Plant Circular RNA Database

Detail information of Zm00001d047540_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d047540_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010047
					
						Alias
						Zm09circ00060, zma_circ_0003031, GRMZM2G462803_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 134450526-134458316  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d047540						
					
						Parent gene annotation
						
							Guanine nucleotide exchange factor SPIKE 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d047540_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  
						
							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
						Zm00001d047540_T008:8
Zm00001d047540_T025:8
Zm00001d047540_T033:8
Zm00001d047540_T024:8
Zm00001d047540_T006:8
Zm00001d047540_T034:8
Zm00001d047540_T002:8
Zm00001d047540_T007:8
Zm00001d047540_T005:3
Zm00001d047540_T036:8
Zm00001d047540_T003:8
Zm00001d047540_T029:8
Zm00001d047540_T010:7
Zm00001d047540_T009:8
Zm00001d047540_T014:8
Zm00001d047540_T001:8
Zm00001d047540_T004:8
Zm00001d047540_T031:8

General Information
CircRNA Name	Zm00001d047540_circ_g.3
ID in PlantcircBase	zma_circ_010047
Alias	Zm09circ00060, zma_circ_0003031, GRMZM2G462803_C1
Organism	Zea mays
Position	chr9: 134450526-134458316 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d047540
Parent gene annotation	Guanine nucleotide exchange factor SPIKE 1
Parent gene strand	-
Alternative splicing	Zm00001d047540_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	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	Zm00001d047540_T008:8 Zm00001d047540_T025:8 Zm00001d047540_T033:8 Zm00001d047540_T024:8 Zm00001d047540_T006:8 Zm00001d047540_T034:8 Zm00001d047540_T002:8 Zm00001d047540_T007:8 Zm00001d047540_T005:3 Zm00001d047540_T036:8 Zm00001d047540_T003:8 Zm00001d047540_T029:8 Zm00001d047540_T010:7 Zm00001d047540_T009:8 Zm00001d047540_T014:8 Zm00001d047540_T001:8 Zm00001d047540_T004:8 Zm00001d047540_T031:8

			
						 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  
						
							CACAGGTGCTTGCCGACCGCCGAAGTCATCAAAAGCAAAATCAACATAATTAATAAGGAATCTA
TTTCTCTCAGCCCCATCTGATGACTCCTGCTGCACAccttatttcatgccttgaagcctccgac
aaatatgcattgactgatggggataatcgctcagagtactttgggggtgcagggcgctcaacat
ctgggctc

						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: 1111
Transcript exons: 134450526-134450669,134451412-134451594,134452697-134452
807,134452964-134453039,134453643-134453773,134453954-13
4454147,134454241-134454367,134458172-134458316
CCTTATTTCATGCCTTGAAGCCTCCGACAAATATGCATTGACTGATGGGGATAATCGCTCAGAG
TACTTTGGGGGTGCAGGGCGCTCAACATCTGGGCTCCGAGAACTAGCACCAAGTAGCATGCTGC
CTCCTGTTTTGTTGTGCTCAAAATGGGTTATACATTCTTCAAGAAGCTTGAAGAACAATCTGGT
TCTAGCAATGCTTTGTTGCCATGCTTTGATAAGAGTTGCATCATCCAAGTTCCTTACAATTTGC
AAAATGACAACTAGCACTTCACGCTTTTCGATGGCATTCAGATTATAGAAAACAGGCATCTCAT
CAAGGATCTGCCCTATAAGAGAGAAGTACAGCTGAGCAATGTACAGCTTGTCTTCACTTTTTTG
ATAGCGTGCATCAAATTCATGTTTGCATATAAGGACAACCAGAATCCGAGCAGCCTTCGCTCGT
TGAGACAAATCATCATGGTCTAAGGTCAGAAAGATCTCTTGAATAAGAACTGACGAGAGATAGT
TTCTATCAGAGGGATCCCGCCCAGGCATCTCAACGAATAGATCATGGTCGCATATTATCTGCAG
GAATGTCAATTTGCAGTCATGAAGGACTGCTTGACAAACTCCTGCAAACTTGTCCATGTACAAC
GAAACCAGCTCAAAAACTTGGCGAGGCTCAATTATTGATAAAAGATCATAGCAAAAGAAAGCAA
GCGTGCTGTTCAAGCGTTTTGCCAAGCTTAAACCCTTTTTACAGCGTTCATGAACCTCAGTTAG
AAGGCAATCAAAGAGCTGCATGATGCACCTGAAGACACCTTCTTTCAATTGTAGCGGTGGGACA
TCTTCACCTAATGGAAGGTTGTGGTAGAAGAGACGACTTTGTTCCAATCCCATTGATTTTACAA
TAAGCTCCAGAAAAAACCAAGCCATTGCCAACACATCATCATACACAGGACCAACTCTATAACC
TTTCGCCTTACTCCTAGCAAGACTTCCCCAAACAGTAGACAGACCAGGATACACAGGTGCTTGC
CGACCGCCGAAGTCATCAAAAGCAAAATCAACATAATTAATAAGGAATCTATTTCTCTCAGCCC
CATCTGATGACTCCTGCTGCACA
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CACAGGTGCTTGCCGACCGCCGAAGTCATCAAAAGCAAAATCAACATAATTAATAAGGAATCTA TTTCTCTCAGCCCCATCTGATGACTCCTGCTGCACAccttatttcatgccttgaagcctccgac aaatatgcattgactgatggggataatcgctcagagtactttgggggtgcagggcgctcaacat ctgggctc
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: 1111 Transcript exons: 134450526-134450669,134451412-134451594,134452697-134452 807,134452964-134453039,134453643-134453773,134453954-13 4454147,134454241-134454367,134458172-134458316 CCTTATTTCATGCCTTGAAGCCTCCGACAAATATGCATTGACTGATGGGGATAATCGCTCAGAG TACTTTGGGGGTGCAGGGCGCTCAACATCTGGGCTCCGAGAACTAGCACCAAGTAGCATGCTGC CTCCTGTTTTGTTGTGCTCAAAATGGGTTATACATTCTTCAAGAAGCTTGAAGAACAATCTGGT TCTAGCAATGCTTTGTTGCCATGCTTTGATAAGAGTTGCATCATCCAAGTTCCTTACAATTTGC AAAATGACAACTAGCACTTCACGCTTTTCGATGGCATTCAGATTATAGAAAACAGGCATCTCAT CAAGGATCTGCCCTATAAGAGAGAAGTACAGCTGAGCAATGTACAGCTTGTCTTCACTTTTTTG ATAGCGTGCATCAAATTCATGTTTGCATATAAGGACAACCAGAATCCGAGCAGCCTTCGCTCGT TGAGACAAATCATCATGGTCTAAGGTCAGAAAGATCTCTTGAATAAGAACTGACGAGAGATAGT TTCTATCAGAGGGATCCCGCCCAGGCATCTCAACGAATAGATCATGGTCGCATATTATCTGCAG GAATGTCAATTTGCAGTCATGAAGGACTGCTTGACAAACTCCTGCAAACTTGTCCATGTACAAC GAAACCAGCTCAAAAACTTGGCGAGGCTCAATTATTGATAAAAGATCATAGCAAAAGAAAGCAA GCGTGCTGTTCAAGCGTTTTGCCAAGCTTAAACCCTTTTTACAGCGTTCATGAACCTCAGTTAG AAGGCAATCAAAGAGCTGCATGATGCACCTGAAGACACCTTCTTTCAATTGTAGCGGTGGGACA TCTTCACCTAATGGAAGGTTGTGGTAGAAGAGACGACTTTGTTCCAATCCCATTGATTTTACAA TAAGCTCCAGAAAAAACCAAGCCATTGCCAACACATCATCATACACAGGACCAACTCTATAACC TTTCGCCTTACTCCTAGCAAGACTTCCCCAAACAGTAGACAGACCAGGATACACAGGTGCTTGC CGACCGCCGAAGTCATCAAAAGCAAAATCAACATAATTAATAAGGAATCTATTTCTCTCAGCCC CATCTGATGACTCCTGCTGCACA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.143336405

Conservation Information
Conserved circRNAs	NA
PMCS	0.143336405

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							134458301-134451568(+)
134454324-134458289(-)
						
						Potential amino acid sequence
						
							MTPAAHLISCLEASDKYALTDGDNRSEYFGGAGRSTSGLRELAPSSMLPPVLLCSKWVIHSSRS
LKNNLVLAMLCCHALIRVASSKFLTICKMTTSTSRFSMAFRL*(+)
MAWFFLELIVKSMGLEQSRLFYHNLPLGEDVPPLQLKEGVFRCIMQLFDCLLTEVHERCKKGLS
LAKRLNSTLAFFCYDLLSIIEPRQVFELVSLYMDKFAGVCQAVLHDCKLTFLQIICDHDLFVEM
PGRDPSDRNYLSSVLIQEIFLTLDHDDLSQRAKAARILVVLICKHEFDARYQKSEDKLYIAQLY
FSLIGQILDEMPVFYNLNAIEKREVLVVILQIVRNLDDATLIKAWQQSIARTRLFFKLLEECIT
HFEHNKTGGSMLLGASSRSPDVERPAPPKYSERLSPSVNAYLSEASRHEIRCAAGVIRWG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	134458301-134451568(+) 134454324-134458289(-)
Potential amino acid sequence	MTPAAHLISCLEASDKYALTDGDNRSEYFGGAGRSTSGLRELAPSSMLPPVLLCSKWVIHSSRS LKNNLVLAMLCCHALIRVASSKFLTICKMTTSTSRFSMAFRL(+) MAWFFLELIVKSMGLEQSRLFYHNLPLGEDVPPLQLKEGVFRCIMQLFDCLLTEVHERCKKGLS LAKRLNSTLAFFCYDLLSIIEPRQVFELVSLYMDKFAGVCQAVLHDCKLTFLQIICDHDLFVEM PGRDPSDRNYLSSVLIQEIFLTLDHDDLSQRAKAARILVVLICKHEFDARYQKSEDKLYIAQLY FSLIGQILDEMPVFYNLNAIEKREVLVVILQIVRNLDDATLIKAWQQSIARTRLFFKLLEECIT HFEHNKTGGSMLLGASSRSPDVERPAPPKYSERLSPSVNAYLSEASRHEIRCAAGVIRWG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d047540_circ_g.3

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