Plant Circular RNA Database

Detail information of Zm00001d001415_circ_ig.2

			
						 General Information
					
						CircRNA Name
						Zm00001d001415_circ_ig.2
					
						ID in PlantcircBase
						zma_circ_009015
					
						Alias
						Zm06circ00044, zma_circ_0002148
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 115323758-115326796  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Zm00001d037196_circ_g.1 Zm00001d037196_circ_igg.1 Zm00001d001415_circ_ig.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, root
					
						Exon boundary  
						
							NA-NA							"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
						NA

General Information
CircRNA Name	Zm00001d001415_circ_ig.2
ID in PlantcircBase	zma_circ_009015
Alias	Zm06circ00044, zma_circ_0002148
Organism	Zea mays
Position	chr6: 115323758-115326796 JBrowse»
Reference genome	AGPv4.38
Type	ig-circRNA
Identification method	CIRI2, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Zm00001d037196_circ_g.1 Zm00001d037196_circ_igg.1 Zm00001d001415_circ_ig.1
Support reads	NA
Tissues	leaf, endosperm, root
Exon boundary	NA-NA "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	NA

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: TTGCGATGATATTGAGTGATTATG
 R: CCAGAGGTTTGATGAGAAGG
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	Yes 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	F: TTGCGATGATATTGAGTGATTATG R: CCAGAGGTTTGATGAGAAGG 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  
						
							AAGAATCTACTAAGGAAATCAATAATCAACTACCTTGGATGGGCACGATGGAGGAAGATTTATA
CGATTCCCAGCCTCCAGCTCAGGATAGACCTTGAAGcttgtaggggagtatgtttttcccagaa
acacttaaactcgtcttcagtttccacgggaatgtctatatcagccttcagctcatttgttctc
ctgaatgc

									
								

					

						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
						
							CTTGTAGGGGAGTATGTTTTTCCCAGAAACACTTAAACTCGTCTTCAGTTTCCACGGGAATGTC
TATATCAGCCTTCAGCTCATTTGTTCTCCTGAATGCAGTCATCCGTAAACATAAGAACAACAAA
TGAAAGGAACTGGCATTGTTCAGACTTGAATCAGAAACAAGAAAGCATCATTTGGGCAAATAAA
AATAGCTGCAAACTACTAGCCTAAATATATGACTACTGATGACATCTGATCTGAGTACTTTGGT
ACATGGTGATAAGGAAACTACAATGCAGTGAGCAAAGCAAAACTAGCCAATGAGTCAGATCATA
GGCTGTAGACAAAGACCCTTATTTTGTTGGTTGCATACAAGCCAGGCATAAGAAAGCATGAACA
ATTTTCAACTAGAATTAACATGGTAAATCTTATTGCTGGTATCACAGGTAGGGGTGACAATGGG
CTCTAAATTTTACACTATAAGATTTAAGAATCGGATCGGATTAAGATCGGGTCTGTCGGCGTTT
CGACCCCGGGGGGGGGGGGGTCCCTGGACCGACGAGTGAATTGTCGCCGCGTGTCCCAGCCCAG
ATGGGTCGGCGCGAGACGGAGCACGAAGGGGGGTAGAAGAGAGAGGGGAAAGCCCGCGGCCTCC
GTGTTTGTCCTGCGCCCAGGTCAGGTGCGCTTGCAGTAGGGGGTTACAAGCGTCCGCGTGGGGG
GGAGAGCGAGGGACTCTACGCGTCGCCCCGTCCTCCCGCGCGGCCAACCTTCTCGTAAGAGAGC
CTTGGACCTTCCTTTTATAGGCGTAAGGAGAGGGTCCAGGTGTACAATGGGGGGTGTAGCAGTG
CGCTATCGTGTCTAGCAGAGAGGAGCTAGTGCCCTAAGTACATGCCGTCGTGGCAGCCAGAGAG
GTTTTGGCACCCTGTTCACGTGATGTCGTAGCCGTCGGAGGAGCGTTGGAGCCTTGCGGAAGGA
CAGCTGTCGGGGCTGTCGAGTCCTTGCTGACGTCTCCTTGCTTCCGTAAGGGTTTGAGAATCGC
CGTCGTCATGGAGCACGCGGGGCGCCATCATTATCTGTTTTCCGGGGCGAGCCAGATGGGACGC
CGGTCCTGTTACCCGTAGCCTGAGCTAGCTAGGGATAGGGTAATGATGGCCCCCCTGTGACGTG
GTCGGTCCGAGCCCTGGGTCGGGCGAGGCGGAGGCTCCTCCGAGGTCGGGGTCGAGTTGGTCTT
CCGAGGCCGAGCCCGAGTCCGAGCCCTGGGGTCGGGCGAGGCGGAGTTCGTCGTCTTCCGGGGC
CGAGCCCGAGTCCGAGCCCTGGGGTCGGGCGAGGCGGAGTTCATCGTCTTCCGGGGTCGAGCCC
GAGTCCGAGCCCTGGGGTCGGGCGAGGCGGAGTTTCCTATGGCGCCCGAGGCCAGACTTGGCTG
CTGTCAGCCTCACTCTGTCGAGTGGCACAGCAGTCGGAGCGACGCAGGCGGCGCTGTCTTCTTG
TCAGGCCGGTCAGTGGAGCGGCGAAGTGACTGCGGTCACTTTCGGCTCTGTCGACTGAAGGGCG
TATGGCAGGATAAGATGTCAGGCCATCCTTGCATTAAATGCTCCTGCGATTCGGTTGGTTGGTG
TGGCGATCTGGCCAAGGTTGCTTCTTGGCGAAGACTGGGCCTCGGGCGAGCCGAAGGTGTGTAC
GCCGCTTGAGGGGGTCCTCAGGCGAGACGTGAATCTTCCGGGGTCGGCTGCCCTTGCCCGAGGC
TGGGCTCGGGCGAGGCGAGGTCGTGTCCCTTGAGTGGACCGAGCCTTGGCTTAATCGCACCCAT
CAGGCCTTTGCAGCTTTGTGCTGATGGGGGTTACCAGCTGAGATTAGGAGTCTTGGGGGTACCC
CTAATTATGGTCCCCGACAGGGCCCTATTTCTATTCATTTTTGAAACAAAATTTATTTAGGGCC
CTACTATTTTGTGAAGAAGCATTTGGATCGTGACCCATTACCACCCCTAATCACAGGATCGATC
TCGATGCATGAACATGACCCTCCAGATTCTTGTCAACCATACTATGCTATGAAATACTTCAGAG
AATAAAAAAATTGCAATTGACTAATCATGTAGCTGAAAATATGACTAAACTTCTAATGCTCAAG
AGATTCGAAGTTAATAGAATCAAAACTTGCTTTGACGACCAAATTATAGATAATCAAATTACCT
CACATAATTAGCAAGCAGCATAGGATCAAGGTTGGACCGCACATCCTTAATATCAGGAGACCAT
TTGGCAGATAATATACCCGTAATAATGACATCATCTGAAGAAACACCCAAAACAGTTAAGTATA
ATAATGGATGACCATTGTACGCATCTCATGTAATGCATACAACATATTCCTGTTTTAACTTTTT
CATCTTGAAAAAACAAGAAACCAGCATTGAAATGTTATAAAATGAACTGTTCGAGCTGTTCCAA
ACAGTATCAAAGCTCCTGAATTTTTCGAGCTCTGAACACAACTGGGAAATTTGAAAAATGGAAA
GAAAAAATGCAGGATAAGGGCTGAGGACATGAAGGGCAAAATAATATCAACAGTCGATCCACAT
GATCCTTTGGATAATGCACAAAGAGGCTGCTTACCTCCAGCTTTAATGTTATCAACAAGGTCAT
CCATCAAAATTACAGGTATGGAACGGGGTATAGACCCAACACCAAGAAGTTGTACATTCTCTTG
AATTTTGATTTCTTGGTAATCATGGCAAATGGTGCTACCTTCTACAAACTGGAAAGAAACACTT
GTACAGCTTCTCGAATCCTAGATGGCCAGCAAAATCATCAATAGCAGCTTCCACAGCAGTTCAA
GCAAAAGTACAACCAATTATAAAAATGTAACAGGCAAGAAAAATAGTACTCCTATCACGGAGAA
CAATGCAAATGTTCACCACATGTCAAAAAAATATATTTAAAACAAAAAAACAACAGTAAAAGAA
TCTACTAAGGAAATCAATAATCAACTACCTTGGATGGGCACGATGGAGGAAGATTTATACGATT
CCCAGCCTCCAGCTCAGGATAGACCTTGAAG
						
					

			
		

Sequences
Splice junction sequence	AAGAATCTACTAAGGAAATCAATAATCAACTACCTTGGATGGGCACGATGGAGGAAGATTTATA CGATTCCCAGCCTCCAGCTCAGGATAGACCTTGAAGcttgtaggggagtatgtttttcccagaa acacttaaactcgtcttcagtttccacgggaatgtctatatcagccttcagctcatttgttctc ctgaatgc
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	CTTGTAGGGGAGTATGTTTTTCCCAGAAACACTTAAACTCGTCTTCAGTTTCCACGGGAATGTC TATATCAGCCTTCAGCTCATTTGTTCTCCTGAATGCAGTCATCCGTAAACATAAGAACAACAAA TGAAAGGAACTGGCATTGTTCAGACTTGAATCAGAAACAAGAAAGCATCATTTGGGCAAATAAA AATAGCTGCAAACTACTAGCCTAAATATATGACTACTGATGACATCTGATCTGAGTACTTTGGT ACATGGTGATAAGGAAACTACAATGCAGTGAGCAAAGCAAAACTAGCCAATGAGTCAGATCATA GGCTGTAGACAAAGACCCTTATTTTGTTGGTTGCATACAAGCCAGGCATAAGAAAGCATGAACA ATTTTCAACTAGAATTAACATGGTAAATCTTATTGCTGGTATCACAGGTAGGGGTGACAATGGG CTCTAAATTTTACACTATAAGATTTAAGAATCGGATCGGATTAAGATCGGGTCTGTCGGCGTTT CGACCCCGGGGGGGGGGGGGTCCCTGGACCGACGAGTGAATTGTCGCCGCGTGTCCCAGCCCAG ATGGGTCGGCGCGAGACGGAGCACGAAGGGGGGTAGAAGAGAGAGGGGAAAGCCCGCGGCCTCC GTGTTTGTCCTGCGCCCAGGTCAGGTGCGCTTGCAGTAGGGGGTTACAAGCGTCCGCGTGGGGG GGAGAGCGAGGGACTCTACGCGTCGCCCCGTCCTCCCGCGCGGCCAACCTTCTCGTAAGAGAGC CTTGGACCTTCCTTTTATAGGCGTAAGGAGAGGGTCCAGGTGTACAATGGGGGGTGTAGCAGTG CGCTATCGTGTCTAGCAGAGAGGAGCTAGTGCCCTAAGTACATGCCGTCGTGGCAGCCAGAGAG GTTTTGGCACCCTGTTCACGTGATGTCGTAGCCGTCGGAGGAGCGTTGGAGCCTTGCGGAAGGA CAGCTGTCGGGGCTGTCGAGTCCTTGCTGACGTCTCCTTGCTTCCGTAAGGGTTTGAGAATCGC CGTCGTCATGGAGCACGCGGGGCGCCATCATTATCTGTTTTCCGGGGCGAGCCAGATGGGACGC CGGTCCTGTTACCCGTAGCCTGAGCTAGCTAGGGATAGGGTAATGATGGCCCCCCTGTGACGTG GTCGGTCCGAGCCCTGGGTCGGGCGAGGCGGAGGCTCCTCCGAGGTCGGGGTCGAGTTGGTCTT CCGAGGCCGAGCCCGAGTCCGAGCCCTGGGGTCGGGCGAGGCGGAGTTCGTCGTCTTCCGGGGC CGAGCCCGAGTCCGAGCCCTGGGGTCGGGCGAGGCGGAGTTCATCGTCTTCCGGGGTCGAGCCC GAGTCCGAGCCCTGGGGTCGGGCGAGGCGGAGTTTCCTATGGCGCCCGAGGCCAGACTTGGCTG CTGTCAGCCTCACTCTGTCGAGTGGCACAGCAGTCGGAGCGACGCAGGCGGCGCTGTCTTCTTG TCAGGCCGGTCAGTGGAGCGGCGAAGTGACTGCGGTCACTTTCGGCTCTGTCGACTGAAGGGCG TATGGCAGGATAAGATGTCAGGCCATCCTTGCATTAAATGCTCCTGCGATTCGGTTGGTTGGTG TGGCGATCTGGCCAAGGTTGCTTCTTGGCGAAGACTGGGCCTCGGGCGAGCCGAAGGTGTGTAC GCCGCTTGAGGGGGTCCTCAGGCGAGACGTGAATCTTCCGGGGTCGGCTGCCCTTGCCCGAGGC TGGGCTCGGGCGAGGCGAGGTCGTGTCCCTTGAGTGGACCGAGCCTTGGCTTAATCGCACCCAT CAGGCCTTTGCAGCTTTGTGCTGATGGGGGTTACCAGCTGAGATTAGGAGTCTTGGGGGTACCC CTAATTATGGTCCCCGACAGGGCCCTATTTCTATTCATTTTTGAAACAAAATTTATTTAGGGCC CTACTATTTTGTGAAGAAGCATTTGGATCGTGACCCATTACCACCCCTAATCACAGGATCGATC TCGATGCATGAACATGACCCTCCAGATTCTTGTCAACCATACTATGCTATGAAATACTTCAGAG AATAAAAAAATTGCAATTGACTAATCATGTAGCTGAAAATATGACTAAACTTCTAATGCTCAAG AGATTCGAAGTTAATAGAATCAAAACTTGCTTTGACGACCAAATTATAGATAATCAAATTACCT CACATAATTAGCAAGCAGCATAGGATCAAGGTTGGACCGCACATCCTTAATATCAGGAGACCAT TTGGCAGATAATATACCCGTAATAATGACATCATCTGAAGAAACACCCAAAACAGTTAAGTATA ATAATGGATGACCATTGTACGCATCTCATGTAATGCATACAACATATTCCTGTTTTAACTTTTT CATCTTGAAAAAACAAGAAACCAGCATTGAAATGTTATAAAATGAACTGTTCGAGCTGTTCCAA ACAGTATCAAAGCTCCTGAATTTTTCGAGCTCTGAACACAACTGGGAAATTTGAAAAATGGAAA GAAAAAATGCAGGATAAGGGCTGAGGACATGAAGGGCAAAATAATATCAACAGTCGATCCACAT GATCCTTTGGATAATGCACAAAGAGGCTGCTTACCTCCAGCTTTAATGTTATCAACAAGGTCAT CCATCAAAATTACAGGTATGGAACGGGGTATAGACCCAACACCAAGAAGTTGTACATTCTCTTG AATTTTGATTTCTTGGTAATCATGGCAAATGGTGCTACCTTCTACAAACTGGAAAGAAACACTT GTACAGCTTCTCGAATCCTAGATGGCCAGCAAAATCATCAATAGCAGCTTCCACAGCAGTTCAA GCAAAAGTACAACCAATTATAAAAATGTAACAGGCAAGAAAAATAGTACTCCTATCACGGAGAA CAATGCAAATGTTCACCACATGTCAAAAAAATATATTTAAAACAAAAAAACAACAGTAAAAGAA TCTACTAAGGAAATCAATAATCAACTACCTTGGATGGGCACGATGGAGGAAGATTTATACGATT CCCAGCCTCCAGCTCAGGATAGACCTTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.139650666

Conservation Information
Conserved circRNAs	NA
PMCS	0.139650666

			
						 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
						regulating the response to N deficiency  (validated)

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	regulating the response to N deficiency (validated)

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

circRNA

Detail information of Zm00001d001415_circ_ig.2

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