Plant Circular RNA Database

Detail information of Zm00001d029095_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d029095_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006523
					
						Alias
						zma_circ_0000675, GRMZM2G353147_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 57659425-57660477  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d029095						
					
						Parent gene annotation
						
							Putative GTP diphosphokinase RSH1 chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d029095_circ_g.1 Zm00001d029095_circ_g.2 Zm00001d029095_circ_g.4 Zm00001d029095_circ_g.5 Zm00001d029095_circ_g.6 						
					
						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
						Zm00001d029095_T014:3
Zm00001d029095_T004:3
Zm00001d029095_T001:3
Zm00001d029095_T002:3
Zm00001d029095_T017:3
Zm00001d029095_T011:3
Zm00001d029095_T003:3
Zm00001d029095_T009:3
Zm00001d029095_T006:3
Zm00001d029095_T015:3
Zm00001d029095_T005:3

General Information
CircRNA Name	Zm00001d029095_circ_g.3
ID in PlantcircBase	zma_circ_006523
Alias	zma_circ_0000675, GRMZM2G353147_C1
Organism	Zea mays
Position	chr1: 57659425-57660477 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d029095
Parent gene annotation	Putative GTP diphosphokinase RSH1 chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d029095_circ_g.1 Zm00001d029095_circ_g.2 Zm00001d029095_circ_g.4 Zm00001d029095_circ_g.5 Zm00001d029095_circ_g.6
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	Zm00001d029095_T014:3 Zm00001d029095_T004:3 Zm00001d029095_T001:3 Zm00001d029095_T002:3 Zm00001d029095_T017:3 Zm00001d029095_T011:3 Zm00001d029095_T003:3 Zm00001d029095_T009:3 Zm00001d029095_T006:3 Zm00001d029095_T015:3 Zm00001d029095_T005:3

			
						 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  
						
							ACCGCAGTTGGCATATGAAGCACACAGTGGACAAAAACGGCGAAGTGGAGAACCATTCATTATT
CATCCTGTTGAAGTTGCTCGTATTCTTGGAGAGCATttaccgcgcatcaccctggatgaggaca
tcaatagagggaaatttggttatgatccatcgcgtgcctactctacaagttttgtcagatcttg
gtctacta

						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: 333
Transcript exons: 57659425-57659598,57660231-57660296,57660385-57660477
TTACCGCGCATCACCCTGGATGAGGACATCAATAGAGGGAAATTTGGTTATGATCCATCGCGTG
CCTACTCTACAAGTTTTGTCAGATCTTGGTCTACTATTGTTGACCGAACATGGAGATCTTACTG
CTATTCATCATCTGATTCTTTCATCTCTCCAGAGACTTTGTGGGAGGATCTCAAACCAGCTGTT
TCATATCTTCAACCTGAAGAGTTAAAATTTGTGCATGATGCTTTGAAGTTGGCATATGAAGCAC
ACAGTGGACAAAAACGGCGAAGTGGAGAACCATTCATTATTCATCCTGTTGAAGTTGCTCGTAT
TCTTGGAGAGCAT
						
						Genomic sequence
						
							TTACCGCGCATCACCCTGGATGAGGACATCAATAGAGGGAAATTTGGTTATGATCCATCGCGTG
CCTACTCTACAAGTTTTGTCAGATCTTGGTCTACTATTGTTGACCGAACATGGAGATCTTACTG
CTATTCATCATCTGATTCTTTCATCTCTCCAGAGACTTTGTGGGAGGTGTGTCATTGAATCACT
TATGTAATTTGCACTTTTGCACATATCTGAAGAGCTACATTTTCTAGCTTCGATCAAATCCCTC
GATTTGGTTTGCAGCCTTATGACCATTCAAAGTTCTTTTGGGGCAGCAAAAAACACAACAGTGT
AGGGGTTTTCCCTTTTATTAAATATATGATATATATAGTGCTTTCCACCTTGTCTCTAACATTT
GCACAAATATTCTAGAATATGTAAGGAATAGGGATCGTTCTATTCCTGGTAATGGAACACCACA
ATTATTTCCTGCTCCATGGTGCCAACACATGTTTTAACTAGAAGAAATTAGATAGGAGTCAAGC
TCATTGGTGCTTTTGAAATGTAGTTCTGGCCAGAGTAAAATACATTCATTTCAACAGCCACATG
GCCACACTAGTTTTACCAAATGGTACCCGTTTGTTGTTAGTTGTTACTTGGTAGTATGTTTTGC
TCCTTTGAGTTCGAAACAACATTTTTTTATGTTCAAGTTTACCTACAAACCTCGGGTGCTACTA
AGTCCTTAGGTGAGGCAAGGCTCGACTTTAATGCTAGATTTTCTTATGCGAATCAAGAATCACT
TCAATCATAGTGAATTGTAACTTTTTTCTGCATAACAGGATCTCAAACCAGCTGTTTCATATCT
TCAACCTGAAGAGTTAAAATTTGTGCATGATGCTTTGAAGGTAACTGGTTCACAATATCTTCCT
TCAGTGCTATTTGAGAAAAGACTGCACGAACGTCTGCATCACTATAGTTCATTAATAACCGCAG
TTGGCATATGAAGCACACAGTGGACAAAAACGGCGAAGTGGAGAACCATTCATTATTCATCCTG
TTGAAGTTGCTCGTATTCTTGGAGAGCAT

Sequences
Splice junction sequence	ACCGCAGTTGGCATATGAAGCACACAGTGGACAAAAACGGCGAAGTGGAGAACCATTCATTATT CATCCTGTTGAAGTTGCTCGTATTCTTGGAGAGCATttaccgcgcatcaccctggatgaggaca tcaatagagggaaatttggttatgatccatcgcgtgcctactctacaagttttgtcagatcttg gtctacta
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: 333 Transcript exons: 57659425-57659598,57660231-57660296,57660385-57660477 TTACCGCGCATCACCCTGGATGAGGACATCAATAGAGGGAAATTTGGTTATGATCCATCGCGTG CCTACTCTACAAGTTTTGTCAGATCTTGGTCTACTATTGTTGACCGAACATGGAGATCTTACTG CTATTCATCATCTGATTCTTTCATCTCTCCAGAGACTTTGTGGGAGGATCTCAAACCAGCTGTT TCATATCTTCAACCTGAAGAGTTAAAATTTGTGCATGATGCTTTGAAGTTGGCATATGAAGCAC ACAGTGGACAAAAACGGCGAAGTGGAGAACCATTCATTATTCATCCTGTTGAAGTTGCTCGTAT TCTTGGAGAGCAT
Genomic sequence	TTACCGCGCATCACCCTGGATGAGGACATCAATAGAGGGAAATTTGGTTATGATCCATCGCGTG CCTACTCTACAAGTTTTGTCAGATCTTGGTCTACTATTGTTGACCGAACATGGAGATCTTACTG CTATTCATCATCTGATTCTTTCATCTCTCCAGAGACTTTGTGGGAGGTGTGTCATTGAATCACT TATGTAATTTGCACTTTTGCACATATCTGAAGAGCTACATTTTCTAGCTTCGATCAAATCCCTC GATTTGGTTTGCAGCCTTATGACCATTCAAAGTTCTTTTGGGGCAGCAAAAAACACAACAGTGT AGGGGTTTTCCCTTTTATTAAATATATGATATATATAGTGCTTTCCACCTTGTCTCTAACATTT GCACAAATATTCTAGAATATGTAAGGAATAGGGATCGTTCTATTCCTGGTAATGGAACACCACA ATTATTTCCTGCTCCATGGTGCCAACACATGTTTTAACTAGAAGAAATTAGATAGGAGTCAAGC TCATTGGTGCTTTTGAAATGTAGTTCTGGCCAGAGTAAAATACATTCATTTCAACAGCCACATG GCCACACTAGTTTTACCAAATGGTACCCGTTTGTTGTTAGTTGTTACTTGGTAGTATGTTTTGC TCCTTTGAGTTCGAAACAACATTTTTTTATGTTCAAGTTTACCTACAAACCTCGGGTGCTACTA AGTCCTTAGGTGAGGCAAGGCTCGACTTTAATGCTAGATTTTCTTATGCGAATCAAGAATCACT TCAATCATAGTGAATTGTAACTTTTTTCTGCATAACAGGATCTCAAACCAGCTGTTTCATATCT TCAACCTGAAGAGTTAAAATTTGTGCATGATGCTTTGAAGGTAACTGGTTCACAATATCTTCCT TCAGTGCTATTTGAGAAAAGACTGCACGAACGTCTGCATCACTATAGTTCATTAATAACCGCAG TTGGCATATGAAGCACACAGTGGACAAAAACGGCGAAGTGGAGAACCATTCATTATTCATCCTG TTGAAGTTGCTCGTATTCTTGGAGAGCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.115504486

Conservation Information
Conserved circRNAs	NA
PMCS	0.115504486

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							57660393-57660270(+)
57659455-57660443(-)
						
						Potential amino acid sequence
						
							MKHTVDKNGEVENHSLFILLKLLVFLESIYRASPWMRTSIEGNLVMIHRVPTLQVLSDLGLLLL
TEHGDLTAIHHLILSSLQRLCGRISNQLFHIFNLKS*(+)
MSSSRVMRGKCSPRIRATSTG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	57660393-57660270(+) 57659455-57660443(-)
Potential amino acid sequence	MKHTVDKNGEVENHSLFILLKLLVFLESIYRASPWMRTSIEGNLVMIHRVPTLQVLSDLGLLLL TEHGDLTAIHHLILSSLQRLCGRISNQLFHIFNLKS(+) MSSSRVMRGKCSPRIRATSTG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d029095_circ_g.3

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