Plant Circular RNA Database

Detail information of Zm00001d048175_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d048175_circ_g.1
					
						ID in PlantcircBase
						zma_circ_010079
					
						Alias
						zma_circ_0003108
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 151503685-151506419  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d048175						
					
						Parent gene annotation
						
							J domain-containing protein required for chloroplast accumulatio
n response 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d048175_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  
						
							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
						Zm00001d048175_T002:5
Zm00001d048175_T001:5
Zm00001d048175_T003:5
Zm00001d048175_T004:2

General Information
CircRNA Name	Zm00001d048175_circ_g.1
ID in PlantcircBase	zma_circ_010079
Alias	zma_circ_0003108
Organism	Zea mays
Position	chr9: 151503685-151506419 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d048175
Parent gene annotation	J domain-containing protein required for chloroplast accumulatio n response 1
Parent gene strand	-
Alternative splicing	Zm00001d048175_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	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	Zm00001d048175_T002:5 Zm00001d048175_T001:5 Zm00001d048175_T003:5 Zm00001d048175_T004:2

			
						 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  
						
							GCTTACCATTAGAAGCGGCCTCATTACTTCCCGTAGCTGTATCCATTTTACTATTCGCTGTCAA
AACTGGTTTGTCCAACCTCTCTTGCACTTCAGTCATctgtaaaatgtcaaaaaccttctctgct
atacacttctgatgcatggcagcacctcgttgctgcaacttatctggatgaaggcacaataatg
ctttctgg

									
								

					

						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: 489
Transcript exons: 151503685-151503861,151504188-151504265,151504358-151504
417,151505813-151505892,151506326-151506419
CTGTAAAATGTCAAAAACCTTCTCTGCTATACACTTCTGATGCATGGCAGCACCTCGTTGCTGC
AACTTATCTGGATGAAGGCACAATAATGCTTTCTGGTAAGCCTTCTTAACTGCTGCTCCTTCAA
TTATATCAACAAGTGGAACTGGTTTCCATCCACTCTCAGGCCATAAGACATATTGCAGTGTTGA
AAGCAATGACCTAATATTTCCTTCTTTTCCCCTAGACCATTCGCGAATTTTAGCTTCTGATATC
TTTATTAGCTCCTTTTCCTGATCATTATGAAGAACATGATCTTCAGAAAAATGCTCAACCACAC
ATCCATCAAGATCTTCAATGTCCTCATGCTCTATTGTGTTGGCCGCTTTGTCTTTTGTATCATC
ATGGATGGGCTCATTAGAAGCGGCCTCATTACTTCCCGTAGCTGTATCCATTTTACTATTCGCT
GTCAAAACTGGTTTGTCCAACCTCTCTTGCACTTCAGTCAT
						
					

						Genomic sequence
						
							CTGTAAAATGTCAAAAACCTTCTCTGCTATACACTTCTGATGCATGGCAGCACCTCGTTGCTGC
AACTTATCTGGATGAAGGCACAATAATGCTTTCTGGTAAGCCTTCTTAACTGCTGCTCCTTCAA
TTATATCAACAAGTGGAACTGGTTTCCATCCACTCTCAGGCCATAAGACCTAAAATGAGCACAA
ACTTTTGTAATTCCGAAGTGGTGGGACCGTGGGAGACATTATTTATGATCTACTTCAAAGAGAA
TAAAACAAAAGGGAAATAATTTCACGCAGCATTTCCAGAAGACATAAAACAAGAATAAAATATG
TAGAATATTTTTTCCGTATATATAAAATCAGGCGATGCCATCAGCCATTAAAGAAGAACAATAA
CATAAGCAAAACCTAGGCTAGAGCAAAAGAGAGGATAAAACATTTATCATTCTTAGGAAGAAAA
GATTAGCAATAGTAAACAGTAAGAAATTACGCACGGTTGATACTCTTGCACTTACATATTGCAG
TGTTGAAAGCAATGACCTAATATTTCCTTCTTTTCCCCTAGACCATTCGCGAATTTTAGCTTCT
GATATCTACATTCCAGGAAACAATAAAATTGGACAAATAGAATATGGAAGTGAAACAAGAAGAC
TTAGAGGCCACATATTTATCCTCCATATTGTACCTTTATTAGCTCCTTTTCCTGATCATTATGA
AGAACATGATCTTCAGAAAAATGCTCAACCTGATTGACGAAATATAAATTTGTTAGGTAAAGAA
GCCATAACAAGAGAACATTTCCATATGACAGGGAACAGCTAAAAATGTGCACCTGAGAAAACAT
TCTTTGCTACATCTTGAGGCTCTAGTTTACTATTAACTATGGATCAACAATAGTTTATGTTGTA
AAACAAATTCATGCTGATTTTTGTTACTGCACGATGACTGTAGGTTGACATTCTTTGCCACAGT
GCCATGAATTACACTCATCTAACAACCCCTCAAACTCAAGGTAGAGGCCGTAACAAGTACAAAT
GCGACATGCGAGAAAAAAAACGTAGAGAAGGGAAGAATCCTAACCCTAAAAATTAGCTCTTTAT
ACCATTGTTATAAATTGCACTGTATTTAAAATGAGGGCACTAGACCCGAATATATAGACGATAC
AAAATAGAGACTGTAGAACAAGAACTCTCTATATGAGACCAAATACAACAAAGACACATGCATA
GGCATCTATACCCTTCAGTCAATTTGCTTAATACAACAGTAAATGACACTTATTGGGTGTTAGT
TTAGAATCTCATAGGTACATTTGTGGATATCAAGGTGTAGGAGCAGTGTTTTAAACAAAGTGTT
AGCCATGGAACAAAGGTGTAGCAACTGAATCTCAAAAATGTGCACTCGGTATCTGTCTATCTGA
TGTGCAGGAAACCAGTAGCTAGATGCTAAATGCCACTATAATGCATATTAAAACACCAGGTTTT
ACTAAGTAGGACTCATATCATCCAGGCTTTGAGCTTTGGCTAGGTTTTTTCATGAAATATTGAA
CTACATGATGGAATAGAAAAAAAGTTTGTCAAATCATCCAGGCTTGAGTATTTGGCAATTAAAT
TAGGCCAGTTTCTAGCAGTCATGAGCCTTGGTTGGGTGGAAACACATATAAATCAATAGGTCAC
CTAGTGCCATCTAATGCTGAATTTCACCTTCCAAGACGTTGTAGGACATTTGATGGGAATTTGG
TTGTATGAATAATTTGGTTGATGGATTGGCAAATATTACAGCTGTAGCTGCCAACTGCATGTCT
AATAAAACAATAAATCTAAAAAATAAAAAAGACTTTGACCCCCCCCTCTCTACCCACAGGGTAA
GACAACCCTTGGATATTCTTATTAAGGTAGAAGATAACCTTCTCACACAGGTTGAGAAAACTCC
CAAATCTCTTCCCCAAGACACTATTGCTCATGTGAGAACCTAGGCCAGTCCTTTGACCTATACT
TTGGTTTGGACAAATAAGGGATTTTTTTAACCTCAATCTTCTTCGCTCCCATGGGGAGTCGAAG
TGCTAATAGCCTACTAAAGCCACCTAACAAACTTCGCTAGGCACCCATTTGCATAGAAAGACTT
TGCAGTTTGCACATACCACACATCCATCAAGATCTTCAATGTCCTCATGCTCTATTGTGTTGGC
CGCTTTGTCTTTTGTATCATCATGGATGGGCTCTGAAAAACAGAAAAATAAGAAATACCATATA
TGTGATTTGTTCTTGGGAACAAGAACACAAGTTCATGATAATAAATGAAAAATATCACAGAGAG
CATGCATTTGGAAATTTCTGTGTTATTTATGGCACATCTGCAAACATACGGCCCATTGGTCAGT
ACAAATCTCAACCATTCACGAGCCAGAGAAGTCCATTCGTGAAAACAAATTTCAACTGTAGCTA
AATAATCTATGCAACAAGGTCCCAAAATGTTATGGTAAACACATATCAATAAAGCCTATTGTGG
CCTTTAATGTAGGAATAACCAAGAAAAACCAATACAAACAATGGTTAGTGGTTATGATAAATTT
GAACTTTCCTTTTGAAAGTGAGGTGGATATTCAACACATTCACAAGCACACTTGGGACAATCCC
TCCTTGTCAGGGCTTACCATTAGAAGCGGCCTCATTACTTCCCGTAGCTGTATCCATTTTACTA
TTCGCTGTCAAAACTGGTTTGTCCAACCTCTCTTGCACTTCAGTCAT
						
					

			
		

Sequences
Splice junction sequence	GCTTACCATTAGAAGCGGCCTCATTACTTCCCGTAGCTGTATCCATTTTACTATTCGCTGTCAA AACTGGTTTGTCCAACCTCTCTTGCACTTCAGTCATctgtaaaatgtcaaaaaccttctctgct atacacttctgatgcatggcagcacctcgttgctgcaacttatctggatgaaggcacaataatg ctttctgg
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: 489 Transcript exons: 151503685-151503861,151504188-151504265,151504358-151504 417,151505813-151505892,151506326-151506419 CTGTAAAATGTCAAAAACCTTCTCTGCTATACACTTCTGATGCATGGCAGCACCTCGTTGCTGC AACTTATCTGGATGAAGGCACAATAATGCTTTCTGGTAAGCCTTCTTAACTGCTGCTCCTTCAA TTATATCAACAAGTGGAACTGGTTTCCATCCACTCTCAGGCCATAAGACATATTGCAGTGTTGA AAGCAATGACCTAATATTTCCTTCTTTTCCCCTAGACCATTCGCGAATTTTAGCTTCTGATATC TTTATTAGCTCCTTTTCCTGATCATTATGAAGAACATGATCTTCAGAAAAATGCTCAACCACAC ATCCATCAAGATCTTCAATGTCCTCATGCTCTATTGTGTTGGCCGCTTTGTCTTTTGTATCATC ATGGATGGGCTCATTAGAAGCGGCCTCATTACTTCCCGTAGCTGTATCCATTTTACTATTCGCT GTCAAAACTGGTTTGTCCAACCTCTCTTGCACTTCAGTCAT
Genomic sequence	CTGTAAAATGTCAAAAACCTTCTCTGCTATACACTTCTGATGCATGGCAGCACCTCGTTGCTGC AACTTATCTGGATGAAGGCACAATAATGCTTTCTGGTAAGCCTTCTTAACTGCTGCTCCTTCAA TTATATCAACAAGTGGAACTGGTTTCCATCCACTCTCAGGCCATAAGACCTAAAATGAGCACAA ACTTTTGTAATTCCGAAGTGGTGGGACCGTGGGAGACATTATTTATGATCTACTTCAAAGAGAA TAAAACAAAAGGGAAATAATTTCACGCAGCATTTCCAGAAGACATAAAACAAGAATAAAATATG TAGAATATTTTTTCCGTATATATAAAATCAGGCGATGCCATCAGCCATTAAAGAAGAACAATAA CATAAGCAAAACCTAGGCTAGAGCAAAAGAGAGGATAAAACATTTATCATTCTTAGGAAGAAAA GATTAGCAATAGTAAACAGTAAGAAATTACGCACGGTTGATACTCTTGCACTTACATATTGCAG TGTTGAAAGCAATGACCTAATATTTCCTTCTTTTCCCCTAGACCATTCGCGAATTTTAGCTTCT GATATCTACATTCCAGGAAACAATAAAATTGGACAAATAGAATATGGAAGTGAAACAAGAAGAC TTAGAGGCCACATATTTATCCTCCATATTGTACCTTTATTAGCTCCTTTTCCTGATCATTATGA AGAACATGATCTTCAGAAAAATGCTCAACCTGATTGACGAAATATAAATTTGTTAGGTAAAGAA GCCATAACAAGAGAACATTTCCATATGACAGGGAACAGCTAAAAATGTGCACCTGAGAAAACAT TCTTTGCTACATCTTGAGGCTCTAGTTTACTATTAACTATGGATCAACAATAGTTTATGTTGTA AAACAAATTCATGCTGATTTTTGTTACTGCACGATGACTGTAGGTTGACATTCTTTGCCACAGT GCCATGAATTACACTCATCTAACAACCCCTCAAACTCAAGGTAGAGGCCGTAACAAGTACAAAT GCGACATGCGAGAAAAAAAACGTAGAGAAGGGAAGAATCCTAACCCTAAAAATTAGCTCTTTAT ACCATTGTTATAAATTGCACTGTATTTAAAATGAGGGCACTAGACCCGAATATATAGACGATAC AAAATAGAGACTGTAGAACAAGAACTCTCTATATGAGACCAAATACAACAAAGACACATGCATA GGCATCTATACCCTTCAGTCAATTTGCTTAATACAACAGTAAATGACACTTATTGGGTGTTAGT TTAGAATCTCATAGGTACATTTGTGGATATCAAGGTGTAGGAGCAGTGTTTTAAACAAAGTGTT AGCCATGGAACAAAGGTGTAGCAACTGAATCTCAAAAATGTGCACTCGGTATCTGTCTATCTGA TGTGCAGGAAACCAGTAGCTAGATGCTAAATGCCACTATAATGCATATTAAAACACCAGGTTTT ACTAAGTAGGACTCATATCATCCAGGCTTTGAGCTTTGGCTAGGTTTTTTCATGAAATATTGAA CTACATGATGGAATAGAAAAAAAGTTTGTCAAATCATCCAGGCTTGAGTATTTGGCAATTAAAT TAGGCCAGTTTCTAGCAGTCATGAGCCTTGGTTGGGTGGAAACACATATAAATCAATAGGTCAC CTAGTGCCATCTAATGCTGAATTTCACCTTCCAAGACGTTGTAGGACATTTGATGGGAATTTGG TTGTATGAATAATTTGGTTGATGGATTGGCAAATATTACAGCTGTAGCTGCCAACTGCATGTCT AATAAAACAATAAATCTAAAAAATAAAAAAGACTTTGACCCCCCCCTCTCTACCCACAGGGTAA GACAACCCTTGGATATTCTTATTAAGGTAGAAGATAACCTTCTCACACAGGTTGAGAAAACTCC CAAATCTCTTCCCCAAGACACTATTGCTCATGTGAGAACCTAGGCCAGTCCTTTGACCTATACT TTGGTTTGGACAAATAAGGGATTTTTTTAACCTCAATCTTCTTCGCTCCCATGGGGAGTCGAAG TGCTAATAGCCTACTAAAGCCACCTAACAAACTTCGCTAGGCACCCATTTGCATAGAAAGACTT TGCAGTTTGCACATACCACACATCCATCAAGATCTTCAATGTCCTCATGCTCTATTGTGTTGGC CGCTTTGTCTTTTGTATCATCATGGATGGGCTCTGAAAAACAGAAAAATAAGAAATACCATATA TGTGATTTGTTCTTGGGAACAAGAACACAAGTTCATGATAATAAATGAAAAATATCACAGAGAG CATGCATTTGGAAATTTCTGTGTTATTTATGGCACATCTGCAAACATACGGCCCATTGGTCAGT ACAAATCTCAACCATTCACGAGCCAGAGAAGTCCATTCGTGAAAACAAATTTCAACTGTAGCTA AATAATCTATGCAACAAGGTCCCAAAATGTTATGGTAAACACATATCAATAAAGCCTATTGTGG CCTTTAATGTAGGAATAACCAAGAAAAACCAATACAAACAATGGTTAGTGGTTATGATAAATTT GAACTTTCCTTTTGAAAGTGAGGTGGATATTCAACACATTCACAAGCACACTTGGGACAATCCC TCCTTGTCAGGGCTTACCATTAGAAGCGGCCTCATTACTTCCCGTAGCTGTATCCATTTTACTA TTCGCTGTCAAAACTGGTTTGTCCAACCTCTCTTGCACTTCAGTCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.143980956

Conservation Information
Conserved circRNAs	NA
PMCS	0.143980956

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							151504386-151503687(+)
151505836-151503721(+)
151506421-151503687(-)
						
						Potential amino acid sequence
						
							MKNMIFRKMLNHTSIKIFNVLMLYCVGRFVFCIIMDGLIRSGLITSRSCIHFTIRCQNWFVQPL
LHFSHL*(+)
MSSCSIVLAALSFVSSWMGSLEAASLLPVAVSILLFAVKTGLSNLSCTSVICKMSKTFSAIHF*
(+)
MTEVQERLDKPVLTANSKMDTATGSNEAASNEPIHDDTKDKAANTIEHEDIEDLDGCVVEHFSE
DHVLHNDQEKELIKISEAKIREWSRGKEGNIRSLLSTLQYVLWPESGWKPVPLVDIIEGAAVKK
AYQKALLCLHPDKLQQRGAAMHQKCIAEKVFDILQMTEVQERLDKPVLTANSKMDTATGSNEAA
SNEPIHDDTKDKAANTIEHEDIEDLDGCVVEHFSEDHVLHNDQEKELIKISEAKIREWSRGKEG
NIRSLLSTLQYVLWPESGWKPVPLVDIIEGAAVKKAYQKALLCLHPDKLQQRGAAMHQKCIAEK
VFDILQMTEVQERLDKPVLTANSKMDTATGSNEAASNEPIHDDTKDKAANTIEHEDIEDLDGCV
VEHFSEDHVLHNDQEKELIKISEAKIREWSRGKEGNIRSLLSTLQYVLWPESGWKPVPLVDIIE
GAAVKKAYQKALLCLHPDKLQQRGAAMHQKCIAEKVFDILQMTEVQERLDKPVLTANSKMDTAT
GSNEAASNEPIHDDTKDKAANTIEHEDIEDLDGCVVEHFSEDHVLHNDQEKELIKISEAKIREW
SRGKEGNIRSLLSTLQYVLWPESGWKPVPLVDIIEGAAVKKAYQKALLCLHPDKLQQRGAAMHQ
KCIAEKVFDILQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	151504386-151503687(+) 151505836-151503721(+) 151506421-151503687(-)
Potential amino acid sequence	MKNMIFRKMLNHTSIKIFNVLMLYCVGRFVFCIIMDGLIRSGLITSRSCIHFTIRCQNWFVQPL LHFSHL(+) MSSCSIVLAALSFVSSWMGSLEAASLLPVAVSILLFAVKTGLSNLSCTSVICKMSKTFSAIHF (+) MTEVQERLDKPVLTANSKMDTATGSNEAASNEPIHDDTKDKAANTIEHEDIEDLDGCVVEHFSE DHVLHNDQEKELIKISEAKIREWSRGKEGNIRSLLSTLQYVLWPESGWKPVPLVDIIEGAAVKK AYQKALLCLHPDKLQQRGAAMHQKCIAEKVFDILQMTEVQERLDKPVLTANSKMDTATGSNEAA SNEPIHDDTKDKAANTIEHEDIEDLDGCVVEHFSEDHVLHNDQEKELIKISEAKIREWSRGKEG NIRSLLSTLQYVLWPESGWKPVPLVDIIEGAAVKKAYQKALLCLHPDKLQQRGAAMHQKCIAEK VFDILQMTEVQERLDKPVLTANSKMDTATGSNEAASNEPIHDDTKDKAANTIEHEDIEDLDGCV VEHFSEDHVLHNDQEKELIKISEAKIREWSRGKEGNIRSLLSTLQYVLWPESGWKPVPLVDIIE GAAVKKAYQKALLCLHPDKLQQRGAAMHQKCIAEKVFDILQMTEVQERLDKPVLTANSKMDTAT GSNEAASNEPIHDDTKDKAANTIEHEDIEDLDGCVVEHFSEDHVLHNDQEKELIKISEAKIREW SRGKEGNIRSLLSTLQYVLWPESGWKPVPLVDIIEGAAVKKAYQKALLCLHPDKLQQRGAAMHQ KCIAEKVFDILQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d048175_circ_g.1

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