAATCATGATGTATT
TAATTGAGAAAACAATTAAAGGTGATATTATATCATCAGCATCTGCTCCTTTCCGAAGAACCTG
AGTGGTAAAGTCAAGCA
						
						Genomic sequence
						
							CTCTGGTAAATTGGACAGGATGTGATATATAATATCAAGTCCATTGCAAAGGACAAGCTGGATA
TCTTCAATATCCTTAAGACCATGATAATTGCTCCTATATGAGTCCTGAAAAAAATTTTACAGAT
TATCATGTAAAGGTCACAAAGCTAATGATCATTAATACTAACAGGAAGAATATCCTTACATGCA
GTAATCGTGTTAGTACAGATAATATGCTCCAGAGTACACCGTGGACAGATGAATCATATAGTAG
AATTTCCCAAATGATGCCACCAAGCTTTGATGAGAATGGTTTTACTTGAAGACAGCTTTTCACC
AATTCAAACACCTAGTCAAGTACAGTTCAGTGGCAATATTTAGCTTCTCTATTATTAATGGTAA
CAACAAATAAAAACAAGATCAACAAAACTGAAATGTTTCTAAAATAAATCTACTAAAATGAAAT
AAGAATCACAGCCAACTAAGTTGAAAATTTTACTTTGTCTATTAGGTTCAATCAACAGAAAAAA
GGGCTGTGGCTCACAAGTACTAAAAATATCACAGGTAACAAGCAATACTATCATTATATTGAAC
AAACATAAAAAAAACATACCCGTAGGGTTGTCTTCCAACGACTACATTCCTTGTGTTTCCAGTT
CACATGATTAATCATGATGTATTTAATTGAGAAAACAATTAAAGGTGATATTATATCATCAGCA
TCTGCTCCTTTCCGAAGAACCTGAGTGGTAAAGTCAAGCA

Sequences
Splice junction sequence	TGATTAATCATGATGTATTTAATTGAGAAAACAATTAAAGGTGATATTATATCATCAGCATCTG CTCCTTTCCGAAGAACCTGAGTGGTAAAGTCAAGCActctggtaaattggacaggatgtgatat ataatatcaagtccattgcaaaggacaagctggatatcttcaatatccttaagaccatgataat tgctccta
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: 401 Transcript exons: 123401298-123401405,123401485-123401628,123401893-123402 041 CTCTGGTAAATTGGACAGGATGTGATATATAATATCAAGTCCATTGCAAAGGACAAGCTGGATA TCTTCAATATCCTTAAGACCATGATAATTGCTCCTATATGAGTCATGCAGTAATCGTGTTAGTA CAGATAATATGCTCCAGAGTACACCGTGGACAGATGAATCATATAGTAGAATTTCCCAAATGAT GCCACCAAGCTTTGATGAGAATGGTTTTACTTGAAGACAGCTTTTCACCAATTCAAACACCCGT AGGGTTGTCTTCCAACGACTACATTCCTTGTGTTTCCAGTTCACATGATTAATCATGATGTATT TAATTGAGAAAACAATTAAAGGTGATATTATATCATCAGCATCTGCTCCTTTCCGAAGAACCTG AGTGGTAAAGTCAAGCA
Genomic sequence	CTCTGGTAAATTGGACAGGATGTGATATATAATATCAAGTCCATTGCAAAGGACAAGCTGGATA TCTTCAATATCCTTAAGACCATGATAATTGCTCCTATATGAGTCCTGAAAAAAATTTTACAGAT TATCATGTAAAGGTCACAAAGCTAATGATCATTAATACTAACAGGAAGAATATCCTTACATGCA GTAATCGTGTTAGTACAGATAATATGCTCCAGAGTACACCGTGGACAGATGAATCATATAGTAG AATTTCCCAAATGATGCCACCAAGCTTTGATGAGAATGGTTTTACTTGAAGACAGCTTTTCACC AATTCAAACACCTAGTCAAGTACAGTTCAGTGGCAATATTTAGCTTCTCTATTATTAATGGTAA CAACAAATAAAAACAAGATCAACAAAACTGAAATGTTTCTAAAATAAATCTACTAAAATGAAAT AAGAATCACAGCCAACTAAGTTGAAAATTTTACTTTGTCTATTAGGTTCAATCAACAGAAAAAA GGGCTGTGGCTCACAAGTACTAAAAATATCACAGGTAACAAGCAATACTATCATTATATTGAAC AAACATAAAAAAAACATACCCGTAGGGTTGTCTTCCAACGACTACATTCCTTGTGTTTCCAGTT CACATGATTAATCATGATGTATTTAATTGAGAAAACAATTAAAGGTGATATTATATCATCAGCA TCTGCTCCTTTCCGAAGAACCTGAGTGGTAAAGTCAAGCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.090125946

Conservation Information
Conserved circRNAs	NA
PMCS	0.090125946

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							123401488-123402037(-)
123401954-123401990(-)
						
						Potential amino acid sequence
						
							MTHIGAIIMVLRILKISSLSFAMDLILYITSCPIYQSA*(-)
MINHVNWKHKECSRWKTTLRVFELVKSCLQVKPFSSKLGGIIWEILLYDSSVHGVLWSILSVLT
RLLHDSYRSNYHGLKDIEDIQLVLCNGLDIIYHILSNLPECLTLPLRFFGKEQMLMI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	123401488-123402037(-) 123401954-123401990(-)
Potential amino acid sequence	MTHIGAIIMVLRILKISSLSFAMDLILYITSCPIYQSA(-) MINHVNWKHKECSRWKTTLRVFELVKSCLQVKPFSSKLGGIIWEILLYDSSVHGVLWSILSVLT RLLHDSYRSNYHGLKDIEDIQLVLCNGLDIIYHILSNLPECLTLPLRFFGKEQMLMI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d030340_circ_g.3

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