Plant Circular RNA Database

Detail information of Zm00001d039526_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d039526_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007478
					
						Alias
						Zm03circ00006
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 7125804-7126815  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d039526						
					
						Parent gene annotation
						
							AGC (cAMP-dependent cGMP-dependent and protein kinase C) kinase 
family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d039526_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d039526_T001:4
Zm00001d039526_T007:3
Zm00001d039526_T004:4
Zm00001d039526_T003:4
Zm00001d039526_T006:4
Zm00001d039526_T005:4
Zm00001d039526_T002:4

General Information
CircRNA Name	Zm00001d039526_circ_g.2
ID in PlantcircBase	zma_circ_007478
Alias	Zm03circ00006
Organism	Zea mays
Position	chr3: 7125804-7126815 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d039526
Parent gene annotation	AGC (cAMP-dependent cGMP-dependent and protein kinase C) kinase family protein
Parent gene strand	+
Alternative splicing	Zm00001d039526_circ_g.1
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d039526_T001:4 Zm00001d039526_T007:3 Zm00001d039526_T004:4 Zm00001d039526_T003:4 Zm00001d039526_T006:4 Zm00001d039526_T005:4 Zm00001d039526_T002:4

			
						 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  
						
							TTGTTTTATTCCCAGGTGGTCTCTGGGCGCGATCATGTATGAGATGCTAGTTGGGTATCCACCA
TTTTATGCTGATGATCCAATAACTACATGCAGAAAGgtggaacatgttagagctgaaagaaact
tgttggccgaagttgctagtcatcactgcattgtgaagctttactattctttccaagacactga
gtatcttt

									
								

					

						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: 654
Transcript exons: 7125804-7126048,7126130-7126373,7126546-7126625,7126731-
7126815
GTGGAACATGTTAGAGCTGAAAGAAACTTGTTGGCCGAAGTTGCTAGTCATCACTGCATTGTGA
AGCTTTACTATTCTTTCCAAGACACTGAGTATCTTTACCTTATTATGGAGTACCTCCCTGGTGG
TGATATCATGACCCTTCTCATGAGAGAGGATACCTTGACTGAACATGTGGCACGATTCTACGTT
GCTGAGACTATTCTTGCTATCGAATCCATCCATAAACATAACTACATCCACAGAGATATTAAGC
CTGATAATTTGCTTCTAGATAAGAATGGTCACATGAAGCTGTCAGATTTTGGGCTGTGTAAGCC
AATTGATTGTTCAAAGCTCTCAACTTTGAATGAAGATGAACCCATGAGTGATGACAACTTGAGG
GAATCAATGGATATTGATAGTTCTTTGTCTGATACAGCAAATGGTAGAAGATGGAGAAGTCAAC
ACGAACAGCTTCAGCACTGGCAGATGAACAGGAGAAAACTGGCATTCTCAACTGTTGGAACACC
GGATTATATTGCTCCAGAGGTTCTTCTAAAGAAGGGATATGGAATGGAATGCGATTGGTGGTCT
CTGGGCGCGATCATGTATGAGATGCTAGTTGGGTATCCACCATTTTATGCTGATGATCCAATAA
CTACATGCAGAAAG
						
					

						Genomic sequence
						
							GTGGAACATGTTAGAGCTGAAAGAAACTTGTTGGCCGAAGTTGCTAGTCATCACTGCATTGTGA
AGCTTTACTATTCTTTCCAAGACACTGAGTATCTTTACCTTATTATGGAGTACCTCCCTGGTGG
TGATATCATGACCCTTCTCATGAGAGAGGATACCTTGACTGAACATGTGGCACGATTCTACGTT
GCTGAGACTATTCTTGCTATCGAATCCATCCATAAACATAACTACATCCACAGGTTAGTCTTTA
TTTAATGGCATCTATGTATTGTGGTCCTACCATTTTGCTGATTTGAATACTTGCTTTGATACCA
TTGCAGAGATATTAAGCCTGATAATTTGCTTCTAGATAAGAATGGTCACATGAAGCTGTCAGAT
TTTGGGCTGTGTAAGCCAATTGATTGTTCAAAGCTCTCAACTTTGAATGAAGATGAACCCATGA
GTGATGACAACTTGAGGGAATCAATGGATATTGATAGTTCTTTGTCTGATACAGCAAATGGTAG
AAGATGGAGAAGTCAACACGAACAGCTTCAGCACTGGCAGATGAACAGGAGAAAACTGGTATAC
TTATGTACAGTTTACCTATTGGGGATTGCACCAGTCTTTATGATTTTTATTTTGCTTGGATAGT
ATCTTGTAGCGATCCTTACCTGGAACAGAATTGATACTCTTTGTGTACAATGTACAACCTCAAT
ATTTCTTATTAGCTTTTCTTGAATTTATGTTTATGCAGGCATTCTCAACTGTTGGAACACCGGA
TTATATTGCTCCAGAGGTTCTTCTAAAGAAGGGATATGGAATGGAATGCGATTGGTATACTTTG
TTGGAATAATGCTTGCATAATCAAGTTAATGTCGAGGTTCTTATATGTGTCTTGAGTTTTAATA
ACTGGTTTATTATTCTTTGTTTTATTCCCAGGTGGTCTCTGGGCGCGATCATGTATGAGATGCT
AGTTGGGTATCCACCATTTTATGCTGATGATCCAATAACTACATGCAGAAAG
						
					

			
		

Sequences
Splice junction sequence	TTGTTTTATTCCCAGGTGGTCTCTGGGCGCGATCATGTATGAGATGCTAGTTGGGTATCCACCA TTTTATGCTGATGATCCAATAACTACATGCAGAAAGgtggaacatgttagagctgaaagaaact tgttggccgaagttgctagtcatcactgcattgtgaagctttactattctttccaagacactga gtatcttt
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: 654 Transcript exons: 7125804-7126048,7126130-7126373,7126546-7126625,7126731- 7126815 GTGGAACATGTTAGAGCTGAAAGAAACTTGTTGGCCGAAGTTGCTAGTCATCACTGCATTGTGA AGCTTTACTATTCTTTCCAAGACACTGAGTATCTTTACCTTATTATGGAGTACCTCCCTGGTGG TGATATCATGACCCTTCTCATGAGAGAGGATACCTTGACTGAACATGTGGCACGATTCTACGTT GCTGAGACTATTCTTGCTATCGAATCCATCCATAAACATAACTACATCCACAGAGATATTAAGC CTGATAATTTGCTTCTAGATAAGAATGGTCACATGAAGCTGTCAGATTTTGGGCTGTGTAAGCC AATTGATTGTTCAAAGCTCTCAACTTTGAATGAAGATGAACCCATGAGTGATGACAACTTGAGG GAATCAATGGATATTGATAGTTCTTTGTCTGATACAGCAAATGGTAGAAGATGGAGAAGTCAAC ACGAACAGCTTCAGCACTGGCAGATGAACAGGAGAAAACTGGCATTCTCAACTGTTGGAACACC GGATTATATTGCTCCAGAGGTTCTTCTAAAGAAGGGATATGGAATGGAATGCGATTGGTGGTCT CTGGGCGCGATCATGTATGAGATGCTAGTTGGGTATCCACCATTTTATGCTGATGATCCAATAA CTACATGCAGAAAG
Genomic sequence	GTGGAACATGTTAGAGCTGAAAGAAACTTGTTGGCCGAAGTTGCTAGTCATCACTGCATTGTGA AGCTTTACTATTCTTTCCAAGACACTGAGTATCTTTACCTTATTATGGAGTACCTCCCTGGTGG TGATATCATGACCCTTCTCATGAGAGAGGATACCTTGACTGAACATGTGGCACGATTCTACGTT GCTGAGACTATTCTTGCTATCGAATCCATCCATAAACATAACTACATCCACAGGTTAGTCTTTA TTTAATGGCATCTATGTATTGTGGTCCTACCATTTTGCTGATTTGAATACTTGCTTTGATACCA TTGCAGAGATATTAAGCCTGATAATTTGCTTCTAGATAAGAATGGTCACATGAAGCTGTCAGAT TTTGGGCTGTGTAAGCCAATTGATTGTTCAAAGCTCTCAACTTTGAATGAAGATGAACCCATGA GTGATGACAACTTGAGGGAATCAATGGATATTGATAGTTCTTTGTCTGATACAGCAAATGGTAG AAGATGGAGAAGTCAACACGAACAGCTTCAGCACTGGCAGATGAACAGGAGAAAACTGGTATAC TTATGTACAGTTTACCTATTGGGGATTGCACCAGTCTTTATGATTTTTATTTTGCTTGGATAGT ATCTTGTAGCGATCCTTACCTGGAACAGAATTGATACTCTTTGTGTACAATGTACAACCTCAAT ATTTCTTATTAGCTTTTCTTGAATTTATGTTTATGCAGGCATTCTCAACTGTTGGAACACCGGA TTATATTGCTCCAGAGGTTCTTCTAAAGAAGGGATATGGAATGGAATGCGATTGGTATACTTTG TTGGAATAATGCTTGCATAATCAAGTTAATGTCGAGGTTCTTATATGTGTCTTGAGTTTTAATA ACTGGTTTATTATTCTTTGTTTTATTCCCAGGTGGTCTCTGGGCGCGATCATGTATGAGATGCT AGTTGGGTATCCACCATTTTATGCTGATGATCCAATAACTACATGCAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							pop_circ_001991 						
					
						PMCS
						0.289020541

Conservation Information
Conserved circRNAs	pop_circ_001991
PMCS	0.289020541

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7125913-7126812(+)
7126036-7126764(-)
						
						Potential amino acid sequence
						
							MEYLPGGDIMTLLMREDTLTEHVARFYVAETILAIESIHKHNYIHRDIKPDNLLLDKNGHMKLS
DFGLCKPIDCSKLSTLNEDEPMSDDNLRESMDIDSSLSDTANGRRWRSQHEQLQHWQMNRRKLA
FSTVGTPDYIAPEVLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPITTCRKVEHVRAERNL
LAEVASHHCIVKLYYSFQDTEYLYLIMEYLPGGDIMTLLMREDTLTEHVARFYVAETILAIESI
HKHNYIHRDIKPDNLLLDKNGHMKLSDFGLCKPIDCSKLSTLNEDEPMSDDNLRESMDIDSSLS
DTANGRRWRSQHEQLQHWQMNRRKLAFSTVGTPDYIAPEVLLKKGYGMECDWWSLGAIMYEMLV
GYPPFYADDPITTCRKVEHVRAERNLLAEVASHHCIVKLYYSFQDTEYLYLIMEYLPGGDIMTL
LMREDTLTEHVARFYVAETILAIESIHKHNYIHRDIKPDNLLLDKNGHMKLSDFGLCKPIDCSK
LSTLNEDEPMSDDNLRESMDIDSSLSDTANGRRWRSQHEQLQHWQMNRRKLAFSTVGTPDYIAP
EVLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPITTCRKVEHVRAERNLLAEVASHHCIVK
LYYSFQDTEYLYLIMEYLPGGDIMTLLMREDTLTEHVARFYVAETILAIESIHKHNYIHRDIKP
DNLLLDKNGHMKLSDFGLCKPIDCSKLSTLNEDEPMSDDNLRESMDIDSSLSDTANGRRWRSQH
EQLQHWQMNRRKLAFSTVGTPDYIAPEVLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPIT
TCRK(+)
MFMDGFDSKNSLSNVESCHMFSQGILSHEKGHDITTREVLHNKVKILSVLERIVKLHNAVMTSN
FGQQVSFSSNMFHLSACSYWIISIKWWIPN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7125913-7126812(+) 7126036-7126764(-)
Potential amino acid sequence	MEYLPGGDIMTLLMREDTLTEHVARFYVAETILAIESIHKHNYIHRDIKPDNLLLDKNGHMKLS DFGLCKPIDCSKLSTLNEDEPMSDDNLRESMDIDSSLSDTANGRRWRSQHEQLQHWQMNRRKLA FSTVGTPDYIAPEVLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPITTCRKVEHVRAERNL LAEVASHHCIVKLYYSFQDTEYLYLIMEYLPGGDIMTLLMREDTLTEHVARFYVAETILAIESI HKHNYIHRDIKPDNLLLDKNGHMKLSDFGLCKPIDCSKLSTLNEDEPMSDDNLRESMDIDSSLS DTANGRRWRSQHEQLQHWQMNRRKLAFSTVGTPDYIAPEVLLKKGYGMECDWWSLGAIMYEMLV GYPPFYADDPITTCRKVEHVRAERNLLAEVASHHCIVKLYYSFQDTEYLYLIMEYLPGGDIMTL LMREDTLTEHVARFYVAETILAIESIHKHNYIHRDIKPDNLLLDKNGHMKLSDFGLCKPIDCSK LSTLNEDEPMSDDNLRESMDIDSSLSDTANGRRWRSQHEQLQHWQMNRRKLAFSTVGTPDYIAP EVLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPITTCRKVEHVRAERNLLAEVASHHCIVK LYYSFQDTEYLYLIMEYLPGGDIMTLLMREDTLTEHVARFYVAETILAIESIHKHNYIHRDIKP DNLLLDKNGHMKLSDFGLCKPIDCSKLSTLNEDEPMSDDNLRESMDIDSSLSDTANGRRWRSQH EQLQHWQMNRRKLAFSTVGTPDYIAPEVLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPIT TCRK(+) MFMDGFDSKNSLSNVESCHMFSQGILSHEKGHDITTREVLHNKVKILSVLERIVKLHNAVMTSN FGQQVSFSSNMFHLSACSYWIISIKWWIPN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d039526_circ_g.2

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