Plant Circular RNA Database

Detail information of Zm00001d035089_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d035089_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008877
					
						Alias
						zma_circ_0002471
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 4704822-4713211  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d035089						
					
						Parent gene annotation
						
							pleckstrin homology (PH) domain-containing protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d035089_circ_g.3 Zm00001d035089_circ_g.5 Zm00001d035089_circ_g.6 						
					
						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
						Zm00001d035089_T007:10
Zm00001d035089_T003:10
Zm00001d035089_T006:11
Zm00001d035089_T005:10

General Information
CircRNA Name	Zm00001d035089_circ_g.4
ID in PlantcircBase	zma_circ_008877
Alias	zma_circ_0002471
Organism	Zea mays
Position	chr6: 4704822-4713211 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d035089
Parent gene annotation	pleckstrin homology (PH) domain-containing protein
Parent gene strand	-
Alternative splicing	Zm00001d035089_circ_g.3 Zm00001d035089_circ_g.5 Zm00001d035089_circ_g.6
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	Zm00001d035089_T007:10 Zm00001d035089_T003:10 Zm00001d035089_T006:11 Zm00001d035089_T005:10

			
						 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  
						
							AGAATCAAGCCAAGCAAGAATAGTTGCTGCATCATCCCATATTTTACATTCCATACCAAGCCCA
GAAAACATTGTATCTACAAGCTTCGTGCCAAACCTCccttccatcgcttagcagaagagaccct
ttcctcaatcctgccttgaatgccacagaataaaaagaggatgcagatgatgcagcaggaaatt
tgagttcc

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AGAATCAAGCCAAGCAAGAATAGTTGCTGCATCATCCCATATTTTACATTCCATACCAAGCCCA GAAAACATTGTATCTACAAGCTTCGTGCCAAACCTCccttccatcgcttagcagaagagaccct ttcctcaatcctgccttgaatgccacagaataaaaagaggatgcagatgatgcagcaggaaatt tgagttcc
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110820822

Conservation Information
Conserved circRNAs	NA
PMCS	0.110820822

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							4712770-4704833(+)
4713185-4713157(-)
4704831-4713157(-)
						
					

						Potential amino acid sequence
						
							MALNSWTTTLVEASDLSFDLGKSTWILTTGAPRPSPVLHFSAHKIFVLFSGLITRRESSQARIV
AASSHILHSIPSPENIVSTSFVPNLPSIA*(+)
MFSGLGMECKIWDDAATILAWLDSLRVINPLNKTKILWAEKCSTGDGLGAPVVSIQVDFPKSNE
RSEASTRVVVQEFNAIYEPEFFVNVLYIYNVFSAFQFQHDRVLSSLNRFNNLGTRLVSKLKYMS
ANRKKLIWDLRIYHFVIRIPSQNCERKELAMVIDAGDVFIQSKDTIDDISRTQESNSFLDHISK
SLPSYFSDDLLLGIQLDELYNQFELGLTGFQVKVLLPDRHNVSSTLIKLDASIALRLCVFLDEP
VLKQLEVGFIVSSIDAYLSQTMYSTIVNLPRMKETNLFKNSVFDNTKTHVPKKLALNVSVSLKL
AKLGLHVDLDGNFEESSGLIVGIEDIDIRYAICELSDLSLAMKTVNVTFRYWKDKSDSHVLCLS
GNLTRCPENSVETCLDLHYRTHKHDDQIHHVYRLILCDVDLHVNPSVIGQIRMFLRKLDSGPSI
GSDVESTMIGQSSMKSGAANGILPMFFLSNLCGADGTVFAGVSVDHFPFLVADHSCGYNFGCLG
TQNVEAQESLYSKNEHCHDTSGLNGYHASDLTSNTYGKTQRSDCSSGSSNDPKNASRTVLDLSL
ISVRIHFPESCGTLVTITIPESISTLTYFDASSWDLLLSANNLTLASPWTPPNVNELVWGTASH
RNASVLNVRVKKDLPALSTEVCVGIQNVCCVLPSKLLAMFVGFFLLDDWNRIAEQEFLVADNNL
EGLRESHDCVTYKFDISDCVVFFPVEEQGLSCLKLEVPHFFCEFIANGSSVEFAKRIPKEFFSS
ECIVSRRVDVICIYARNASISLLIVSDQTDFMLKLDENVPKRIHSLIEKLDADVWIQVPCKDIP
YSQQPTSPTSVMSKISRCNLIAEDLYFINGMETVIGVVDQLISIGNESKMYKGNASQFLDHRSF
CEGNPDPNECTNLTISIKDLMILLGQSKAKGLALERIATANMEFDVSAVLVGEKPERIDFDVVS
LTLQSPGGYTLISIVSDGPLSPVFFKFTKHHTGQDEILLSVPLFEIWLYLQDWNTIINHSHSYI
KTEVNSMPVEHAAALSQFPEMVSSPLIASEFGSPDDFNLVVTCETISGVLHIPIWGKEENHTSN
HMGVTPASFPMEVGTHETDDIQYCEPKGCKFVTLTFDTKHFVVMSGDSCINFRCDLERLKVLLE
MIQENKGTSVPFVHISKVKSSGYVRQSERNLEHLSVDLQAEYMDVSFSHQIFNFWHNMELKFPA
ASSASSFYSVAFKAGLRKGSLLLSDGREVWHEACRYNVFWAWYGM*(-)
MEGRFGTKLVDTMFSGLGMECKIWDDAATILAWLDSLRVINPLNKTKILWAEKCSTGDGLGAPV
VSIQVDFPKSNERSEASTRVVVQEFNAIYEPEFFVNVLYIYNVFSAFQFQHDRVLSSLNRFNNL
GTRLVSKLKYMSANRKKLIWDLRIYHFVIRIPSQNCERKELAMVIDAGDVFIQSKDTIDDISRT
QESNSFLDHISKSLPSYFSDDLLLGIQLDELYNQFELGLTGFQVKVLLPDRHNVSSTLIKLDAS
IALRLCVFLDEPVLKQLEVGFIVSSIDAYLSQTMYSTIVNLPRMKETNLFKNSVFDNTKTHVPK
KLALNVSVSLKLAKLGLHVDLDGNFEESSGLIVGIEDIDIRYAICELSDLSLAMKTVNVTFRYW
KDKSDSHVLCLSGNLTRCPENSVETCLDLHYRTHKHDDQIHHVYRLILCDVDLHVNPSVIGQIR
MFLRKLDSGPSIGSDVESTMIGQSSMKSGAANGILPMFFLSNLCGADGTVFAGVSVDHFPFLVA
DHSCGYNFGCLGTQNVEAQESLYSKNEHCHDTSGLNGYHASDLTSNTYGKTQRSDCSSGSSNDP
KNASRTVLDLSLISVRIHFPESCGTLVTITIPESISTLTYFDASSWDLLLSANNLTLASPWTPP
NVNELVWGTASHRNASVLNVRVKKDLPALSTEVCVGIQNVCCVLPSKLLAMFVGFFLLDDWNRI
AEQEFLVADNNLEGLRESHDCVTYKFDISDCVVFFPVEEQGLSCLKLEVPHFFCEFIANGSSVE
FAKRIPKEFFSSECIVSRRVDVICIYARNASISLLIVSDQTDFMLKLDENVPKRIHSLIEKLDA
DVWIQVPCKDIPYSQQPTSPTSVMSKISRCNLIAEDLYFINGMETVIGVVDQLISIGNESKMYK
GNASQFLDHRSFCEGNPDPNECTNLTISIKDLMILLGQSKAKGLALERIATANMEFDVSAVLVG
EKPERIDFDVVSLTLQSPGGYTLISIVSDGPLSPVFFKFTKHHTGQDEILLSVPLFEIWLYLQD
WNTIINHSHSYIKTEVNSMPVEHAAALSQFPEMVSSPLIASEFGSPDDFNLVVTCETISGVLHI
PIWGKEENHTSNHMGVTPASFPMEVGTHETDDIQYCEPKGCKFVTLTFDTKHFVVMSGDSCINF
RCDLERLKVLLEMIQENKGTSVPFVHISKVKSSGYVRQSERNLEHLSVDLQAEYMDVSFSHQIF
NFWHNMELKFPAASSASSFYSVAFKAGLRKGSLLLSDGREVWHEACRYNVFWAWYGM*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	4712770-4704833(+) 4713185-4713157(-) 4704831-4713157(-)
Potential amino acid sequence	MALNSWTTTLVEASDLSFDLGKSTWILTTGAPRPSPVLHFSAHKIFVLFSGLITRRESSQARIV AASSHILHSIPSPENIVSTSFVPNLPSIA(+) MFSGLGMECKIWDDAATILAWLDSLRVINPLNKTKILWAEKCSTGDGLGAPVVSIQVDFPKSNE RSEASTRVVVQEFNAIYEPEFFVNVLYIYNVFSAFQFQHDRVLSSLNRFNNLGTRLVSKLKYMS ANRKKLIWDLRIYHFVIRIPSQNCERKELAMVIDAGDVFIQSKDTIDDISRTQESNSFLDHISK SLPSYFSDDLLLGIQLDELYNQFELGLTGFQVKVLLPDRHNVSSTLIKLDASIALRLCVFLDEP VLKQLEVGFIVSSIDAYLSQTMYSTIVNLPRMKETNLFKNSVFDNTKTHVPKKLALNVSVSLKL AKLGLHVDLDGNFEESSGLIVGIEDIDIRYAICELSDLSLAMKTVNVTFRYWKDKSDSHVLCLS GNLTRCPENSVETCLDLHYRTHKHDDQIHHVYRLILCDVDLHVNPSVIGQIRMFLRKLDSGPSI GSDVESTMIGQSSMKSGAANGILPMFFLSNLCGADGTVFAGVSVDHFPFLVADHSCGYNFGCLG TQNVEAQESLYSKNEHCHDTSGLNGYHASDLTSNTYGKTQRSDCSSGSSNDPKNASRTVLDLSL ISVRIHFPESCGTLVTITIPESISTLTYFDASSWDLLLSANNLTLASPWTPPNVNELVWGTASH RNASVLNVRVKKDLPALSTEVCVGIQNVCCVLPSKLLAMFVGFFLLDDWNRIAEQEFLVADNNL EGLRESHDCVTYKFDISDCVVFFPVEEQGLSCLKLEVPHFFCEFIANGSSVEFAKRIPKEFFSS ECIVSRRVDVICIYARNASISLLIVSDQTDFMLKLDENVPKRIHSLIEKLDADVWIQVPCKDIP YSQQPTSPTSVMSKISRCNLIAEDLYFINGMETVIGVVDQLISIGNESKMYKGNASQFLDHRSF CEGNPDPNECTNLTISIKDLMILLGQSKAKGLALERIATANMEFDVSAVLVGEKPERIDFDVVS LTLQSPGGYTLISIVSDGPLSPVFFKFTKHHTGQDEILLSVPLFEIWLYLQDWNTIINHSHSYI KTEVNSMPVEHAAALSQFPEMVSSPLIASEFGSPDDFNLVVTCETISGVLHIPIWGKEENHTSN HMGVTPASFPMEVGTHETDDIQYCEPKGCKFVTLTFDTKHFVVMSGDSCINFRCDLERLKVLLE MIQENKGTSVPFVHISKVKSSGYVRQSERNLEHLSVDLQAEYMDVSFSHQIFNFWHNMELKFPA ASSASSFYSVAFKAGLRKGSLLLSDGREVWHEACRYNVFWAWYGM(-) MEGRFGTKLVDTMFSGLGMECKIWDDAATILAWLDSLRVINPLNKTKILWAEKCSTGDGLGAPV VSIQVDFPKSNERSEASTRVVVQEFNAIYEPEFFVNVLYIYNVFSAFQFQHDRVLSSLNRFNNL GTRLVSKLKYMSANRKKLIWDLRIYHFVIRIPSQNCERKELAMVIDAGDVFIQSKDTIDDISRT QESNSFLDHISKSLPSYFSDDLLLGIQLDELYNQFELGLTGFQVKVLLPDRHNVSSTLIKLDAS IALRLCVFLDEPVLKQLEVGFIVSSIDAYLSQTMYSTIVNLPRMKETNLFKNSVFDNTKTHVPK KLALNVSVSLKLAKLGLHVDLDGNFEESSGLIVGIEDIDIRYAICELSDLSLAMKTVNVTFRYW KDKSDSHVLCLSGNLTRCPENSVETCLDLHYRTHKHDDQIHHVYRLILCDVDLHVNPSVIGQIR MFLRKLDSGPSIGSDVESTMIGQSSMKSGAANGILPMFFLSNLCGADGTVFAGVSVDHFPFLVA DHSCGYNFGCLGTQNVEAQESLYSKNEHCHDTSGLNGYHASDLTSNTYGKTQRSDCSSGSSNDP KNASRTVLDLSLISVRIHFPESCGTLVTITIPESISTLTYFDASSWDLLLSANNLTLASPWTPP NVNELVWGTASHRNASVLNVRVKKDLPALSTEVCVGIQNVCCVLPSKLLAMFVGFFLLDDWNRI AEQEFLVADNNLEGLRESHDCVTYKFDISDCVVFFPVEEQGLSCLKLEVPHFFCEFIANGSSVE FAKRIPKEFFSSECIVSRRVDVICIYARNASISLLIVSDQTDFMLKLDENVPKRIHSLIEKLDA DVWIQVPCKDIPYSQQPTSPTSVMSKISRCNLIAEDLYFINGMETVIGVVDQLISIGNESKMYK GNASQFLDHRSFCEGNPDPNECTNLTISIKDLMILLGQSKAKGLALERIATANMEFDVSAVLVG EKPERIDFDVVSLTLQSPGGYTLISIVSDGPLSPVFFKFTKHHTGQDEILLSVPLFEIWLYLQD WNTIINHSHSYIKTEVNSMPVEHAAALSQFPEMVSSPLIASEFGSPDDFNLVVTCETISGVLHI PIWGKEENHTSNHMGVTPASFPMEVGTHETDDIQYCEPKGCKFVTLTFDTKHFVVMSGDSCINF RCDLERLKVLLEMIQENKGTSVPFVHISKVKSSGYVRQSERNLEHLSVDLQAEYMDVSFSHQIF NFWHNMELKFPAASSASSFYSVAFKAGLRKGSLLLSDGREVWHEACRYNVFWAWYGM*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d035089_circ_g.4

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