Plant Circular RNA Database

Detail information of Zm00001d046041_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d046041_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009947
					
						Alias
						Zm09circ00039, zma_circ_0002978, ZmciR404
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 58184826-58186465  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d046041						
					
						Parent gene annotation
						
							HEAT repeat-containing protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d046041_circ_g.1 						
					
						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
						Zm00001d046039_T001:4
Zm00001d046039_T021:4
Zm00001d046039_T015:4
Zm00001d046039_T014:4
Zm00001d046039_T006:4
Zm00001d046039_T033:4
Zm00001d046039_T037:4
Zm00001d046039_T031:4
Zm00001d046039_T024:4
Zm00001d046039_T004:4
Zm00001d046039_T011:4
Zm00001d046039_T017:4
Zm00001d046039_T040:4
Zm00001d046039_T035:4
Zm00001d046039_T039:4
Zm00001d046039_T029:4
Zm00001d046039_T010:4
Zm00001d046039_T007:4
Zm00001d046039_T052:4
Zm00001d046039_T027:4
Zm00001d046039_T033:4
Zm00001d046039_T006:4
Zm00001d046039_T014:4
Zm00001d046039_T015:4
Zm00001d046039_T021:4
Zm00001d046039_T001:4
Zm00001d046039_T027:4
Zm00001d046039_T052:4
Zm00001d046039_T007:4
Zm00001d046039_T010:4
Zm00001d046039_T029:4
Zm00001d046039_T039:4
Zm00001d046039_T035:4
Zm00001d046041_T001:4
Zm00001d046039_T040:4
Zm00001d046039_T017:4
Zm00001d046039_T011:4
Zm00001d046039_T004:4
Zm00001d046039_T037:4
Zm00001d046039_T031:4
Zm00001d046039_T024:4

General Information
CircRNA Name	Zm00001d046041_circ_g.2
ID in PlantcircBase	zma_circ_009947
Alias	Zm09circ00039, zma_circ_0002978, ZmciR404
Organism	Zea mays
Position	chr9: 58184826-58186465 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d046041
Parent gene annotation	HEAT repeat-containing protein
Parent gene strand	-
Alternative splicing	Zm00001d046041_circ_g.1
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	Zm00001d046039_T001:4 Zm00001d046039_T021:4 Zm00001d046039_T015:4 Zm00001d046039_T014:4 Zm00001d046039_T006:4 Zm00001d046039_T033:4 Zm00001d046039_T037:4 Zm00001d046039_T031:4 Zm00001d046039_T024:4 Zm00001d046039_T004:4 Zm00001d046039_T011:4 Zm00001d046039_T017:4 Zm00001d046039_T040:4 Zm00001d046039_T035:4 Zm00001d046039_T039:4 Zm00001d046039_T029:4 Zm00001d046039_T010:4 Zm00001d046039_T007:4 Zm00001d046039_T052:4 Zm00001d046039_T027:4 Zm00001d046039_T033:4 Zm00001d046039_T006:4 Zm00001d046039_T014:4 Zm00001d046039_T015:4 Zm00001d046039_T021:4 Zm00001d046039_T001:4 Zm00001d046039_T027:4 Zm00001d046039_T052:4 Zm00001d046039_T007:4 Zm00001d046039_T010:4 Zm00001d046039_T029:4 Zm00001d046039_T039:4 Zm00001d046039_T035:4 Zm00001d046041_T001:4 Zm00001d046039_T040:4 Zm00001d046039_T017:4 Zm00001d046039_T011:4 Zm00001d046039_T004:4 Zm00001d046039_T037:4 Zm00001d046039_T031:4 Zm00001d046039_T024:4

			
						 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  
						
							TACTTCATGAGTTTAGCTACAATGCTTGATGTCTCAATCAGCCCTGCAGTAATCTTGCGTCCAA
ATAAACGGTAAATTTCCCCCAGACATTGTGCTGCACctttgacaaatggcacaatcaaatgctt
ctgcacaccatcttcaattttctttgcagaagcagtttgttttttcccgcctttcttcacctat
caaataag

									
								

					

						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: 519
Transcript exons: 58184826-58184913,58184981-58185070,58185167-58185400,58
186359-58186465
CTTTGACAAATGGCACAATCAAATGCTTCTGCACACCATCTTCAATTTTCTTTGCAGAAGCAGT
TTGTTTTTTCCCGCCTTTCTTCACCTGGGCATCTGGATTCACTGCAAGAGCAAGTATGGCACCA
AGTGCTTCGGCAAATGAATCTCTAACTGAAGATACACTATCTTCCAAACCCTTCACACAATAAG
ACATAGAAGAATCGAAATCAGCCATCCCCAATGCAGGCCCACCAATATTAGCAAATGCCTTCAA
GCAACGTGCTGCCGCTGCTCTGACAATGAACGATTTATCACTTACACCTCGCATGATGATACGA
AAAGCCTCTTGATAAGCTGCAGCAGCACCACCACCACCTGAGCCTTCCAATGCATTCTCAAGCA
AGAGAAGAGCATCTTGTCTCACAAAGTCCTCATGATACTTCATGAGTTTAGCTACAATGCTTGA
TGTCTCAATCAGCCCTGCAGTAATCTTGCGTCCAAATAAACGGTAAATTTCCCCCAGACATTGT
GCTGCAC
						
					

						Genomic sequence
						
							CTTTGACAAATGGCACAATCAAATGCTTCTGCACACCATCTTCAATTTTCTTTGCAGAAGCAGT
TTGTTTTTTCCCGCCTTTCTTCACCTATCAAATAAGCTTGTATCTAAATCGTAAAAAGAAAATG
GTTAAGAAAAATGTGAGAATGATATACCTGGGCATCTGGATTCACTGCAAGAGCAAGTATGGCA
CCAAGTGCTTCGGCAAATGAATCTCTAACTGAAGATACACTATCTTCCAAACCCTGTGATAAAA
CATCAACAAAAGGAACAGATTCAACATGTGCTTTTCAGCTAGCTGAGCCACATTAAGCATGAGA
AAGAAGGTAAATAAACAATACCTTCACACAATAAGACATAGAAGAATCGAAATCAGCCATCCCC
AATGCAGGCCCACCAATATTAGCAAATGCCTTCAAGCAACGTGCTGCCGCTGCTCTGACAATGA
ACGATTTATCACTTACACCTCGCATGATGATACGAAAAGCCTCTTGATAAGCTGCAGCAGCACC
ACCACCACCTGAGCCTTCCAATGCATTCTCAAGCAAGAGAAGAGCATCTTGTCTCACAAAGTCC
TGACAAATTTGTTTGAGAAAACTGTTAGAATTCCTTTTAGGGCGTGATATACAGCACAACTCAA
GCCAGCTGCCAGCATAAATGAATACAATGTCATGGTATTTTGTTGTCGGCACTACTACCCATGA
GGATATGGAAAGAGGCGGCAAAAAGACTTGAAAGGATGAAATATAACTAAAAATTTAGCATTAA
ATAGGAGTGCGTAAAAACAGCTATCCATGTGTCTGAACCTTGACTTGCGGTTTTTGTTGAGTGT
TAACTCTAGCCTACTCCAACTTGGACTAAAAAGCTTTGATGATGGTGGTGGTGGTGGTGGTGGT
GGTGTGATGGTGTTTTCTAGTCGGCATACGCAAACTGCATTTGTTAAGGTTGTGTTTAGTTGCT
TATATTGTGTTGCATGTAGTCATCACCATGTGCTAGTAGATATCTCATGATCTGGTAGATGTGG
GGGAGGTGAAAAGATTTCCTTTTTGTGTGCTCCCATCAGCTTGTCCAGTTCTGGATTTCCTGAT
ACGACCAAATCTGTCTTACTAGCTAATGTCGCACTGGGACTGCTTTAAGCAATGTGCAAGCCTA
CATAAAGGCCACTGCAGTCAACCAAACATACCCTTATTTGATAGAAAATGAATTGGGCCCACAA
AACACCAAAATGGAGAAGTCTAGATAGATGTCAACAAGCAGTAGTTCAAGACCATCAGAGATTA
ATAAAGATTAGGGGAAAAACACCCAACAAGAAATCAACAGGTACACTATTGCTGCAATTTCCCG
TCTTTTATTCATCATCGTTTGTTGATACGCAAATAAATATTTTCCATACACCTAAACCAAAATG
AAGTATTCCAGAACAAATTTGAAAAAAAAATACATACAAAGAATTGTCAATATTCAGATTTACT
AAAGAAGACACAAGAATGAGTAAATAAAGAACACTAACAGAATCGCAGTGAAGCATACAACCTC
ATGATACTTCATGAGTTTAGCTACAATGCTTGATGTCTCAATCAGCCCTGCAGTAATCTTGCGT
CCAAATAAACGGTAAATTTCCCCCAGACATTGTGCTGCAC
						
					

			
		

Sequences
Splice junction sequence	TACTTCATGAGTTTAGCTACAATGCTTGATGTCTCAATCAGCCCTGCAGTAATCTTGCGTCCAA ATAAACGGTAAATTTCCCCCAGACATTGTGCTGCACctttgacaaatggcacaatcaaatgctt ctgcacaccatcttcaattttctttgcagaagcagtttgttttttcccgcctttcttcacctat caaataag
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: 519 Transcript exons: 58184826-58184913,58184981-58185070,58185167-58185400,58 186359-58186465 CTTTGACAAATGGCACAATCAAATGCTTCTGCACACCATCTTCAATTTTCTTTGCAGAAGCAGT TTGTTTTTTCCCGCCTTTCTTCACCTGGGCATCTGGATTCACTGCAAGAGCAAGTATGGCACCA AGTGCTTCGGCAAATGAATCTCTAACTGAAGATACACTATCTTCCAAACCCTTCACACAATAAG ACATAGAAGAATCGAAATCAGCCATCCCCAATGCAGGCCCACCAATATTAGCAAATGCCTTCAA GCAACGTGCTGCCGCTGCTCTGACAATGAACGATTTATCACTTACACCTCGCATGATGATACGA AAAGCCTCTTGATAAGCTGCAGCAGCACCACCACCACCTGAGCCTTCCAATGCATTCTCAAGCA AGAGAAGAGCATCTTGTCTCACAAAGTCCTCATGATACTTCATGAGTTTAGCTACAATGCTTGA TGTCTCAATCAGCCCTGCAGTAATCTTGCGTCCAAATAAACGGTAAATTTCCCCCAGACATTGT GCTGCAC
Genomic sequence	CTTTGACAAATGGCACAATCAAATGCTTCTGCACACCATCTTCAATTTTCTTTGCAGAAGCAGT TTGTTTTTTCCCGCCTTTCTTCACCTATCAAATAAGCTTGTATCTAAATCGTAAAAAGAAAATG GTTAAGAAAAATGTGAGAATGATATACCTGGGCATCTGGATTCACTGCAAGAGCAAGTATGGCA CCAAGTGCTTCGGCAAATGAATCTCTAACTGAAGATACACTATCTTCCAAACCCTGTGATAAAA CATCAACAAAAGGAACAGATTCAACATGTGCTTTTCAGCTAGCTGAGCCACATTAAGCATGAGA AAGAAGGTAAATAAACAATACCTTCACACAATAAGACATAGAAGAATCGAAATCAGCCATCCCC AATGCAGGCCCACCAATATTAGCAAATGCCTTCAAGCAACGTGCTGCCGCTGCTCTGACAATGA ACGATTTATCACTTACACCTCGCATGATGATACGAAAAGCCTCTTGATAAGCTGCAGCAGCACC ACCACCACCTGAGCCTTCCAATGCATTCTCAAGCAAGAGAAGAGCATCTTGTCTCACAAAGTCC TGACAAATTTGTTTGAGAAAACTGTTAGAATTCCTTTTAGGGCGTGATATACAGCACAACTCAA GCCAGCTGCCAGCATAAATGAATACAATGTCATGGTATTTTGTTGTCGGCACTACTACCCATGA GGATATGGAAAGAGGCGGCAAAAAGACTTGAAAGGATGAAATATAACTAAAAATTTAGCATTAA ATAGGAGTGCGTAAAAACAGCTATCCATGTGTCTGAACCTTGACTTGCGGTTTTTGTTGAGTGT TAACTCTAGCCTACTCCAACTTGGACTAAAAAGCTTTGATGATGGTGGTGGTGGTGGTGGTGGT GGTGTGATGGTGTTTTCTAGTCGGCATACGCAAACTGCATTTGTTAAGGTTGTGTTTAGTTGCT TATATTGTGTTGCATGTAGTCATCACCATGTGCTAGTAGATATCTCATGATCTGGTAGATGTGG GGGAGGTGAAAAGATTTCCTTTTTGTGTGCTCCCATCAGCTTGTCCAGTTCTGGATTTCCTGAT ACGACCAAATCTGTCTTACTAGCTAATGTCGCACTGGGACTGCTTTAAGCAATGTGCAAGCCTA CATAAAGGCCACTGCAGTCAACCAAACATACCCTTATTTGATAGAAAATGAATTGGGCCCACAA AACACCAAAATGGAGAAGTCTAGATAGATGTCAACAAGCAGTAGTTCAAGACCATCAGAGATTA ATAAAGATTAGGGGAAAAACACCCAACAAGAAATCAACAGGTACACTATTGCTGCAATTTCCCG TCTTTTATTCATCATCGTTTGTTGATACGCAAATAAATATTTTCCATACACCTAAACCAAAATG AAGTATTCCAGAACAAATTTGAAAAAAAAATACATACAAAGAATTGTCAATATTCAGATTTACT AAAGAAGACACAAGAATGAGTAAATAAAGAACACTAACAGAATCGCAGTGAAGCATACAACCTC ATGATACTTCATGAGTTTAGCTACAATGCTTGATGTCTCAATCAGCCCTGCAGTAATCTTGCGT CCAAATAAACGGTAAATTTCCCCCAGACATTGTGCTGCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.180008264

Conservation Information
Conserved circRNAs	NA
PMCS	0.180008264

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58186375-58184828(-)
						
						Potential amino acid sequence
						
							MKYHEDFVRQDALLLLENALEGSGGGGAAAAYQEAFRIIMRGVSDKSFIVRAAAARCLKAFANI
GGPALGMADFDSSMSYCVKGLEDSVSSVRDSFAEALGAILALAVNPDAQVKKGGKKQTASAKKI
EDGVQKHLIVPFVKGAAQCLGEIYRLFGRKITAGLIETSSIVAKLMKYHEDFVRQDALLLLENA
LEGSGGGGAAAAYQEAFRIIMRGVSDKSFIVRAAAARCLKAFANIGGPALGMADFDSSMSYCVK
GLEDSVSSVRDSFAEALGAILALAVNPDAQVKKGGKKQTASAKKIEDGVQKHLIVPFVKGAAQC
LGEIYRLFGRKITAGLIETSSIVAKLMKYHEDFVRQDALLLLENALEGSGGGGAAAAYQEAFRI
IMRGVSDKSFIVRAAAARCLKAFANIGGPALGMADFDSSMSYCVKGLEDSVSSVRDSFAEALGA
ILALAVNPDAQVKKGGKKQTASAKKIEDGVQKHLIVPFVKGAAQCLGEIYRLFGRKITAGLIET
SSIVAKLMKYHEDFVRQDALLLLENALEGSGGGGAAAAYQEAFRIIMRGVSDKSFIVRAAAARC
LKAFANIGGPALGMADFDSSMSYCVKGLEDSVSSVRDSFAEALGAILALAVNPDAQVKKGGKKQ
TASAKKIEDGVQKHLIVPFVK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	58186375-58184828(-)
Potential amino acid sequence	MKYHEDFVRQDALLLLENALEGSGGGGAAAAYQEAFRIIMRGVSDKSFIVRAAAARCLKAFANI GGPALGMADFDSSMSYCVKGLEDSVSSVRDSFAEALGAILALAVNPDAQVKKGGKKQTASAKKI EDGVQKHLIVPFVKGAAQCLGEIYRLFGRKITAGLIETSSIVAKLMKYHEDFVRQDALLLLENA LEGSGGGGAAAAYQEAFRIIMRGVSDKSFIVRAAAARCLKAFANIGGPALGMADFDSSMSYCVK GLEDSVSSVRDSFAEALGAILALAVNPDAQVKKGGKKQTASAKKIEDGVQKHLIVPFVKGAAQC LGEIYRLFGRKITAGLIETSSIVAKLMKYHEDFVRQDALLLLENALEGSGGGGAAAAYQEAFRI IMRGVSDKSFIVRAAAARCLKAFANIGGPALGMADFDSSMSYCVKGLEDSVSSVRDSFAEALGA ILALAVNPDAQVKKGGKKQTASAKKIEDGVQKHLIVPFVKGAAQCLGEIYRLFGRKITAGLIET SSIVAKLMKYHEDFVRQDALLLLENALEGSGGGGAAAAYQEAFRIIMRGVSDKSFIVRAAAARC LKAFANIGGPALGMADFDSSMSYCVKGLEDSVSSVRDSFAEALGAILALAVNPDAQVKKGGKKQ TASAKKIEDGVQKHLIVPFVK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d046041_circ_g.2

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