Plant Circular RNA Database

Detail information of Zm00001d042470_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d042470_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007701
					
						Alias
						zma_circ_0001215
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 168702704-168704243  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d042470						
					
						Parent gene annotation
						
							Protein kinase superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d042470_circ_g.1 Zm00001d042470_circ_g.3 Zm00001d042470_circ_g.4 						
					
						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
						Zm00001d042470_T010:4
Zm00001d042470_T006:4
Zm00001d042470_T003:4
Zm00001d042470_T001:3
Zm00001d042470_T004:4
Zm00001d042470_T011:4
Zm00001d042470_T012:1
Zm00001d042470_T002:3
Zm00001d042470_T005:3
Zm00001d042470_T008:4
Zm00001d042470_T007:4

General Information
CircRNA Name	Zm00001d042470_circ_g.2
ID in PlantcircBase	zma_circ_007701
Alias	zma_circ_0001215
Organism	Zea mays
Position	chr3: 168702704-168704243 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d042470
Parent gene annotation	Protein kinase superfamily protein
Parent gene strand	+
Alternative splicing	Zm00001d042470_circ_g.1 Zm00001d042470_circ_g.3 Zm00001d042470_circ_g.4
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	Zm00001d042470_T010:4 Zm00001d042470_T006:4 Zm00001d042470_T003:4 Zm00001d042470_T001:3 Zm00001d042470_T004:4 Zm00001d042470_T011:4 Zm00001d042470_T012:1 Zm00001d042470_T002:3 Zm00001d042470_T005:3 Zm00001d042470_T008:4 Zm00001d042470_T007:4

			
						 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  
						
							GCGAAGCAAGTGCAATGGAAAGAATTCGAGAATTCCTACGTATCACCAATAAGAAACCTCCGGT
TATGGTGCCCCGTGTGATTCCTGGGATGGTTACCAGgctgctcaaattctggggaaacctgacc
tggcacctatggcttgggtgaagagacttgttacgctgtgtgacaaggccccagccacgccatt
tgatgtgg

									
								

					

						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: 497
Transcript exons: 168702704-168702898,168703101-168703148,168703235-168703
363,168704119-168704243
GCTGCTCAAATTCTGGGGAAACCTGACCTGGCACCTATGGCTTGGGTGAAGAGACTTGTTACGC
TGTGTGACAAGGCCCCAGCCACGCCATTTGATGTGGTTAGAGATGTTGTGGAGAAACAGTTCAT
GAAGAATTTCGATGACATATTCGAATTCTTCGATGTTGAGCCTGTTGGGTCTGCTTCTATTGCA
CAGGTGCATCGAGCAAGGCTTAAATTGTCAAATACTGATGTTGCTGTCAAGGTTCAACATCCAG
GAGCCGAACATCTGATGATGGTTGATATTCGGAATATGCAAGCAATGGCCTTGTTTCTGCAGAA
GTATGACATAAACTTCGATCTATTCTCTGCCACGAAAGAGATGGAAAAGCAGATATGCTATGAG
TTTGACTTTGTGCGCGAAGCAAGTGCAATGGAAAGAATTCGAGAATTCCTACGTATCACCAATA
AGAAACCTCCGGTTATGGTGCCCCGTGTGATTCCTGGGATGGTTACCAG
						
					

						Genomic sequence
						
							GCTGCTCAAATTCTGGGGAAACCTGACCTGGCACCTATGGCTTGGGTGAAGAGACTTGTTACGC
TGTGTGACAAGGCCCCAGCCACGCCATTTGATGTGGTTAGAGATGTTGTGGAGAAACAGTTCAT
GAAGAATTTCGATGACATATTCGAATTCTTCGATGTTGAGCCTGTTGGGTCTGCTTCTATTGCA
CAGGTTCGTGCTTAGGTATTTCTCTTCATCTGTGAAATCTGGGGAGTGAACTTTCTACCATTCC
TGCCAATGTTAGGCCTTTGCAAATGTTGTTTCCTTGTTTTGTAACATATAAGTACATAACATCA
CATACATACTGGGAACATATCATTTATTTTCTCACTAAAGATGGTTTCCAAGATATATTTTGAT
TCATATTTGATAGGTGCATCGAGCAAGGCTTAAATTGTCAAATACTGATGTTGCTGTCAAGGTT
AGTAATATGCTTATGTGTTTTGCAAACAGTAATTTGATACCTCAGATTTTTTCAGATGTCATAA
TGAATTAGGAATTGACCAGGTTCAACATCCAGGAGCCGAACATCTGATGATGGTTGATATTCGG
AATATGCAAGCAATGGCCTTGTTTCTGCAGAAGTATGACATAAACTTCGATCTATTCTCTGCCA
CGAAAGAGATGGAAAAGCAGGTTTCTCCCGCATCCCCATATCTTTCTTTTTGTTGCTTGTCCCA
GTAATCTAGTGTACTTTTCTACCCTTTCGTAAAACACCAACAAAAAATGTTGAGCCTCTTTCTG
CATTTATAATTGTGTTGAGATAAAAATAAGTCGTCTGCCGTGTTTCAAGTTACTATTGAACCCT
GTTAAACTGCACAAATTCTTACTATACGCAAATCATTTTATAGAGCTATACACATCATAGATTT
CTGGTATCTACTATCTTATATCTGATTATTCAGTAACTTCCAAATTTAGTAAAATAGGGTTTCA
ACCTTTTTCTTATCTGTTTTTTTCTTCAATCATCACTATGAAAATTTTAAGCTCCTTATGTTAG
AACAAATGTGAAAGTTCATTGTATAGTACATGGTAACTAATATGTATCTTTGGTGAAGCAGTAA
TGCAATGCAAGGTTAATAGAATCTTCAAATATTAGATTTATGCATGTGCACAAAAGAATAAGCT
GTCATTCTTTCTATATATTAGCTCGAAGAACAACGATGACAAATTTAGAGTTCTCATTGAGTGT
TATACTGTTATAAACAAGAAGCATCTCCTATTTGCATCTGGACCATTATTGACCAGTTATATAA
TTATTTACATTAGCCAAAGGAGGTTAGCTGTTCAAATATATTGGTCTTCATAAACATCGATATC
TCACACCAGTGTGTGCCTTGTGTGGTATTAAAGTATTGATATCGTTTTTTATTGATGTTTGCTT
TCTGAAGATATGCTATGAGTTTGACTTTGTGCGCGAAGCAAGTGCAATGGAAAGAATTCGAGAA
TTCCTACGTATCACCAATAAGAAACCTCCGGTTATGGTGCCCCGTGTGATTCCTGGGATGGTTA
CCAG
						
					

			
		

Sequences
Splice junction sequence	GCGAAGCAAGTGCAATGGAAAGAATTCGAGAATTCCTACGTATCACCAATAAGAAACCTCCGGT TATGGTGCCCCGTGTGATTCCTGGGATGGTTACCAGgctgctcaaattctggggaaacctgacc tggcacctatggcttgggtgaagagacttgttacgctgtgtgacaaggccccagccacgccatt tgatgtgg
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: 497 Transcript exons: 168702704-168702898,168703101-168703148,168703235-168703 363,168704119-168704243 GCTGCTCAAATTCTGGGGAAACCTGACCTGGCACCTATGGCTTGGGTGAAGAGACTTGTTACGC TGTGTGACAAGGCCCCAGCCACGCCATTTGATGTGGTTAGAGATGTTGTGGAGAAACAGTTCAT GAAGAATTTCGATGACATATTCGAATTCTTCGATGTTGAGCCTGTTGGGTCTGCTTCTATTGCA CAGGTGCATCGAGCAAGGCTTAAATTGTCAAATACTGATGTTGCTGTCAAGGTTCAACATCCAG GAGCCGAACATCTGATGATGGTTGATATTCGGAATATGCAAGCAATGGCCTTGTTTCTGCAGAA GTATGACATAAACTTCGATCTATTCTCTGCCACGAAAGAGATGGAAAAGCAGATATGCTATGAG TTTGACTTTGTGCGCGAAGCAAGTGCAATGGAAAGAATTCGAGAATTCCTACGTATCACCAATA AGAAACCTCCGGTTATGGTGCCCCGTGTGATTCCTGGGATGGTTACCAG
Genomic sequence	GCTGCTCAAATTCTGGGGAAACCTGACCTGGCACCTATGGCTTGGGTGAAGAGACTTGTTACGC TGTGTGACAAGGCCCCAGCCACGCCATTTGATGTGGTTAGAGATGTTGTGGAGAAACAGTTCAT GAAGAATTTCGATGACATATTCGAATTCTTCGATGTTGAGCCTGTTGGGTCTGCTTCTATTGCA CAGGTTCGTGCTTAGGTATTTCTCTTCATCTGTGAAATCTGGGGAGTGAACTTTCTACCATTCC TGCCAATGTTAGGCCTTTGCAAATGTTGTTTCCTTGTTTTGTAACATATAAGTACATAACATCA CATACATACTGGGAACATATCATTTATTTTCTCACTAAAGATGGTTTCCAAGATATATTTTGAT TCATATTTGATAGGTGCATCGAGCAAGGCTTAAATTGTCAAATACTGATGTTGCTGTCAAGGTT AGTAATATGCTTATGTGTTTTGCAAACAGTAATTTGATACCTCAGATTTTTTCAGATGTCATAA TGAATTAGGAATTGACCAGGTTCAACATCCAGGAGCCGAACATCTGATGATGGTTGATATTCGG AATATGCAAGCAATGGCCTTGTTTCTGCAGAAGTATGACATAAACTTCGATCTATTCTCTGCCA CGAAAGAGATGGAAAAGCAGGTTTCTCCCGCATCCCCATATCTTTCTTTTTGTTGCTTGTCCCA GTAATCTAGTGTACTTTTCTACCCTTTCGTAAAACACCAACAAAAAATGTTGAGCCTCTTTCTG CATTTATAATTGTGTTGAGATAAAAATAAGTCGTCTGCCGTGTTTCAAGTTACTATTGAACCCT GTTAAACTGCACAAATTCTTACTATACGCAAATCATTTTATAGAGCTATACACATCATAGATTT CTGGTATCTACTATCTTATATCTGATTATTCAGTAACTTCCAAATTTAGTAAAATAGGGTTTCA ACCTTTTTCTTATCTGTTTTTTTCTTCAATCATCACTATGAAAATTTTAAGCTCCTTATGTTAG AACAAATGTGAAAGTTCATTGTATAGTACATGGTAACTAATATGTATCTTTGGTGAAGCAGTAA TGCAATGCAAGGTTAATAGAATCTTCAAATATTAGATTTATGCATGTGCACAAAAGAATAAGCT GTCATTCTTTCTATATATTAGCTCGAAGAACAACGATGACAAATTTAGAGTTCTCATTGAGTGT TATACTGTTATAAACAAGAAGCATCTCCTATTTGCATCTGGACCATTATTGACCAGTTATATAA TTATTTACATTAGCCAAAGGAGGTTAGCTGTTCAAATATATTGGTCTTCATAAACATCGATATC TCACACCAGTGTGTGCCTTGTGTGGTATTAAAGTATTGATATCGTTTTTTATTGATGTTTGCTT TCTGAAGATATGCTATGAGTTTGACTTTGTGCGCGAAGCAAGTGCAATGGAAAGAATTCGAGAA TTCCTACGTATCACCAATAAGAAACCTCCGGTTATGGTGCCCCGTGTGATTCCTGGGATGGTTA CCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.139548788

Conservation Information
Conserved circRNAs	NA
PMCS	0.139548788

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							168702741-168702749(+)
168703108-168704126(-)
						
						Potential amino acid sequence
						
							MAWVKRLVTLCDKAPATPFDVVRDVVEKQFMKNFDDIFEFFDVEPVGSASIAQVHRARLKLSNT
DVAVKVQHPGAEHLMMVDIRNMQAMALFLQKYDINFDLFSATKEMEKQICYEFDFVREASAMER
IREFLRITNKKPPVMVPRVIPGMVTRLLKFWGNLTWHLWLG*(+)
MHLCNRSRPNRLNIEEFEYVIEILHELFLHNISNHIKWRGWGLVTQRNKSLHPSHRCQVRFPQN
LSSLVTIPGITRGTITGGFLLVIRRNSRILSIALASRTKSNS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	168702741-168702749(+) 168703108-168704126(-)
Potential amino acid sequence	MAWVKRLVTLCDKAPATPFDVVRDVVEKQFMKNFDDIFEFFDVEPVGSASIAQVHRARLKLSNT DVAVKVQHPGAEHLMMVDIRNMQAMALFLQKYDINFDLFSATKEMEKQICYEFDFVREASAMER IREFLRITNKKPPVMVPRVIPGMVTRLLKFWGNLTWHLWLG(+) MHLCNRSRPNRLNIEEFEYVIEILHELFLHNISNHIKWRGWGLVTQRNKSLHPSHRCQVRFPQN LSSLVTIPGITRGTITGGFLLVIRRNSRILSIALASRTKSNS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d042470_circ_g.2

Address

Any questions?

Supported by