Plant Circular RNA Database

Detail information of Zm00001d041880_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d041880_circ_g.4
					
						ID in PlantcircBase
						zma_circ_007652
					
						Alias
						Zm03circ00046, zma_circ_0001140, GRMZM2G073584_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 142140828-142142879  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d041880						
					
						Parent gene annotation
						
							Beta-galactosidase 9
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d041880_circ_g.2 Zm00001d041880_circ_g.3 Zm00001d041880_circ_g.5 						
					
						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
						Zm00001d041880_T010:4
Zm00001d041880_T004:4
Zm00001d041880_T002:5
Zm00001d041880_T001:4
Zm00001d041880_T005:4
Zm00001d041880_T006:5
Zm00001d041880_T009:4

General Information
CircRNA Name	Zm00001d041880_circ_g.4
ID in PlantcircBase	zma_circ_007652
Alias	Zm03circ00046, zma_circ_0001140, GRMZM2G073584_C1
Organism	Zea mays
Position	chr3: 142140828-142142879 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d041880
Parent gene annotation	Beta-galactosidase 9
Parent gene strand	+
Alternative splicing	Zm00001d041880_circ_g.2 Zm00001d041880_circ_g.3 Zm00001d041880_circ_g.5
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	Zm00001d041880_T010:4 Zm00001d041880_T004:4 Zm00001d041880_T002:5 Zm00001d041880_T001:4 Zm00001d041880_T005:4 Zm00001d041880_T006:5 Zm00001d041880_T009:4

			
						 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  
						
							CTTTTTGGCAGCTCAATACTTGCAATGCCTTTTACTGTGATGGGTTCAAACCAAATTCCTACAA
CAAGCCAACAATATGGACTGAGGATTGGGATGGATGtggtttcccagtttggttgcgcgatgtc
cctgggatagaattccgcactgacaatgaaccctacaaggtagatgaaccactaagcatagatt
ttgtcttc

									
								

					

						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: 393
Transcript exons: 142140828-142140894,142140985-142141077,142142542-142142
685,142142791-142142879
TGGTTTCCCAGTTTGGTTGCGCGATGTCCCTGGGATAGAATTCCGCACTGACAATGAACCCTAC
AAGGCTGAAATGCAGATTTTTGTGACAAAAATTGTAGATATCATGAAAGAGGAGAAGCTTTATT
CTTGGCAAGGTGGTCCCATTATACTGCAGCAGATTGAAAATGAATACGGTAACATTCAAGGCCA
TTATGGTCAAGCAGGGAAGAGATACATGCTATGGGCAGCTCAGATGGCACTTGCACTTGATACT
GGTGTTCCTTGGGTAATGTGTAGGCAAACAGATGCTCCAGAACAAATTCTCAATACTTGCAATG
CCTTTTACTGTGATGGGTTCAAACCAAATTCCTACAACAAGCCAACAATATGGACTGAGGATTG
GGATGGATG
						
					

						Genomic sequence
						
							TGGTTTCCCAGTTTGGTTGCGCGATGTCCCTGGGATAGAATTCCGCACTGACAATGAACCCTAC
AAGGTAGATGAACCACTAAGCATAGATTTTGTCTTCCTATGATGAACATTTTTCATTTATTTGA
ATTCACTAATCCTTAAAATTGTCGTACAGGCTGAAATGCAGATTTTTGTGACAAAAATTGTAGA
TATCATGAAAGAGGAGAAGCTTTATTCTTGGCAAGGTGGTCCCATTATACTGCAGCAGGTCTGA
AAACTTTTCTCGAAGTTCACTTATTGGTGTTTCTTTTCTCCTCCCTCCCTCCCTCCTAGGAGAC
CCCTTGCATAAAGCACTCTATCTTGTTGAGGAGACGAGAGAGGTTCAGGTTTGGACAATTGGAC
AAATAAAGAAACCATCTGAAAAGAGGAAAAAACCCGGACTCAACCAGGGCTGGTTATTAAACCC
TCAACAAGACCTAGACCATGTTCTTGAAGTTTACGTAATGTATACATGTCTTAGGGGTGTCTTT
AGTACAACTTCGTCTTCCGTCATCCCCTTAGCGTCATCTTTCATCATGCGTAGGCGTATGCCTT
GTACGGTGTATTGCCCTGCCCCCTCCGGCGTATGGGTCACTGTAGAGACCCTGATGCTGAGGTC
TCTATGGCTGGAGCCTTCTGGTCCCACTAGTCAGCGGGGATACGTATCCGGCGTCGTGCTTTGA
CAGAGACCTCTCGGTACCGCTTCCACAGTCTGGGCATGGCTCGGTGATGTCCCATCGTGTCGAC
GTGGCTTGATAGTACTAGGTGGGCTCTTCTTGAGAGCCGGCTGTCGTTTTGCTGGGTTGCTCGG
CAGCCTCGCCTCGTTGGGTTGCTCAGCGGGCAGGTTGCTCGGCAGCCTCGTCTCGTTGGGTTGC
TTCGCGGGCAGGTTGCTCGGTAGCCCCGCCTCGCTGGGTTGCTCGGCGGACATTAGTTCGTTGG
GCCGATCGGCTTGGTAGGCCGTCCCTGGGCGGCCTTTTGGTCTTTCCCGCCGATTTGTTTGGCA
GGCGGGCTGCTCGGTTCGTGGGTTGTCTTTGGGAGGCCTTCGGGCCTTCTTTGGGTACCCTGTT
TCCAGGTACCCAACAGTTAGCTAAGCTATCACCCATTAATCAGTACACAGAGATCTGAAAAATA
TCAATGACAAGTGGATATTATGTTATATGTGGCTTAAGTAATTTTTGGTTGGTGCCATTTGGTG
ACAACATTGCTTAGTATCTTTGATGTTCAGTTAATTCCTTTGTTTAATAAAACTGTTAGATGGC
GTTCTATATATGGATGGTGCTCATGATAGAGTTAAACATTGAACCATAATGTGGTAAAGGATAC
AATTCTGAAGTATGTTATGTAGCCAAAAGCTAGATGCTGGCTGTTTTACCTTCTGAAGTAGCAA
TACTTATGGTGTTGGCTCTGTGCTCTAGTTAATTCAGCACAAACACCTGAAATTTGGTGGATGT
AAGAGGCTCATATTAATAAAAACTTGACCAATCTAGGAGGAACTAGGCATCTTTTACTTTTAGT
AAGAAGAAAAAGGCACTGAAATTTGACTGGGAAAGGACTTGAACATGAGTGGTCAACCAAATGA
GCAGGTCTCAGTTTCTTAAGAGTTAAGAGGCTTATATTCATGCTTAATGTGTCAGTTGAATTAT
GTATTACATTAAAATGCGTATAATTGTTTTGTCTGAAAAATGTTTGACAGATTGAAAATGAATA
CGGTAACATTCAAGGCCATTATGGTCAAGCAGGGAAGAGATACATGCTATGGGCAGCTCAGATG
GCACTTGCACTTGATACTGGTGTTCCTTGGGTAATGTGTAGGCAAACAGATGCTCCAGAACAAA
TTGTAGGTTGCCTCAAAATCTATTGAGATCGACTTCACATTACATTAGAGATTGTCAAATGTGC
TTACTGCAAAGTAAATAGATTACTGCCTTGTCCTTTTTGGCAGCTCAATACTTGCAATGCCTTT
TACTGTGATGGGTTCAAACCAAATTCCTACAACAAGCCAACAATATGGACTGAGGATTGGGATG
GATG
						
					

			
		

Sequences
Splice junction sequence	CTTTTTGGCAGCTCAATACTTGCAATGCCTTTTACTGTGATGGGTTCAAACCAAATTCCTACAA CAAGCCAACAATATGGACTGAGGATTGGGATGGATGtggtttcccagtttggttgcgcgatgtc cctgggatagaattccgcactgacaatgaaccctacaaggtagatgaaccactaagcatagatt ttgtcttc
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: 393 Transcript exons: 142140828-142140894,142140985-142141077,142142542-142142 685,142142791-142142879 TGGTTTCCCAGTTTGGTTGCGCGATGTCCCTGGGATAGAATTCCGCACTGACAATGAACCCTAC AAGGCTGAAATGCAGATTTTTGTGACAAAAATTGTAGATATCATGAAAGAGGAGAAGCTTTATT CTTGGCAAGGTGGTCCCATTATACTGCAGCAGATTGAAAATGAATACGGTAACATTCAAGGCCA TTATGGTCAAGCAGGGAAGAGATACATGCTATGGGCAGCTCAGATGGCACTTGCACTTGATACT GGTGTTCCTTGGGTAATGTGTAGGCAAACAGATGCTCCAGAACAAATTCTCAATACTTGCAATG CCTTTTACTGTGATGGGTTCAAACCAAATTCCTACAACAAGCCAACAATATGGACTGAGGATTG GGATGGATG
Genomic sequence	TGGTTTCCCAGTTTGGTTGCGCGATGTCCCTGGGATAGAATTCCGCACTGACAATGAACCCTAC AAGGTAGATGAACCACTAAGCATAGATTTTGTCTTCCTATGATGAACATTTTTCATTTATTTGA ATTCACTAATCCTTAAAATTGTCGTACAGGCTGAAATGCAGATTTTTGTGACAAAAATTGTAGA TATCATGAAAGAGGAGAAGCTTTATTCTTGGCAAGGTGGTCCCATTATACTGCAGCAGGTCTGA AAACTTTTCTCGAAGTTCACTTATTGGTGTTTCTTTTCTCCTCCCTCCCTCCCTCCTAGGAGAC CCCTTGCATAAAGCACTCTATCTTGTTGAGGAGACGAGAGAGGTTCAGGTTTGGACAATTGGAC AAATAAAGAAACCATCTGAAAAGAGGAAAAAACCCGGACTCAACCAGGGCTGGTTATTAAACCC TCAACAAGACCTAGACCATGTTCTTGAAGTTTACGTAATGTATACATGTCTTAGGGGTGTCTTT AGTACAACTTCGTCTTCCGTCATCCCCTTAGCGTCATCTTTCATCATGCGTAGGCGTATGCCTT GTACGGTGTATTGCCCTGCCCCCTCCGGCGTATGGGTCACTGTAGAGACCCTGATGCTGAGGTC TCTATGGCTGGAGCCTTCTGGTCCCACTAGTCAGCGGGGATACGTATCCGGCGTCGTGCTTTGA CAGAGACCTCTCGGTACCGCTTCCACAGTCTGGGCATGGCTCGGTGATGTCCCATCGTGTCGAC GTGGCTTGATAGTACTAGGTGGGCTCTTCTTGAGAGCCGGCTGTCGTTTTGCTGGGTTGCTCGG CAGCCTCGCCTCGTTGGGTTGCTCAGCGGGCAGGTTGCTCGGCAGCCTCGTCTCGTTGGGTTGC TTCGCGGGCAGGTTGCTCGGTAGCCCCGCCTCGCTGGGTTGCTCGGCGGACATTAGTTCGTTGG GCCGATCGGCTTGGTAGGCCGTCCCTGGGCGGCCTTTTGGTCTTTCCCGCCGATTTGTTTGGCA GGCGGGCTGCTCGGTTCGTGGGTTGTCTTTGGGAGGCCTTCGGGCCTTCTTTGGGTACCCTGTT TCCAGGTACCCAACAGTTAGCTAAGCTATCACCCATTAATCAGTACACAGAGATCTGAAAAATA TCAATGACAAGTGGATATTATGTTATATGTGGCTTAAGTAATTTTTGGTTGGTGCCATTTGGTG ACAACATTGCTTAGTATCTTTGATGTTCAGTTAATTCCTTTGTTTAATAAAACTGTTAGATGGC GTTCTATATATGGATGGTGCTCATGATAGAGTTAAACATTGAACCATAATGTGGTAAAGGATAC AATTCTGAAGTATGTTATGTAGCCAAAAGCTAGATGCTGGCTGTTTTACCTTCTGAAGTAGCAA TACTTATGGTGTTGGCTCTGTGCTCTAGTTAATTCAGCACAAACACCTGAAATTTGGTGGATGT AAGAGGCTCATATTAATAAAAACTTGACCAATCTAGGAGGAACTAGGCATCTTTTACTTTTAGT AAGAAGAAAAAGGCACTGAAATTTGACTGGGAAAGGACTTGAACATGAGTGGTCAACCAAATGA GCAGGTCTCAGTTTCTTAAGAGTTAAGAGGCTTATATTCATGCTTAATGTGTCAGTTGAATTAT GTATTACATTAAAATGCGTATAATTGTTTTGTCTGAAAAATGTTTGACAGATTGAAAATGAATA CGGTAACATTCAAGGCCATTATGGTCAAGCAGGGAAGAGATACATGCTATGGGCAGCTCAGATG GCACTTGCACTTGATACTGGTGTTCCTTGGGTAATGTGTAGGCAAACAGATGCTCCAGAACAAA TTGTAGGTTGCCTCAAAATCTATTGAGATCGACTTCACATTACATTAGAGATTGTCAAATGTGC TTACTGCAAAGTAAATAGATTACTGCCTTGTCCTTTTTGGCAGCTCAATACTTGCAATGCCTTT TACTGTGATGGGTTCAAACCAAATTCCTACAACAAGCCAACAATATGGACTGAGGATTGGGATG GATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_011362 						
					
						PMCS
						0.087153918

Conservation Information
Conserved circRNAs	osa_circ_011362
PMCS	0.087153918

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							142140992-142142876(+)
142142670-142140862(+)
142142576-142142604(-)
						
						Potential amino acid sequence
						
							MQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQMALALDTGVP
WVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDGCGFPVWLRDVPGIEFRTDNEPY
KAEMQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQMALALDT
GVPWVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDGCGFPVWLRDVPGIEFRTDN
EPYKAEMQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQMALA
LDTGVPWVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDGCGFPVWLRDVPGIEFR
TDNEPYKAEMQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQM
ALALDTGVPWVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDG(+)
MLQNKFSILAMPFTVMGSNQIPTTSQQYGLRIGMDVVSQFGCAMSLG*(+)
MALNVTVFIFNLLQYNGTTLPRIKLLLFHDIYNFCHKNLHFSLVGFIVSAEFYPRDIAQPNWET
TSIPILSPYCWLVVGIWFEPITVKGIASIENLFWSICLPTHYPRNTSIKCKCHLSCP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	142140992-142142876(+) 142142670-142140862(+) 142142576-142142604(-)
Potential amino acid sequence	MQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQMALALDTGVP WVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDGCGFPVWLRDVPGIEFRTDNEPY KAEMQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQMALALDT GVPWVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDGCGFPVWLRDVPGIEFRTDN EPYKAEMQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQMALA LDTGVPWVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDGCGFPVWLRDVPGIEFR TDNEPYKAEMQIFVTKIVDIMKEEKLYSWQGGPIILQQIENEYGNIQGHYGQAGKRYMLWAAQM ALALDTGVPWVMCRQTDAPEQILNTCNAFYCDGFKPNSYNKPTIWTEDWDG(+) MLQNKFSILAMPFTVMGSNQIPTTSQQYGLRIGMDVVSQFGCAMSLG(+) MALNVTVFIFNLLQYNGTTLPRIKLLLFHDIYNFCHKNLHFSLVGFIVSAEFYPRDIAQPNWET TSIPILSPYCWLVVGIWFEPITVKGIASIENLFWSICLPTHYPRNTSIKCKCHLSCP(-)
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 Zm00001d041880_circ_g.4

Address

Any questions?

Supported by