Plant Circular RNA Database

Detail information of Zm00001d014340_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d014340_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008464
					
						Alias
						Zm05circ00037, zma_circ_0001794, GRMZM2G151195_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 41559585-41560528  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d014340						
					
						Parent gene annotation
						
							Whole genome shotgun sequence of line PN40024 scaffold_7.assembl
y12x (Fragment)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d014340_circ_g.1 Zm00001d014340_circ_g.2 Zm00001d014340_circ_g.3 Zm00001d014340_circ_g.5 Zm00001d014340_circ_g.6 Zm00001d014340_circ_g.7 						
					
						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  
						
							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
						Zm00001d014340_T014:3
Zm00001d014340_T001:3
Zm00001d014340_T006:2
Zm00001d014340_T004:3
Zm00001d014340_T007:3
Zm00001d014340_T012:3
Zm00001d014340_T008:3
Zm00001d014340_T010:3
Zm00001d014340_T009:3
Zm00001d014340_T002:3
Zm00001d014340_T013:3

General Information
CircRNA Name	Zm00001d014340_circ_g.4
ID in PlantcircBase	zma_circ_008464
Alias	Zm05circ00037, zma_circ_0001794, GRMZM2G151195_C1
Organism	Zea mays
Position	chr5: 41559585-41560528 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d014340
Parent gene annotation	Whole genome shotgun sequence of line PN40024 scaffold_7.assembl y12x (Fragment)
Parent gene strand	-
Alternative splicing	Zm00001d014340_circ_g.1 Zm00001d014340_circ_g.2 Zm00001d014340_circ_g.3 Zm00001d014340_circ_g.5 Zm00001d014340_circ_g.6 Zm00001d014340_circ_g.7
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	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	Zm00001d014340_T014:3 Zm00001d014340_T001:3 Zm00001d014340_T006:2 Zm00001d014340_T004:3 Zm00001d014340_T007:3 Zm00001d014340_T012:3 Zm00001d014340_T008:3 Zm00001d014340_T010:3 Zm00001d014340_T009:3 Zm00001d014340_T002:3 Zm00001d014340_T013:3

			
						 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  
						
							GCAGCGAGGTTCCCTTCGCATGCGTTTTAGTTCCTTGAGCTCCTTGAATTCGCGAATAACATTC
CTTCTGCAGTCTCTGCAGAATCTCTTGCTGTCGAATctgttctttgaagataacagcagcagca
tccaggagaaattctcttgcaagttcagggctcttggcatgcttctgtggatgagcgatatcac
catcaggg

									
								

					

						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: 646
Transcript exons: 41559585-41559716,41559839-41560210,41560387-41560528
CTGTTCTTTGAAGATAACAGCAGCAGCATCCAGGAGAAATTCTCTTGCAAGTTCAGGGCTCTTG
GCATGCTTCTGTGGATGAGCGATATCACCATCAGGGTCATTGCTGTCTCTGTCCACTACATCAT
CTTCATCCTCTTCCTCTGCTTCTTCAGCATACTCAAAGAAACTTCTAATACTTTCACCTTTGGT
AATTGTCACAAATCCATCCCCCACAATTAGCCTCCGGTGAACACATGATTGGCCCTTCAAGGCA
TGCGCCTTCACACAGAATTCAGTACAGCGACCATCCAGCCTCCATGCTCTCAGTGTAACAAAAT
AGTCTTCAAAGTGATCAAGATCGAGGCCTTTCCTGTGGACTTGTCCATTCATGCCCACATTTTC
AAAGTTTAGAATATCAGATTTTCCTTCATCTGTTCCAATAGCCCACTCGAAATGATGGTATATT
CCATCTTGCTCCAATAAAGATTGATGCCAATCAACAAGAATAGCATCCTCGAACACCTCACACT
TAAATGTGGTATCTGCAACACAAAACCAACTAGTGCAGCGAGGTTCCCTTCGCATGCGTTTTAG
TTCCTTGAGCTCCTTGAATTCGCGAATAACATTCCTTCTGCAGTCTCTGCAGAATCTCTTGCTG
TCGAAT
						
					

						Genomic sequence
						
							CTGTTCTTTGAAGATAACAGCAGCAGCATCCAGGAGAAATTCTCTTGCAAGTTCAGGGCTCTTG
GCATGCTTCTGTGGATGAGCGATATCACCATCAGGGTCATTGCTGTCTCTGTCCACTACATCAT
CTTCCTGCTCATGATTATGTCATTGAATCAAGCTATATGAATTCCCAACACCATGCTTGTTCAA
GTGCTGAAAAACAAATACTGTGATCATGTTTGATAATATGATTTAAAATATAAGGCACTTACAT
CCTCTTCCTCTGCTTCTTCAGCATACTCAAAGAAACTTCTAATACTTTCACCTTTGGTAATTGT
CACAAATCCATCCCCCACAATTAGCCTCCGGTGAACACATGATTGGCCCTTCAAGGCATGCGCC
TTCACACAGAATTCAGTACAGCGACCATCCAGCCTCCATGCTCTCAGTGTAACAAAATAGTCTT
CAAAGTGATCAAGATCGAGGCCTTTCCTGTGGACTTGTCCATTCATGCCCACATTTTCAAAGTT
TAGAATATCAGATTTTCCTTCATCTGTTCCAATAGCCCACTCGAAATGATGGTATATTCCATCT
TGCTCCAATAAAGATTGATGCCAATCAACAAGAATAGCATCCTCGAACACCTGCAAATATACAA
ATAAAGTCACAAAATGTGAATGCAAGATCCTTGACTCTTACTGTTTTATAGGGATTTTCTCCAT
ATGGTCTTACCAAAACAGGATGCGTGCCCCAAAGAAAAAAACACAAAAACAAACATGAGCTTTT
AGATAGGAATGATGACAAGGAATAGTATCCTCACCTCACACTTAAATGTGGTATCTGCAACACA
AAACCAACTAGTGCAGCGAGGTTCCCTTCGCATGCGTTTTAGTTCCTTGAGCTCCTTGAATTCG
CGAATAACATTCCTTCTGCAGTCTCTGCAGAATCTCTTGCTGTCGAAT
						
					

			
		

Sequences
Splice junction sequence	GCAGCGAGGTTCCCTTCGCATGCGTTTTAGTTCCTTGAGCTCCTTGAATTCGCGAATAACATTC CTTCTGCAGTCTCTGCAGAATCTCTTGCTGTCGAATctgttctttgaagataacagcagcagca tccaggagaaattctcttgcaagttcagggctcttggcatgcttctgtggatgagcgatatcac catcaggg
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: 646 Transcript exons: 41559585-41559716,41559839-41560210,41560387-41560528 CTGTTCTTTGAAGATAACAGCAGCAGCATCCAGGAGAAATTCTCTTGCAAGTTCAGGGCTCTTG GCATGCTTCTGTGGATGAGCGATATCACCATCAGGGTCATTGCTGTCTCTGTCCACTACATCAT CTTCATCCTCTTCCTCTGCTTCTTCAGCATACTCAAAGAAACTTCTAATACTTTCACCTTTGGT AATTGTCACAAATCCATCCCCCACAATTAGCCTCCGGTGAACACATGATTGGCCCTTCAAGGCA TGCGCCTTCACACAGAATTCAGTACAGCGACCATCCAGCCTCCATGCTCTCAGTGTAACAAAAT AGTCTTCAAAGTGATCAAGATCGAGGCCTTTCCTGTGGACTTGTCCATTCATGCCCACATTTTC AAAGTTTAGAATATCAGATTTTCCTTCATCTGTTCCAATAGCCCACTCGAAATGATGGTATATT CCATCTTGCTCCAATAAAGATTGATGCCAATCAACAAGAATAGCATCCTCGAACACCTCACACT TAAATGTGGTATCTGCAACACAAAACCAACTAGTGCAGCGAGGTTCCCTTCGCATGCGTTTTAG TTCCTTGAGCTCCTTGAATTCGCGAATAACATTCCTTCTGCAGTCTCTGCAGAATCTCTTGCTG TCGAAT
Genomic sequence	CTGTTCTTTGAAGATAACAGCAGCAGCATCCAGGAGAAATTCTCTTGCAAGTTCAGGGCTCTTG GCATGCTTCTGTGGATGAGCGATATCACCATCAGGGTCATTGCTGTCTCTGTCCACTACATCAT CTTCCTGCTCATGATTATGTCATTGAATCAAGCTATATGAATTCCCAACACCATGCTTGTTCAA GTGCTGAAAAACAAATACTGTGATCATGTTTGATAATATGATTTAAAATATAAGGCACTTACAT CCTCTTCCTCTGCTTCTTCAGCATACTCAAAGAAACTTCTAATACTTTCACCTTTGGTAATTGT CACAAATCCATCCCCCACAATTAGCCTCCGGTGAACACATGATTGGCCCTTCAAGGCATGCGCC TTCACACAGAATTCAGTACAGCGACCATCCAGCCTCCATGCTCTCAGTGTAACAAAATAGTCTT CAAAGTGATCAAGATCGAGGCCTTTCCTGTGGACTTGTCCATTCATGCCCACATTTTCAAAGTT TAGAATATCAGATTTTCCTTCATCTGTTCCAATAGCCCACTCGAAATGATGGTATATTCCATCT TGCTCCAATAAAGATTGATGCCAATCAACAAGAATAGCATCCTCGAACACCTGCAAATATACAA ATAAAGTCACAAAATGTGAATGCAAGATCCTTGACTCTTACTGTTTTATAGGGATTTTCTCCAT ATGGTCTTACCAAAACAGGATGCGTGCCCCAAAGAAAAAAACACAAAAACAAACATGAGCTTTT AGATAGGAATGATGACAAGGAATAGTATCCTCACCTCACACTTAAATGTGGTATCTGCAACACA AAACCAACTAGTGCAGCGAGGTTCCCTTCGCATGCGTTTTAGTTCCTTGAGCTCCTTGAATTCG CGAATAACATTCCTTCTGCAGTCTCTGCAGAATCTCTTGCTGTCGAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.127474842

Conservation Information
Conserved circRNAs	NA
PMCS	0.127474842

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							41560449-41559925(+)
41560451-41560426(-)
41559690-41560426(-)
						
						Potential amino acid sequence
						
							MRFSSLSSLNSRITFLLQSLQNLLLSNLFFEDNSSSIQEKFSCKFRALGMLLWMSDITIRVIAV
SVHYIIFILFLCFFSILKETSNTFTFGNCHKSIPHN*(+)
MRREPRCTSWFCVADTTFKCEVFEDAILVDWHQSLLEQDGIYHHFEWAIGTDEGKSDILNFENV
GMNGQVHRKGLDLDHFEDYFVTLRAWRLDGRCTEFCVKAHALKGQSCVHRRLIVGDGFVTITKG
ESIRSFFEYAEEAEEEDEDDVVDRDSNDPDGDIAHPQKHAKSPELAREFLLDAAAVIFKEQIRQ
QEILQRLQKECYSRIQGAQGTKTHAKGTSLH*(-)
MTLMVISLIHRSMPRALNLQENFSWMLLLLSSKNRFDSKRFCRDCRRNVIREFKELKELKRMRR
EPRCTSWFCVADTTFKCEVFEDAILVDWHQSLLEQDGIYHHFEWAIGTDEGKSDILNFENVGMN
GQVHRKGLDLDHFEDYFVTLRAWRLDGRCTEFCVKAHALKGQSCVHRRLIVGDGFVTITKGESI
RSFFEYAEEAEEEDEDDVVDRDSNDPDGDIAHPQKHAKSPELAREFLLDAAAVIFKEQIRQQEI
LQRLQKECYSRIQGAQGTKTHAKGTSLH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	41560449-41559925(+) 41560451-41560426(-) 41559690-41560426(-)
Potential amino acid sequence	MRFSSLSSLNSRITFLLQSLQNLLLSNLFFEDNSSSIQEKFSCKFRALGMLLWMSDITIRVIAV SVHYIIFILFLCFFSILKETSNTFTFGNCHKSIPHN(+) MRREPRCTSWFCVADTTFKCEVFEDAILVDWHQSLLEQDGIYHHFEWAIGTDEGKSDILNFENV GMNGQVHRKGLDLDHFEDYFVTLRAWRLDGRCTEFCVKAHALKGQSCVHRRLIVGDGFVTITKG ESIRSFFEYAEEAEEEDEDDVVDRDSNDPDGDIAHPQKHAKSPELAREFLLDAAAVIFKEQIRQ QEILQRLQKECYSRIQGAQGTKTHAKGTSLH(-) MTLMVISLIHRSMPRALNLQENFSWMLLLLSSKNRFDSKRFCRDCRRNVIREFKELKELKRMRR EPRCTSWFCVADTTFKCEVFEDAILVDWHQSLLEQDGIYHHFEWAIGTDEGKSDILNFENVGMN GQVHRKGLDLDHFEDYFVTLRAWRLDGRCTEFCVKAHALKGQSCVHRRLIVGDGFVTITKGESI RSFFEYAEEAEEEDEDDVVDRDSNDPDGDIAHPQKHAKSPELAREFLLDAAAVIFKEQIRQQEI LQRLQKECYSRIQGAQGTKTHAKGTSLH*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d014340_circ_g.4

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