Plant Circular RNA Database

Detail information of Zm00001d006428_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d006428_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007362
					
						Alias
						Zm02circ00101, zma_circ_0000870, ZmciR108
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 207719184-207720944  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d006428						
					
						Parent gene annotation
						
							Protein CHROMATIN REMODELING 4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d006428_T029:2
Zm00001d006428_T021:2
Zm00001d006428_T018:1
Zm00001d006428_T004:3
Zm00001d006428_T005:2
Zm00001d006428_T010:2
Zm00001d006428_T001:2
Zm00001d006428_T002:2
Zm00001d006428_T026:2
Zm00001d006428_T023:2
Zm00001d006428_T015:2
Zm00001d006428_T024:2
Zm00001d006428_T003:2
Zm00001d006428_T008:2
Zm00001d006428_T012:2
Zm00001d006428_T032:2
Zm00001d006428_T028:2
Zm00001d006428_T033:2

General Information
CircRNA Name	Zm00001d006428_circ_g.3
ID in PlantcircBase	zma_circ_007362
Alias	Zm02circ00101, zma_circ_0000870, ZmciR108
Organism	Zea mays
Position	chr2: 207719184-207720944 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d006428
Parent gene annotation	Protein CHROMATIN REMODELING 4
Parent gene strand	+
Alternative splicing	NA
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	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	Zm00001d006428_T029:2 Zm00001d006428_T021:2 Zm00001d006428_T018:1 Zm00001d006428_T004:3 Zm00001d006428_T005:2 Zm00001d006428_T010:2 Zm00001d006428_T001:2 Zm00001d006428_T002:2 Zm00001d006428_T026:2 Zm00001d006428_T023:2 Zm00001d006428_T015:2 Zm00001d006428_T024:2 Zm00001d006428_T003:2 Zm00001d006428_T008:2 Zm00001d006428_T012:2 Zm00001d006428_T032:2 Zm00001d006428_T028:2 Zm00001d006428_T033:2

			
						 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  
						
							AATAGAGGAGGAGGCATCTCTTGGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAG
ACATTTGCAACACTTCCTAATGAAGCATTAAGTGAGtcaatagactggaatgatgagctgaatg
accaccctggtaccaatgaggatattgcacctattgataatgatgggagtgagttggcatctga
atcaaagc

									
								

					

						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: 1761
Transcript exons: 207719184-207720944
TCAATAGACTGGAATGATGAGCTGAATGACCACCCTGGTACCAATGAGGATATTGCACCTATTG
ATAATGATGGGAGTGAGTTGGCATCTGAATCAAAGCAAGGTGCTACTAATCGTTTAGAAGAAAA
TGAATGGGATAAACTTTTACGTGTCAGATGGGAGCAATATCAAATAGAGGAGGAGGCATCTCTT
GGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAGACATTTGCAACACTTCCTAATG
AAGCATTAAGTGAG
Transcript length: 270
Transcript exons: 207719184-207719338,207720830-207720944
TCAATAGACTGGAATGATGAGCTGAATGACCACCCTGGTACCAATGAGGATATTGCACCTATTG
ATAATGATGGGAGTGAGTTGGCATCTGAATCAAAGCAAGGTGCTACTAATCGTTTAGAAGAAAA
TGAATGGGATAAACTTTTACGTGTCAGATGGGAGCAATATCAAATAGAGGAGGAGGCATCTCTT
GGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAGACATTTGCAACACTTCCTAATG
AAGCATTAAGTGAG
						
					

						Genomic sequence
						
							TCAATAGACTGGAATGATGAGCTGAATGACCACCCTGGTACCAATGAGGATATTGCACCTATTG
ATAATGATGGGAGTGAGTTGGCATCTGAATCAAAGCAAGGTGCTACTAATCGTTTAGAAGAAAA
TGAATGGGATAAACTTTTACGTGTCAGGTACTCTGCAATACTGTATAAACTTGTATCTTTTTGT
TTAACAATCCCATCATTTTGAGGGTTAAGTAGGTGCAATGTGATGGTCCTAATGATGTACTTAA
AAAACTTCTTTTATTTTTAAAAATTATAATTGCCACAAAGGAAAACAAGTGGAAGAATGAATAC
TATAACACTAGCATGTATTTTTGTTCTCGAAAGGCGCAGGAGAACTGCACCCCCTTATAATAAG
AAGATAAAAAGAAAGGTCCAAAACATAGACCAGAATACAGAGACTTCCCTTACGGAGGTCGAAA
ACACAGGAAAAACAGGAGATCCATCCAAAAAGAAACTAGAAAAAACACCAGAAACTATGCAGCC
GAGGGAAGGGCAGTAAGGTATGAAAAACTTTTAGCCCCAGCCATCTCCCACATCAATCTCTCTT
CACCCGCCATCTTGAGAGCTAGAGAAACATTAGGAGACCAGCCGTCGAAGATACACTTATTCCG
GTGATTCCAGATTATCCAAGCTCCCAAAACAACAAGGGAATTGAAACCATTCTTGGCTTGACCA
ATAACTGAATCTGAGGCACTTTCCCACCAGTTCATAAAGGAGGAAGAACTAGGCTGCGGTGATA
TATTCTGCAGACCGTAAGGTTGCAAAAGCTGAACCAAAACACCCTTGAGAAAACACAAGAAACT
AGAAGGTGATCCAATGTTTCAGCTTCTTGATCACAGAGGGGGCAGCTGGCTGGATGATCCAAAC
CTCTTTTAGCAAGTATGTTAGCCGTCCAACATCTCTCATGACTCATGAGCAGCGAGCCAGATAA
AAAAACCTGCATTTCGGAGGAGCCCATGTTTTCCACACCCTAGTGTAGGGGCCAAAATGCCAAA
TAAAGTTGAGCCTGCAAAGAAGCCCTCATAAGCAGCCTTTGCCGAGTAGCAACCATCTGATGCA
AGGCTGAAAATGTGTTTATCATCTTGATCCGGCCGAAGCTCAACATTTGAAAGTAGATCCCACA
GCTGAATATAATCCACTAAAACTCCAACCGAGAGAGCTCCCTTAAATGTCTTTGATCCATTTTC
TATTTAATAAAACCTCCTGGACAGTCCTTTATACTTTAAATTGTGGTTTATAATCACTCATTTA
AATTGTGGTTTATCAACTTTTATGCTTTATGCCATCATAATGGAGCCAAGTTTGTGTTATTTCT
TCTCCTGCGCTTTCGAAAAAAAAGTTTGTGTTATTTCTTATTAGGGAAAAAATGTACGTGCATG
CACTATCCTTGATTTGTACGGTGGATGCAGTTGTGCTGAATTGACATAATCTGTTGCCCCTCAT
GTGCGTCAAAATCTCATTTGAACCTAGGAATTTACAGTGAGAATCTATCTACTTAAGCATAGTT
TGGTGAGAAGCAAAGACCTGGGTTCTTCTATATTGCGATAATTGACCTGCTTGCTTTGTGTAGT
CGTTTTATCTCTTTGGACCTTGAGGAATAATAATAATGTTATCCAGATGGGAGCAATATCAAAT
AGAGGAGGAGGCATCTCTTGGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAGACA
TTTGCAACACTTCCTAATGAAGCATTAAGTGAG
						
					

			
		

Sequences
Splice junction sequence	AATAGAGGAGGAGGCATCTCTTGGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAG ACATTTGCAACACTTCCTAATGAAGCATTAAGTGAGtcaatagactggaatgatgagctgaatg accaccctggtaccaatgaggatattgcacctattgataatgatgggagtgagttggcatctga atcaaagc
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: 1761 Transcript exons: 207719184-207720944 TCAATAGACTGGAATGATGAGCTGAATGACCACCCTGGTACCAATGAGGATATTGCACCTATTG ATAATGATGGGAGTGAGTTGGCATCTGAATCAAAGCAAGGTGCTACTAATCGTTTAGAAGAAAA TGAATGGGATAAACTTTTACGTGTCAGATGGGAGCAATATCAAATAGAGGAGGAGGCATCTCTT GGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAGACATTTGCAACACTTCCTAATG AAGCATTAAGTGAG Transcript length: 270 Transcript exons: 207719184-207719338,207720830-207720944 TCAATAGACTGGAATGATGAGCTGAATGACCACCCTGGTACCAATGAGGATATTGCACCTATTG ATAATGATGGGAGTGAGTTGGCATCTGAATCAAAGCAAGGTGCTACTAATCGTTTAGAAGAAAA TGAATGGGATAAACTTTTACGTGTCAGATGGGAGCAATATCAAATAGAGGAGGAGGCATCTCTT GGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAGACATTTGCAACACTTCCTAATG AAGCATTAAGTGAG
Genomic sequence	TCAATAGACTGGAATGATGAGCTGAATGACCACCCTGGTACCAATGAGGATATTGCACCTATTG ATAATGATGGGAGTGAGTTGGCATCTGAATCAAAGCAAGGTGCTACTAATCGTTTAGAAGAAAA TGAATGGGATAAACTTTTACGTGTCAGGTACTCTGCAATACTGTATAAACTTGTATCTTTTTGT TTAACAATCCCATCATTTTGAGGGTTAAGTAGGTGCAATGTGATGGTCCTAATGATGTACTTAA AAAACTTCTTTTATTTTTAAAAATTATAATTGCCACAAAGGAAAACAAGTGGAAGAATGAATAC TATAACACTAGCATGTATTTTTGTTCTCGAAAGGCGCAGGAGAACTGCACCCCCTTATAATAAG AAGATAAAAAGAAAGGTCCAAAACATAGACCAGAATACAGAGACTTCCCTTACGGAGGTCGAAA ACACAGGAAAAACAGGAGATCCATCCAAAAAGAAACTAGAAAAAACACCAGAAACTATGCAGCC GAGGGAAGGGCAGTAAGGTATGAAAAACTTTTAGCCCCAGCCATCTCCCACATCAATCTCTCTT CACCCGCCATCTTGAGAGCTAGAGAAACATTAGGAGACCAGCCGTCGAAGATACACTTATTCCG GTGATTCCAGATTATCCAAGCTCCCAAAACAACAAGGGAATTGAAACCATTCTTGGCTTGACCA ATAACTGAATCTGAGGCACTTTCCCACCAGTTCATAAAGGAGGAAGAACTAGGCTGCGGTGATA TATTCTGCAGACCGTAAGGTTGCAAAAGCTGAACCAAAACACCCTTGAGAAAACACAAGAAACT AGAAGGTGATCCAATGTTTCAGCTTCTTGATCACAGAGGGGGCAGCTGGCTGGATGATCCAAAC CTCTTTTAGCAAGTATGTTAGCCGTCCAACATCTCTCATGACTCATGAGCAGCGAGCCAGATAA AAAAACCTGCATTTCGGAGGAGCCCATGTTTTCCACACCCTAGTGTAGGGGCCAAAATGCCAAA TAAAGTTGAGCCTGCAAAGAAGCCCTCATAAGCAGCCTTTGCCGAGTAGCAACCATCTGATGCA AGGCTGAAAATGTGTTTATCATCTTGATCCGGCCGAAGCTCAACATTTGAAAGTAGATCCCACA GCTGAATATAATCCACTAAAACTCCAACCGAGAGAGCTCCCTTAAATGTCTTTGATCCATTTTC TATTTAATAAAACCTCCTGGACAGTCCTTTATACTTTAAATTGTGGTTTATAATCACTCATTTA AATTGTGGTTTATCAACTTTTATGCTTTATGCCATCATAATGGAGCCAAGTTTGTGTTATTTCT TCTCCTGCGCTTTCGAAAAAAAAGTTTGTGTTATTTCTTATTAGGGAAAAAATGTACGTGCATG CACTATCCTTGATTTGTACGGTGGATGCAGTTGTGCTGAATTGACATAATCTGTTGCCCCTCAT GTGCGTCAAAATCTCATTTGAACCTAGGAATTTACAGTGAGAATCTATCTACTTAAGCATAGTT TGGTGAGAAGCAAAGACCTGGGTTCTTCTATATTGCGATAATTGACCTGCTTGCTTTGTGTAGT CGTTTTATCTCTTTGGACCTTGAGGAATAATAATAATGTTATCCAGATGGGAGCAATATCAAAT AGAGGAGGAGGCATCTCTTGGTCGAGGTAAACGTTTAAGGAAGGCTGTTTCTTACAGAGAGACA TTTGCAACACTTCCTAATGAAGCATTAAGTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.091558751

Conservation Information
Conserved circRNAs	NA
PMCS	0.091558751

			
						 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
						responsive to drought stress

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	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d006428_circ_g.3

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