Plant Circular RNA Database

Detail information of Zm00001d039612_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d039612_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007489
					
						Alias
						Zm03circ00009, zma_circ_0000977
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 9055087-9055908  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d039612						
					
						Parent gene annotation
						
							embryo defective 2410
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d039612_circ_g.1 Zm00001d039612_circ_g.2 Zm00001d039612_circ_g.3 Zm00001d039612_circ_g.5 Zm00001d039612_circ_g.6 Zm00001d039612_circ_g.7 Zm00001d039612_circ_g.8 Zm00001d039612_circ_g.9 Zm00001d039612_circ_g.10 Zm00001d039612_circ_g.11 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d039612_T025:1
Zm00001d039612_T023:1
Zm00001d039612_T016:1
Zm00001d039612_T015:1
Zm00001d039612_T014:1
Zm00001d039612_T001:1
Zm00001d039612_T004:1
Zm00001d039612_T011:1
Zm00001d039612_T028:1
Zm00001d039612_T019:1
Zm00001d039612_T002:1
Zm00001d039612_T009:1
Zm00001d039612_T021:1
Zm00001d039612_T007:1
Zm00001d039612_T027:1
Zm00001d039612_T013:1

General Information
CircRNA Name	Zm00001d039612_circ_g.4
ID in PlantcircBase	zma_circ_007489
Alias	Zm03circ00009, zma_circ_0000977
Organism	Zea mays
Position	chr3: 9055087-9055908 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d039612
Parent gene annotation	embryo defective 2410
Parent gene strand	-
Alternative splicing	Zm00001d039612_circ_g.1 Zm00001d039612_circ_g.2 Zm00001d039612_circ_g.3 Zm00001d039612_circ_g.5 Zm00001d039612_circ_g.6 Zm00001d039612_circ_g.7 Zm00001d039612_circ_g.8 Zm00001d039612_circ_g.9 Zm00001d039612_circ_g.10 Zm00001d039612_circ_g.11
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d039612_T025:1 Zm00001d039612_T023:1 Zm00001d039612_T016:1 Zm00001d039612_T015:1 Zm00001d039612_T014:1 Zm00001d039612_T001:1 Zm00001d039612_T004:1 Zm00001d039612_T011:1 Zm00001d039612_T028:1 Zm00001d039612_T019:1 Zm00001d039612_T002:1 Zm00001d039612_T009:1 Zm00001d039612_T021:1 Zm00001d039612_T007:1 Zm00001d039612_T027:1 Zm00001d039612_T013:1

			
						 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  
						
							GACGCAGACCATCATTATTGCTGAATGAACCAGATGCGAGAACTCGCTGTGTCTTGTAAGTTCC
CCATTCCCAATCTTCACCATTGAAATCAAAATCTGCctgcaggagaacatcagcatagccttga
agccagtttgcataaggactcaatgcagttatcagcatcatacccccatcctttatatctgcat
ctatcctc

									
								

					

						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: 822
Transcript exons: 9055087-9055908
CTGCAGGAGAACATCAGCATAGCCTTGAAGCCAGTTTGCATAAGGACTCAATGCAGTTATCAGC
ATCATACCCCCATCCTTTATATCTGCATCTATCCTCACTTCACCTGGTTCTAGCATGTTATAAC
TTAAACCTTTAAGTTTTTCAGCTAATTGAAATTCCCAGCCCTCCTCTGTCTTGTCTCTCACCAT
TCTTGCTTCACTGATCTCATTCGATGATCCTCTGTCTCTTGCCCAAACAGGGATTCTTATGATA
CCTTGTTTCCCATCTGCCTCTTCTGGACTTTCCTCTATCGAGCTGTTGTCTACATAAGTGACTG
GTATACTACCTTGAATGTTTACATGTCCACTTTGTATTGTCGGTTCGAAATTTGCATCAAATAC
GAAACGACTTGTAGGGGTAACAGAAGCTAATACTTCTGCTCTTCCAAGATCGATGCCTCCAATA
GTGCCATCAAGCAGCCTTATTTGAACATCACATTCTGGTTTTGCCAGAGTACCTCTCAAGTCTC
CCTCCATGTGCAAAATACCTTTGATGGGAGTCAACCATTGCCTCAGAAAATGAATTGAGTCTGT
GGTTGATGATTCTATAGCCTGAACTAAAGCTGGTATAAGGCCGACTGGGAAGTTAAGCACAGCA
AAGTGAAGATTTGTAAGCGGCCCAAGAATCGAACCATCAGCATGAAGGGTGGCATTATCTTTCT
GGATAAATAATTTATCAAGACGCAGACCATCATTATTGCTGAATGAACCAGATGCGAGAACTCG
CTGTGTCTTGTAAGTTCCCCATTCCCAATCTTCACCATTGAAATCAAAATCTGC
						
					

						Genomic sequence
						
							CTGCAGGAGAACATCAGCATAGCCTTGAAGCCAGTTTGCATAAGGACTCAATGCAGTTATCAGC
ATCATACCCCCATCCTTTATATCTGCATCTATCCTCACTTCACCTGGTTCTAGCATGTTATAAC
TTAAACCTTTAAGTTTTTCAGCTAATTGAAATTCCCAGCCCTCCTCTGTCTTGTCTCTCACCAT
TCTTGCTTCACTGATCTCATTCGATGATCCTCTGTCTCTTGCCCAAACAGGGATTCTTATGATA
CCTTGTTTCCCATCTGCCTCTTCTGGACTTTCCTCTATCGAGCTGTTGTCTACATAAGTGACTG
GTATACTACCTTGAATGTTTACATGTCCACTTTGTATTGTCGGTTCGAAATTTGCATCAAATAC
GAAACGACTTGTAGGGGTAACAGAAGCTAATACTTCTGCTCTTCCAAGATCGATGCCTCCAATA
GTGCCATCAAGCAGCCTTATTTGAACATCACATTCTGGTTTTGCCAGAGTACCTCTCAAGTCTC
CCTCCATGTGCAAAATACCTTTGATGGGAGTCAACCATTGCCTCAGAAAATGAATTGAGTCTGT
GGTTGATGATTCTATAGCCTGAACTAAAGCTGGTATAAGGCCGACTGGGAAGTTAAGCACAGCA
AAGTGAAGATTTGTAAGCGGCCCAAGAATCGAACCATCAGCATGAAGGGTGGCATTATCTTTCT
GGATAAATAATTTATCAAGACGCAGACCATCATTATTGCTGAATGAACCAGATGCGAGAACTCG
CTGTGTCTTGTAAGTTCCCCATTCCCAATCTTCACCATTGAAATCAAAATCTGC
						
					

			
		

Sequences
Splice junction sequence	GACGCAGACCATCATTATTGCTGAATGAACCAGATGCGAGAACTCGCTGTGTCTTGTAAGTTCC CCATTCCCAATCTTCACCATTGAAATCAAAATCTGCctgcaggagaacatcagcatagccttga agccagtttgcataaggactcaatgcagttatcagcatcatacccccatcctttatatctgcat ctatcctc
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: 822 Transcript exons: 9055087-9055908 CTGCAGGAGAACATCAGCATAGCCTTGAAGCCAGTTTGCATAAGGACTCAATGCAGTTATCAGC ATCATACCCCCATCCTTTATATCTGCATCTATCCTCACTTCACCTGGTTCTAGCATGTTATAAC TTAAACCTTTAAGTTTTTCAGCTAATTGAAATTCCCAGCCCTCCTCTGTCTTGTCTCTCACCAT TCTTGCTTCACTGATCTCATTCGATGATCCTCTGTCTCTTGCCCAAACAGGGATTCTTATGATA CCTTGTTTCCCATCTGCCTCTTCTGGACTTTCCTCTATCGAGCTGTTGTCTACATAAGTGACTG GTATACTACCTTGAATGTTTACATGTCCACTTTGTATTGTCGGTTCGAAATTTGCATCAAATAC GAAACGACTTGTAGGGGTAACAGAAGCTAATACTTCTGCTCTTCCAAGATCGATGCCTCCAATA GTGCCATCAAGCAGCCTTATTTGAACATCACATTCTGGTTTTGCCAGAGTACCTCTCAAGTCTC CCTCCATGTGCAAAATACCTTTGATGGGAGTCAACCATTGCCTCAGAAAATGAATTGAGTCTGT GGTTGATGATTCTATAGCCTGAACTAAAGCTGGTATAAGGCCGACTGGGAAGTTAAGCACAGCA AAGTGAAGATTTGTAAGCGGCCCAAGAATCGAACCATCAGCATGAAGGGTGGCATTATCTTTCT GGATAAATAATTTATCAAGACGCAGACCATCATTATTGCTGAATGAACCAGATGCGAGAACTCG CTGTGTCTTGTAAGTTCCCCATTCCCAATCTTCACCATTGAAATCAAAATCTGC
Genomic sequence	CTGCAGGAGAACATCAGCATAGCCTTGAAGCCAGTTTGCATAAGGACTCAATGCAGTTATCAGC ATCATACCCCCATCCTTTATATCTGCATCTATCCTCACTTCACCTGGTTCTAGCATGTTATAAC TTAAACCTTTAAGTTTTTCAGCTAATTGAAATTCCCAGCCCTCCTCTGTCTTGTCTCTCACCAT TCTTGCTTCACTGATCTCATTCGATGATCCTCTGTCTCTTGCCCAAACAGGGATTCTTATGATA CCTTGTTTCCCATCTGCCTCTTCTGGACTTTCCTCTATCGAGCTGTTGTCTACATAAGTGACTG GTATACTACCTTGAATGTTTACATGTCCACTTTGTATTGTCGGTTCGAAATTTGCATCAAATAC GAAACGACTTGTAGGGGTAACAGAAGCTAATACTTCTGCTCTTCCAAGATCGATGCCTCCAATA GTGCCATCAAGCAGCCTTATTTGAACATCACATTCTGGTTTTGCCAGAGTACCTCTCAAGTCTC CCTCCATGTGCAAAATACCTTTGATGGGAGTCAACCATTGCCTCAGAAAATGAATTGAGTCTGT GGTTGATGATTCTATAGCCTGAACTAAAGCTGGTATAAGGCCGACTGGGAAGTTAAGCACAGCA AAGTGAAGATTTGTAAGCGGCCCAAGAATCGAACCATCAGCATGAAGGGTGGCATTATCTTTCT GGATAAATAATTTATCAAGACGCAGACCATCATTATTGCTGAATGAACCAGATGCGAGAACTCG CTGTGTCTTGTAAGTTCCCCATTCCCAATCTTCACCATTGAAATCAAAATCTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.30279474

Conservation Information
Conserved circRNAs	NA
PMCS	0.30279474

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9055607-9055089(-)
9055129-9055688(-)
						
						Potential amino acid sequence
						
							MEGDLRGTLAKPECDVQIRLLDGTIGGIDLGRAEVLASVTPTSRFVFDANFEPTIQSGHVNIQG
SIPVTYVDNSSIEESPEEADGKQGIIRIPVWARDRGSSNEISEARMVRDKTEEGWEFQLAEKLK
GLSYNMLEPGEVRIDADIKDGGMMLITALSPYANWLQGYADVLLQADFDFNGEDWEWGTYKTQR
VLASGSFSNNDGLRLDKLFIQKDNATLHADGSILGPLTNLHFAVLNFPVGLIPALVQAIESSTT
DSIHFLRQWLTPIKGILHMEGDLRGTLAKPECDVQIRLLDGTIGGIDLGRAEVLASVTPTSRFV
FDANFEPTIQSGHVNIQGSIPVTYVDNSSIEESPEEADGKQGIIRIPVWARDRGSSNEISEARM
VRDKTEEGWEFQLAEKLKGLSYNMLEPGEVRIDADIKDGGMMLITALSPYANWLQGYADVLLQA
DFDFNGEDWEWGTYKTQRVLASGSFSNNDGLRLDKLFIQKDNATLHADGSILGPLTNLHFAVLN
FPVGLIPALVQAIESSTTDSIHFLRQWLTPIKGILHMEGDLRGTLAKPECDVQIRLLDGTIGGI
DLGRAEVLASVTPTSRFVFDANFEPTIQSGHVNIQGSIPVTYVDNSSIEESPEEADGKQGIIRI
PVWARDRGSSNEISEARMVRDKTEEGWEFQLAEKLKGLSYNMLEPGEVRIDADIKDGGMMLITA
LSPYANWLQGYADVLLQADFDFNGEDWEWGTYKTQRVLASGSFSNNDGLRLDKLFIQKDNATLH
ADGSILGPLTNLHFAVLNFPVGLIPALVQAIESSTTDSIHFLRQWLTPIKGILHMEGDLRGTLA
KPECDVQIRLLDGTIGGIDLGRAEVLASVTPTSRFVFDANFEPTIQSGHVNIQGSIPVTYVDNS
SIEESPEEADGKQGIIRIPVWARDRGSSNEISEARMVRDKTEEGWEFQLAEKLKGLSYNMLEPG
EVRIDADIKDGGMMLITALSPYANWLQGYADVLLQ(-)
MQTGFKAMLMFSCRQILISMVKIGNGELTRHSEFSHLVHSAIMMVCVLINYLSRKIMPPFMLMV
RFLGRLQIFTLLCLTSQSALYQL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9055607-9055089(-) 9055129-9055688(-)
Potential amino acid sequence	MEGDLRGTLAKPECDVQIRLLDGTIGGIDLGRAEVLASVTPTSRFVFDANFEPTIQSGHVNIQG SIPVTYVDNSSIEESPEEADGKQGIIRIPVWARDRGSSNEISEARMVRDKTEEGWEFQLAEKLK GLSYNMLEPGEVRIDADIKDGGMMLITALSPYANWLQGYADVLLQADFDFNGEDWEWGTYKTQR VLASGSFSNNDGLRLDKLFIQKDNATLHADGSILGPLTNLHFAVLNFPVGLIPALVQAIESSTT DSIHFLRQWLTPIKGILHMEGDLRGTLAKPECDVQIRLLDGTIGGIDLGRAEVLASVTPTSRFV FDANFEPTIQSGHVNIQGSIPVTYVDNSSIEESPEEADGKQGIIRIPVWARDRGSSNEISEARM VRDKTEEGWEFQLAEKLKGLSYNMLEPGEVRIDADIKDGGMMLITALSPYANWLQGYADVLLQA DFDFNGEDWEWGTYKTQRVLASGSFSNNDGLRLDKLFIQKDNATLHADGSILGPLTNLHFAVLN FPVGLIPALVQAIESSTTDSIHFLRQWLTPIKGILHMEGDLRGTLAKPECDVQIRLLDGTIGGI DLGRAEVLASVTPTSRFVFDANFEPTIQSGHVNIQGSIPVTYVDNSSIEESPEEADGKQGIIRI PVWARDRGSSNEISEARMVRDKTEEGWEFQLAEKLKGLSYNMLEPGEVRIDADIKDGGMMLITA LSPYANWLQGYADVLLQADFDFNGEDWEWGTYKTQRVLASGSFSNNDGLRLDKLFIQKDNATLH ADGSILGPLTNLHFAVLNFPVGLIPALVQAIESSTTDSIHFLRQWLTPIKGILHMEGDLRGTLA KPECDVQIRLLDGTIGGIDLGRAEVLASVTPTSRFVFDANFEPTIQSGHVNIQGSIPVTYVDNS SIEESPEEADGKQGIIRIPVWARDRGSSNEISEARMVRDKTEEGWEFQLAEKLKGLSYNMLEPG EVRIDADIKDGGMMLITALSPYANWLQGYADVLLQ(-) MQTGFKAMLMFSCRQILISMVKIGNGELTRHSEFSHLVHSAIMMVCVLINYLSRKIMPPFMLMV RFLGRLQIFTLLCLTSQSALYQL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d039612_circ_g.4

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