Plant Circular RNA Database

Detail information of Zm00001d041889_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d041889_circ_g.3
					

						ID in PlantcircBase
						zma_circ_004224
					

						Alias
						ear_test_circ_002280
					

						Organism
						
							Zea mays						
					

						Position
						
							chr3: 142437097-142439838  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d041889						
					

						Parent gene annotation
						
							protein_coding
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d041889_circ_g.1 Zm00001d041889_circ_g.2 Zm00001d041889_circ_g.4 Zm00001d041889_circ_g.5 Zm00001d041889_circ_g.6 Zm00001d041889_circ_g.7 Zm00001d041889_circ_g.8 Zm00001d041889_circ_g.9 Zm00001d041889_circ_g.10 Zm00001d041889_circ_g.11 Zm00001d041889_circ_g.12 Zm00001d041889_circ_g.13 Zm00001d041889_circ_g.14 Zm00001d041889_circ_g.15 Zm00001d041889_circ_g.16 Zm00001d041889_circ_g.17 Zm00001d041889_circ_g.18 Zm00001d041889_circ_g.19 						
					

						Support reads
						NA
					

						Tissues
						ear
					

						Exon boundary  
						
							No-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-CA							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
						Zm00001d041889_T029:7
Zm00001d041889_T003:9
Zm00001d041889_T033:9
Zm00001d041889_T054:9
Zm00001d041889_T002:9
Zm00001d041889_T010:7
Zm00001d041889_T117:9
Zm00001d041889_T148:2
Zm00001d041889_T070:9
Zm00001d041889_T005:9
Zm00001d041889_T042:9
Zm00001d041889_T116:7
Zm00001d041889_T142:5
Zm00001d041889_T065:9
Zm00001d041889_T081:9
Zm00001d041889_T066:9
Zm00001d041889_T045:7
Zm00001d041889_T147:3
Zm00001d041889_T106:9
Zm00001d041889_T073:8
Zm00001d041889_T135:9
Zm00001d041889_T047:8
Zm00001d041889_T108:9
Zm00001d041889_T150:2
Zm00001d041889_T092:9
Zm00001d041889_T077:8
Zm00001d041889_T134:9
Zm00001d041889_T027:9
Zm00001d041889_T129:9
Zm00001d041889_T001:9
Zm00001d041889_T041:9
Zm00001d041889_T107:8
Zm00001d041889_T082:9
Zm00001d041889_T075:7
Zm00001d041889_T036:9
Zm00001d041889_T025:9
Zm00001d041889_T139:7
Zm00001d041889_T149:2
Zm00001d041889_T086:8
Zm00001d041889_T097:9
Zm00001d041889_T089:9
Zm00001d041889_T151:1
Zm00001d041889_T090:8
Zm00001d041889_T094:9
Zm00001d041889_T096:9
Zm00001d041889_T021:8
Zm00001d041889_T138:7
Zm00001d041889_T087:9
Zm00001d041889_T113:9
Zm00001d041889_T099:7
Zm00001d041889_T079:9
Zm00001d041889_T145:6
Zm00001d041889_T101:7
Zm00001d041889_T144:5
Zm00001d041889_T016:9
Zm00001d041889_T085:7
Zm00001d041889_T057:8
Zm00001d041889_T031:7
Zm00001d041889_T131:9
Zm00001d041889_T140:4
Zm00001d041889_T034:7
Zm00001d041889_T068:8
Zm00001d041889_T083:9
Zm00001d041889_T019:10
Zm00001d041889_T141:6
Zm00001d041889_T018:9
Zm00001d041889_T064:9
Zm00001d041889_T022:9
Zm00001d041889_T143:5
Zm00001d041889_T007:9
Zm00001d041889_T048:9
Zm00001d041889_T051:9
Zm00001d041889_T062:9
Zm00001d041889_T103:9
Zm00001d041889_T136:7
Zm00001d041889_T059:9
Zm00001d041889_T035:9
Zm00001d041889_T014:9
Zm00001d041889_T049:8
Zm00001d041889_T012:9
Zm00001d041889_T132:8
Zm00001d041889_T115:8
Zm00001d041889_T039:7
Zm00001d041889_T137:7
Zm00001d041889_T102:6
Zm00001d041889_T146:3
Zm00001d041889_T061:9
Zm00001d041889_T114:8
Zm00001d041889_T152:1

					

			
		

General Information
CircRNA Name	Zm00001d041889_circ_g.3
ID in PlantcircBase	zma_circ_004224
Alias	ear_test_circ_002280
Organism	Zea mays
Position	chr3: 142437097-142439838 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d041889
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d041889_circ_g.1 Zm00001d041889_circ_g.2 Zm00001d041889_circ_g.4 Zm00001d041889_circ_g.5 Zm00001d041889_circ_g.6 Zm00001d041889_circ_g.7 Zm00001d041889_circ_g.8 Zm00001d041889_circ_g.9 Zm00001d041889_circ_g.10 Zm00001d041889_circ_g.11 Zm00001d041889_circ_g.12 Zm00001d041889_circ_g.13 Zm00001d041889_circ_g.14 Zm00001d041889_circ_g.15 Zm00001d041889_circ_g.16 Zm00001d041889_circ_g.17 Zm00001d041889_circ_g.18 Zm00001d041889_circ_g.19
Support reads	NA
Tissues	ear
Exon boundary	No-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-CA 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	Zm00001d041889_T029:7 Zm00001d041889_T003:9 Zm00001d041889_T033:9 Zm00001d041889_T054:9 Zm00001d041889_T002:9 Zm00001d041889_T010:7 Zm00001d041889_T117:9 Zm00001d041889_T148:2 Zm00001d041889_T070:9 Zm00001d041889_T005:9 Zm00001d041889_T042:9 Zm00001d041889_T116:7 Zm00001d041889_T142:5 Zm00001d041889_T065:9 Zm00001d041889_T081:9 Zm00001d041889_T066:9 Zm00001d041889_T045:7 Zm00001d041889_T147:3 Zm00001d041889_T106:9 Zm00001d041889_T073:8 Zm00001d041889_T135:9 Zm00001d041889_T047:8 Zm00001d041889_T108:9 Zm00001d041889_T150:2 Zm00001d041889_T092:9 Zm00001d041889_T077:8 Zm00001d041889_T134:9 Zm00001d041889_T027:9 Zm00001d041889_T129:9 Zm00001d041889_T001:9 Zm00001d041889_T041:9 Zm00001d041889_T107:8 Zm00001d041889_T082:9 Zm00001d041889_T075:7 Zm00001d041889_T036:9 Zm00001d041889_T025:9 Zm00001d041889_T139:7 Zm00001d041889_T149:2 Zm00001d041889_T086:8 Zm00001d041889_T097:9 Zm00001d041889_T089:9 Zm00001d041889_T151:1 Zm00001d041889_T090:8 Zm00001d041889_T094:9 Zm00001d041889_T096:9 Zm00001d041889_T021:8 Zm00001d041889_T138:7 Zm00001d041889_T087:9 Zm00001d041889_T113:9 Zm00001d041889_T099:7 Zm00001d041889_T079:9 Zm00001d041889_T145:6 Zm00001d041889_T101:7 Zm00001d041889_T144:5 Zm00001d041889_T016:9 Zm00001d041889_T085:7 Zm00001d041889_T057:8 Zm00001d041889_T031:7 Zm00001d041889_T131:9 Zm00001d041889_T140:4 Zm00001d041889_T034:7 Zm00001d041889_T068:8 Zm00001d041889_T083:9 Zm00001d041889_T019:10 Zm00001d041889_T141:6 Zm00001d041889_T018:9 Zm00001d041889_T064:9 Zm00001d041889_T022:9 Zm00001d041889_T143:5 Zm00001d041889_T007:9 Zm00001d041889_T048:9 Zm00001d041889_T051:9 Zm00001d041889_T062:9 Zm00001d041889_T103:9 Zm00001d041889_T136:7 Zm00001d041889_T059:9 Zm00001d041889_T035:9 Zm00001d041889_T014:9 Zm00001d041889_T049:8 Zm00001d041889_T012:9 Zm00001d041889_T132:8 Zm00001d041889_T115:8 Zm00001d041889_T039:7 Zm00001d041889_T137:7 Zm00001d041889_T102:6 Zm00001d041889_T146:3 Zm00001d041889_T061:9 Zm00001d041889_T114:8 Zm00001d041889_T152:1

			
						 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  
						
							GAATCTGCAGGAAAACCCCTAACTGTCATCTTTTCTAACGATCTCCACACCAAACATCTGCAAC
ATGATTGTGATGTGCTAATTAAGGAGACTGGTGAAGgaagttttagctcaggagaattgtaatg
accagcctgttcctgcccagactgaccaagaaattaagttaaacgatgaacttgctgatccggg
tatggact

									
								

					

						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
						
							GAAGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAGACTGACCAAGAAATTA
AGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATTTACCAATTTTAAACATAC
TGAGTTCTAAGTCAAGTTGTTGGTTACTTTCATTCTAATTATTTTTAATAGGCTTTATGTTTGT
TCTATCTGCAACAGCTAGGCACATGTTTCATTGTCATTTATTGTCTTTTAAGTATCTGACATTT
ATTTTTTAAATGTATTCTTTCCCTTTATCAGATGTTTTAGCTCAGGAGAATTGTAATGACCAGC
CCGTTCCTGCCCAGACTGACCTAGAAATTAAGTTACACGATGAACTTGCTGATCCGGGTATGTA
CTGTGTTTAATTTACCAATTTTCAACATACTGAGTTCTAAGTCAAATTATTGGCTACGTGTAAT
TCTAATTATTAGATTTGTGCATTATTGTCATGTTATATACTGAAAGGAAGACTTTGTCGTTCCA
AAATCACCAAATGGTTTATCAATTAGTTTCACTGTTGCAGACCATGAAGAGCAAAGCCCTGTAT
CCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCCTGAGGAAAAGAACCTAGCTAA
CGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGCATGATAATGGCAGAATAGCTGAAGAG
ACTGATAAAGGTACAACTGAATTAATCCTGTATCCCCAATAAAAGCTCTGCAACATTGATGAGT
GAAGATAATATGTATGCTGAACATCTAAATCCACCTGTGCCAGCTCTCATTCACTGTTTTTTTC
TAAAGATCTTGCTTCAAGATTTTCAATTCACTAAATTAAACTTGCTAAATCTCCAGATGTTTTG
TCTTTTGTTTTCCCTATTGAAGAGCATGAAGAAAAATATGCAGTTAGCCCTATAGCCGTTGAAA
AGAGCTTCCGTCAGGAAGCAAGTGCAATTGAATCTGCAGGAAAACCCCTAACTGTCATCTTTTC
TAACGATCTCCACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGACTGGTGAA
GGTAATATTGCATTAATACTTGTTCCACAACTTGTTACTGATCTGCGGAGATGGTGATGAAAAC
TTGTGCTGTTTGCACTGTGTTGACATTTTTTAAATGTATTCTTTCCCTTTCTCAGAAGTTTTAG
CTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAGACCGACCTAGAAATTAAGTTAAATGA
TGAACTTGCTGATCCGGGTATGGACCGTGTTTAATTTACCAATTTTAAACATACCGAGTTCTAA
GTCAAGTTGTTGGCTACTTGTAATTCTAATTGTTTTTAATAGGCTTTATATTTATTCTATCTGC
AAAAGCTAGGCATATGTTTCATTGTCATTTGATGTCTTTTAAGTATCTGACATTTATTTTTTAA
ATGTATTCTTTCCCTTTATCAGATGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTG
CCAACGAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCT
GCAGCATGATAATGACAGAATAGCTGAAGAGACTGATAAAGGTACAACCGAATTAATCCTGCCC
AGACTGACCTAGAAATTAAGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATT
TACCAATTTTAAACATACTGCAGAGTTTTGGTTTATCAATTAGTTTCACTGTTGCAGACCATGA
AGAGCAAAGCAATGTGTTCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCCTGAG
GAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCATGATAATG
ACAGAATAGCTGAAGAGACTGATAAAGGTACAACCGAATTAATCCTGCCCAGACTGACCTAGAA
ATTAAGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATTTACCAATTTTAAAC
ATACTGAGTTCTAAGTCAAATTGTTGGCTACGTGTAATTCTAATCATTAGCTTTGTCCATTATT
GTCATGTTATATACTGAAAGGAAGACTTTGTCGTTCCAAAATCACCAAATGGTTTATCAATTAG
TTTCACTGTTGCAGACCATGAAGAGCAAAGCAATGTGTCCGGAGAACGGAGAGTTAGCTTGGAA
GCAAATGCCAACGAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCA
AAACTCTGCAGCATGATAATGACAGAATAGCTGAAGAGACTGATAAAGGTACAACCGAATTAAT
CCTGTATCCATAATAAAAACTCCGCAACATTGATGAGTGAAGATAATATGTATGCTGAACATCT
AAATCCACCTGTGCCAACTGATTATTCACTATTTTTTTTCTAAAGATCTTGCTTAGTAATCTTG
CTTCAAGATTTTCAATTCACTAAATTAAACTTGCTAAATCTCCAGATGTTTCGTCTTTGGTTTT
CCCTATTGAAGAGCATGAAGAAAAATATGCAGTGAGCCCTATAGCTGTTGAAAAGAGCGTCAGT
CGGGAAGCCAGTGCATGTGAATCTGCAGGAAAACCCCTAACTGTCATCTTTTCTAACGATCTCC
ACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGACTGGTGAAG
						
					

			
		

Sequences
Splice junction sequence	GAATCTGCAGGAAAACCCCTAACTGTCATCTTTTCTAACGATCTCCACACCAAACATCTGCAAC ATGATTGTGATGTGCTAATTAAGGAGACTGGTGAAGgaagttttagctcaggagaattgtaatg accagcctgttcctgcccagactgaccaagaaattaagttaaacgatgaacttgctgatccggg tatggact
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	GAAGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAGACTGACCAAGAAATTA AGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATTTACCAATTTTAAACATAC TGAGTTCTAAGTCAAGTTGTTGGTTACTTTCATTCTAATTATTTTTAATAGGCTTTATGTTTGT TCTATCTGCAACAGCTAGGCACATGTTTCATTGTCATTTATTGTCTTTTAAGTATCTGACATTT ATTTTTTAAATGTATTCTTTCCCTTTATCAGATGTTTTAGCTCAGGAGAATTGTAATGACCAGC CCGTTCCTGCCCAGACTGACCTAGAAATTAAGTTACACGATGAACTTGCTGATCCGGGTATGTA CTGTGTTTAATTTACCAATTTTCAACATACTGAGTTCTAAGTCAAATTATTGGCTACGTGTAAT TCTAATTATTAGATTTGTGCATTATTGTCATGTTATATACTGAAAGGAAGACTTTGTCGTTCCA AAATCACCAAATGGTTTATCAATTAGTTTCACTGTTGCAGACCATGAAGAGCAAAGCCCTGTAT CCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCCTGAGGAAAAGAACCTAGCTAA CGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGCATGATAATGGCAGAATAGCTGAAGAG ACTGATAAAGGTACAACTGAATTAATCCTGTATCCCCAATAAAAGCTCTGCAACATTGATGAGT GAAGATAATATGTATGCTGAACATCTAAATCCACCTGTGCCAGCTCTCATTCACTGTTTTTTTC TAAAGATCTTGCTTCAAGATTTTCAATTCACTAAATTAAACTTGCTAAATCTCCAGATGTTTTG TCTTTTGTTTTCCCTATTGAAGAGCATGAAGAAAAATATGCAGTTAGCCCTATAGCCGTTGAAA AGAGCTTCCGTCAGGAAGCAAGTGCAATTGAATCTGCAGGAAAACCCCTAACTGTCATCTTTTC TAACGATCTCCACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGACTGGTGAA GGTAATATTGCATTAATACTTGTTCCACAACTTGTTACTGATCTGCGGAGATGGTGATGAAAAC TTGTGCTGTTTGCACTGTGTTGACATTTTTTAAATGTATTCTTTCCCTTTCTCAGAAGTTTTAG CTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAGACCGACCTAGAAATTAAGTTAAATGA TGAACTTGCTGATCCGGGTATGGACCGTGTTTAATTTACCAATTTTAAACATACCGAGTTCTAA GTCAAGTTGTTGGCTACTTGTAATTCTAATTGTTTTTAATAGGCTTTATATTTATTCTATCTGC AAAAGCTAGGCATATGTTTCATTGTCATTTGATGTCTTTTAAGTATCTGACATTTATTTTTTAA ATGTATTCTTTCCCTTTATCAGATGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTG CCAACGAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCT GCAGCATGATAATGACAGAATAGCTGAAGAGACTGATAAAGGTACAACCGAATTAATCCTGCCC AGACTGACCTAGAAATTAAGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATT TACCAATTTTAAACATACTGCAGAGTTTTGGTTTATCAATTAGTTTCACTGTTGCAGACCATGA AGAGCAAAGCAATGTGTTCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCCTGAG GAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCATGATAATG ACAGAATAGCTGAAGAGACTGATAAAGGTACAACCGAATTAATCCTGCCCAGACTGACCTAGAA ATTAAGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATTTACCAATTTTAAAC ATACTGAGTTCTAAGTCAAATTGTTGGCTACGTGTAATTCTAATCATTAGCTTTGTCCATTATT GTCATGTTATATACTGAAAGGAAGACTTTGTCGTTCCAAAATCACCAAATGGTTTATCAATTAG TTTCACTGTTGCAGACCATGAAGAGCAAAGCAATGTGTCCGGAGAACGGAGAGTTAGCTTGGAA GCAAATGCCAACGAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCA AAACTCTGCAGCATGATAATGACAGAATAGCTGAAGAGACTGATAAAGGTACAACCGAATTAAT CCTGTATCCATAATAAAAACTCCGCAACATTGATGAGTGAAGATAATATGTATGCTGAACATCT AAATCCACCTGTGCCAACTGATTATTCACTATTTTTTTTCTAAAGATCTTGCTTAGTAATCTTG CTTCAAGATTTTCAATTCACTAAATTAAACTTGCTAAATCTCCAGATGTTTCGTCTTTGGTTTT CCCTATTGAAGAGCATGAAGAAAAATATGCAGTGAGCCCTATAGCTGTTGAAAAGAGCGTCAGT CGGGAAGCCAGTGCATGTGAATCTGCAGGAAAACCCCTAACTGTCATCTTTTCTAACGATCTCC ACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGACTGGTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.130407939

Conservation Information
Conserved circRNAs	NA
PMCS	0.130407939

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tang et al., 2018

circRNA

Detail information of Zm00001d041889_circ_g.3

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