Plant Circular RNA Database

Detail information of Zm00001d025461_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d025461_circ_g.5
					
						ID in PlantcircBase
						zma_circ_003218
					
						Alias
						circ1519
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 119226608-119230129  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d025461						
					
						Parent gene annotation
						
							Regulator of nonsense transcripts UPF3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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-TA							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
						Zm00001d025461_T004:6
Zm00001d025461_T001:6
Zm00001d025461_T003:6
Zm00001d025461_T015:5
Zm00001d025461_T010:6
Zm00001d025461_T006:6
Zm00001d025461_T012:6
Zm00001d025461_T017:6
Zm00001d025461_T008:6
Zm00001d025461_T002:6
Zm00001d025461_T005:6
Zm00001d025461_T014:6
Zm00001d025461_T009:6
Zm00001d025461_T013:6
Zm00001d025461_T011:6
Zm00001d025461_T007:5

General Information
CircRNA Name	Zm00001d025461_circ_g.5
ID in PlantcircBase	zma_circ_003218
Alias	circ1519
Organism	Zea mays
Position	chr10: 119226608-119230129 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d025461
Parent gene annotation	Regulator of nonsense transcripts UPF3
Parent gene strand	-
Alternative splicing	NA
Support reads	2
Tissues	seedling leaves
Exon boundary	No-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-TA 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	Zm00001d025461_T004:6 Zm00001d025461_T001:6 Zm00001d025461_T003:6 Zm00001d025461_T015:5 Zm00001d025461_T010:6 Zm00001d025461_T006:6 Zm00001d025461_T012:6 Zm00001d025461_T017:6 Zm00001d025461_T008:6 Zm00001d025461_T002:6 Zm00001d025461_T005:6 Zm00001d025461_T014:6 Zm00001d025461_T009:6 Zm00001d025461_T013:6 Zm00001d025461_T011:6 Zm00001d025461_T007:5

			
						 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  
						
							ATTCACAAATACGTGCCCATTGAAGACCTCAGCGAACTCAACAACATCCTCGGGGCGCTTGAAA
TTAAGGTAAAGTCGAGAATGTCTATGGTTCTTTTGGccgcctgaatttccagcaacatcttttt
ccctttgtgtatgctcctctctctttggcaccatgatataggttggtttctccttagtgttgtc
tcgtacaa

									
								

					

						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
						
							CCGCCTGAATTTCCAGCAACATCTTTTTCCCTTTGTGTATGCTCCTCTCTCTTTGGCACCATGA
TATAGGTTGGTTTCTCCTTAGTGTTGTCTCGTACAACATACTGCTTGAGAAAATAGAAAAAAAA
CAGTAAAAATGTGAACCTCAGGTCACAATTTATTTCACAGAACAAAAGGAGGGTAGCATTTGTT
GTTTTGTCTCAACATGTAGTCAGATCACTGGATCAGGAGGTCTTGTTACAAAATAACAACACAG
ATACTGAAGGTTTGGTGGTGCCTCAATTGTATCATGCATGATTCTTAAAGAGTAAGGCGAGCAA
GGCGCCTAGGATTTTTTGGGCGCCTGGACGCCTAGGCGACGCCTTTAAAACACTGTTATCATGG
AAACCATACATGCATAGGACTACGAGTTCTGAAGGAAAATTAACTATGCAACTATCACCTAGAA
GGGACCAATTGTAGTGAATTTATTCAGATTATATAACTATAAGGAGCACACTATGCATGGGCGC
CATAAATATAGAAATAAGAGCAATTGTGCTAATTTTCATAAAATACAGTAAACCGTGAGCATAA
TTCATCAGTGACCATCATCTGACAAATGAGGAAAAACATAATGATGAGTTAGTACCATACACAC
GGCAAATCTTAGTGAACAAAAGAATAATGCCAACATAGGAACCCATGTGAAGGTACACCCGTTA
TGTCAAAGAAAGTATGAACTGACAATAGACAGTTTTATCAGAAAAAATCACAAAGTTCCAAATA
GGGCATGTTACCGTGGAGGATCTGCGCTTCTCAGAAGACCTTTTAGGACTGGAACTGCTTACGA
CACTTGCAAGTTTTCTGCTAAGTCTACTTCCAGGTCTCTGCAATTTAAGAAAACAGTAACAAGT
TAACAGTTGATCAAGAAGGGCCCTATGTTATCGGTTAAGGAATAAATGTACCTACATGAACCAT
ACTCTTAGCTGCCCTTTGCTGGCGGACATACATCATAAGAGGTGTCACAACAGGTGCCTCCTTT
CCAGCAGCTGCCACAAAATAATCAATAATCAAATGTGATAACCCCATTTTGTGCTTGGCATATT
TGGAAAGATACATCGATATAGCAAATACTTCCGCCATTTCAAATTATAAGACGTTTTTGCTTTT
CTAGATACATTGTTTCTACTTTGTATATAGACATAGTGTATATCTAAGTGCATAGCAAAAGTTG
TGTATCTAGCAAAGCCAAAACTTCTTATAGTTTGGAGTGGAGTACTACATTGTGGATCGAAAGT
AATGATGGCATATTCTACCTGCCCTTTCAGCTTCTTTCCTTTCGAGCTGAATTTCAGCACTAGG
CAGATGCTCAGTAGGCTTTGAAATAAACTCAAGAAACTCCAAGTACTCCGGATCTAGTAATTCC
AAAAAGACAAAATCCAAGTTTAGAAAATGGTAATATGACAAAACGATGCAATTGGGAAAAGAAT
TAGTTAAAGTGATTGCCTAAGACCTTTCATAATAGTTCCTTCACGGCCATCCTTCTTGATAGTT
GACTTGGGAACCTGTTGTGATGGTGCATATTCCACGAAAGCTTTAAACTGAGCACCTGACAGAA
CCATACACAACATCCATGAGACTCAAATTAGGCAAAGCAGATCATAAATGACACCTCAAATAAA
TCTACAAACATGTGCTTGACAGTTGCAAAAAAAAGCCTTATGCATTATAAGTAGTTTATTTATG
TTTCAGAATAACAATATAACACACTGTACAAGAAATATTATCAAGCCAACATATGCTGTTTTTG
CTTCCTGCCACCAACTCTAGCGCTGACCTAAGTTGGATCGACAAGCACAATAGCATCAAGTACA
ATACTAATGTGAAACAGTATGTCATCATTAATGTGCTAGAATGATGCAACCTAATGTAAGTGCA
TTCAATTCAATTTCAAAATTTCCTTCATATAAAATATTTACTATGTTACACTCATCAAGGACAT
GTATAACAAGGTTGTGACTAGTGTCCGAACAACTGATGGTGATACAAATGTTTTCCCGATTAAC
ATAGGACTACATCAAGGTTCAGCTTTGAGCCCTTATTTGCCTTAGTGATAGATGAGGTCACGAG
GGATATACAAGGAGATATCCCTTGGTGTATGCTTTTCGCTGACGATGTAGTTCTAGTAGATGAA
AGCTGGGAATGAGTAAATAGAAAGCTAGAGTTATGGCATCAGTCCCTAGAGTCAAAAGGATTTA
GAATTAGCAGGGCCAAAAGAGAGTATATGAGATGTGACTTTGGTACTACAATTAGTGAGGATGG
AGATGTAAGTTTGGGAGGCCAGGTAGTACCAAAGGACACCTTCTATTATTTGGGATCGATGCTA
CAGAGAGATGGTGATATTGATGAAGATGTTAGCCATAGAGTCAAAACGGGGTGGATGAAATGGC
GTCAAGCATCGGGAGTCCTATGCGACAAGAGAGTGTCACAGAAGTTGAAAGGCAAGTTCTACAG
GACAGCGATTAGGCCTAATATGTTATATGGGGTTGAGTGTTGGCCTACTAAGAGACGACATATT
CAACAACTAAGTGTCGCAGAGATGTGTATGTTGTGTTGGATATGTGGGCACACAAGATTGGATC
GAGTGAGAAACGATGACATTCTTGATCGTCTAGGAGTAGCACCAATTGAAGAAAAGCTTATTCA
ACACCGGTTGAGATAGTTTGGGCATGTCCAACGGAGTTGTGTTTGGATATCCCAATGGAGTTGT
GTTTGGATAGAAGTGTTTGGAAAGAAGCTATCCACGTGCCCGAACCGTGATTAGGCCTTTTTCC
TTTTAGTGCTCTCAAAAGCTTTTCCCTCCCCTTTCTCTCTCTTTCCCCTTTTGGTGACATTTTG
TTGGGTTTCAACTCTAGCCTACCCCAACTTGCTTGGGACTAAAAGGCTATGTTGATGTTGATGA
TAAAATATTTACTATGTGTCTCTTGGATCCTTCTTCAACACTCACCAAGAGAAACCAGAATCTT
ATACACCATCAGGTCAAGTAGACAGTGTTCTAGAAAGCTAACTGTAACTAGACCCAATCAATAG
AAAGCTAACTATAACTAGACCCAACCATATGCAACAAATTTCAGTTTGATGGCTATCAGGCTAT
GTAAATGCTCAAGCATTAATATTTAACATCAATTTGTGTTTGTGATGCCACATAAGTAGATGAT
AAGGCGTGCACCCATGATAAACTTAGATCACAAGGTTTGTAAACAATGAAATGGGAATGCAACT
TAGAAAAAATATTTTTTCTGGTAAAAGAACTTAATAGTCAGTGCTTGTAACTGATGGAATTGGC
ACAATATGATTGAATCAAAATGTACATAAGGTGCACATCCAGAATATAAATTATCATGGACAAA
ATTCAACAAGATGGAGGAAATACCCTTTTCATTCACAAATACGTGCCCATTGAAGACCTCAGCG
AACTCAACAACATCCTCGGGGCGCTTGAAATTAAGGTAAAGTCGAGAATGTCTATGGTTCTTTT
GG
						
					

			
		

Sequences
Splice junction sequence	ATTCACAAATACGTGCCCATTGAAGACCTCAGCGAACTCAACAACATCCTCGGGGCGCTTGAAA TTAAGGTAAAGTCGAGAATGTCTATGGTTCTTTTGGccgcctgaatttccagcaacatcttttt ccctttgtgtatgctcctctctctttggcaccatgatataggttggtttctccttagtgttgtc tcgtacaa
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	CCGCCTGAATTTCCAGCAACATCTTTTTCCCTTTGTGTATGCTCCTCTCTCTTTGGCACCATGA TATAGGTTGGTTTCTCCTTAGTGTTGTCTCGTACAACATACTGCTTGAGAAAATAGAAAAAAAA CAGTAAAAATGTGAACCTCAGGTCACAATTTATTTCACAGAACAAAAGGAGGGTAGCATTTGTT GTTTTGTCTCAACATGTAGTCAGATCACTGGATCAGGAGGTCTTGTTACAAAATAACAACACAG ATACTGAAGGTTTGGTGGTGCCTCAATTGTATCATGCATGATTCTTAAAGAGTAAGGCGAGCAA GGCGCCTAGGATTTTTTGGGCGCCTGGACGCCTAGGCGACGCCTTTAAAACACTGTTATCATGG AAACCATACATGCATAGGACTACGAGTTCTGAAGGAAAATTAACTATGCAACTATCACCTAGAA GGGACCAATTGTAGTGAATTTATTCAGATTATATAACTATAAGGAGCACACTATGCATGGGCGC CATAAATATAGAAATAAGAGCAATTGTGCTAATTTTCATAAAATACAGTAAACCGTGAGCATAA TTCATCAGTGACCATCATCTGACAAATGAGGAAAAACATAATGATGAGTTAGTACCATACACAC GGCAAATCTTAGTGAACAAAAGAATAATGCCAACATAGGAACCCATGTGAAGGTACACCCGTTA TGTCAAAGAAAGTATGAACTGACAATAGACAGTTTTATCAGAAAAAATCACAAAGTTCCAAATA GGGCATGTTACCGTGGAGGATCTGCGCTTCTCAGAAGACCTTTTAGGACTGGAACTGCTTACGA CACTTGCAAGTTTTCTGCTAAGTCTACTTCCAGGTCTCTGCAATTTAAGAAAACAGTAACAAGT TAACAGTTGATCAAGAAGGGCCCTATGTTATCGGTTAAGGAATAAATGTACCTACATGAACCAT ACTCTTAGCTGCCCTTTGCTGGCGGACATACATCATAAGAGGTGTCACAACAGGTGCCTCCTTT CCAGCAGCTGCCACAAAATAATCAATAATCAAATGTGATAACCCCATTTTGTGCTTGGCATATT TGGAAAGATACATCGATATAGCAAATACTTCCGCCATTTCAAATTATAAGACGTTTTTGCTTTT CTAGATACATTGTTTCTACTTTGTATATAGACATAGTGTATATCTAAGTGCATAGCAAAAGTTG TGTATCTAGCAAAGCCAAAACTTCTTATAGTTTGGAGTGGAGTACTACATTGTGGATCGAAAGT AATGATGGCATATTCTACCTGCCCTTTCAGCTTCTTTCCTTTCGAGCTGAATTTCAGCACTAGG CAGATGCTCAGTAGGCTTTGAAATAAACTCAAGAAACTCCAAGTACTCCGGATCTAGTAATTCC AAAAAGACAAAATCCAAGTTTAGAAAATGGTAATATGACAAAACGATGCAATTGGGAAAAGAAT TAGTTAAAGTGATTGCCTAAGACCTTTCATAATAGTTCCTTCACGGCCATCCTTCTTGATAGTT GACTTGGGAACCTGTTGTGATGGTGCATATTCCACGAAAGCTTTAAACTGAGCACCTGACAGAA CCATACACAACATCCATGAGACTCAAATTAGGCAAAGCAGATCATAAATGACACCTCAAATAAA TCTACAAACATGTGCTTGACAGTTGCAAAAAAAAGCCTTATGCATTATAAGTAGTTTATTTATG TTTCAGAATAACAATATAACACACTGTACAAGAAATATTATCAAGCCAACATATGCTGTTTTTG CTTCCTGCCACCAACTCTAGCGCTGACCTAAGTTGGATCGACAAGCACAATAGCATCAAGTACA ATACTAATGTGAAACAGTATGTCATCATTAATGTGCTAGAATGATGCAACCTAATGTAAGTGCA TTCAATTCAATTTCAAAATTTCCTTCATATAAAATATTTACTATGTTACACTCATCAAGGACAT GTATAACAAGGTTGTGACTAGTGTCCGAACAACTGATGGTGATACAAATGTTTTCCCGATTAAC ATAGGACTACATCAAGGTTCAGCTTTGAGCCCTTATTTGCCTTAGTGATAGATGAGGTCACGAG GGATATACAAGGAGATATCCCTTGGTGTATGCTTTTCGCTGACGATGTAGTTCTAGTAGATGAA AGCTGGGAATGAGTAAATAGAAAGCTAGAGTTATGGCATCAGTCCCTAGAGTCAAAAGGATTTA GAATTAGCAGGGCCAAAAGAGAGTATATGAGATGTGACTTTGGTACTACAATTAGTGAGGATGG AGATGTAAGTTTGGGAGGCCAGGTAGTACCAAAGGACACCTTCTATTATTTGGGATCGATGCTA CAGAGAGATGGTGATATTGATGAAGATGTTAGCCATAGAGTCAAAACGGGGTGGATGAAATGGC GTCAAGCATCGGGAGTCCTATGCGACAAGAGAGTGTCACAGAAGTTGAAAGGCAAGTTCTACAG GACAGCGATTAGGCCTAATATGTTATATGGGGTTGAGTGTTGGCCTACTAAGAGACGACATATT CAACAACTAAGTGTCGCAGAGATGTGTATGTTGTGTTGGATATGTGGGCACACAAGATTGGATC GAGTGAGAAACGATGACATTCTTGATCGTCTAGGAGTAGCACCAATTGAAGAAAAGCTTATTCA ACACCGGTTGAGATAGTTTGGGCATGTCCAACGGAGTTGTGTTTGGATATCCCAATGGAGTTGT GTTTGGATAGAAGTGTTTGGAAAGAAGCTATCCACGTGCCCGAACCGTGATTAGGCCTTTTTCC TTTTAGTGCTCTCAAAAGCTTTTCCCTCCCCTTTCTCTCTCTTTCCCCTTTTGGTGACATTTTG TTGGGTTTCAACTCTAGCCTACCCCAACTTGCTTGGGACTAAAAGGCTATGTTGATGTTGATGA TAAAATATTTACTATGTGTCTCTTGGATCCTTCTTCAACACTCACCAAGAGAAACCAGAATCTT ATACACCATCAGGTCAAGTAGACAGTGTTCTAGAAAGCTAACTGTAACTAGACCCAATCAATAG AAAGCTAACTATAACTAGACCCAACCATATGCAACAAATTTCAGTTTGATGGCTATCAGGCTAT GTAAATGCTCAAGCATTAATATTTAACATCAATTTGTGTTTGTGATGCCACATAAGTAGATGAT AAGGCGTGCACCCATGATAAACTTAGATCACAAGGTTTGTAAACAATGAAATGGGAATGCAACT TAGAAAAAATATTTTTTCTGGTAAAAGAACTTAATAGTCAGTGCTTGTAACTGATGGAATTGGC ACAATATGATTGAATCAAAATGTACATAAGGTGCACATCCAGAATATAAATTATCATGGACAAA ATTCAACAAGATGGAGGAAATACCCTTTTCATTCACAAATACGTGCCCATTGAAGACCTCAGCG AACTCAACAACATCCTCGGGGCGCTTGAAATTAAGGTAAAGTCGAGAATGTCTATGGTTCTTTT GG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.070170166

Conservation Information
Conserved circRNAs	NA
PMCS	0.070170166

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d025461_circ_g.5

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