Plant Circular RNA Database

Detail information of Zm00001d025174_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d025174_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010296
					
						Alias
						Zm10circ00046, GRMZM2G547542_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 107655972-107657590  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d025174						
					
						Parent gene annotation
						
							S-adenosyl-L-methionine-dependent methyltransferases superfamily
 protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025174_circ_g.2 Zm00001d025174_circ_g.3 Zm00001d025174_circ_igg.1 Zm00001d025174_circ_g.2 Zm00001d025174_circ_ig.1 Zm00001d025174_circ_ig.2 						
					
						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
						Zm00001d025174_T001:6

General Information
CircRNA Name	Zm00001d025174_circ_g.3
ID in PlantcircBase	zma_circ_010296
Alias	Zm10circ00046, GRMZM2G547542_C2
Organism	Zea mays
Position	chr10: 107655972-107657590 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d025174
Parent gene annotation	S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
Parent gene strand	-
Alternative splicing	Zm00001d025174_circ_g.2 Zm00001d025174_circ_g.3 Zm00001d025174_circ_igg.1 Zm00001d025174_circ_g.2 Zm00001d025174_circ_ig.1 Zm00001d025174_circ_ig.2
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	Zm00001d025174_T001:6

			
						 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  
						
							GACGACGGAACATTTTCTCAGACATGGAACCTTGATCTCCATCAGCATTTTCATAGACAACATC
TTCCACAACCATTGGACCAGTTATTTCTGAAGTTACcttcaattgctcatccattgaaaagcca
aaatatttctttgctagctcagccaccaaggggtccaactcaacgacctgcaaattttgagaag
tgtgagca

									
								

					

						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: 639
Transcript exons: 107655972-107656046,107656123-107656203,107656401-107656
522,107656661-107656788,107656884-107656945,107657420-10
7657590
CTTCAATTGCTCATCCATTGAAAAGCCAAAATATTTCTTTGCTAGCTCAGCCACCAAGGGGTCC
AACTCAACGACCTCAATATCTACGAAAGGCAGACATCCACGGAGAAACATTGGGAAACAACCAG
CACCAAGGCCTACAACGGTGATGCTGACTTTTTCTCCAGATGAAGCAGCAGCACTCAGAGAAGA
TGCAACTAAAGAAAGCCCAGATATGATACTGCTGTGATATGAGCTACCAAGAAATTTATGGTCA
ATTCTCAGACTGTTCTTGGATCCTGTAGCAGTTCCAACATTCAACAGATCACTAGGGGATTTAT
ATTCCAGATATTTATTATTATTATTCTTTCTATTATCCGAGTAAATCAGATGATGTTTACAATT
CTGGCTAGAACCCATATAGATTATCACACATCTATCGTGTCCCAACAAATAGACGAATTGCCTT
TGAAACAACTGTGGTTGCATCTCATCACTGGGAGGATCTCTGATTAACAACGCTTCAGATTGCA
CTAAACCAGAACTTCTTCCAAAAATAAGACGACGGAACATTTTCTCAGACATGGAACCTTGATC
TCCATCAGCATTTTCATAGACAACATCTTCCACAACCATTGGACCAGTTATTTCTGAAGTTAC
						
					

						Genomic sequence
						
							CTTCAATTGCTCATCCATTGAAAAGCCAAAATATTTCTTTGCTAGCTCAGCCACCAAGGGGTCC
AACTCAACGACCTGCAAATTTTGAGAAGTGTGAGCACCTCATTCAATCAATAGTCGAAGATAAA
AGCCTACCCCCCCCCCCCCTTACCTCAATATCTACGAAAGGCAGACATCCACGGAGAAACATTG
GGAAACAACCAGCACCAAGGCCTACAACGGTGATGCTGACCTACAAAATGCAAATTGAATTAAC
ATACAGAATTGTTTCGCACGCCATAATACCAAAAAATTACGAACAACCTGTACCACAACAAAGC
TGGCATTCAACTTCAACTACTTTAAGGGGCCAACTCCAATAATCTGGATTCATGGTTTCATGCA
CTTAAAAGTTGAATCGTTCACATAGAACAATAGCACAATACTTACTTTTTCTCCAGATGAAGCA
GCAGCACTCAGAGAAGATGCAACTAAAGAAAGCCCAGATATGATACTGCTGTGATATGAGCTAC
CAAGAAATTTATGGTCAATTCTCAGACTGTTCTTGGATCCTGCATATCAGTGACCAACAATTGG
ATTTTAAAACCATGAGAGAAAAACAAATGTAATTTAGTGCCTAATCTTGAATAGCTTATTGAAT
GGGTGAATATAAGATATCAACAGGTACTGAAACAATAAGAATCATGTACCTGTAGCAGTTCCAA
CATTCAACAGATCACTAGGGGATTTATATTCCAGATATTTATTATTATTATTCTTTCTATTATC
CGAGTAAATCAGATGATGTTTACAATTCTGGCTAGAACCCATATAGATTCTGCAGAAATTGTAG
ATTATGGGCAAGCATTGCAATTACTAGATAAAAATTCCTGAACATCCTAGGGAGCAATAGATTA
TGAAAGACTAACGCACATCACACATCTATCGTGTCCCAACAAATAGACGAATTGCCTTTGAAAC
AACTGTGGTTGCATCTAGAACAGCCCAGTGAGCAGTTAAACTGAACAAATATTCACAAAGTAAC
TACATAGACAGAAATTTAGCTACAACCTATAGAAATGAATAAGAACTAGAAGTGACACATCTGA
TCTGCCACATAGAAATATGTGATATACAGCATGCTCTCTCCACAAAATCTAAGAAAATGAGCAA
CATTTGGAATGTAAGATTATCAGCTAAACAGGAACACTTTGATTTTGAATCTATGATTTTAAAA
AGAACCAAACTTCCAACACAAGTATTAGATTGTGCACACACATGATAGCAACAAAAGGTACTAA
GAGCAAGGATATCAACTAGTGCCAATTAAACCAATGAGTATGGCAAGCAAGCACCGCAAAGCAC
CTTGCACATTAAAATTACAGAAACAAGAAGAAACAGAGCAGACCCCTTTTATGGTTCCTTCTTT
TTTTAGATGTTGCAGCTGCACTTTTGTTCTTTTTGTCTACCTCATCACTGGGAGGATCTCTGAT
TAACAACGCTTCAGATTGCACTAAACCAGAACTTCTTCCAAAAATAAGACGACGGAACATTTTC
TCAGACATGGAACCTTGATCTCCATCAGCATTTTCATAGACAACATCTTCCACAACCATTGGAC
CAGTTATTTCTGAAGTTAC
						
					

			
		

Sequences
Splice junction sequence	GACGACGGAACATTTTCTCAGACATGGAACCTTGATCTCCATCAGCATTTTCATAGACAACATC TTCCACAACCATTGGACCAGTTATTTCTGAAGTTACcttcaattgctcatccattgaaaagcca aaatatttctttgctagctcagccaccaaggggtccaactcaacgacctgcaaattttgagaag tgtgagca
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: 639 Transcript exons: 107655972-107656046,107656123-107656203,107656401-107656 522,107656661-107656788,107656884-107656945,107657420-10 7657590 CTTCAATTGCTCATCCATTGAAAAGCCAAAATATTTCTTTGCTAGCTCAGCCACCAAGGGGTCC AACTCAACGACCTCAATATCTACGAAAGGCAGACATCCACGGAGAAACATTGGGAAACAACCAG CACCAAGGCCTACAACGGTGATGCTGACTTTTTCTCCAGATGAAGCAGCAGCACTCAGAGAAGA TGCAACTAAAGAAAGCCCAGATATGATACTGCTGTGATATGAGCTACCAAGAAATTTATGGTCA ATTCTCAGACTGTTCTTGGATCCTGTAGCAGTTCCAACATTCAACAGATCACTAGGGGATTTAT ATTCCAGATATTTATTATTATTATTCTTTCTATTATCCGAGTAAATCAGATGATGTTTACAATT CTGGCTAGAACCCATATAGATTATCACACATCTATCGTGTCCCAACAAATAGACGAATTGCCTT TGAAACAACTGTGGTTGCATCTCATCACTGGGAGGATCTCTGATTAACAACGCTTCAGATTGCA CTAAACCAGAACTTCTTCCAAAAATAAGACGACGGAACATTTTCTCAGACATGGAACCTTGATC TCCATCAGCATTTTCATAGACAACATCTTCCACAACCATTGGACCAGTTATTTCTGAAGTTAC
Genomic sequence	CTTCAATTGCTCATCCATTGAAAAGCCAAAATATTTCTTTGCTAGCTCAGCCACCAAGGGGTCC AACTCAACGACCTGCAAATTTTGAGAAGTGTGAGCACCTCATTCAATCAATAGTCGAAGATAAA AGCCTACCCCCCCCCCCCCTTACCTCAATATCTACGAAAGGCAGACATCCACGGAGAAACATTG GGAAACAACCAGCACCAAGGCCTACAACGGTGATGCTGACCTACAAAATGCAAATTGAATTAAC ATACAGAATTGTTTCGCACGCCATAATACCAAAAAATTACGAACAACCTGTACCACAACAAAGC TGGCATTCAACTTCAACTACTTTAAGGGGCCAACTCCAATAATCTGGATTCATGGTTTCATGCA CTTAAAAGTTGAATCGTTCACATAGAACAATAGCACAATACTTACTTTTTCTCCAGATGAAGCA GCAGCACTCAGAGAAGATGCAACTAAAGAAAGCCCAGATATGATACTGCTGTGATATGAGCTAC CAAGAAATTTATGGTCAATTCTCAGACTGTTCTTGGATCCTGCATATCAGTGACCAACAATTGG ATTTTAAAACCATGAGAGAAAAACAAATGTAATTTAGTGCCTAATCTTGAATAGCTTATTGAAT GGGTGAATATAAGATATCAACAGGTACTGAAACAATAAGAATCATGTACCTGTAGCAGTTCCAA CATTCAACAGATCACTAGGGGATTTATATTCCAGATATTTATTATTATTATTCTTTCTATTATC CGAGTAAATCAGATGATGTTTACAATTCTGGCTAGAACCCATATAGATTCTGCAGAAATTGTAG ATTATGGGCAAGCATTGCAATTACTAGATAAAAATTCCTGAACATCCTAGGGAGCAATAGATTA TGAAAGACTAACGCACATCACACATCTATCGTGTCCCAACAAATAGACGAATTGCCTTTGAAAC AACTGTGGTTGCATCTAGAACAGCCCAGTGAGCAGTTAAACTGAACAAATATTCACAAAGTAAC TACATAGACAGAAATTTAGCTACAACCTATAGAAATGAATAAGAACTAGAAGTGACACATCTGA TCTGCCACATAGAAATATGTGATATACAGCATGCTCTCTCCACAAAATCTAAGAAAATGAGCAA CATTTGGAATGTAAGATTATCAGCTAAACAGGAACACTTTGATTTTGAATCTATGATTTTAAAA AGAACCAAACTTCCAACACAAGTATTAGATTGTGCACACACATGATAGCAACAAAAGGTACTAA GAGCAAGGATATCAACTAGTGCCAATTAAACCAATGAGTATGGCAAGCAAGCACCGCAAAGCAC CTTGCACATTAAAATTACAGAAACAAGAAGAAACAGAGCAGACCCCTTTTATGGTTCCTTCTTT TTTTAGATGTTGCAGCTGCACTTTTGTTCTTTTTGTCTACCTCATCACTGGGAGGATCTCTGAT TAACAACGCTTCAGATTGCACTAAACCAGAACTTCTTCCAAAAATAAGACGACGGAACATTTTC TCAGACATGGAACCTTGATCTCCATCAGCATTTTCATAGACAACATCTTCCACAACCATTGGAC CAGTTATTTCTGAAGTTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.18847298

Conservation Information
Conserved circRNAs	NA
PMCS	0.18847298

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							107657568-107655974(-)
						
						Potential amino acid sequence
						
							MVVEDVVYENADGDQGSMSEKMFRRLIFGRSSGLVQSEALLIRDPPSDEMQPQLFQRQFVYLLG
HDRCVIIYMGSSQNCKHHLIYSDNRKNNNNKYLEYKSPSDLLNVGTATGSKNSLRIDHKFLGSS
YHSSIISGLSLVASSLSAAASSGEKVSITVVGLGAGCFPMFLRGCLPFVDIEVVELDPLVAELA
KKYFGFSMDEQLKVTSEITGPMVVEDVVYENADGDQGSMSEKMFRRLIFGRSSGLVQSEALLIR
DPPSDEMQPQLFQRQFVYLLGHDRCVIIYMGSSQNCKHHLIYSDNRKNNNNKYLEYKSPSDLLN
VGTATGSKNSLRIDHKFLGSSYHSSIISGLSLVASSLSAAASSGEKVSITVVGLGAGCFPMFLR
GCLPFVDIEVVELDPLVAELAKKYFGFSMDEQLKVTSEITGPMVVEDVVYENADGDQGSMSEKM
FRRLIFGRSSGLVQSEALLIRDPPSDEMQPQLFQRQFVYLLGHDRCVIIYMGSSQNCKHHLIYS
DNRKNNNNKYLEYKSPSDLLNVGTATGSKNSLRIDHKFLGSSYHSSIISGLSLVASSLSAAASS
GEKVSITVVGLGAGCFPMFLRGCLPFVDIEVVELDPLVAELAKKYFGFSMDEQLKVTSEITGPM
VVEDVVYENADGDQGSMSEKMFRRLIFGRSSGLVQSEALLIRDPPSDEMQPQLFQRQFVYLLGH
DRCVIIYMGSSQNCKHHLIYSDNRKNNNNKYLEYKSPSDLLNVGTATGSKNSLRIDHKFLGSSY
HSSIISGLSLVASSLSAAASSGEKVSITVVGLGAGCFPMFLRGCLPFVDIEVVELDPLVAELAK
KYFGFSMDEQLK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	107657568-107655974(-)
Potential amino acid sequence	MVVEDVVYENADGDQGSMSEKMFRRLIFGRSSGLVQSEALLIRDPPSDEMQPQLFQRQFVYLLG HDRCVIIYMGSSQNCKHHLIYSDNRKNNNNKYLEYKSPSDLLNVGTATGSKNSLRIDHKFLGSS YHSSIISGLSLVASSLSAAASSGEKVSITVVGLGAGCFPMFLRGCLPFVDIEVVELDPLVAELA KKYFGFSMDEQLKVTSEITGPMVVEDVVYENADGDQGSMSEKMFRRLIFGRSSGLVQSEALLIR DPPSDEMQPQLFQRQFVYLLGHDRCVIIYMGSSQNCKHHLIYSDNRKNNNNKYLEYKSPSDLLN VGTATGSKNSLRIDHKFLGSSYHSSIISGLSLVASSLSAAASSGEKVSITVVGLGAGCFPMFLR GCLPFVDIEVVELDPLVAELAKKYFGFSMDEQLKVTSEITGPMVVEDVVYENADGDQGSMSEKM FRRLIFGRSSGLVQSEALLIRDPPSDEMQPQLFQRQFVYLLGHDRCVIIYMGSSQNCKHHLIYS DNRKNNNNKYLEYKSPSDLLNVGTATGSKNSLRIDHKFLGSSYHSSIISGLSLVASSLSAAASS GEKVSITVVGLGAGCFPMFLRGCLPFVDIEVVELDPLVAELAKKYFGFSMDEQLKVTSEITGPM VVEDVVYENADGDQGSMSEKMFRRLIFGRSSGLVQSEALLIRDPPSDEMQPQLFQRQFVYLLGH DRCVIIYMGSSQNCKHHLIYSDNRKNNNNKYLEYKSPSDLLNVGTATGSKNSLRIDHKFLGSSY HSSIISGLSLVASSLSAAASSGEKVSITVVGLGAGCFPMFLRGCLPFVDIEVVELDPLVAELAK KYFGFSMDEQLK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d025174_circ_g.3

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