Plant Circular RNA Database

Detail information of Zm00001d044506_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d044506_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007916
					
						Alias
						zma_circ_0001394, GRMZM2G030596_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 230173753-230175626  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d044506						
					
						Parent gene annotation
						
							Protein MICRORCHIDIA 6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d044506_T006:5
Zm00001d044506_T002:5
Zm00001d044506_T009:5
Zm00001d044506_T001:5
Zm00001d044506_T013:5
Zm00001d044506_T012:5
Zm00001d044506_T005:5
Zm00001d044506_T003:5
Zm00001d044506_T008:5
Zm00001d044506_T007:5
Zm00001d044506_T011:5

General Information
CircRNA Name	Zm00001d044506_circ_g.1
ID in PlantcircBase	zma_circ_007916
Alias	zma_circ_0001394, GRMZM2G030596_C1
Organism	Zea mays
Position	chr3: 230173753-230175626 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d044506
Parent gene annotation	Protein MICRORCHIDIA 6
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, 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	Zm00001d044506_T006:5 Zm00001d044506_T002:5 Zm00001d044506_T009:5 Zm00001d044506_T001:5 Zm00001d044506_T013:5 Zm00001d044506_T012:5 Zm00001d044506_T005:5 Zm00001d044506_T003:5 Zm00001d044506_T008:5 Zm00001d044506_T007:5 Zm00001d044506_T011:5

			
						 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  
						
							CCAACTTTATCAAACCTACCCATGACAAGCAGGATTTTGAGAAGTCAGTCCTTTATCAAAGACT
TGAGTTCCGCTTGAAAGAAATGACTTACGAATACTGgatatcctcattactggggcccacaaga
aggtgaaaacaaacagtttggacaagattgctgcacagaactacgtctcaactcggcttcgcta
ttctctta

									
								

					

						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
						
							GATATCCTCATTACTGGGGCCCACAAGAAGGTGAAAACAAACAGTTTGGACAAGATTGCTGCAC
AGAACTACGTCTCAACTCGGCTTCGCTATTCTCTTAGAGTTAAGTATATTGGTTCCCGTTTACT
CATATGACACTTCTTGTTTCTTTCTTGAGCTAACATTATTATTCACTTTGGATTCAAACAGGCA
TATGCATCTATCTTGTATCTTCATGTACCTGATACTTTCAGAATTATCCTGCGGGGATGTGATG
TGGAACCACATAATGTAGTTAATGATTTGATGTATCGGGAGTGCGTGTTGTATAAACCACAAAT
TGCTGGACTTACAGAGGTACTGTATAAATCGCATTTGCAAATCATGTTTGCATTTTTTTATCAT
TTTGATTGCTGGAATAAACCTTTCCATTGACTCATACTGTTTTCAATTGCTGTCTCATGAAAGA
GAAATGTCTGTGCATTCAGTTTTTTAGAGTTTAGAATGACTAATGGGGAAAAGAAATGTGAAAA
ATCTACATGAAACAATATTCCATCTGTGAAATGTGGCTACTTAGTACTTTGCCCCCAATTTTAC
CCATGAAGTGCAACATACAACCAACCTTTCTGTGAAACGTAGTCCAGGCAGCATTGGTATTCGT
TTTGTAGCATTTTGTACTGTGCATCGGTGACCTCATGTATTCAAGAATTGCCAAATGGATCTTG
AGGGAGTGCTCTCATAATTGTCCCCTTTGTGTTCATGCCTGTCATAAATATCTAGTGTCATGCT
AGTTTTCCTAACCCATTTTTGGTTTTAGGCAAATACTAATATTTTTTAACCTATTTATACTTGA
CACCTTACCCTCTGGGTGAGGCTATATCCTTGAAAGTGGAAATTGATATGTCCTTGCTGATAGA
TCAGGCAGTCCTTGAGCGTTGCCTTTGATTTCTACTCCAACAAATATTCTCTGATTGCTTTGAG
CATGCGGGTGTAGCCTATGTTTTATTTTTTATTATACTATCAAATCAAAATTTTGATTTTCTTG
TTTTAGAAAATCTCTCTGATTGGCCTCATGTTTTGCAGTCATCGGTAATCACAACCATTGGGTT
TGTTAAAGGTGCACCAGATATAGATGTACAAGGGTTTAATGTATATCACAAAAACCGTCTAATA
TTGGTAAGAGCTCTGCTTTGTATACTACATGGTGCATGATGTATCAATTCACTTTTCTTTCCTG
TTGCTGTCTGTTGCCAGTTGGGCTGTAATCGTTTGAAGCAGAAACATTTGTGTGTTTGTCAAAT
CTTTGTTTAATTTCGAAGCCTTTGTGTTTATGACAAAATGTTGTTTTTAAAATGGAAGAGTAGC
ATATAGTTCTTCCGAAACATAGCATATAACAGAGTAGCACACATAAATATTTTCTTCTTCCATT
GTAGGCACTTGTACTTTGTGTTTCCCATCAGGCTAGCTAAGCTATCAACTTCAATAAAATTTTC
CTTAGGATGCCATTAACTCGATAACCTAGTTTAGGTATGTGCAACATATTGTTTTCCAGAATGA
CATTCTTGGTAAATTTTATATTGCTTTCGCTTAGTGATATCGGTAATGTGTGACATATTTCCAG
AATCTCAAATGTCTGATTTTTTTCAGCCCTTCTGGAAAGTTGCAAACAACTCATACGGGAAAGG
ACGAGGAGTTGTTGGTAAGAAATATTTGAAGGAGTCATCCAAAAATCAAGATATTGGTTAAAAA
GATCTATATTTTCTTTTTTATCATCCCTTTTCAGGCATTCTGGAGGCCAACTTTATCAAACCTA
CCCATGACAAGCAGGATTTTGAGAAGTCAGTCCTTTATCAAAGACTTGAGTTCCGCTTGAAAGA
AATGACTTACGAATACTG
						
					

			
		

Sequences
Splice junction sequence	CCAACTTTATCAAACCTACCCATGACAAGCAGGATTTTGAGAAGTCAGTCCTTTATCAAAGACT TGAGTTCCGCTTGAAAGAAATGACTTACGAATACTGgatatcctcattactggggcccacaaga aggtgaaaacaaacagtttggacaagattgctgcacagaactacgtctcaactcggcttcgcta ttctctta
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	GATATCCTCATTACTGGGGCCCACAAGAAGGTGAAAACAAACAGTTTGGACAAGATTGCTGCAC AGAACTACGTCTCAACTCGGCTTCGCTATTCTCTTAGAGTTAAGTATATTGGTTCCCGTTTACT CATATGACACTTCTTGTTTCTTTCTTGAGCTAACATTATTATTCACTTTGGATTCAAACAGGCA TATGCATCTATCTTGTATCTTCATGTACCTGATACTTTCAGAATTATCCTGCGGGGATGTGATG TGGAACCACATAATGTAGTTAATGATTTGATGTATCGGGAGTGCGTGTTGTATAAACCACAAAT TGCTGGACTTACAGAGGTACTGTATAAATCGCATTTGCAAATCATGTTTGCATTTTTTTATCAT TTTGATTGCTGGAATAAACCTTTCCATTGACTCATACTGTTTTCAATTGCTGTCTCATGAAAGA GAAATGTCTGTGCATTCAGTTTTTTAGAGTTTAGAATGACTAATGGGGAAAAGAAATGTGAAAA ATCTACATGAAACAATATTCCATCTGTGAAATGTGGCTACTTAGTACTTTGCCCCCAATTTTAC CCATGAAGTGCAACATACAACCAACCTTTCTGTGAAACGTAGTCCAGGCAGCATTGGTATTCGT TTTGTAGCATTTTGTACTGTGCATCGGTGACCTCATGTATTCAAGAATTGCCAAATGGATCTTG AGGGAGTGCTCTCATAATTGTCCCCTTTGTGTTCATGCCTGTCATAAATATCTAGTGTCATGCT AGTTTTCCTAACCCATTTTTGGTTTTAGGCAAATACTAATATTTTTTAACCTATTTATACTTGA CACCTTACCCTCTGGGTGAGGCTATATCCTTGAAAGTGGAAATTGATATGTCCTTGCTGATAGA TCAGGCAGTCCTTGAGCGTTGCCTTTGATTTCTACTCCAACAAATATTCTCTGATTGCTTTGAG CATGCGGGTGTAGCCTATGTTTTATTTTTTATTATACTATCAAATCAAAATTTTGATTTTCTTG TTTTAGAAAATCTCTCTGATTGGCCTCATGTTTTGCAGTCATCGGTAATCACAACCATTGGGTT TGTTAAAGGTGCACCAGATATAGATGTACAAGGGTTTAATGTATATCACAAAAACCGTCTAATA TTGGTAAGAGCTCTGCTTTGTATACTACATGGTGCATGATGTATCAATTCACTTTTCTTTCCTG TTGCTGTCTGTTGCCAGTTGGGCTGTAATCGTTTGAAGCAGAAACATTTGTGTGTTTGTCAAAT CTTTGTTTAATTTCGAAGCCTTTGTGTTTATGACAAAATGTTGTTTTTAAAATGGAAGAGTAGC ATATAGTTCTTCCGAAACATAGCATATAACAGAGTAGCACACATAAATATTTTCTTCTTCCATT GTAGGCACTTGTACTTTGTGTTTCCCATCAGGCTAGCTAAGCTATCAACTTCAATAAAATTTTC CTTAGGATGCCATTAACTCGATAACCTAGTTTAGGTATGTGCAACATATTGTTTTCCAGAATGA CATTCTTGGTAAATTTTATATTGCTTTCGCTTAGTGATATCGGTAATGTGTGACATATTTCCAG AATCTCAAATGTCTGATTTTTTTCAGCCCTTCTGGAAAGTTGCAAACAACTCATACGGGAAAGG ACGAGGAGTTGTTGGTAAGAAATATTTGAAGGAGTCATCCAAAAATCAAGATATTGGTTAAAAA GATCTATATTTTCTTTTTTATCATCCCTTTTCAGGCATTCTGGAGGCCAACTTTATCAAACCTA CCCATGACAAGCAGGATTTTGAGAAGTCAGTCCTTTATCAAAGACTTGAGTTCCGCTTGAAAGA AATGACTTACGAATACTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.048640084

Conservation Information
Conserved circRNAs	NA
PMCS	0.048640084

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							230174039-230173783(+)
230173765-230175544(-)
						
						Potential amino acid sequence
						
							MYRECVLYKPQIAGLTESSVITTIGFVKGAPDIDVQGFNVYHKNRLILPFWKVANNSYGKGRGV
VGILEANFIKPTHDKQDFEKSVLYQRLEFRLKEMTYEYWISSLLGPTRR*(+)
MRISSIRKSFLSSGTQVFDKGLTSQNPACHG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	230174039-230173783(+) 230173765-230175544(-)
Potential amino acid sequence	MYRECVLYKPQIAGLTESSVITTIGFVKGAPDIDVQGFNVYHKNRLILPFWKVANNSYGKGRGV VGILEANFIKPTHDKQDFEKSVLYQRLEFRLKEMTYEYWISSLLGPTRR(+) MRISSIRKSFLSSGTQVFDKGLTSQNPACHG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d044506_circ_g.1

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