Plant Circular RNA Database

Detail information of Zm00001d006588_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d006588_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007375
					
						Alias
						Zm02circ00104
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 211697464-211699110  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d006588						
					
						Parent gene annotation
						
							Protein THYLAKOID FORMATION 1 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d006588_T001:2

General Information
CircRNA Name	Zm00001d006588_circ_g.1
ID in PlantcircBase	zma_circ_007375
Alias	Zm02circ00104
Organism	Zea mays
Position	chr2: 211697464-211699110 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d006588
Parent gene annotation	Protein THYLAKOID FORMATION 1 chloroplastic
Parent gene strand	-
Alternative splicing	NA
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	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	Zm00001d006588_T001:2

			
						 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  
						
							TTTCAGAATGGATTCAATTTCACCATCTCTAGAAGAAAAATCAACTAAGGAACTGCCATTCTGG
GAACGTGCCCACCCTTCCATCTTTAGTGCATCAGCTctatccacgtattccttgagaagttcct
tggcttgaaccagctttgagagtatgttgcggtaaacatcaaggtccctatccacacttctttt
attgatgt

									
								

					

						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: 333
Transcript exons: 211697464-211697579,211698894-211699110
CTATCCACGTATTCCTTGAGAAGTTCCTTGGCTTGAACCAGCTTTGAGAGTATGTTGCGGTAAA
CATCAAGGTCCCTATCCACACTTCTTTTATTGATGTTTAGCGCAGCGCAAAGCTTGTCTAGTAC
TGTTGGTTCTGTTGCATTTGCAAGCTCAAGCAAACGGAACAAGCCAACTGCAAAGAATCGGCTG
TAGCTGAAGTTTCCCTTACCCTTGGCCCTTTCTGATATATCTTTCAGAATGGATTCAATTTCAC
CATCTCTAGAAGAAAAATCAACTAAGGAACTGCCATTCTGGGAACGTGCCCACCCTTCCATCTT
TAGTGCATCAGCT
						
					

						Genomic sequence
						
							CTATCCACGTATTCCTTGAGAAGTTCCTTGGCTTGAACCAGCTTTGAGAGTATGTTGCGGTAAA
CATCAAGGTCCCTATCCACACTTCTTTTATTGATGTTTAGCGCAGCGCAAAGCTATCAATCGAG
AAATAAAGTCAGTGTCTGTTGCCAATGCTAGCGTTGTAACGGTTAAAGAGCATTTAATTTTGAT
GTCAACACCAAGCACTACCTTCACTGCTCAAATGTTTTGCCGAAATATTTGTTATACTTTGCAA
AAAAATGACTTTATACAAATGTGCTGAAATATTGAGCACAGTTTTTTTGTTATTAAACCCTAAT
TCGAAGTTCTTAATTGAATAGTGCAGAAAGAGTTACCAACCCATATTAATTCATTTAGGGGTGT
TTGGTTTGTTAAATAAGGTAGTCCATCTTATGCGTTAGTCTTTTGTTTGGTTTAGGGAATGGAA
TGAGATGATCCATCACCACATCATTCCTCACAAACTAATAATAAGTACTAGTATGAGCCTATGA
GGAATGAAGTCATTCCACTAAATTTGAATAATGGAGTCATGATGCATACTTCATCTAGAATGGG
TTGATTCACCAAACCAAGCATTCCATAGATACTAAAGCTGTTCTAACATTCCATAGATACTAAA
GCTGTTCTTTCCTCGGGTTATCCAAAGATACACCAACATAATCATATGTTCAGTGGCAGCATAT
AATTGAATGGTGATCTATCATATTCCCAAGCACCAGACAGAAACATTGCGAGTAAAAAAAAAGT
AAATGCAATGAGTTACAAGGCTACTGTACTGGATAGAAGGGCAGACCAGGTCACCAGACCATGT
CTAGGTCAAAAGTCAAATGAAACTTCAAGAAGGAAACCTAACTTTCATGAGTCTGCCGACACAC
ATATCTAAATAAGTCCCAGAGAAAGCTACCAAGCAGACTTATTTGAATCCTAATTTTAATTTTT
TGATTTGTTAGAAACATCACAAAATTCAGTTCTATTTCATACTGACAATCCCATGACATAATGG
TCAGTATATTTGCAATCTCAATCATGGGAGAACAATATTGAACAGAGCAGTGTACAAATGAAAG
CTATGCAAATGCAATGACAACAAGATGTCACAAATGAATTCAAATTATACGTTGGTCTATGTTT
TCTACCTAAAAAAGTTGCCAATACTAAATATTACATTAATTTTCAGCAACTGATCTGATTTAGG
CTAAATTGTCTCGAGAAAAAAAGGGGGGGGGGGGGGGGGGCTAAATTGTGCGTTCTTGAAGCAA
AAGGCAAACACAGGTCCTTTCTGTAAAAAAAATAGGAACTAAAACTATAGGTGAAATAGGAAGC
ATAATTGAGAACACACAATAAACAAGAAATGCAAAAACAAAAAACTTGACCACATGACAAGAAA
AATTAATAGTGAGAGGAACAACCTTGTCTAGTACTGTTGGTTCTGTTGCATTTGCAAGCTCAAG
CAAACGGAACAAGCCAACTGCAAAGAATCGGCTGTAGCTGAAGTTTCCCTTACCCTTGGCCCTT
TCTGATATATCTTTCAGAATGGATTCAATTTCACCATCTCTAGAAGAAAAATCAACTAAGGAAC
TGCCATTCTGGGAACGTGCCCACCCTTCCATCTTTAGTGCATCAGCT
						
					

			
		

Sequences
Splice junction sequence	TTTCAGAATGGATTCAATTTCACCATCTCTAGAAGAAAAATCAACTAAGGAACTGCCATTCTGG GAACGTGCCCACCCTTCCATCTTTAGTGCATCAGCTctatccacgtattccttgagaagttcct tggcttgaaccagctttgagagtatgttgcggtaaacatcaaggtccctatccacacttctttt attgatgt
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: 333 Transcript exons: 211697464-211697579,211698894-211699110 CTATCCACGTATTCCTTGAGAAGTTCCTTGGCTTGAACCAGCTTTGAGAGTATGTTGCGGTAAA CATCAAGGTCCCTATCCACACTTCTTTTATTGATGTTTAGCGCAGCGCAAAGCTTGTCTAGTAC TGTTGGTTCTGTTGCATTTGCAAGCTCAAGCAAACGGAACAAGCCAACTGCAAAGAATCGGCTG TAGCTGAAGTTTCCCTTACCCTTGGCCCTTTCTGATATATCTTTCAGAATGGATTCAATTTCAC CATCTCTAGAAGAAAAATCAACTAAGGAACTGCCATTCTGGGAACGTGCCCACCCTTCCATCTT TAGTGCATCAGCT
Genomic sequence	CTATCCACGTATTCCTTGAGAAGTTCCTTGGCTTGAACCAGCTTTGAGAGTATGTTGCGGTAAA CATCAAGGTCCCTATCCACACTTCTTTTATTGATGTTTAGCGCAGCGCAAAGCTATCAATCGAG AAATAAAGTCAGTGTCTGTTGCCAATGCTAGCGTTGTAACGGTTAAAGAGCATTTAATTTTGAT GTCAACACCAAGCACTACCTTCACTGCTCAAATGTTTTGCCGAAATATTTGTTATACTTTGCAA AAAAATGACTTTATACAAATGTGCTGAAATATTGAGCACAGTTTTTTTGTTATTAAACCCTAAT TCGAAGTTCTTAATTGAATAGTGCAGAAAGAGTTACCAACCCATATTAATTCATTTAGGGGTGT TTGGTTTGTTAAATAAGGTAGTCCATCTTATGCGTTAGTCTTTTGTTTGGTTTAGGGAATGGAA TGAGATGATCCATCACCACATCATTCCTCACAAACTAATAATAAGTACTAGTATGAGCCTATGA GGAATGAAGTCATTCCACTAAATTTGAATAATGGAGTCATGATGCATACTTCATCTAGAATGGG TTGATTCACCAAACCAAGCATTCCATAGATACTAAAGCTGTTCTAACATTCCATAGATACTAAA GCTGTTCTTTCCTCGGGTTATCCAAAGATACACCAACATAATCATATGTTCAGTGGCAGCATAT AATTGAATGGTGATCTATCATATTCCCAAGCACCAGACAGAAACATTGCGAGTAAAAAAAAAGT AAATGCAATGAGTTACAAGGCTACTGTACTGGATAGAAGGGCAGACCAGGTCACCAGACCATGT CTAGGTCAAAAGTCAAATGAAACTTCAAGAAGGAAACCTAACTTTCATGAGTCTGCCGACACAC ATATCTAAATAAGTCCCAGAGAAAGCTACCAAGCAGACTTATTTGAATCCTAATTTTAATTTTT TGATTTGTTAGAAACATCACAAAATTCAGTTCTATTTCATACTGACAATCCCATGACATAATGG TCAGTATATTTGCAATCTCAATCATGGGAGAACAATATTGAACAGAGCAGTGTACAAATGAAAG CTATGCAAATGCAATGACAACAAGATGTCACAAATGAATTCAAATTATACGTTGGTCTATGTTT TCTACCTAAAAAAGTTGCCAATACTAAATATTACATTAATTTTCAGCAACTGATCTGATTTAGG CTAAATTGTCTCGAGAAAAAAAGGGGGGGGGGGGGGGGGGCTAAATTGTGCGTTCTTGAAGCAA AAGGCAAACACAGGTCCTTTCTGTAAAAAAAATAGGAACTAAAACTATAGGTGAAATAGGAAGC ATAATTGAGAACACACAATAAACAAGAAATGCAAAAACAAAAAACTTGACCACATGACAAGAAA AATTAATAGTGAGAGGAACAACCTTGTCTAGTACTGTTGGTTCTGTTGCATTTGCAAGCTCAAG CAAACGGAACAAGCCAACTGCAAAGAATCGGCTGTAGCTGAAGTTTCCCTTACCCTTGGCCCTT TCTGATATATCTTTCAGAATGGATTCAATTTCACCATCTCTAGAAGAAAAATCAACTAAGGAAC TGCCATTCTGGGAACGTGCCCACCCTTCCATCTTTAGTGCATCAGCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.095667679

Conservation Information
Conserved circRNAs	NA
PMCS	0.095667679

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							211699019-211697496(+)
211699096-211697466(-)
211697532-211699099(-)
						
						Potential amino acid sequence
						
							MDSISPSLEEKSTKELPFWERAHPSIFSASALSTYSLRSSLA*(+)
MEGWARSQNGSSLVDFSSRDGEIESILKDISERAKGKGNFSYSRFFAVGLFRLLELANATEPTV
LDKLCAALNINKRSVDRDLDVYRNILSKLVQAKELLKEYVDRADALKMEGWARSQNGSSLVDFS
SRDGEIESILKDISERAKGKGNFSYSRFFAVGLFRLLELANATEPTVLDKLCAALNINKRSVDR
DLDVYRNILSKLVQAKELLKEYVDRADALKMEGWARSQNGSSLVDFSSRDGEIESILKDISERA
KGKGNFSYSRFFAVGLFRLLELANATEPTVLDKLCAALNINKRSVDRDLDVYRNILSKLVQAKE
LLKEYVDRADALKMEGWARSQNGSSLVDFSSRDGEIESILKDISERAKGKGNFSYSRFFAVGLF
RLLELANATEPTVLDKLCAALNINKRSVDRDLDVYRNILSKLVQAKELLKEYVD(-)
MFTATYSQSWFKPRNFSRNTWIELMH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	211699019-211697496(+) 211699096-211697466(-) 211697532-211699099(-)
Potential amino acid sequence	MDSISPSLEEKSTKELPFWERAHPSIFSASALSTYSLRSSLA(+) MEGWARSQNGSSLVDFSSRDGEIESILKDISERAKGKGNFSYSRFFAVGLFRLLELANATEPTV LDKLCAALNINKRSVDRDLDVYRNILSKLVQAKELLKEYVDRADALKMEGWARSQNGSSLVDFS SRDGEIESILKDISERAKGKGNFSYSRFFAVGLFRLLELANATEPTVLDKLCAALNINKRSVDR DLDVYRNILSKLVQAKELLKEYVDRADALKMEGWARSQNGSSLVDFSSRDGEIESILKDISERA KGKGNFSYSRFFAVGLFRLLELANATEPTVLDKLCAALNINKRSVDRDLDVYRNILSKLVQAKE LLKEYVDRADALKMEGWARSQNGSSLVDFSSRDGEIESILKDISERAKGKGNFSYSRFFAVGLF RLLELANATEPTVLDKLCAALNINKRSVDRDLDVYRNILSKLVQAKELLKEYVD(-) MFTATYSQSWFKPRNFSRNTWIELMH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d006588_circ_g.1

Address

Any questions?

Supported by