Plant Circular RNA Database

Detail information of Zm00001d041889_circ_g.1

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d041889_circ_g.1
					

						ID in PlantcircBase
						zma_circ_007657
					

						Alias
						Zm03circ00050
					

						Organism
						
							Zea mays						
					

						Position
						
							chr3: 142436633-142437810  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI2
					

						Parent gene
						
							Zm00001d041889						
					

						Parent gene annotation
						
							protein_coding
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d041889_circ_g.2 Zm00001d041889_circ_g.3 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
						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  
						
							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
						Zm00001d041889_T106:4
Zm00001d041889_T057:4
Zm00001d041889_T094:4
Zm00001d041889_T018:4
Zm00001d041889_T086:4
Zm00001d041889_T005:3
Zm00001d041889_T036:4
Zm00001d041889_T048:4
Zm00001d041889_T089:4
Zm00001d041889_T141:1
Zm00001d041889_T034:3
Zm00001d041889_T113:4
Zm00001d041889_T049:4
Zm00001d041889_T059:4
Zm00001d041889_T114:4
Zm00001d041889_T087:4
Zm00001d041889_T033:4
Zm00001d041889_T002:4
Zm00001d041889_T039:4
Zm00001d041889_T003:3
Zm00001d041889_T075:4
Zm00001d041889_T140:1
Zm00001d041889_T019:4
Zm00001d041889_T081:4
Zm00001d041889_T061:4
Zm00001d041889_T108:3
Zm00001d041889_T001:3
Zm00001d041889_T047:4
Zm00001d041889_T012:4
Zm00001d041889_T014:4
Zm00001d041889_T137:1
Zm00001d041889_T101:4
Zm00001d041889_T136:1
Zm00001d041889_T096:4
Zm00001d041889_T102:4
Zm00001d041889_T099:4
Zm00001d041889_T083:4
Zm00001d041889_T016:4
Zm00001d041889_T103:4
Zm00001d041889_T022:3
Zm00001d041889_T042:4
Zm00001d041889_T021:3
Zm00001d041889_T035:4
Zm00001d041889_T070:3
Zm00001d041889_T135:3
Zm00001d041889_T132:3
Zm00001d041889_T097:4
Zm00001d041889_T077:4
Zm00001d041889_T066:4
Zm00001d041889_T051:3
Zm00001d041889_T092:4
Zm00001d041889_T031:3
Zm00001d041889_T079:4
Zm00001d041889_T117:4
Zm00001d041889_T134:4
Zm00001d041889_T073:4
Zm00001d041889_T045:3
Zm00001d041889_T029:4
Zm00001d041889_T131:4
Zm00001d041889_T139:1
Zm00001d041889_T062:3
Zm00001d041889_T054:4
Zm00001d041889_T027:4
Zm00001d041889_T068:4
Zm00001d041889_T107:4
Zm00001d041889_T090:3
Zm00001d041889_T025:4
Zm00001d041889_T138:1
Zm00001d041889_T085:4
Zm00001d041889_T065:3
Zm00001d041889_T082:5
Zm00001d041889_T116:4
Zm00001d041889_T064:4
Zm00001d041889_T007:4
Zm00001d041889_T041:4
Zm00001d041889_T115:4
Zm00001d041889_T142:1
Zm00001d041889_T010:3
Zm00001d041889_T129:4

					

			
		

General Information
CircRNA Name	Zm00001d041889_circ_g.1
ID in PlantcircBase	zma_circ_007657
Alias	Zm03circ00050
Organism	Zea mays
Position	chr3: 142436633-142437810 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d041889
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d041889_circ_g.2 Zm00001d041889_circ_g.3 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	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	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	Zm00001d041889_T106:4 Zm00001d041889_T057:4 Zm00001d041889_T094:4 Zm00001d041889_T018:4 Zm00001d041889_T086:4 Zm00001d041889_T005:3 Zm00001d041889_T036:4 Zm00001d041889_T048:4 Zm00001d041889_T089:4 Zm00001d041889_T141:1 Zm00001d041889_T034:3 Zm00001d041889_T113:4 Zm00001d041889_T049:4 Zm00001d041889_T059:4 Zm00001d041889_T114:4 Zm00001d041889_T087:4 Zm00001d041889_T033:4 Zm00001d041889_T002:4 Zm00001d041889_T039:4 Zm00001d041889_T003:3 Zm00001d041889_T075:4 Zm00001d041889_T140:1 Zm00001d041889_T019:4 Zm00001d041889_T081:4 Zm00001d041889_T061:4 Zm00001d041889_T108:3 Zm00001d041889_T001:3 Zm00001d041889_T047:4 Zm00001d041889_T012:4 Zm00001d041889_T014:4 Zm00001d041889_T137:1 Zm00001d041889_T101:4 Zm00001d041889_T136:1 Zm00001d041889_T096:4 Zm00001d041889_T102:4 Zm00001d041889_T099:4 Zm00001d041889_T083:4 Zm00001d041889_T016:4 Zm00001d041889_T103:4 Zm00001d041889_T022:3 Zm00001d041889_T042:4 Zm00001d041889_T021:3 Zm00001d041889_T035:4 Zm00001d041889_T070:3 Zm00001d041889_T135:3 Zm00001d041889_T132:3 Zm00001d041889_T097:4 Zm00001d041889_T077:4 Zm00001d041889_T066:4 Zm00001d041889_T051:3 Zm00001d041889_T092:4 Zm00001d041889_T031:3 Zm00001d041889_T079:4 Zm00001d041889_T117:4 Zm00001d041889_T134:4 Zm00001d041889_T073:4 Zm00001d041889_T045:3 Zm00001d041889_T029:4 Zm00001d041889_T131:4 Zm00001d041889_T139:1 Zm00001d041889_T062:3 Zm00001d041889_T054:4 Zm00001d041889_T027:4 Zm00001d041889_T068:4 Zm00001d041889_T107:4 Zm00001d041889_T090:3 Zm00001d041889_T025:4 Zm00001d041889_T138:1 Zm00001d041889_T085:4 Zm00001d041889_T065:3 Zm00001d041889_T082:5 Zm00001d041889_T116:4 Zm00001d041889_T064:4 Zm00001d041889_T007:4 Zm00001d041889_T041:4 Zm00001d041889_T115:4 Zm00001d041889_T142:1 Zm00001d041889_T010:3 Zm00001d041889_T129:4

			
						 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  
						
							GAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGC
ATGATAATGGCAGAATAGCTGAAGAGACTGATAAAGatgttttgtctttggttttccctattga
agagcatgaagaaaaatatggagtgagccctatagctgttgaaaagtgcgtctgtcgtgaagca
agtgcatg

									
								

					

						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: 543
Transcript exons: 142436633-142436833,142437098-142437187,142437384-142437
473,142437649-142437810
ATGTTTTGTCTTTGGTTTTCCCTATTGAAGAGCATGAAGAAAAATATGGAGTGAGCCCTATAGC
TGTTGAAAAGTGCGTCTGTCGTGAAGCAAGTGCATGTGAATCTGCACGAAAACCCCTAACCGTT
ATCTTTTCTAACAATCTCCACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGA
CTGGTGAAGAAGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAGACTGACCA
AGAAATTAAGTTAAACGATGAACTTGCTGATCCGGATGTTTTAGCTCAGGAGAATTGTAATGAC
CAGCCCGTTCCTGCCCAGACTGACCTAGAAATTAAGTTACACGATGAACTTGCTGATCCGGACC
ATGAAGAGCAAAGCCCTGTATCCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCC
TGAGGAAAAGAACCTAGCTAACGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGCATGAT
AATGGCAGAATAGCTGAAGAGACTGATAAAG
						
					

						Genomic sequence
						
							ATGTTTTGTCTTTGGTTTTCCCTATTGAAGAGCATGAAGAAAAATATGGAGTGAGCCCTATAGC
TGTTGAAAAGTGCGTCTGTCGTGAAGCAAGTGCATGTGAATCTGCACGAAAACCCCTAACCGTT
ATCTTTTCTAACAATCTCCACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGA
CTGGTGAAGGTAATATTGCATTAATACTTGTTCCACAACTTGTTACTGATCTGTGGAGATGGTG
ATGAAAACTTGTGCTGTTTGCACTGTGTTTAATTTACCAATTTTAAACATACTGAGTTCTAAGT
CAAGTTGTTGGCTACTTGTAATTCTAATTATTTTTAATAGGCTTTATGTTTGTTCTATCTGGAA
CAGCTAGGCATATGTTTCATTGTCATTTGTTGTCTTTTAAGTATCTTACATTTTTTTGAATGTA
TTCTTTCCCTTTCTCAGAAGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAG
ACTGACCAAGAAATTAAGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATTTA
CCAATTTTAAACATACTGAGTTCTAAGTCAAGTTGTTGGTTACTTTCATTCTAATTATTTTTAA
TAGGCTTTATGTTTGTTCTATCTGCAACAGCTAGGCACATGTTTCATTGTCATTTATTGTCTTT
TAAGTATCTGACATTTATTTTTTAAATGTATTCTTTCCCTTTATCAGATGTTTTAGCTCAGGAG
AATTGTAATGACCAGCCCGTTCCTGCCCAGACTGACCTAGAAATTAAGTTACACGATGAACTTG
CTGATCCGGGTATGTACTGTGTTTAATTTACCAATTTTCAACATACTGAGTTCTAAGTCAAATT
ATTGGCTACGTGTAATTCTAATTATTAGATTTGTGCATTATTGTCATGTTATATACTGAAAGGA
AGACTTTGTCGTTCCAAAATCACCAAATGGTTTATCAATTAGTTTCACTGTTGCAGACCATGAA
GAGCAAAGCCCTGTATCCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCCTGAGG
AAAAGAACCTAGCTAACGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGCATGATAATGG
CAGAATAGCTGAAGAGACTGATAAAG
						
					

			
		

Sequences
Splice junction sequence	GAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGC ATGATAATGGCAGAATAGCTGAAGAGACTGATAAAGatgttttgtctttggttttccctattga agagcatgaagaaaaatatggagtgagccctatagctgttgaaaagtgcgtctgtcgtgaagca agtgcatg
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: 543 Transcript exons: 142436633-142436833,142437098-142437187,142437384-142437 473,142437649-142437810 ATGTTTTGTCTTTGGTTTTCCCTATTGAAGAGCATGAAGAAAAATATGGAGTGAGCCCTATAGC TGTTGAAAAGTGCGTCTGTCGTGAAGCAAGTGCATGTGAATCTGCACGAAAACCCCTAACCGTT ATCTTTTCTAACAATCTCCACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGA CTGGTGAAGAAGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAGACTGACCA AGAAATTAAGTTAAACGATGAACTTGCTGATCCGGATGTTTTAGCTCAGGAGAATTGTAATGAC CAGCCCGTTCCTGCCCAGACTGACCTAGAAATTAAGTTACACGATGAACTTGCTGATCCGGACC ATGAAGAGCAAAGCCCTGTATCCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCC TGAGGAAAAGAACCTAGCTAACGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGCATGAT AATGGCAGAATAGCTGAAGAGACTGATAAAG
Genomic sequence	ATGTTTTGTCTTTGGTTTTCCCTATTGAAGAGCATGAAGAAAAATATGGAGTGAGCCCTATAGC TGTTGAAAAGTGCGTCTGTCGTGAAGCAAGTGCATGTGAATCTGCACGAAAACCCCTAACCGTT ATCTTTTCTAACAATCTCCACACCAAACATCTGCAACATGATTGTGATGTGCTAATTAAGGAGA CTGGTGAAGGTAATATTGCATTAATACTTGTTCCACAACTTGTTACTGATCTGTGGAGATGGTG ATGAAAACTTGTGCTGTTTGCACTGTGTTTAATTTACCAATTTTAAACATACTGAGTTCTAAGT CAAGTTGTTGGCTACTTGTAATTCTAATTATTTTTAATAGGCTTTATGTTTGTTCTATCTGGAA CAGCTAGGCATATGTTTCATTGTCATTTGTTGTCTTTTAAGTATCTTACATTTTTTTGAATGTA TTCTTTCCCTTTCTCAGAAGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCCAG ACTGACCAAGAAATTAAGTTAAACGATGAACTTGCTGATCCGGGTATGGACTGTGTTTAATTTA CCAATTTTAAACATACTGAGTTCTAAGTCAAGTTGTTGGTTACTTTCATTCTAATTATTTTTAA TAGGCTTTATGTTTGTTCTATCTGCAACAGCTAGGCACATGTTTCATTGTCATTTATTGTCTTT TAAGTATCTGACATTTATTTTTTAAATGTATTCTTTCCCTTTATCAGATGTTTTAGCTCAGGAG AATTGTAATGACCAGCCCGTTCCTGCCCAGACTGACCTAGAAATTAAGTTACACGATGAACTTG CTGATCCGGGTATGTACTGTGTTTAATTTACCAATTTTCAACATACTGAGTTCTAAGTCAAATT ATTGGCTACGTGTAATTCTAATTATTAGATTTGTGCATTATTGTCATGTTATATACTGAAAGGA AGACTTTGTCGTTCCAAAATCACCAAATGGTTTATCAATTAGTTTCACTGTTGCAGACCATGAA GAGCAAAGCCCTGTATCCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACGAGCCTGAGG AAAAGAACCTAGCTAACGTCATATCAATTGATCTCCACACCAAAAGTCTGCAGCATGATAATGG CAGAATAGCTGAAGAGACTGATAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.428506143

Conservation Information
Conserved circRNAs	NA
PMCS	0.428506143

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							142436669-142437746(-)
						
						Potential amino acid sequence
						
							MLFNRENQRQNIFISLFSYSAIIMLQTFGVEIN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	142436669-142437746(-)
Potential amino acid sequence	MLFNRENQRQNIFISLFSYSAIIMLQTFGVEIN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d041889_circ_g.1

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