Plant Circular RNA Database

Detail information of Zm00001d025003_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d025003_circ_g.4
					
						ID in PlantcircBase
						zma_circ_010263
					
						Alias
						zma_circ_0000210, GRMZM2G007721_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 99123962-99131493  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d025003						
					
						Parent gene annotation
						
							Putative glycosyl transferase family 28 protein  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d025003_circ_g.1 Zm00001d025003_circ_g.2 Zm00001d025003_circ_g.3 						
					
						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
						Zm00001d025003_T002:6
Zm00001d025003_T003:5
Zm00001d025003_T004:6
Zm00001d025003_T001:6

General Information
CircRNA Name	Zm00001d025003_circ_g.4
ID in PlantcircBase	zma_circ_010263
Alias	zma_circ_0000210, GRMZM2G007721_C3
Organism	Zea mays
Position	chr10: 99123962-99131493 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d025003
Parent gene annotation	Putative glycosyl transferase family 28 protein
Parent gene strand	+
Alternative splicing	Zm00001d025003_circ_g.1 Zm00001d025003_circ_g.2 Zm00001d025003_circ_g.3
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	Zm00001d025003_T002:6 Zm00001d025003_T003:5 Zm00001d025003_T004:6 Zm00001d025003_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  
						
							CCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGTTTGGTTTGCAGAAG
TTGGTCGACGCTATAACATTCATGATGAAACCAGAGctttcttatcaaattgtggactccatga
tttggcttggaataagggatatgataaatgagttcagaaagaaaaagctgaagctgcgtccagt
aacatatc

						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: 687
Transcript exons: 99123962-99124139,99124811-99124941,99125967-99126069,99
126157-99126233,99126357-99126404,99131344-99131493
CTTTCTTATCAAATTGTGGACTCCATGATTTGGCTTGGAATAAGGGATATGATAAATGAGTTCA
GAAAGAAAAAGCTGAAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGA
CATTCCGCATGGATACATTTGGAGTCCTCATCTTGTTCCGAAACCAAAAGATTGGGGCCCAAAG
ATCGATGTTGTTGGATTTTGCTTCCTTGATCTTGCTTCCAATTACGTACCTCCTGAACCACTTG
TGGAATGGCTTGAAGCCGGTGACAAGCCCATATATGTTGGTTTTGGTAGTCTTCCAGTTCAAGA
TCCACAAAAGATGACTGAAATTATTGTCAAAGCACTGGAAATTACTGGACAGAGAGGTATCATT
AACAAAGGCTGGGGTGGCCTTGGAACCTTGTCAGAACCAAAAGATTTTGTGTATCTACTAGACA
ACTGCCCTCATGACTGGCTTTTTCTGCACTGCAAAGCAGTGGTGCATCATGGTGGTGCTGGAAC
GACAGCCGCAGGTCTTAAAGCAGCGTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCT
TTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGTTTG
GTTTGCAGAAGTTGGTCGACGCTATAACATTCATGATGAAACCAGAG
						
						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	CCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGTTTGGTTTGCAGAAG TTGGTCGACGCTATAACATTCATGATGAAACCAGAGctttcttatcaaattgtggactccatga tttggcttggaataagggatatgataaatgagttcagaaagaaaaagctgaagctgcgtccagt aacatatc
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: 687 Transcript exons: 99123962-99124139,99124811-99124941,99125967-99126069,99 126157-99126233,99126357-99126404,99131344-99131493 CTTTCTTATCAAATTGTGGACTCCATGATTTGGCTTGGAATAAGGGATATGATAAATGAGTTCA GAAAGAAAAAGCTGAAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGA CATTCCGCATGGATACATTTGGAGTCCTCATCTTGTTCCGAAACCAAAAGATTGGGGCCCAAAG ATCGATGTTGTTGGATTTTGCTTCCTTGATCTTGCTTCCAATTACGTACCTCCTGAACCACTTG TGGAATGGCTTGAAGCCGGTGACAAGCCCATATATGTTGGTTTTGGTAGTCTTCCAGTTCAAGA TCCACAAAAGATGACTGAAATTATTGTCAAAGCACTGGAAATTACTGGACAGAGAGGTATCATT AACAAAGGCTGGGGTGGCCTTGGAACCTTGTCAGAACCAAAAGATTTTGTGTATCTACTAGACA ACTGCCCTCATGACTGGCTTTTTCTGCACTGCAAAGCAGTGGTGCATCATGGTGGTGCTGGAAC GACAGCCGCAGGTCTTAAAGCAGCGTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCT TTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGTTTG GTTTGCAGAAGTTGGTCGACGCTATAACATTCATGATGAAACCAGAG
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
						0.139194824

Conservation Information
Conserved circRNAs	NA
PMCS	0.139194824

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							99123987-99131490(+)
						
						Potential amino acid sequence
						
							MIWLGIRDMINEFRKKKLKLRPVTYLSGSQGSGNDIPHGYIWSPHLVPKPKDWGPKIDVVGFCF
LDLASNYVPPEPLVEWLEAGDKPIYVGFGSLPVQDPQKMTEIIVKALEITGQRGIINKGWGGLG
TLSEPKDFVYLLDNCPHDWLFLHCKAVVHHGGAGTTAAGLKAACPTTIVPFFGDQPFWGDRVHA
RGLGPPPIPVDQFGLQKLVDAITFMMKPELSYQIVDSMIWLGIRDMINEFRKKKLKLRPVTYLS
GSQGSGNDIPHGYIWSPHLVPKPKDWGPKIDVVGFCFLDLASNYVPPEPLVEWLEAGDKPIYVG
FGSLPVQDPQKMTEIIVKALEITGQRGIINKGWGGLGTLSEPKDFVYLLDNCPHDWLFLHCKAV
VHHGGAGTTAAGLKAACPTTIVPFFGDQPFWGDRVHARGLGPPPIPVDQFGLQKLVDAITFMMK
PELSYQIVDSMIWLGIRDMINEFRKKKLKLRPVTYLSGSQGSGNDIPHGYIWSPHLVPKPKDWG
PKIDVVGFCFLDLASNYVPPEPLVEWLEAGDKPIYVGFGSLPVQDPQKMTEIIVKALEITGQRG
IINKGWGGLGTLSEPKDFVYLLDNCPHDWLFLHCKAVVHHGGAGTTAAGLKAACPTTIVPFFGD
QPFWGDRVHARGLGPPPIPVDQFGLQKLVDAITFMMKPELSYQIVDSMIWLGIRDMINEFRKKK
LKLRPVTYLSGSQGSGNDIPHGYIWSPHLVPKPKDWGPKIDVVGFCFLDLASNYVPPEPLVEWL
EAGDKPIYVGFGSLPVQDPQKMTEIIVKALEITGQRGIINKGWGGLGTLSEPKDFVYLLDNCPH
DWLFLHCKAVVHHGGAGTTAAGLKAACPTTIVPFFGDQPFWGDRVHARGLGPPPIPVDQFGLQK
LVDAITFMMKPE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	99123987-99131490(+)
Potential amino acid sequence	MIWLGIRDMINEFRKKKLKLRPVTYLSGSQGSGNDIPHGYIWSPHLVPKPKDWGPKIDVVGFCF LDLASNYVPPEPLVEWLEAGDKPIYVGFGSLPVQDPQKMTEIIVKALEITGQRGIINKGWGGLG TLSEPKDFVYLLDNCPHDWLFLHCKAVVHHGGAGTTAAGLKAACPTTIVPFFGDQPFWGDRVHA RGLGPPPIPVDQFGLQKLVDAITFMMKPELSYQIVDSMIWLGIRDMINEFRKKKLKLRPVTYLS GSQGSGNDIPHGYIWSPHLVPKPKDWGPKIDVVGFCFLDLASNYVPPEPLVEWLEAGDKPIYVG FGSLPVQDPQKMTEIIVKALEITGQRGIINKGWGGLGTLSEPKDFVYLLDNCPHDWLFLHCKAV VHHGGAGTTAAGLKAACPTTIVPFFGDQPFWGDRVHARGLGPPPIPVDQFGLQKLVDAITFMMK PELSYQIVDSMIWLGIRDMINEFRKKKLKLRPVTYLSGSQGSGNDIPHGYIWSPHLVPKPKDWG PKIDVVGFCFLDLASNYVPPEPLVEWLEAGDKPIYVGFGSLPVQDPQKMTEIIVKALEITGQRG IINKGWGGLGTLSEPKDFVYLLDNCPHDWLFLHCKAVVHHGGAGTTAAGLKAACPTTIVPFFGD QPFWGDRVHARGLGPPPIPVDQFGLQKLVDAITFMMKPELSYQIVDSMIWLGIRDMINEFRKKK LKLRPVTYLSGSQGSGNDIPHGYIWSPHLVPKPKDWGPKIDVVGFCFLDLASNYVPPEPLVEWL EAGDKPIYVGFGSLPVQDPQKMTEIIVKALEITGQRGIINKGWGGLGTLSEPKDFVYLLDNCPH DWLFLHCKAVVHHGGAGTTAAGLKAACPTTIVPFFGDQPFWGDRVHARGLGPPPIPVDQFGLQK LVDAITFMMKPE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d025003_circ_g.4

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