Plant Circular RNA Database

Detail information of Zm00001d053155_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d053155_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008249
					
						Alias
						Zm04circ00092
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 216752533-216754439  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d053155						
					
						Parent gene annotation
						
							Phox-associated domain;Phox-like;Sorting nexin C-terminal
							
						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
						Zm00001d053155_T003:7
Zm00001d053155_T002:7
Zm00001d053155_T005:7
Zm00001d053155_T001:7
Zm00001d053155_T006:7
Zm00001d053155_T014:7
Zm00001d053155_T012:7
Zm00001d053155_T004:7
Zm00001d053155_T007:7
Zm00001d053155_T016:7

General Information
CircRNA Name	Zm00001d053155_circ_g.2
ID in PlantcircBase	zma_circ_008249
Alias	Zm04circ00092
Organism	Zea mays
Position	chr4: 216752533-216754439 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d053155
Parent gene annotation	Phox-associated domain;Phox-like;Sorting nexin C-terminal
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	Zm00001d053155_T003:7 Zm00001d053155_T002:7 Zm00001d053155_T005:7 Zm00001d053155_T001:7 Zm00001d053155_T006:7 Zm00001d053155_T014:7 Zm00001d053155_T012:7 Zm00001d053155_T004:7 Zm00001d053155_T007:7 Zm00001d053155_T016:7

			
						 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  
						
							TTCTTTTCACAAACCAGCTCTTGTTATCCGCATCAGTCACCACAATAGAATAAACTGCAAAAGA
TTTTGAACCTTGTTTCTCAAAATATGCACCAACAACatcttgaatccaatgtattccttgtacg
atgacatcttctcttcggagccaattgatttgtcttatgatccattcatcaattgcatcttcca
tgaccaac

									
								

					

						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
						
							ATCTTGAATCCAATGTATTCCTTGTACGATGACATCTTCTCTTCGGAGCCAATTGATTTGTCTT
ATGATCCATTCATCAATTGCATCTTCCATGACCAACTGCAAAATTTGTTTTGATATCCAAAGAA
CCTGTCTCCTACAGATTACATAACATTAGTAAAACCCCATGTTTTGTAATTGAAAGAATGAAAC
AGCTAGATTGCAGAAGTGATTGAGTTGTAGAATTGAAGCATAGATGGTGAAAACACAAGTGTGT
GTGTGCATGGCTATGAAAACAAAAAAAAAATTGTGACAACCCACCCAAATTTCATTAGCATCTA
AACAAACATCGGAGAATATACTGCCAAGATACATGGAATGGGAACCATATGCTGATATCTAGTA
ACCAGTCCTTCCAATCAGGCCAATTAAATGCCTTTGGGTTACAAGTTTCTACAGTATTTCAGTG
TATCGTTTACTTTATTTGTACTATGTAACAGTAATCTGAAACTACTAAAGTACTAAGCAAATTC
TGAGGAACAAATTTGATAAAGTTAATTATAAAGAAACTAACCGTATCCAACCCCGTCGCTTTAG
CTGGAATACTTTGTCAACCAGGTTCAATAAAGGCACACTAACATTTGTTGGCATCCACTGCCAA
AATAGAAGAGAAGGTTTATCAGTAAAAGGAAAAACAGTAACAACACATGTTCCCTATGATCTGT
ATCAAATAAATTATGTAGTAGCAGGGTATGGTGTACCTCAGGAGGAATTCCTGTTGGATCCTCA
AATGCATTTAGAGATGACATGTTTGAAGAATCAGAATATTCCTTTGCAGGTTTTCCTATTTGGT
CGCTGGCTTGTTTATCCAAACTAGAGCATGTTTCGATGTGCTCAACATCATTTGAAGTATGTCC
TCTATTATTGACCTCATTGTCTGAATGGCATCCACTATTCACAGAAGAGATGTGATCTTCATAG
TTACTATCACCATCTGAAAGGCTATGAGCCCTTTCCAAGTTTCTTTGATGCAAGTTGTGGTTAT
CTTTCTCTTCCTGGTTCCAAGATAGAGACATCCTATTATCTGCAAATTGGGCAGTTGCACTAGA
AGGTGATGTGCCGACCGCCCGTTTCAAACCATCTGAAACTCCTTTAAATTGTCGAACAATGTCA
TCCATTGCATCATCAACATTAACTGTTTTAAGAAAAATAAAATGTCTTCAAGAAAAGAACATAG
CAAGTTACAGCTTTTAAGGGGGAATACAAGTATGGGGCATGCATACCAGCCAAGGTTTTCATAA
CAGAGGAGGACTTTCCAGCAGAGTAAGTCTACAAAGTGGAGAAGAATTGAAGTGCTAAGAACCT
CAAGAAAGCAGAAGCACTGAATGAAGATGTGTGCATTCCTTGTCATTAAGGACAAGGCTATAAG
GATTTGCTTGGTGTAAATCACACACCTTTGAGGATGCACTCAGAAAATCCAAAACTTCATGCTG
CTCTGCAATATTAGCTATAGACAAGAGATCCTATTGAACACAAAATGAATATTATACATTTAAA
GTAAAAGATGAGCAAAAATGCAAGAGAACCAAACATACTTGAAGATATTTGTCCAGGAGAATGC
ACCGTTGGTGCACAAGATAATCATCAACGCTAGATGAAAGAAAACTCTTTGGAGGCAGATGTAA
TGAATAATTAGGTATCTCCTTCAGTTGTCGATGAAGACGTTCAAAATTCCGGTATCTACAGATA
CAAGCTATAGGTCAGGACCATACATGTTCCTCTCTCGAAGCTGCAATTAATTTACAAATATGTC
AAGTAAAACCATGCCTTCTTTTCACAAACCAGCTCTTGTTATCCGCATCAGTCACCACAATAGA
ATAAACTGCAAAAGATTTTGAACCTTGTTTCTCAAAATATGCACCAACAAC
						
					

			
		

Sequences
Splice junction sequence	TTCTTTTCACAAACCAGCTCTTGTTATCCGCATCAGTCACCACAATAGAATAAACTGCAAAAGA TTTTGAACCTTGTTTCTCAAAATATGCACCAACAACatcttgaatccaatgtattccttgtacg atgacatcttctcttcggagccaattgatttgtcttatgatccattcatcaattgcatcttcca tgaccaac
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	ATCTTGAATCCAATGTATTCCTTGTACGATGACATCTTCTCTTCGGAGCCAATTGATTTGTCTT ATGATCCATTCATCAATTGCATCTTCCATGACCAACTGCAAAATTTGTTTTGATATCCAAAGAA CCTGTCTCCTACAGATTACATAACATTAGTAAAACCCCATGTTTTGTAATTGAAAGAATGAAAC AGCTAGATTGCAGAAGTGATTGAGTTGTAGAATTGAAGCATAGATGGTGAAAACACAAGTGTGT GTGTGCATGGCTATGAAAACAAAAAAAAAATTGTGACAACCCACCCAAATTTCATTAGCATCTA AACAAACATCGGAGAATATACTGCCAAGATACATGGAATGGGAACCATATGCTGATATCTAGTA ACCAGTCCTTCCAATCAGGCCAATTAAATGCCTTTGGGTTACAAGTTTCTACAGTATTTCAGTG TATCGTTTACTTTATTTGTACTATGTAACAGTAATCTGAAACTACTAAAGTACTAAGCAAATTC TGAGGAACAAATTTGATAAAGTTAATTATAAAGAAACTAACCGTATCCAACCCCGTCGCTTTAG CTGGAATACTTTGTCAACCAGGTTCAATAAAGGCACACTAACATTTGTTGGCATCCACTGCCAA AATAGAAGAGAAGGTTTATCAGTAAAAGGAAAAACAGTAACAACACATGTTCCCTATGATCTGT ATCAAATAAATTATGTAGTAGCAGGGTATGGTGTACCTCAGGAGGAATTCCTGTTGGATCCTCA AATGCATTTAGAGATGACATGTTTGAAGAATCAGAATATTCCTTTGCAGGTTTTCCTATTTGGT CGCTGGCTTGTTTATCCAAACTAGAGCATGTTTCGATGTGCTCAACATCATTTGAAGTATGTCC TCTATTATTGACCTCATTGTCTGAATGGCATCCACTATTCACAGAAGAGATGTGATCTTCATAG TTACTATCACCATCTGAAAGGCTATGAGCCCTTTCCAAGTTTCTTTGATGCAAGTTGTGGTTAT CTTTCTCTTCCTGGTTCCAAGATAGAGACATCCTATTATCTGCAAATTGGGCAGTTGCACTAGA AGGTGATGTGCCGACCGCCCGTTTCAAACCATCTGAAACTCCTTTAAATTGTCGAACAATGTCA TCCATTGCATCATCAACATTAACTGTTTTAAGAAAAATAAAATGTCTTCAAGAAAAGAACATAG CAAGTTACAGCTTTTAAGGGGGAATACAAGTATGGGGCATGCATACCAGCCAAGGTTTTCATAA CAGAGGAGGACTTTCCAGCAGAGTAAGTCTACAAAGTGGAGAAGAATTGAAGTGCTAAGAACCT CAAGAAAGCAGAAGCACTGAATGAAGATGTGTGCATTCCTTGTCATTAAGGACAAGGCTATAAG GATTTGCTTGGTGTAAATCACACACCTTTGAGGATGCACTCAGAAAATCCAAAACTTCATGCTG CTCTGCAATATTAGCTATAGACAAGAGATCCTATTGAACACAAAATGAATATTATACATTTAAA GTAAAAGATGAGCAAAAATGCAAGAGAACCAAACATACTTGAAGATATTTGTCCAGGAGAATGC ACCGTTGGTGCACAAGATAATCATCAACGCTAGATGAAAGAAAACTCTTTGGAGGCAGATGTAA TGAATAATTAGGTATCTCCTTCAGTTGTCGATGAAGACGTTCAAAATTCCGGTATCTACAGATA CAAGCTATAGGTCAGGACCATACATGTTCCTCTCTCGAAGCTGCAATTAATTTACAAATATGTC AAGTAAAACCATGCCTTCTTTTCACAAACCAGCTCTTGTTATCCGCATCAGTCACCACAATAGA ATAAACTGCAAAAGATTTTGAACCTTGTTTCTCAAAATATGCACCAACAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.131284876

Conservation Information
Conserved circRNAs	NA
PMCS	0.131284876

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							216753812-216752535(-)
216752569-216754378(-)
216752607-216754422(-)
						
					

						Potential amino acid sequence
						
							MKTLAVNVDDAMDDIVRQFKGVSDGLKRAVGTSPSSATAQFADNRMSLSWNQEEKDNHNLHQRN
LERAHSLSDGDSNYEDHISSVNSGCHSDNEVNNRGHTSNDVEHIETCSSLDKQASDQIGKPAKE
YSDSSNMSSLNAFEDPTGIPPEWMPTNVSVPLLNLVDKVFQLKRRGWIRRQVLWISKQILQLVM
EDAIDEWIIRQINWLRREDVIVQGIHWIQDVVGAYFEKQGSKSFAVYSIVVTDADNKSWFVKRR
YRNFERLHRQLKEIPNYSLHLPPKSFLSSSVDDYLVHQRCILLDKYLQDLLSIANIAEQHEVLD
FLSASSKTYSAGKSSSVMKTLAVNVDDAMDDIVRQFKGVSDGLKRAVGTSPSSATAQFADNRMS
LSWNQEEKDNHNLHQRNLERAHSLSDGDSNYEDHISSVNSGCHSDNEVNNRGHTSNDVEHIETC
SSLDKQASDQIGKPAKEYSDSSNMSSLNAFEDPTGIPPEWMPTNVSVPLLNLVDKVFQLKRRGW
IRRQVLWISKQILQLVMEDAIDEWIIRQINWLRREDVIVQGIHWIQDVVGAYFEKQGSKSFAVY
SIVVTDADNKSWFVKRRYRNFERLHRQLKEIPNYSLHLPPKSFLSSSVDDYLVHQRCILLDKYL
QDLLSIANIAEQHEVLDFLSASSKTYSAGKSSSVMKTLAVNVDDAMDDIVRQFKGVSDGLKRAV
GTSPSSATAQFADNRMSLSWNQEEKDNHNLHQRNLERAHSLSDGDSNYEDHISSVNSGCHSDNE
VNNRGHTSNDVEHIETCSSLDKQASDQIGKPAKEYSDSSNMSSLNAFEDPTGIPPEWMPTNVSV
PLLNLVDKVFQLKRRGWIRRQVLWISKQILQLVMEDAIDEWIIRQINWLRREDVIVQGIHWIQD
VVGAYFEKQGSKSFAVYSIVVTDADNKSWFVKRRYRNFERLHRQLKEIPNYSLHLPPKSFLSSS
VDDYLVHQRCILLDKYLQDLLSIANIAEQHEVLDFLSASSKTYSAGKSSSVMKTLAVNVDDAMD
DIVRQFKGVSDGLKRAVGTSPSSATAQFADNRMSLSWNQEEKDNHNLHQRNLERAHSLSDGDSN
YEDHISSVNSGCHSDNEVNNRGHTSNDVEHIETCSSLDKQASDQIGKPAKEYSDSSNMSSLNAF
EDPTGIPPEWMPTNVSVPLLNLVDKVFQLKRRGWIRRQVLWISKQILQLVMEDAIDEWIIRQIN
WLRREDVIVQGIHWIQD(-)
MSSYKEYIGFKMLLVHILRNKVQNLLQFILLW*(-)
MDHKTNQLAPKRRCHRTRNTLDSRCCWCIF*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	216753812-216752535(-) 216752569-216754378(-) 216752607-216754422(-)
Potential amino acid sequence	MKTLAVNVDDAMDDIVRQFKGVSDGLKRAVGTSPSSATAQFADNRMSLSWNQEEKDNHNLHQRN LERAHSLSDGDSNYEDHISSVNSGCHSDNEVNNRGHTSNDVEHIETCSSLDKQASDQIGKPAKE YSDSSNMSSLNAFEDPTGIPPEWMPTNVSVPLLNLVDKVFQLKRRGWIRRQVLWISKQILQLVM EDAIDEWIIRQINWLRREDVIVQGIHWIQDVVGAYFEKQGSKSFAVYSIVVTDADNKSWFVKRR YRNFERLHRQLKEIPNYSLHLPPKSFLSSSVDDYLVHQRCILLDKYLQDLLSIANIAEQHEVLD FLSASSKTYSAGKSSSVMKTLAVNVDDAMDDIVRQFKGVSDGLKRAVGTSPSSATAQFADNRMS LSWNQEEKDNHNLHQRNLERAHSLSDGDSNYEDHISSVNSGCHSDNEVNNRGHTSNDVEHIETC SSLDKQASDQIGKPAKEYSDSSNMSSLNAFEDPTGIPPEWMPTNVSVPLLNLVDKVFQLKRRGW IRRQVLWISKQILQLVMEDAIDEWIIRQINWLRREDVIVQGIHWIQDVVGAYFEKQGSKSFAVY SIVVTDADNKSWFVKRRYRNFERLHRQLKEIPNYSLHLPPKSFLSSSVDDYLVHQRCILLDKYL QDLLSIANIAEQHEVLDFLSASSKTYSAGKSSSVMKTLAVNVDDAMDDIVRQFKGVSDGLKRAV GTSPSSATAQFADNRMSLSWNQEEKDNHNLHQRNLERAHSLSDGDSNYEDHISSVNSGCHSDNE VNNRGHTSNDVEHIETCSSLDKQASDQIGKPAKEYSDSSNMSSLNAFEDPTGIPPEWMPTNVSV PLLNLVDKVFQLKRRGWIRRQVLWISKQILQLVMEDAIDEWIIRQINWLRREDVIVQGIHWIQD VVGAYFEKQGSKSFAVYSIVVTDADNKSWFVKRRYRNFERLHRQLKEIPNYSLHLPPKSFLSSS VDDYLVHQRCILLDKYLQDLLSIANIAEQHEVLDFLSASSKTYSAGKSSSVMKTLAVNVDDAMD DIVRQFKGVSDGLKRAVGTSPSSATAQFADNRMSLSWNQEEKDNHNLHQRNLERAHSLSDGDSN YEDHISSVNSGCHSDNEVNNRGHTSNDVEHIETCSSLDKQASDQIGKPAKEYSDSSNMSSLNAF EDPTGIPPEWMPTNVSVPLLNLVDKVFQLKRRGWIRRQVLWISKQILQLVMEDAIDEWIIRQIN WLRREDVIVQGIHWIQD(-) MSSYKEYIGFKMLLVHILRNKVQNLLQFILLW(-) MDHKTNQLAPKRRCHRTRNTLDSRCCWCIF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d053155_circ_g.2

Address

Any questions?

Supported by