Plant Circular RNA Database

Detail information of Zm00001d048783_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d048783_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007957
					
						Alias
						zma_circ_0001796
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 5481540-5491110  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d048783						
					
						Parent gene annotation
						
							Beta-galactosidase 5
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d048783_circ_g.2 						
					
						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
						Zm00001d048783_T006:5
Zm00001d048783_T005:7
Zm00001d048783_T001:12
Zm00001d048783_T003:10
Zm00001d048783_T004:10
Zm00001d048783_T002:10

General Information
CircRNA Name	Zm00001d048783_circ_g.1
ID in PlantcircBase	zma_circ_007957
Alias	zma_circ_0001796
Organism	Zea mays
Position	chr4: 5481540-5491110 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d048783
Parent gene annotation	Beta-galactosidase 5
Parent gene strand	+
Alternative splicing	Zm00001d048783_circ_g.2
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	Zm00001d048783_T006:5 Zm00001d048783_T005:7 Zm00001d048783_T001:12 Zm00001d048783_T003:10 Zm00001d048783_T004:10 Zm00001d048783_T002:10

			
						 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  
						
							TCATCTGAAAACTTTCTACAAGGTGGCGGCAAGCCTCTGTCTCTCAGTGTGCAGTCTGCTGGTC
ATGCCTTGCATGTCTTTGTCAATGGACAGCTTCAAGgttctgcatatggtactagggaagattg
aagaatcaaatacaatggcaatgctaaccttcgagccggtactaacaaaatttccatgctgagt
gttgcctg

									
								

					

						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: 1408
Transcript exons: 5481540-5481605,5481733-5481843,5487983-5488057,5488154-
5488273,5488716-5488859,5489277-5489365,5489483-5489617,
5489840-5489927,5490130-5490255,5490326-5490487,5490610-
5490788,5490998-5491110
GTTCTGCATATGGTACTAGGGAAGATTGAAGAATCAAATACAATGGCAATGCTAACCTTCGAGC
CGAATGTTGGAGTGCATTATGAGACGTGGAACACTGGTGTTGGTGGTCCTGTTGTGCTTCATAG
GCTGGATGAAGGTTCACGAGACCTTACTTGGCAGACTTGGTCCTATCAGTGGCTTCCCAGTTTG
GTTGAAGTATGTACCGGACTACCGGGCATCAGCTTCAGGACAGACAACGAACCTTTCAAGATGG
CCATGCAGGGTTTCACTCAGAAAATTGTGGGAATGATGAAGAGCGAAAACCTCTTTGCATCCCA
AGGTGTCCCAATTATCCTCTCTCAGGCAAGTATAATATTTTCCTTAGGTTTGATTGAGAATGAA
TACGGGCCAGAAGGCAGGGAGTTTCGTCCCGCAGGTCAGGCATATATCAACAAGGCAGCAAAGA
TGGCAGTCGGATTGGGTACTGGTGTGCCGTGGGTGATGTGGAAGGAGGAGGATGCACCTGATCC
AGTGATCAATGCATGCAATGGTTTCTACTGTGATGCATTTTCTCCTAACAAACCTTACAAGCCC
ACAATGTGGACTGAAGCTTGGAGTGGCTACAAGTGTGCCCTAACAAATGTCCACAACATTTTAG
GTTCACGGAATTTGTTGGGACCATCCGCCAACGGCCGGTTGAAGATCTTGCATTTGCTCGATTT
GTACAAAAGGGTGGTTCTTTTATCAATTACTACATGTACCATGGAGGAACAAATTTTGGGCGCA
CTGCTGGGGGTCCCTTCATCACAACAAGCTATGATTATGATGCTCCAATTGATGAATATGGACT
TTTTAGAGAACCAAAGCACAGTCATCTTAAAGAACTCCACAGAGCTGTTAAGTTATGCGAGCAG
GCTTTGGTTTCTGTTGACCCAGCAATTACTACCCTTGTACCATGCAAGAGGTATGCTGGCCCAC
GTCTTCCAATCTCCATCTGGTTGTGCAGCTTTCCTTGCAAACTACAATTCTAACTCCTATGCGA
ATGTTGTATTCAACAATGAGCAATACAGCCTACCACATTGGTCGATTAGCATCCTTCCTGATTG
CAAAAATGTTGTTTTTAACAGTGTCACAGTTGGTGTTCAGACATCTCAGATGCAAATGTGTGGA
GATGATGCCTCATCAATGACGTGGAAGAGGTATGATGAGGAGGTTTATTCTCTGGCAGCTGCTC
CATTGCTCACCACGACTAGTTTGCTTGAGCAGCTTAATGTCACGAGAGACAACAGTGATTATTT
GTGGTACATCACCAGTGTTGACATAAGCTCATCTGAAAACTTTCTACAAGGTGGCGGCAAGCCT
CTGTCTCTCAGTGTGCAGTCTGCTGGTCATGCCTTGCATGTCTTTGTCAATGGACAGCTTCAAG
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	TCATCTGAAAACTTTCTACAAGGTGGCGGCAAGCCTCTGTCTCTCAGTGTGCAGTCTGCTGGTC ATGCCTTGCATGTCTTTGTCAATGGACAGCTTCAAGgttctgcatatggtactagggaagattg aagaatcaaatacaatggcaatgctaaccttcgagccggtactaacaaaatttccatgctgagt gttgcctg
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: 1408 Transcript exons: 5481540-5481605,5481733-5481843,5487983-5488057,5488154- 5488273,5488716-5488859,5489277-5489365,5489483-5489617, 5489840-5489927,5490130-5490255,5490326-5490487,5490610- 5490788,5490998-5491110 GTTCTGCATATGGTACTAGGGAAGATTGAAGAATCAAATACAATGGCAATGCTAACCTTCGAGC CGAATGTTGGAGTGCATTATGAGACGTGGAACACTGGTGTTGGTGGTCCTGTTGTGCTTCATAG GCTGGATGAAGGTTCACGAGACCTTACTTGGCAGACTTGGTCCTATCAGTGGCTTCCCAGTTTG GTTGAAGTATGTACCGGACTACCGGGCATCAGCTTCAGGACAGACAACGAACCTTTCAAGATGG CCATGCAGGGTTTCACTCAGAAAATTGTGGGAATGATGAAGAGCGAAAACCTCTTTGCATCCCA AGGTGTCCCAATTATCCTCTCTCAGGCAAGTATAATATTTTCCTTAGGTTTGATTGAGAATGAA TACGGGCCAGAAGGCAGGGAGTTTCGTCCCGCAGGTCAGGCATATATCAACAAGGCAGCAAAGA TGGCAGTCGGATTGGGTACTGGTGTGCCGTGGGTGATGTGGAAGGAGGAGGATGCACCTGATCC AGTGATCAATGCATGCAATGGTTTCTACTGTGATGCATTTTCTCCTAACAAACCTTACAAGCCC ACAATGTGGACTGAAGCTTGGAGTGGCTACAAGTGTGCCCTAACAAATGTCCACAACATTTTAG GTTCACGGAATTTGTTGGGACCATCCGCCAACGGCCGGTTGAAGATCTTGCATTTGCTCGATTT GTACAAAAGGGTGGTTCTTTTATCAATTACTACATGTACCATGGAGGAACAAATTTTGGGCGCA CTGCTGGGGGTCCCTTCATCACAACAAGCTATGATTATGATGCTCCAATTGATGAATATGGACT TTTTAGAGAACCAAAGCACAGTCATCTTAAAGAACTCCACAGAGCTGTTAAGTTATGCGAGCAG GCTTTGGTTTCTGTTGACCCAGCAATTACTACCCTTGTACCATGCAAGAGGTATGCTGGCCCAC GTCTTCCAATCTCCATCTGGTTGTGCAGCTTTCCTTGCAAACTACAATTCTAACTCCTATGCGA ATGTTGTATTCAACAATGAGCAATACAGCCTACCACATTGGTCGATTAGCATCCTTCCTGATTG CAAAAATGTTGTTTTTAACAGTGTCACAGTTGGTGTTCAGACATCTCAGATGCAAATGTGTGGA GATGATGCCTCATCAATGACGTGGAAGAGGTATGATGAGGAGGTTTATTCTCTGGCAGCTGCTC CATTGCTCACCACGACTAGTTTGCTTGAGCAGCTTAATGTCACGAGAGACAACAGTGATTATTT GTGGTACATCACCAGTGTTGACATAAGCTCATCTGAAAACTTTCTACAAGGTGGCGGCAAGCCT CTGTCTCTCAGTGTGCAGTCTGCTGGTCATGCCTTGCATGTCTTTGTCAATGGACAGCTTCAAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.631859355

Conservation Information
Conserved circRNAs	NA
PMCS	0.631859355

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5481550-5481565(+)
5491076-5481565(+)
						
						Potential amino acid sequence
						
							MVLGKIEESNTMAMLTFEPNVGVHYETWNTGVGGPVVLHRLDEGSRDLTWQTWSYQWLPSLVEV
CTGLPGISFRTDNEPFKMAMQGFTQKIVGMMKSENLFASQGVPIILSQASIIFSLGLIENEYGP
EGREFRPAGQAYINKAAKMAVGLGTGVPWVMWKEEDAPDPVINACNGFYCDAFSPNKPYKPTMW
TEAWSGYKCALTNVHNILGSRNLLGPSANGRLKILHLLDLYKRVVLLSITTCTMEEQILGALLG
VPSSQQAMIMMLQLMNMDFLENQSTVILKNSTELLSYASRLWFLLTQQLLPLYHARGMLAHVFQ
SPSGCAAFLANYNSNSYANVVFNNEQYSLPHWSISILPDCKNVVFNSVTVGVQTSQMQMCGDDA
SSMTWKRYDEEVYSLAAAPLLTTTSLLEQLNVTRDNSDYLWYITSVDISSSENFLQGGGKPLSL
SVQSAGHALHVFVNGQLQGSAYGTRED*(+)
MPCMSLSMDSFKVLHMVLGKIEESNTMAMLTFEPNVGVHYETWNTGVGGPVVLHRLDEGSRDLT
WQTWSYQWLPSLVEVCTGLPGISFRTDNEPFKMAMQGFTQKIVGMMKSENLFASQGVPIILSQA
SIIFSLGLIENEYGPEGREFRPAGQAYINKAAKMAVGLGTGVPWVMWKEEDAPDPVINACNGFY
CDAFSPNKPYKPTMWTEAWSGYKCALTNVHNILGSRNLLGPSANGRLKILHLLDLYKRVVLLSI
TTCTMEEQILGALLGVPSSQQAMIMMLQLMNMDFLENQSTVILKNSTELLSYASRLWFLLTQQL
LPLYHARGMLAHVFQSPSGCAAFLANYNSNSYANVVFNNEQYSLPHWSISILPDCKNVVFNSVT
VGVQTSQMQMCGDDASSMTWKRYDEEVYSLAAAPLLTTTSLLEQLNVTRDNSDYLWYITSVDIS
SSENFLQGGGKPLSLSVQSAGHALHVFVNGQLQGSAYGTRED*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5481550-5481565(+) 5491076-5481565(+)
Potential amino acid sequence	MVLGKIEESNTMAMLTFEPNVGVHYETWNTGVGGPVVLHRLDEGSRDLTWQTWSYQWLPSLVEV CTGLPGISFRTDNEPFKMAMQGFTQKIVGMMKSENLFASQGVPIILSQASIIFSLGLIENEYGP EGREFRPAGQAYINKAAKMAVGLGTGVPWVMWKEEDAPDPVINACNGFYCDAFSPNKPYKPTMW TEAWSGYKCALTNVHNILGSRNLLGPSANGRLKILHLLDLYKRVVLLSITTCTMEEQILGALLG VPSSQQAMIMMLQLMNMDFLENQSTVILKNSTELLSYASRLWFLLTQQLLPLYHARGMLAHVFQ SPSGCAAFLANYNSNSYANVVFNNEQYSLPHWSISILPDCKNVVFNSVTVGVQTSQMQMCGDDA SSMTWKRYDEEVYSLAAAPLLTTTSLLEQLNVTRDNSDYLWYITSVDISSSENFLQGGGKPLSL SVQSAGHALHVFVNGQLQGSAYGTRED(+) MPCMSLSMDSFKVLHMVLGKIEESNTMAMLTFEPNVGVHYETWNTGVGGPVVLHRLDEGSRDLT WQTWSYQWLPSLVEVCTGLPGISFRTDNEPFKMAMQGFTQKIVGMMKSENLFASQGVPIILSQA SIIFSLGLIENEYGPEGREFRPAGQAYINKAAKMAVGLGTGVPWVMWKEEDAPDPVINACNGFY CDAFSPNKPYKPTMWTEAWSGYKCALTNVHNILGSRNLLGPSANGRLKILHLLDLYKRVVLLSI TTCTMEEQILGALLGVPSSQQAMIMMLQLMNMDFLENQSTVILKNSTELLSYASRLWFLLTQQL LPLYHARGMLAHVFQSPSGCAAFLANYNSNSYANVVFNNEQYSLPHWSISILPDCKNVVFNSVT VGVQTSQMQMCGDDASSMTWKRYDEEVYSLAAAPLLTTTSLLEQLNVTRDNSDYLWYITSVDIS SSENFLQGGGKPLSLSVQSAGHALHVFVNGQLQGSAYGTRED(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d048783_circ_g.1

Address

Any questions?

Supported by