Plant Circular RNA Database

Detail information of Zm00001d024327_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d024327_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010205
					
						Alias
						Zm10circ00023, GRMZM2G404426_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 64827820-64837830  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d024327						
					
						Parent gene annotation
						
							RING/FYVE/PHD zinc finger superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d024327_circ_g.1 Zm00001d024327_circ_g.2 Zm00001d024327_circ_g.4 Zm00001d024327_circ_g.5 						
					
						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  
						
							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
						Zm00001d024327_T003:9
Zm00001d024327_T001:9
Zm00001d024327_T002:9

General Information
CircRNA Name	Zm00001d024327_circ_g.3
ID in PlantcircBase	zma_circ_010205
Alias	Zm10circ00023, GRMZM2G404426_C2
Organism	Zea mays
Position	chr10: 64827820-64837830 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d024327
Parent gene annotation	RING/FYVE/PHD zinc finger superfamily protein
Parent gene strand	-
Alternative splicing	Zm00001d024327_circ_g.1 Zm00001d024327_circ_g.2 Zm00001d024327_circ_g.4 Zm00001d024327_circ_g.5
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	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	Zm00001d024327_T003:9 Zm00001d024327_T001:9 Zm00001d024327_T002:9

			
						 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  
						
							ACGTGTTTCGCGCCTGGTAAATAACACCTTTTCCATCTGATGCTCTTATTAGCATACCACGTCG
TCCAGTTATTTCTGCAACATTGTCAGGACCACCAAGctcccaagaaactccacggtcaactgta
aaagtatataatattgtactagcaccggacacagtatcaacatgaacagtctgcacaaatataa
ttcaattg

						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: 978
Transcript exons: 64827820-64827897,64827977-64828100,64828163-64828295,64
836460-64836577,64836673-64836760,64836855-64836950,6483
7340-64837446,64837526-64837661,64837733-64837830
CTCCCAAGAAACTCCACGGTCAACTGTAAAAGTATATAATATTGTACTAGCACCGGACACAGTA
TCAACATGAACAGTCTTTGGTGATTCTTTCATTTCGACACTTTTAGCTTTGATATCAACAATAC
CAGAATCAAGTTGTCCTTCAATTCGTGCATTCTGAATGACTATATCAAGTATGCTTGTGAAAAG
GTCAAATAATTTGTGTTCAGATAAAACTTGCCTATTCTGAATGTCTGGAAACAATCCCAGAATA
CGATTAAGGAAACGGGCAACATCATGCATATCAGAATCAATAATCCTACCAGTAAGCTTTCCAC
CATTTTTACCATTGCACATTATAGGGTCCCTAATAATTCCAACTGACACTAAAGCAGCTTTTGC
TTTAGTGATGAACTCTTCAAGGGTAGCTTGATTCTCAGAGCATTCGAAAGGCACAACAGGAAAG
GCATCCTGTTCCATTATTCCTCTGTACATCATTGTCAGGGCTTTCTTTCCATAATTACTGTCAT
AGTTGAAGGCGCTAAGTGATGGTCCAGCCCTTCGATCTCCTTGCGTTAAAGCTCCAAGAGACTC
CAGTCTCTTTGCCACGATTGATGCAAATCGCTTTTCACCACCAAGGTTTGTGAAAAGAAGCCTA
TATTCAGGTGCAGAAGTTTGATTAGAACGATGGGTTCTCCCAAACTGCTGAATCGCACGGTCTG
CACTCCAAGGAAGCTCTAGTGTTATGTGCACTCTTCTCCTCTGATTTTTTGCCCTTCGATCAGC
ATGTAGAGAAACGCCAGCTGATCCTGCTTCTGATATTATGGCAACATTCTTTTCTCCATCCATG
AATTGCTGCTTTTCATGCATATTGATCATGTCCAATGCAACTTCTTTCGTGTTTCGCGCCTGGT
AAATAACACCTTTTCCATCTGATGCTCTTATTAGCATACCACGTCGTCCAGTTATTTCTGCAAC
ATTGTCAGGACCACCAAG
						
						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	ACGTGTTTCGCGCCTGGTAAATAACACCTTTTCCATCTGATGCTCTTATTAGCATACCACGTCG TCCAGTTATTTCTGCAACATTGTCAGGACCACCAAGctcccaagaaactccacggtcaactgta aaagtatataatattgtactagcaccggacacagtatcaacatgaacagtctgcacaaatataa ttcaattg
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: 978 Transcript exons: 64827820-64827897,64827977-64828100,64828163-64828295,64 836460-64836577,64836673-64836760,64836855-64836950,6483 7340-64837446,64837526-64837661,64837733-64837830 CTCCCAAGAAACTCCACGGTCAACTGTAAAAGTATATAATATTGTACTAGCACCGGACACAGTA TCAACATGAACAGTCTTTGGTGATTCTTTCATTTCGACACTTTTAGCTTTGATATCAACAATAC CAGAATCAAGTTGTCCTTCAATTCGTGCATTCTGAATGACTATATCAAGTATGCTTGTGAAAAG GTCAAATAATTTGTGTTCAGATAAAACTTGCCTATTCTGAATGTCTGGAAACAATCCCAGAATA CGATTAAGGAAACGGGCAACATCATGCATATCAGAATCAATAATCCTACCAGTAAGCTTTCCAC CATTTTTACCATTGCACATTATAGGGTCCCTAATAATTCCAACTGACACTAAAGCAGCTTTTGC TTTAGTGATGAACTCTTCAAGGGTAGCTTGATTCTCAGAGCATTCGAAAGGCACAACAGGAAAG GCATCCTGTTCCATTATTCCTCTGTACATCATTGTCAGGGCTTTCTTTCCATAATTACTGTCAT AGTTGAAGGCGCTAAGTGATGGTCCAGCCCTTCGATCTCCTTGCGTTAAAGCTCCAAGAGACTC CAGTCTCTTTGCCACGATTGATGCAAATCGCTTTTCACCACCAAGGTTTGTGAAAAGAAGCCTA TATTCAGGTGCAGAAGTTTGATTAGAACGATGGGTTCTCCCAAACTGCTGAATCGCACGGTCTG CACTCCAAGGAAGCTCTAGTGTTATGTGCACTCTTCTCCTCTGATTTTTTGCCCTTCGATCAGC ATGTAGAGAAACGCCAGCTGATCCTGCTTCTGATATTATGGCAACATTCTTTTCTCCATCCATG AATTGCTGCTTTTCATGCATATTGATCATGTCCAATGCAACTTCTTTCGTGTTTCGCGCCTGGT AAATAACACCTTTTCCATCTGATGCTCTTATTAGCATACCACGTCGTCCAGTTATTTCTGCAAC ATTGTCAGGACCACCAAG
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
						0.126455557

Conservation Information
Conserved circRNAs	NA
PMCS	0.126455557

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							64837771-64827845(+)
64837787-64827822(-)
64827892-64837802(-)
						
					

						Potential amino acid sequence
						
							MLLLAYHVVQLFLQHCQDHQAPKKLHGQL*(+)
MLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISEAGSAGVSLHADRRAKNQR
RRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKRFASIVAKRLESLGALTQG
DRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQATLEEFITKAKAALVSVG
IIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQVLSEHKLFDLFTSILDIV
IQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTFTVDRGVSWELGGPDNVAE
ITGRRGMLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISEAGSAGVSLHADR
RAKNQRRRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKRFASIVAKRLESL
GALTQGDRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQATLEEFITKAKA
ALVSVGIIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQVLSEHKLFDLFT
SILDIVIQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTFTVDRGVSWELGG
PDNVAEITGRRGMLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISEAGSAGV
SLHADRRAKNQRRRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKRFASIVA
KRLESLGALTQGDRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQATLEEF
ITKAKAALVSVGIIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQVLSEHK
LFDLFTSILDIVIQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTFTVDRGV
SWELGGPDNVAEITGRRGMLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISE
AGSAGVSLHADRRAKNQRRRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKR
FASIVAKRLESLGALTQGDRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQ
ATLEEFITKAKAALVSVGIIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQ
VLSEHKLFDLFTSILDIVIQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTF
TVDRGVSWE(-)
MLILCPVLVQYYILLQLTVEFLGSLVVLTMLQK*(-)
						
					

						Sponge-miRNAs
						
							zma-miR399i-5p 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						responsive to drought stress
					

			
		

Functional Information
Coding potential	Y
Potential coding position	64837771-64827845(+) 64837787-64827822(-) 64827892-64837802(-)
Potential amino acid sequence	MLLLAYHVVQLFLQHCQDHQAPKKLHGQL(+) MLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISEAGSAGVSLHADRRAKNQR RRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKRFASIVAKRLESLGALTQG DRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQATLEEFITKAKAALVSVG IIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQVLSEHKLFDLFTSILDIV IQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTFTVDRGVSWELGGPDNVAE ITGRRGMLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISEAGSAGVSLHADR RAKNQRRRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKRFASIVAKRLESL GALTQGDRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQATLEEFITKAKA ALVSVGIIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQVLSEHKLFDLFT SILDIVIQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTFTVDRGVSWELGG PDNVAEITGRRGMLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISEAGSAGV SLHADRRAKNQRRRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKRFASIVA KRLESLGALTQGDRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQATLEEF ITKAKAALVSVGIIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQVLSEHK LFDLFTSILDIVIQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTFTVDRGV SWELGGPDNVAEITGRRGMLIRASDGKGVIYQARNTKEVALDMINMHEKQQFMDGEKNVAIISE AGSAGVSLHADRRAKNQRRRVHITLELPWSADRAIQQFGRTHRSNQTSAPEYRLLFTNLGGEKR FASIVAKRLESLGALTQGDRRAGPSLSAFNYDSNYGKKALTMMYRGIMEQDAFPVVPFECSENQ ATLEEFITKAKAALVSVGIIRDPIMCNGKNGGKLTGRIIDSDMHDVARFLNRILGLFPDIQNRQ VLSEHKLFDLFTSILDIVIQNARIEGQLDSGIVDIKAKSVEMKESPKTVHVDTVSGASTILYTF TVDRGVSWE(-) MLILCPVLVQYYILLQLTVEFLGSLVVLTMLQK(-)
Sponge-miRNAs	zma-miR399i-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d024327_circ_g.3

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