Plant Circular RNA Database

Detail information of Zm00001d028380_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d028380_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006452
					
						Alias
						zma_circ_0000606, GRMZM2G085427_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 32683673-32686060  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d028380						
					
						Parent gene annotation
						
							TSL-kinase interacting protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d028380_T005:6
Zm00001d028380_T003:4
Zm00001d028380_T004:6
Zm00001d028380_T001:4
Zm00001d028380_T007:5
Zm00001d028380_T002:6
Zm00001d028380_T006:6

General Information
CircRNA Name	Zm00001d028380_circ_g.1
ID in PlantcircBase	zma_circ_006452
Alias	zma_circ_0000606, GRMZM2G085427_C1
Organism	Zea mays
Position	chr1: 32683673-32686060 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d028380
Parent gene annotation	TSL-kinase interacting protein 1
Parent gene strand	+
Alternative splicing	NA
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	Zm00001d028380_T005:6 Zm00001d028380_T003:4 Zm00001d028380_T004:6 Zm00001d028380_T001:4 Zm00001d028380_T007:5 Zm00001d028380_T002:6 Zm00001d028380_T006:6

			
						 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  
						
							GTAAGTGAAATATCTTTAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCCAAGTCAAAT
CGCCATCAGGAGATAAGGCTTGTGTTCAAAGTGATGgtggtctctgcttgagaaatttagctgc
actgcatcaaagttgcatctcaaacctcggaggttcaaaacatttgtagaagcactggtgagtt
gctttgtc

									
								

					

						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: 941
Transcript exons: 32683673-32683757,32683853-32684126,32684301-32684477,32
684601-32684704,32685000-32685163,32685924-32686060
GTGGTCTCTGCTTGAGAAATTTAGCTGCACTGCATCAAAGTTGCATCTCAAACCTCGGAGGTTC
AAAACATTTGTAGAAGCACTGGGGAAACAACTGCTAAAGGACAGAAATAAGTCCAGGAGAAAGC
GTTCACGAGTGGATATGTGCCTACCTTCTCCATCTCCAATTATCAGCAAAGCTCCTGGGAATGA
GAATCCTCCTGTAAAGTTCCTGTCAGTAGATGCTCAGAATGGTAGCAGAGTAGCATCTCCTAAA
GGGTCAATTTTCAAGCAGGTTGCAGAACCGATTTCTAACAAGCCAGGGACAACTAAAGGGGAAC
TCTCTGCCACAAGAACCGTGAAACAAAAAAGGAAGGCAGGTGGCGCTGTTGCATCTGCTGCATA
TAAGAAATGGGAGAGAGCAGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCAGCTGAGGAGCTC
GAGCGCAACACGATTAACCCAGGCATTTTTTGTAATGTTGATGCAAGAACACTGACTTCATTAT
CAGAAAGACTTTCTAGCATTGATGGCATTAGCACAAATCATATGAAGGAAGCAGATTCACAGGC
ACCTGTGAAGCTGAAGCTACAGTTATTTCCAATAAATGAAGCTACTCGGAAGGCATTGGAGAAG
GATGACCATAATCCTCATCTAGAGCTCACATTAAGCTCTAGAAAGAAAATATCATCTGTGCTAG
AACATCTAAACCGAAAATGGGGTAACTCAAACATCGCATCTGGAGAGCTTATTCTTTTTCCATA
TTGTGCTAATCAAGAGGATTTGGCTACATATCAGAGGTATGGTTGGGTTTCCCTTGTTGAGCTT
GGAGCAGGAGTAAGTGAAATATCTTTAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCC
AAGTCAAATCGCCATCAGGAGATAAGGCTTGTGTTCAAAGTGATG
						
					

						Genomic sequence
						
							GTGGTCTCTGCTTGAGAAATTTAGCTGCACTGCATCAAAGTTGCATCTCAAACCTCGGAGGTTC
AAAACATTTGTAGAAGCACTGGTGAGTTGCTTTGTCCCCATGTTCCTTTTCTCGTTATAAAACG
TCGACAGTTTATTTCTTCTTTCTCATGCTATGTGTCTCCTTTTGTTTGCTAGGGGAAACAACTG
CTAAAGGACAGAAATAAGTCCAGGAGAAAGCGTTCACGAGTGGATATGTGCCTACCTTCTCCAT
CTCCAATTATCAGCAAAGCTCCTGGGAATGAGAATCCTCCTGTAAAGTTCCTGTCAGTAGATGC
TCAGAATGGTAGCAGAGTAGCATCTCCTAAAGGGTCAATTTTCAAGCAGGTTGCAGAACCGATT
TCTAACAAGCCAGGGACAACTAAAGGGGAACTCTCTGCCACAAGAACCGTGAAACAAAAAAGGA
AGGCAGGTGGGCACATATTCTCTTTCCCTTTGTTATGACCTAGCCTTGCCTATCTTTTGTCAAA
ATCTGTGTGGTTAGAGTTTTGGTGAAATTGTTTTTGATTAATTATCATGTAGAGGACCCTCTCT
AGTGGTGAATCTTTGTTGCATTAATGTGGATAGCTGGTGAGCTATGTTTTAGGTGGCGCTGTTG
CATCTGCTGCATATAAGAAATGGGAGAGAGCAGCCATGGCTGGTGTTTCTTTAGTTGCTGATGC
AGCTGAGGAGCTCGAGCGCAACACGATTAACCCAGGCATTTTTTGTAATGTTGATGCAAGAACA
CTGACTTCATTATCAGAAAGACTTTCTAGCATTGATGGTATGGCTTCTAGCAACTGGATTTTAG
TTTTTGTATTTGTGGAACTTTGTTCAACACAGTCGTTGAAGTTAACAGTAGCAAATACAGGTCT
ATTATCCTGATGTTTTTATTCTGCACTTGCAGGCATTAGCACAAATCATATGAAGGAAGCAGAT
TCACAGGCACCTGTGAAGCTGAAGCTACAGTTATTTCCAATAAATGAAGCTACTCGGAAGGCAT
TGGAGAAGGTAAAGCATGGTTTCTTGCTACTAGCAAGCTGCATATGAATCACAATTTTCCTCAG
TCGCTGTATTTTTAACTTGTCAGTTATTACTGGTGAATTATTGACCAAGCACTCGGGTTCTTGT
TGTTGAATTCATGCATGTTATAGATGAATGATGATGAATAGATTACTTGATTAGTGTCCCTTTG
CATTTTGCTCAAACTTTTCTTTGTATCTGGTTTGGGTCTGAGTTGTTTTGTTCTGTTCTCCAAT
CTTTGAGCAATTTGAACATTACATGGTGCTTTTTCTCCTCTTATCAGGATGACCATAATCCTCA
TCTAGAGCTCACATTAAGCTCTAGAAAGAAAATATCATCTGTGCTAGAACATCTAAACCGAAAA
TGGGGTAACTCAAACATCGCATCTGGAGAGCTTATTCTTTTTCCATATTGTGCTAATCAAGAGG
ATTTGGCTACATATCAGAGGTGGACAACAAGAGATACTGTTGCAGTAGCTGATGTGTTTCTTTC
TGTGAATAGCCCGTCTGTTTTCCGTTTAAGGTATATAATTTCTCTAATTGATAGGAAGTCACAA
CCTTTTTTTTTCGTGAACGCACAGGAGAGCTGCACATCATTAAATTAAGAGAAGAAAACAGTCC
AAAATGGACCAAAGTACAATGCTAAAATAGGCAAAACACAAGACCACCAAATCCTGCTACGCAC
AGAACTGCAGCCTCCTTCTGCGCATGAAAACAGCAGCACGCAAAAGAAGAACAACAGCAAAAGT
GCCAGCAGGCCACACACCCACACAACTGCTCCTCACTAAGCACCCAATAGAACCCTTGATCTGA
AAATTGCAGCACCAGGACCCAAAGCCTCAAGATGTCTAGCACCGGCAAGCCTCCAGCATTCAAA
TTCATCCAAAAAACTGATTTTATTCCATGAATGGAAGGTCTGACACCATCAAAAACCACCTTAT
TACGATGAAGCCATAAACACCAAGCCCCCAAGATGATGATACTGTTAAAGCCTTTTCTTTTGGA
TTTGTGCACTTGCTTACACACCTCCCACCAGTCAGCAAAAGCAGACTCATTAGAGGCAGGGGAA
AGATTAGCCAGTCCCAATGAAGAAAGAATGTAGTATCAAAATTGCCGCGCAAAAATGCAAGTGC
GAAGGAAGTCACAACCTAACGAGTCACTTCTAGCGCATAATGCTTGCTAATTGTTGTCAACATT
TTGTTGTTCAGGTATGGTTGGGTTTCCCTTGTTGAGCTTGGAGCAGGAGTAAGTGAAATATCTT
TAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCCAAGTCAAATCGCCATCAGGAGATAA
GGCTTGTGTTCAAAGTGATG
						
					

			
		

Sequences
Splice junction sequence	GTAAGTGAAATATCTTTAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCCAAGTCAAAT CGCCATCAGGAGATAAGGCTTGTGTTCAAAGTGATGgtggtctctgcttgagaaatttagctgc actgcatcaaagttgcatctcaaacctcggaggttcaaaacatttgtagaagcactggtgagtt gctttgtc
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: 941 Transcript exons: 32683673-32683757,32683853-32684126,32684301-32684477,32 684601-32684704,32685000-32685163,32685924-32686060 GTGGTCTCTGCTTGAGAAATTTAGCTGCACTGCATCAAAGTTGCATCTCAAACCTCGGAGGTTC AAAACATTTGTAGAAGCACTGGGGAAACAACTGCTAAAGGACAGAAATAAGTCCAGGAGAAAGC GTTCACGAGTGGATATGTGCCTACCTTCTCCATCTCCAATTATCAGCAAAGCTCCTGGGAATGA GAATCCTCCTGTAAAGTTCCTGTCAGTAGATGCTCAGAATGGTAGCAGAGTAGCATCTCCTAAA GGGTCAATTTTCAAGCAGGTTGCAGAACCGATTTCTAACAAGCCAGGGACAACTAAAGGGGAAC TCTCTGCCACAAGAACCGTGAAACAAAAAAGGAAGGCAGGTGGCGCTGTTGCATCTGCTGCATA TAAGAAATGGGAGAGAGCAGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCAGCTGAGGAGCTC GAGCGCAACACGATTAACCCAGGCATTTTTTGTAATGTTGATGCAAGAACACTGACTTCATTAT CAGAAAGACTTTCTAGCATTGATGGCATTAGCACAAATCATATGAAGGAAGCAGATTCACAGGC ACCTGTGAAGCTGAAGCTACAGTTATTTCCAATAAATGAAGCTACTCGGAAGGCATTGGAGAAG GATGACCATAATCCTCATCTAGAGCTCACATTAAGCTCTAGAAAGAAAATATCATCTGTGCTAG AACATCTAAACCGAAAATGGGGTAACTCAAACATCGCATCTGGAGAGCTTATTCTTTTTCCATA TTGTGCTAATCAAGAGGATTTGGCTACATATCAGAGGTATGGTTGGGTTTCCCTTGTTGAGCTT GGAGCAGGAGTAAGTGAAATATCTTTAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCC AAGTCAAATCGCCATCAGGAGATAAGGCTTGTGTTCAAAGTGATG
Genomic sequence	GTGGTCTCTGCTTGAGAAATTTAGCTGCACTGCATCAAAGTTGCATCTCAAACCTCGGAGGTTC AAAACATTTGTAGAAGCACTGGTGAGTTGCTTTGTCCCCATGTTCCTTTTCTCGTTATAAAACG TCGACAGTTTATTTCTTCTTTCTCATGCTATGTGTCTCCTTTTGTTTGCTAGGGGAAACAACTG CTAAAGGACAGAAATAAGTCCAGGAGAAAGCGTTCACGAGTGGATATGTGCCTACCTTCTCCAT CTCCAATTATCAGCAAAGCTCCTGGGAATGAGAATCCTCCTGTAAAGTTCCTGTCAGTAGATGC TCAGAATGGTAGCAGAGTAGCATCTCCTAAAGGGTCAATTTTCAAGCAGGTTGCAGAACCGATT TCTAACAAGCCAGGGACAACTAAAGGGGAACTCTCTGCCACAAGAACCGTGAAACAAAAAAGGA AGGCAGGTGGGCACATATTCTCTTTCCCTTTGTTATGACCTAGCCTTGCCTATCTTTTGTCAAA ATCTGTGTGGTTAGAGTTTTGGTGAAATTGTTTTTGATTAATTATCATGTAGAGGACCCTCTCT AGTGGTGAATCTTTGTTGCATTAATGTGGATAGCTGGTGAGCTATGTTTTAGGTGGCGCTGTTG CATCTGCTGCATATAAGAAATGGGAGAGAGCAGCCATGGCTGGTGTTTCTTTAGTTGCTGATGC AGCTGAGGAGCTCGAGCGCAACACGATTAACCCAGGCATTTTTTGTAATGTTGATGCAAGAACA CTGACTTCATTATCAGAAAGACTTTCTAGCATTGATGGTATGGCTTCTAGCAACTGGATTTTAG TTTTTGTATTTGTGGAACTTTGTTCAACACAGTCGTTGAAGTTAACAGTAGCAAATACAGGTCT ATTATCCTGATGTTTTTATTCTGCACTTGCAGGCATTAGCACAAATCATATGAAGGAAGCAGAT TCACAGGCACCTGTGAAGCTGAAGCTACAGTTATTTCCAATAAATGAAGCTACTCGGAAGGCAT TGGAGAAGGTAAAGCATGGTTTCTTGCTACTAGCAAGCTGCATATGAATCACAATTTTCCTCAG TCGCTGTATTTTTAACTTGTCAGTTATTACTGGTGAATTATTGACCAAGCACTCGGGTTCTTGT TGTTGAATTCATGCATGTTATAGATGAATGATGATGAATAGATTACTTGATTAGTGTCCCTTTG CATTTTGCTCAAACTTTTCTTTGTATCTGGTTTGGGTCTGAGTTGTTTTGTTCTGTTCTCCAAT CTTTGAGCAATTTGAACATTACATGGTGCTTTTTCTCCTCTTATCAGGATGACCATAATCCTCA TCTAGAGCTCACATTAAGCTCTAGAAAGAAAATATCATCTGTGCTAGAACATCTAAACCGAAAA TGGGGTAACTCAAACATCGCATCTGGAGAGCTTATTCTTTTTCCATATTGTGCTAATCAAGAGG ATTTGGCTACATATCAGAGGTGGACAACAAGAGATACTGTTGCAGTAGCTGATGTGTTTCTTTC TGTGAATAGCCCGTCTGTTTTCCGTTTAAGGTATATAATTTCTCTAATTGATAGGAAGTCACAA CCTTTTTTTTTCGTGAACGCACAGGAGAGCTGCACATCATTAAATTAAGAGAAGAAAACAGTCC AAAATGGACCAAAGTACAATGCTAAAATAGGCAAAACACAAGACCACCAAATCCTGCTACGCAC AGAACTGCAGCCTCCTTCTGCGCATGAAAACAGCAGCACGCAAAAGAAGAACAACAGCAAAAGT GCCAGCAGGCCACACACCCACACAACTGCTCCTCACTAAGCACCCAATAGAACCCTTGATCTGA AAATTGCAGCACCAGGACCCAAAGCCTCAAGATGTCTAGCACCGGCAAGCCTCCAGCATTCAAA TTCATCCAAAAAACTGATTTTATTCCATGAATGGAAGGTCTGACACCATCAAAAACCACCTTAT TACGATGAAGCCATAAACACCAAGCCCCCAAGATGATGATACTGTTAAAGCCTTTTCTTTTGGA TTTGTGCACTTGCTTACACACCTCCCACCAGTCAGCAAAAGCAGACTCATTAGAGGCAGGGGAA AGATTAGCCAGTCCCAATGAAGAAAGAATGTAGTATCAAAATTGCCGCGCAAAAATGCAAGTGC GAAGGAAGTCACAACCTAACGAGTCACTTCTAGCGCATAATGCTTGCTAATTGTTGTCAACATT TTGTTGTTCAGGTATGGTTGGGTTTCCCTTGTTGAGCTTGGAGCAGGAGTAAGTGAAATATCTT TAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCCAAGTCAAATCGCCATCAGGAGATAA GGCTTGTGTTCAAAGTGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.10956256

Conservation Information
Conserved circRNAs	NA
PMCS	0.10956256

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							32683911-32683746(+)
						
						Potential amino acid sequence
						
							MCLPSPSPIISKAPGNENPPVKFLSVDAQNGSRVASPKGSIFKQVAEPISNKPGTTKGELSATR
TVKQKRKAGGAVASAAYKKWERAAMAGVSLVADAAEELERNTINPGIFCNVDARTLTSLSERLS
SIDGISTNHMKEADSQAPVKLKLQLFPINEATRKALEKDDHNPHLELTLSSRKKISSVLEHLNR
KWGNSNIASGELILFPYCANQEDLATYQRYGWVSLVELGAGVSEISLTHFEDCMIPEVIQVKSP
SGDKACVQSDGGLCLRNLAALHQSCISNLGGSKHL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	32683911-32683746(+)
Potential amino acid sequence	MCLPSPSPIISKAPGNENPPVKFLSVDAQNGSRVASPKGSIFKQVAEPISNKPGTTKGELSATR TVKQKRKAGGAVASAAYKKWERAAMAGVSLVADAAEELERNTINPGIFCNVDARTLTSLSERLS SIDGISTNHMKEADSQAPVKLKLQLFPINEATRKALEKDDHNPHLELTLSSRKKISSVLEHLNR KWGNSNIASGELILFPYCANQEDLATYQRYGWVSLVELGAGVSEISLTHFEDCMIPEVIQVKSP SGDKACVQSDGGLCLRNLAALHQSCISNLGGSKHL*(+)
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 Zm00001d028380_circ_g.1

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