Plant Circular RNA Database

Detail information of Zm00001d004383_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d004383_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007240
					
						Alias
						zma_circ_0000764
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 107700386-107701534  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d004383						
					
						Parent gene annotation
						
							 leunig-related6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d004383_circ_g.2 Zm00001d004383_circ_g.3 Zm00001d004383_circ_g.5 Zm00001d004383_circ_g.6 						
					
						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
						Zm00001d004383_T003:4
Zm00001d004383_T005:4
Zm00001d004383_T001:4
Zm00001d004383_T002:4
Zm00001d004383_T004:4

General Information
CircRNA Name	Zm00001d004383_circ_g.4
ID in PlantcircBase	zma_circ_007240
Alias	zma_circ_0000764
Organism	Zea mays
Position	chr2: 107700386-107701534 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d004383
Parent gene annotation	leunig-related6
Parent gene strand	+
Alternative splicing	Zm00001d004383_circ_g.2 Zm00001d004383_circ_g.3 Zm00001d004383_circ_g.5 Zm00001d004383_circ_g.6
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	Zm00001d004383_T003:4 Zm00001d004383_T005:4 Zm00001d004383_T001:4 Zm00001d004383_T002:4 Zm00001d004383_T004:4

			
						 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  
						
							GAGAAATAATAACTCCTTTGCAACATGTTCAACCGATAACATGATCTATGTTTGCAAGATTGGG
GAACAGCGTCCAATTAAAGCATTCAGTGGTCATCAGatcaggagactcaactgctagaatctgg
acaattccatatggtccatgtggttccgacatgcaaccatattctcctggtgttcatgttttga
aacatttt

									
								

					

						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: 496
Transcript exons: 107700386-107700536,107700766-107700829,107701146-107701
304,107701413-107701534
ATCAGGAGACTCAACTGCTAGAATCTGGACAATTCCATATGGTCCATGTGGTTCCGACATGCAA
CCATATTCTCCTGGTGTTCATGTTTTGAAACATTTTAAAGGTCGGACCAATGAAAAGAGCAAGG
ATGTCACCACGCTTGACTGGAATGGTGAAGGTACACTACTCGCTACGGGCTCCTACGATGGACA
GGCAAGAATATGGAGTAGAGATGGAGACCTGAAGCAGACACTGTTCAAACATAAGGGACCCATA
TTTTCATTGAAATGGAATAAGAAAGGAGATTTTCTCCTAAGTGGAAGTGTTGATAAAACTGCTA
TTGTTTGGGATACAAAGACATGGGAATGCAAGCAGCAGTTTGAATTTCATTCAGCTCCAACACT
AGATGTTGATTGGAGAAATAATAACTCCTTTGCAACATGTTCAACCGATAACATGATCTATGTT
TGCAAGATTGGGGAACAGCGTCCAATTAAAGCATTCAGTGGTCATCAG
						
					

						Genomic sequence
						
							ATCAGGAGACTCAACTGCTAGAATCTGGACAATTCCATATGGTCCATGTGGTTCCGACATGCAA
CCATATTCTCCTGGTGTTCATGTTTTGAAACATTTTAAAGGTCGGACCAATGAAAAGAGCAAGG
ATGTCACCACGCTTGACTGGAATGTGAGTTTCTTCCTGCTGCAAAATTTTGTTTATATCCCATG
TTTTTCTTACATTTCATTTTTCTGGGTGAAGACCAATGGGAACATATCATGGAATGCTATTTAT
AGCCACCTGTTCTATTAGTCTACCTGTTAATTTGTTTGTCATGCAAAAAATTCTATGTTTGCAT
CTACATTCCTTAACTATTTCATACTCATCATTGTATTTGCTTTTCTGCCATCCCTTACAGGGTG
AAGGTACACTACTCGCTACGGGCTCCTACGATGGACAGGCAAGAATATGGAGTAGAGATGGTGA
GTGAACAACTGTATCTGTATCATACCTAGTTGGCTTTAGCTCTTCATTCTGATGTTAAGGTTTG
TTTGATAGACAATGTGGGCCCATCATAAATGTAGGATTCTTGTTTTTGACTAATGGTGCACATT
ATTCATTGTGCCTTAAATTTCTGTAAAAATGATCTGGTGATAGGCTGTTTGTTGATCTGGCATA
AACTCATTGTATTTTTAATTCTTATAACATTTGAAGAAATCATATATAGGTCATACATTCTAGA
TGTTTTATTTCTCCCCTCTTGTGTTATCCTTACTTGTGATGAAATGGATTTTTCAGGAGACCTG
AAGCAGACACTGTTCAAACATAAGGGACCCATATTTTCATTGAAATGGAATAAGAAAGGAGATT
TTCTCCTAAGTGGAAGTGTTGATAAAACTGCTATTGTTTGGGATACAAAGACATGGGAATGCAA
GCAGCAGTTTGAATTTCATTCAGGTACAATTGGCATTCCTGAATGGTGTTTGTTTTAACCTGAT
AGTTCATTCTGTATTGCATAGATGTATCTGTGGTGACCATACCTAACTCCCACCTGCTTCTATG
TAGCTCCAACACTAGATGTTGATTGGAGAAATAATAACTCCTTTGCAACATGTTCAACCGATAA
CATGATCTATGTTTGCAAGATTGGGGAACAGCGTCCAATTAAAGCATTCAGTGGTCATCAG
						
					

			
		

Sequences
Splice junction sequence	GAGAAATAATAACTCCTTTGCAACATGTTCAACCGATAACATGATCTATGTTTGCAAGATTGGG GAACAGCGTCCAATTAAAGCATTCAGTGGTCATCAGatcaggagactcaactgctagaatctgg acaattccatatggtccatgtggttccgacatgcaaccatattctcctggtgttcatgttttga aacatttt
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: 496 Transcript exons: 107700386-107700536,107700766-107700829,107701146-107701 304,107701413-107701534 ATCAGGAGACTCAACTGCTAGAATCTGGACAATTCCATATGGTCCATGTGGTTCCGACATGCAA CCATATTCTCCTGGTGTTCATGTTTTGAAACATTTTAAAGGTCGGACCAATGAAAAGAGCAAGG ATGTCACCACGCTTGACTGGAATGGTGAAGGTACACTACTCGCTACGGGCTCCTACGATGGACA GGCAAGAATATGGAGTAGAGATGGAGACCTGAAGCAGACACTGTTCAAACATAAGGGACCCATA TTTTCATTGAAATGGAATAAGAAAGGAGATTTTCTCCTAAGTGGAAGTGTTGATAAAACTGCTA TTGTTTGGGATACAAAGACATGGGAATGCAAGCAGCAGTTTGAATTTCATTCAGCTCCAACACT AGATGTTGATTGGAGAAATAATAACTCCTTTGCAACATGTTCAACCGATAACATGATCTATGTT TGCAAGATTGGGGAACAGCGTCCAATTAAAGCATTCAGTGGTCATCAG
Genomic sequence	ATCAGGAGACTCAACTGCTAGAATCTGGACAATTCCATATGGTCCATGTGGTTCCGACATGCAA CCATATTCTCCTGGTGTTCATGTTTTGAAACATTTTAAAGGTCGGACCAATGAAAAGAGCAAGG ATGTCACCACGCTTGACTGGAATGTGAGTTTCTTCCTGCTGCAAAATTTTGTTTATATCCCATG TTTTTCTTACATTTCATTTTTCTGGGTGAAGACCAATGGGAACATATCATGGAATGCTATTTAT AGCCACCTGTTCTATTAGTCTACCTGTTAATTTGTTTGTCATGCAAAAAATTCTATGTTTGCAT CTACATTCCTTAACTATTTCATACTCATCATTGTATTTGCTTTTCTGCCATCCCTTACAGGGTG AAGGTACACTACTCGCTACGGGCTCCTACGATGGACAGGCAAGAATATGGAGTAGAGATGGTGA GTGAACAACTGTATCTGTATCATACCTAGTTGGCTTTAGCTCTTCATTCTGATGTTAAGGTTTG TTTGATAGACAATGTGGGCCCATCATAAATGTAGGATTCTTGTTTTTGACTAATGGTGCACATT ATTCATTGTGCCTTAAATTTCTGTAAAAATGATCTGGTGATAGGCTGTTTGTTGATCTGGCATA AACTCATTGTATTTTTAATTCTTATAACATTTGAAGAAATCATATATAGGTCATACATTCTAGA TGTTTTATTTCTCCCCTCTTGTGTTATCCTTACTTGTGATGAAATGGATTTTTCAGGAGACCTG AAGCAGACACTGTTCAAACATAAGGGACCCATATTTTCATTGAAATGGAATAAGAAAGGAGATT TTCTCCTAAGTGGAAGTGTTGATAAAACTGCTATTGTTTGGGATACAAAGACATGGGAATGCAA GCAGCAGTTTGAATTTCATTCAGGTACAATTGGCATTCCTGAATGGTGTTTGTTTTAACCTGAT AGTTCATTCTGTATTGCATAGATGTATCTGTGGTGACCATACCTAACTCCCACCTGCTTCTATG TAGCTCCAACACTAGATGTTGATTGGAGAAATAATAACTCCTTTGCAACATGTTCAACCGATAA CATGATCTATGTTTGCAAGATTGGGGAACAGCGTCCAATTAAAGCATTCAGTGGTCATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.174780383

Conservation Information
Conserved circRNAs	NA
PMCS	0.174780383

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							107700445-107700403(+)
107701483-107700403(+)
107700447-107701465(-)
						
						Potential amino acid sequence
						
							MQPYSPGVHVLKHFKGRTNEKSKDVTTLDWNGEGTLLATGSYDGQARIWSRDGDLKQTLFKHKG
PIFSLKWNKKGDFLLSGSVDKTAIVWDTKTWECKQQFEFHSAPTLDVDWRNNNSFATCSTDNMI
YVCKIGEQRPIKAFSGHQIRRLNC*(+)
MFARLGNSVQLKHSVVIRSGDSTARIWTIPYGPCGSDMQPYSPGVHVLKHFKGRTNEKSKDVTT
LDWNGEGTLLATGSYDGQARIWSRDGDLKQTLFKHKGPIFSLKWNKKGDFLLSGSVDKTAIVWD
TKTWECKQQFEFHSAPTLDVDWRNNNSFATCSTDNMIYVCKIGEQRPIKAFSGHQIRRLNC*(+
)
MSEPHGPYGIVQILAVESPDLMTTECFNWTLFPNLANIDHVIG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	107700445-107700403(+) 107701483-107700403(+) 107700447-107701465(-)
Potential amino acid sequence	MQPYSPGVHVLKHFKGRTNEKSKDVTTLDWNGEGTLLATGSYDGQARIWSRDGDLKQTLFKHKG PIFSLKWNKKGDFLLSGSVDKTAIVWDTKTWECKQQFEFHSAPTLDVDWRNNNSFATCSTDNMI YVCKIGEQRPIKAFSGHQIRRLNC(+) MFARLGNSVQLKHSVVIRSGDSTARIWTIPYGPCGSDMQPYSPGVHVLKHFKGRTNEKSKDVTT LDWNGEGTLLATGSYDGQARIWSRDGDLKQTLFKHKGPIFSLKWNKKGDFLLSGSVDKTAIVWD TKTWECKQQFEFHSAPTLDVDWRNNNSFATCSTDNMIYVCKIGEQRPIKAFSGHQIRRLNC(+ ) MSEPHGPYGIVQILAVESPDLMTTECFNWTLFPNLANIDHVIG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d004383_circ_g.4

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