Plant Circular RNA Database

Detail information of Zm00001d021541_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d021541_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009420
					
						Alias
						Zm07circ00078, zma_circ_0002476
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 155406765-155407637  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d021541						
					
						Parent gene annotation
						
							Protein CHROMATIN REMODELING 4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d021541_T024:2
Zm00001d021541_T027:2
Zm00001d021541_T038:2
Zm00001d021541_T036:2
Zm00001d021541_T004:2
Zm00001d021541_T005:2
Zm00001d021541_T010:2
Zm00001d021541_T002:2
Zm00001d021541_T001:2
Zm00001d021541_T007:2
Zm00001d021541_T009:2
Zm00001d021541_T016:2
Zm00001d021541_T018:2
Zm00001d021541_T039:1
Zm00001d021541_T006:2
Zm00001d021541_T032:2
Zm00001d021541_T023:2
Zm00001d021541_T028:2
Zm00001d021541_T022:1
Zm00001d021541_T003:2
Zm00001d021541_T034:2
Zm00001d021541_T020:2
Zm00001d021541_T008:2

General Information
CircRNA Name	Zm00001d021541_circ_g.1
ID in PlantcircBase	zma_circ_009420
Alias	Zm07circ00078, zma_circ_0002476
Organism	Zea mays
Position	chr7: 155406765-155407637 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d021541
Parent gene annotation	Protein CHROMATIN REMODELING 4
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d021541_T024:2 Zm00001d021541_T027:2 Zm00001d021541_T038:2 Zm00001d021541_T036:2 Zm00001d021541_T004:2 Zm00001d021541_T005:2 Zm00001d021541_T010:2 Zm00001d021541_T002:2 Zm00001d021541_T001:2 Zm00001d021541_T007:2 Zm00001d021541_T009:2 Zm00001d021541_T016:2 Zm00001d021541_T018:2 Zm00001d021541_T039:1 Zm00001d021541_T006:2 Zm00001d021541_T032:2 Zm00001d021541_T023:2 Zm00001d021541_T028:2 Zm00001d021541_T022:1 Zm00001d021541_T003:2 Zm00001d021541_T034:2 Zm00001d021541_T020:2 Zm00001d021541_T008:2

			
						 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  
						
							ATCACCACCAAAAAGAAAACACTCAGATGGAAAAGCACCTTCATCCAGTACCAAGAAAGGGAAA
AAGAAAGTGAAATTTGTTGAGAAAAAGCACTCTGAGtattttttcgagtgcgtagaatgtgatc
ttggtggcaatttgctatgttgtgatagctgtcctcgtgtttaccacttggaatgcctcaatcc
tcctctta

									
								

					

						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: 780
Transcript exons: 155406765-155406866,155406960-155407637
TATTTTTTCGAGTGCGTAGAATGTGATCTTGGTGGCAATTTGCTATGTTGTGATAGCTGTCCTC
GTGTTTACCACTTGGAATGCCTCAATCCTCCTCTTAAGCGTGCACCCCCTGGGAAGTGGCAATG
TCCAAGATGCCGTCCGAAAAAAGTTAGCTTGAAGCTGTTAGGTAATGCAGATGTTGACACTTCT
AAACGTGAAAAAAGTACAAGGACATATGCAAGTACGGCATCAGATAGTCCACCTTCGCATACAA
AAGTCTCCTTTAAGACCAGGAACTCCACACAAGACAAAACTGGATTAAACGAACAAGGAAAAGA
GTCATCTGGTGGCACAATGAATGGGGGTGAAACCAGTACGAAGAATAATGAAGTTGAGAAAAAG
AAGACACTGATATTACATTTGAAGAAGCGTTCAACCAAGGAATTGTCAGAGAACACTAAACCCT
CGAAGTCAGAATTTGTTGAACTTTCAGAAGAGAAAATTGTAAAACATGGAAGTGTTTTGAAACT
CAAGAAACATCCACATCGTATGGACTTGTCTCCAAGTAAATCTAAAACCAGGAGGCAAAGTAGC
CAGAGAGAGAGTAAAAGATCTGGCACAAAAAAGATTAAATATTCCATGTCTGATGATGACAGTG
TTTCCTCATCAGAACCATCGACATCTCTTGATAACAGTGAATCACCACCAAAAAGAAAACACTC
AGATGGAAAAGCACCTTCATCCAGTACCAAGAAAGGGAAAAAGAAAGTGAAATTTGTTGAGAAA
AAGCACTCTGAG
						
					

						Genomic sequence
						
							TATTTTTTCGAGTGCGTAGAATGTGATCTTGGTGGCAATTTGCTATGTTGTGATAGCTGTCCTC
GTGTTTACCACTTGGAATGCCTCAATCCTCCTCTTAAGGTTTGTATTGGGCCCTCACGTTTGGT
TCAGAAGTTACAAATTTTCATTTATAATGATCAGAATTTTAATCATTGCCTTCTGTCCCCAATC
TAGCGTGCACCCCCTGGGAAGTGGCAATGTCCAAGATGCCGTCCGAAAAAAGTTAGCTTGAAGC
TGTTAGGTAATGCAGATGTTGACACTTCTAAACGTGAAAAAAGTACAAGGACATATGCAAGTAC
GGCATCAGATAGTCCACCTTCGCATACAAAAGTCTCCTTTAAGACCAGGAACTCCACACAAGAC
AAAACTGGATTAAACGAACAAGGAAAAGAGTCATCTGGTGGCACAATGAATGGGGGTGAAACCA
GTACGAAGAATAATGAAGTTGAGAAAAAGAAGACACTGATATTACATTTGAAGAAGCGTTCAAC
CAAGGAATTGTCAGAGAACACTAAACCCTCGAAGTCAGAATTTGTTGAACTTTCAGAAGAGAAA
ATTGTAAAACATGGAAGTGTTTTGAAACTCAAGAAACATCCACATCGTATGGACTTGTCTCCAA
GTAAATCTAAAACCAGGAGGCAAAGTAGCCAGAGAGAGAGTAAAAGATCTGGCACAAAAAAGAT
TAAATATTCCATGTCTGATGATGACAGTGTTTCCTCATCAGAACCATCGACATCTCTTGATAAC
AGTGAATCACCACCAAAAAGAAAACACTCAGATGGAAAAGCACCTTCATCCAGTACCAAGAAAG
GGAAAAAGAAAGTGAAATTTGTTGAGAAAAAGCACTCTGAG
						
					

			
		

Sequences
Splice junction sequence	ATCACCACCAAAAAGAAAACACTCAGATGGAAAAGCACCTTCATCCAGTACCAAGAAAGGGAAA AAGAAAGTGAAATTTGTTGAGAAAAAGCACTCTGAGtattttttcgagtgcgtagaatgtgatc ttggtggcaatttgctatgttgtgatagctgtcctcgtgtttaccacttggaatgcctcaatcc tcctctta
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: 780 Transcript exons: 155406765-155406866,155406960-155407637 TATTTTTTCGAGTGCGTAGAATGTGATCTTGGTGGCAATTTGCTATGTTGTGATAGCTGTCCTC GTGTTTACCACTTGGAATGCCTCAATCCTCCTCTTAAGCGTGCACCCCCTGGGAAGTGGCAATG TCCAAGATGCCGTCCGAAAAAAGTTAGCTTGAAGCTGTTAGGTAATGCAGATGTTGACACTTCT AAACGTGAAAAAAGTACAAGGACATATGCAAGTACGGCATCAGATAGTCCACCTTCGCATACAA AAGTCTCCTTTAAGACCAGGAACTCCACACAAGACAAAACTGGATTAAACGAACAAGGAAAAGA GTCATCTGGTGGCACAATGAATGGGGGTGAAACCAGTACGAAGAATAATGAAGTTGAGAAAAAG AAGACACTGATATTACATTTGAAGAAGCGTTCAACCAAGGAATTGTCAGAGAACACTAAACCCT CGAAGTCAGAATTTGTTGAACTTTCAGAAGAGAAAATTGTAAAACATGGAAGTGTTTTGAAACT CAAGAAACATCCACATCGTATGGACTTGTCTCCAAGTAAATCTAAAACCAGGAGGCAAAGTAGC CAGAGAGAGAGTAAAAGATCTGGCACAAAAAAGATTAAATATTCCATGTCTGATGATGACAGTG TTTCCTCATCAGAACCATCGACATCTCTTGATAACAGTGAATCACCACCAAAAAGAAAACACTC AGATGGAAAAGCACCTTCATCCAGTACCAAGAAAGGGAAAAAGAAAGTGAAATTTGTTGAGAAA AAGCACTCTGAG
Genomic sequence	TATTTTTTCGAGTGCGTAGAATGTGATCTTGGTGGCAATTTGCTATGTTGTGATAGCTGTCCTC GTGTTTACCACTTGGAATGCCTCAATCCTCCTCTTAAGGTTTGTATTGGGCCCTCACGTTTGGT TCAGAAGTTACAAATTTTCATTTATAATGATCAGAATTTTAATCATTGCCTTCTGTCCCCAATC TAGCGTGCACCCCCTGGGAAGTGGCAATGTCCAAGATGCCGTCCGAAAAAAGTTAGCTTGAAGC TGTTAGGTAATGCAGATGTTGACACTTCTAAACGTGAAAAAAGTACAAGGACATATGCAAGTAC GGCATCAGATAGTCCACCTTCGCATACAAAAGTCTCCTTTAAGACCAGGAACTCCACACAAGAC AAAACTGGATTAAACGAACAAGGAAAAGAGTCATCTGGTGGCACAATGAATGGGGGTGAAACCA GTACGAAGAATAATGAAGTTGAGAAAAAGAAGACACTGATATTACATTTGAAGAAGCGTTCAAC CAAGGAATTGTCAGAGAACACTAAACCCTCGAAGTCAGAATTTGTTGAACTTTCAGAAGAGAAA ATTGTAAAACATGGAAGTGTTTTGAAACTCAAGAAACATCCACATCGTATGGACTTGTCTCCAA GTAAATCTAAAACCAGGAGGCAAAGTAGCCAGAGAGAGAGTAAAAGATCTGGCACAAAAAAGAT TAAATATTCCATGTCTGATGATGACAGTGTTTCCTCATCAGAACCATCGACATCTCTTGATAAC AGTGAATCACCACCAAAAAGAAAACACTCAGATGGAAAAGCACCTTCATCCAGTACCAAGAAAG GGAAAAAGAAAGTGAAATTTGTTGAGAAAAAGCACTCTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.202632934

Conservation Information
Conserved circRNAs	NA
PMCS	0.202632934

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							155407195-155407634(+)
						
						Potential amino acid sequence
						
							MNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVKHGSVLKLKKHPH
RMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSESPPKRKHSDGKAP
SSSTKKGKKKVKFVEKKHSEYFFECVECDLGGNLLCCDSCPRVYHLECLNPPLKRAPPGKWQCP
RCRPKKVSLKLLGNADVDTSKREKSTRTYASTASDSPPSHTKVSFKTRNSTQDKTGLNEQGKES
SGGTMNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVKHGSVLKLK
KHPHRMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSESPPKRKHSD
GKAPSSSTKKGKKKVKFVEKKHSEYFFECVECDLGGNLLCCDSCPRVYHLECLNPPLKRAPPGK
WQCPRCRPKKVSLKLLGNADVDTSKREKSTRTYASTASDSPPSHTKVSFKTRNSTQDKTGLNEQ
GKESSGGTMNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVKHGSV
LKLKKHPHRMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSESPPKR
KHSDGKAPSSSTKKGKKKVKFVEKKHSEYFFECVECDLGGNLLCCDSCPRVYHLECLNPPLKRA
PPGKWQCPRCRPKKVSLKLLGNADVDTSKREKSTRTYASTASDSPPSHTKVSFKTRNSTQDKTG
LNEQGKESSGGTMNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVK
HGSVLKLKKHPHRMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSES
PPKRKHSDGKAPSSSTKKGKKKVKFVEKKHSE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	155407195-155407634(+)
Potential amino acid sequence	MNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVKHGSVLKLKKHPH RMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSESPPKRKHSDGKAP SSSTKKGKKKVKFVEKKHSEYFFECVECDLGGNLLCCDSCPRVYHLECLNPPLKRAPPGKWQCP RCRPKKVSLKLLGNADVDTSKREKSTRTYASTASDSPPSHTKVSFKTRNSTQDKTGLNEQGKES SGGTMNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVKHGSVLKLK KHPHRMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSESPPKRKHSD GKAPSSSTKKGKKKVKFVEKKHSEYFFECVECDLGGNLLCCDSCPRVYHLECLNPPLKRAPPGK WQCPRCRPKKVSLKLLGNADVDTSKREKSTRTYASTASDSPPSHTKVSFKTRNSTQDKTGLNEQ GKESSGGTMNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVKHGSV LKLKKHPHRMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSESPPKR KHSDGKAPSSSTKKGKKKVKFVEKKHSEYFFECVECDLGGNLLCCDSCPRVYHLECLNPPLKRA PPGKWQCPRCRPKKVSLKLLGNADVDTSKREKSTRTYASTASDSPPSHTKVSFKTRNSTQDKTG LNEQGKESSGGTMNGGETSTKNNEVEKKKTLILHLKKRSTKELSENTKPSKSEFVELSEEKIVK HGSVLKLKKHPHRMDLSPSKSKTRRQSSQRESKRSGTKKIKYSMSDDDSVSSSEPSTSLDNSES PPKRKHSDGKAPSSSTKKGKKKVKFVEKKHSE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d021541_circ_g.1

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