Plant Circular RNA Database

Detail information of Zm00001d049959_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d049959_circ_g.1
					
						ID in PlantcircBase
						zma_circ_008028
					
						Alias
						Zm04circ00028
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 55910460-55912177  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d049959						
					
						Parent gene annotation
						
							Cytochrome c1 1 heme protein mitochondrial
							
						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
						Zm00001d049959_T001:4
Zm00001d049959_T004:4
Zm00001d049959_T002:4
Zm00001d049959_T006:3
Zm00001d049959_T003:4
Zm00001d049959_T005:4

General Information
CircRNA Name	Zm00001d049959_circ_g.1
ID in PlantcircBase	zma_circ_008028
Alias	Zm04circ00028
Organism	Zea mays
Position	chr4: 55910460-55912177 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d049959
Parent gene annotation	Cytochrome c1 1 heme protein mitochondrial
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	Zm00001d049959_T001:4 Zm00001d049959_T004:4 Zm00001d049959_T002:4 Zm00001d049959_T006:3 Zm00001d049959_T003:4 Zm00001d049959_T005:4

			
						 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  
						
							CAAATAAACAAAGAGTTCACCAAAACACTTACAGCGGACTGGTTGTGGAGAATTCTCTTCAGAA
GCTGGTTAATGCCCCTTGCGGCAGCCATCAAGCACTctgaacaccagcaggtggatcacggtat
ccagtaagaagagcgaaaacatagttctgaccattgtgccttgcctggatgaatgcaatgcaaa
cagtaagc

									
								

					

						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
						
							CTGAACACCAGCAGGTGGATCACGGTATCCAGTAAGAAGAGCGAAAACATAGTTCTGACCATTG
TGCCTTGCCTGGATGAATGCAATGCAAACAGTAAGCCATAATCAGTGAAAGGCCACATCAAAGC
AATGCAACACCATTAACTGCAATTACCTTTGTGATAAGACTAAGGTCCGGCGGGTAGGCGCCAC
CATTAGCAAATCGGGCTGCTTGCTCATTTGCATAAGGCTGTGGAAAGCGATCGCTGAGTTTACC
AGGGCGGGTGAACATTTCACCCTCATCATTAGGACCATCAACGACCTCAATCTCAGCAGCCATT
GCCTTTGTTTCCTCCTCAGTATAGGCCACCCCAACCAAATCACGGTATGAAATCAAGGACATGG
AGTGACAAGAAGCACAAACTTGTGTGTAAACTTGATGCCCTCGGCGAATTCTGTGCAATAATAT
TTTTATAAGATAAATTAGAGCAACATACAAGAAAACAAGGTACTAGCACTTCAACAAGAATTTA
TCCTAGAAACAAGACAACTAAAGAATGACTTCAGTTGTAATTCTTAAATCACTACAGCATGCCA
TTTAAGAATTATATACCCCAGTACACAATCAGGTTGTCAATCTCTGTCAACAATCCATATTTCA
TAAATAAGGCTTACATGAATTTGTAAACATCACGCCATATCATATGAAACAAAGCTTCATGAAA
AGAAGAAGCTATGGTTGACTTACGATGCATGATCATAAGAGCTCATGATGCCAGCATGTGGCCA
CGGATAATCTGGGGCTGCCAAACCATGCTCAGCTTCATCAGCAGATGCTATTGTAGCAAAACTC
AAAAGACCGGAGGCACCAACTCCAAGAAGCGCCAATGCTCTCAATCCAGCAGAGGACTCTTCAT
GATTTCCCCGAAATGAAGAAAGCAGCCATGGACCCTGAAGATCATGATGATGATGTTAGACACA
ACTGAGACACACAGAAAAATGGAACTTGTCTAACCAACCGGTAAATATGATCTTCTAGATAACT
ATTGATTTCCATAAATACTATCTTTTATTCAGAATGGAGGGTCACAGTAAAAATATGATTAGCA
GTCAATGTCTAGTCAACAGAACTTAAAATGCACTCCCTCCGTTCACAAATATATGACACCATTG
ATTTTTTTCCAAAACATTGACCACTCATCTTATTCAAAGAAAATCGTGAGTTACCATTTATTTT
GTTGTGATTTGTTTTATCACTTAAGGTTGTTTGACCGTGACTTGAAATTTTACATTTTCGAATA
AGACGAGTGGTAAAGTTTTGAAAAAAAAATCAATGGCGTCATATATATGTGAAAGGAGGCACTA
CTATAATTTATGTTATTTGGTTCAAATCGATACAGTAGGAGAGGACAAAACTGGCAAGCATGAG
CCACACAAGAAACACATACAGCAGTGTATATCATCACTCCATGTTGAGAATGTCGATTCTAACA
GGCTAAGCATGTTCCCTACGACTTGTTTTTAAGGATGAACAATAGGTTCCAGTCAGATAGATTC
CATATCGTGATGGTGTACCCAAGATGGATGTGGAAATAAAAAACACATAAGATTGAATATGGAC
GCATTTTAGAGCAACATGCAAATAAACAAAGAGTTCACCAAAACACTTACAGCGGACTGGTTGT
GGAGAATTCTCTTCAGAAGCTGGTTAATGCCCCTTGCGGCAGCCATCAAGCACT
						
					

			
		

Sequences
Splice junction sequence	CAAATAAACAAAGAGTTCACCAAAACACTTACAGCGGACTGGTTGTGGAGAATTCTCTTCAGAA GCTGGTTAATGCCCCTTGCGGCAGCCATCAAGCACTctgaacaccagcaggtggatcacggtat ccagtaagaagagcgaaaacatagttctgaccattgtgccttgcctggatgaatgcaatgcaaa cagtaagc
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	CTGAACACCAGCAGGTGGATCACGGTATCCAGTAAGAAGAGCGAAAACATAGTTCTGACCATTG TGCCTTGCCTGGATGAATGCAATGCAAACAGTAAGCCATAATCAGTGAAAGGCCACATCAAAGC AATGCAACACCATTAACTGCAATTACCTTTGTGATAAGACTAAGGTCCGGCGGGTAGGCGCCAC CATTAGCAAATCGGGCTGCTTGCTCATTTGCATAAGGCTGTGGAAAGCGATCGCTGAGTTTACC AGGGCGGGTGAACATTTCACCCTCATCATTAGGACCATCAACGACCTCAATCTCAGCAGCCATT GCCTTTGTTTCCTCCTCAGTATAGGCCACCCCAACCAAATCACGGTATGAAATCAAGGACATGG AGTGACAAGAAGCACAAACTTGTGTGTAAACTTGATGCCCTCGGCGAATTCTGTGCAATAATAT TTTTATAAGATAAATTAGAGCAACATACAAGAAAACAAGGTACTAGCACTTCAACAAGAATTTA TCCTAGAAACAAGACAACTAAAGAATGACTTCAGTTGTAATTCTTAAATCACTACAGCATGCCA TTTAAGAATTATATACCCCAGTACACAATCAGGTTGTCAATCTCTGTCAACAATCCATATTTCA TAAATAAGGCTTACATGAATTTGTAAACATCACGCCATATCATATGAAACAAAGCTTCATGAAA AGAAGAAGCTATGGTTGACTTACGATGCATGATCATAAGAGCTCATGATGCCAGCATGTGGCCA CGGATAATCTGGGGCTGCCAAACCATGCTCAGCTTCATCAGCAGATGCTATTGTAGCAAAACTC AAAAGACCGGAGGCACCAACTCCAAGAAGCGCCAATGCTCTCAATCCAGCAGAGGACTCTTCAT GATTTCCCCGAAATGAAGAAAGCAGCCATGGACCCTGAAGATCATGATGATGATGTTAGACACA ACTGAGACACACAGAAAAATGGAACTTGTCTAACCAACCGGTAAATATGATCTTCTAGATAACT ATTGATTTCCATAAATACTATCTTTTATTCAGAATGGAGGGTCACAGTAAAAATATGATTAGCA GTCAATGTCTAGTCAACAGAACTTAAAATGCACTCCCTCCGTTCACAAATATATGACACCATTG ATTTTTTTCCAAAACATTGACCACTCATCTTATTCAAAGAAAATCGTGAGTTACCATTTATTTT GTTGTGATTTGTTTTATCACTTAAGGTTGTTTGACCGTGACTTGAAATTTTACATTTTCGAATA AGACGAGTGGTAAAGTTTTGAAAAAAAAATCAATGGCGTCATATATATGTGAAAGGAGGCACTA CTATAATTTATGTTATTTGGTTCAAATCGATACAGTAGGAGAGGACAAAACTGGCAAGCATGAG CCACACAAGAAACACATACAGCAGTGTATATCATCACTCCATGTTGAGAATGTCGATTCTAACA GGCTAAGCATGTTCCCTACGACTTGTTTTTAAGGATGAACAATAGGTTCCAGTCAGATAGATTC CATATCGTGATGGTGTACCCAAGATGGATGTGGAAATAAAAAACACATAAGATTGAATATGGAC GCATTTTAGAGCAACATGCAAATAAACAAAGAGTTCACCAAAACACTTACAGCGGACTGGTTGT GGAGAATTCTCTTCAGAAGCTGGTTAATGCCCCTTGCGGCAGCCATCAAGCACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.128397502

Conservation Information
Conserved circRNAs	NA
PMCS	0.128397502

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							55912151-55910491(+)
55910755-55912149(-)
55912171-55912171(-)
						
						Potential amino acid sequence
						
							MPLAAAIKHSEHQQVDHGIQ*(+)
MVLMMRVKCSPALVNSAIAFHSLMQMSKQPDLLMVAPTRRTLVLSQRQGTMVRTMFSLFLLDTV
IHLLVFRVLDGCRKGH*(-)
MAAARGINQLLKRILHNQSAGPWLLSSFRGNHEESSAGLRALALLGVGASGLLSFATIASADEA
EHGLAAPDYPWPHAGIMSSYDHASIRRGHQVYTQVCASCHSMSLISYRDLVGVAYTEEETKAMA
AEIEVVDGPNDEGEMFTRPGKLSDRFPQPYANEQAARFANGGAYPPDLSLITKARHNGQNYVFA
LLTGYRDPPAGVQSA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	55912151-55910491(+) 55910755-55912149(-) 55912171-55912171(-)
Potential amino acid sequence	MPLAAAIKHSEHQQVDHGIQ(+) MVLMMRVKCSPALVNSAIAFHSLMQMSKQPDLLMVAPTRRTLVLSQRQGTMVRTMFSLFLLDTV IHLLVFRVLDGCRKGH(-) MAAARGINQLLKRILHNQSAGPWLLSSFRGNHEESSAGLRALALLGVGASGLLSFATIASADEA EHGLAAPDYPWPHAGIMSSYDHASIRRGHQVYTQVCASCHSMSLISYRDLVGVAYTEEETKAMA AEIEVVDGPNDEGEMFTRPGKLSDRFPQPYANEQAARFANGGAYPPDLSLITKARHNGQNYVFA LLTGYRDPPAGVQSA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d049959_circ_g.1

Address

Any questions?

Supported by