Plant Circular RNA Database

Detail information of Zm00001d010546_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d010546_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009673
					
						Alias
						Zm08circ00046, zma_circ_0002759, GRMZM2G390400_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 120075635-120076679  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d010546						
					
						Parent gene annotation
						
							Putative SAC3/GANP family protein  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d010546_circ_g.1 Zm00001d010546_circ_g.2 						
					
						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
						Zm00001d010546_T022:3
Zm00001d010546_T005:3
Zm00001d010546_T015:3
Zm00001d010546_T023:3
Zm00001d010546_T019:3
Zm00001d010546_T008:3
Zm00001d010546_T006:3
Zm00001d010546_T001:3
Zm00001d010546_T016:3
Zm00001d010546_T004:3
Zm00001d010546_T012:3
Zm00001d010546_T021:3
Zm00001d010546_T002:3
Zm00001d010546_T003:3
Zm00001d010546_T018:3
Zm00001d010546_T025:3
Zm00001d010546_T007:3
Zm00001d010546_T013:3
Zm00001d010546_T017:3

General Information
CircRNA Name	Zm00001d010546_circ_g.3
ID in PlantcircBase	zma_circ_009673
Alias	Zm08circ00046, zma_circ_0002759, GRMZM2G390400_C2
Organism	Zea mays
Position	chr8: 120075635-120076679 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d010546
Parent gene annotation	Putative SAC3/GANP family protein
Parent gene strand	-
Alternative splicing	Zm00001d010546_circ_g.1 Zm00001d010546_circ_g.2
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	Zm00001d010546_T022:3 Zm00001d010546_T005:3 Zm00001d010546_T015:3 Zm00001d010546_T023:3 Zm00001d010546_T019:3 Zm00001d010546_T008:3 Zm00001d010546_T006:3 Zm00001d010546_T001:3 Zm00001d010546_T016:3 Zm00001d010546_T004:3 Zm00001d010546_T012:3 Zm00001d010546_T021:3 Zm00001d010546_T002:3 Zm00001d010546_T003:3 Zm00001d010546_T018:3 Zm00001d010546_T025:3 Zm00001d010546_T007:3 Zm00001d010546_T013:3 Zm00001d010546_T017:3

			
						 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  
						
							TTCCACCTTATTGGTAACATTTTCATCCACAACAGGCTCCCATCTACTTTTCACACGTTTCCTT
GGGGTAGATACTGACAAGAAGGGACTTAAATCACTGctttacagtcagttcattctggattctc
tgaactgtaagatcttgccggatagattttagttgatcacacttgtaaaggtaattcttttctg
atgtttca

									
								

					

						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: 784
Transcript exons: 120075635-120075775,120075904-120076383,120076517-120076
679
CTTTACAGTCAGTTCATTCTGGATTCTCTGAACTGTAAGATCTTGCCGGATAGATTTTAGTTGA
TCACACTTGTAAAGGTAATTCTTTTCTGATGTTTCAACCATTGCAAGGGCCTTCTCCAGAACAT
CTTCTGGCCTTACTTTGGCAGGATCAGGTGCTTCTGTAAGTCGTAGATAGCGTTTCTCAATTTC
CTGACATGTTCCTTTGACTGTCAGTGCATCCCAATCCATATCCTCCACAGCCAAAGTGCCTTCT
TCATAGGTTCTAGTACGAAGAGACGAAATTGCCCTTCTTGCACGAAAACTAGCCATACCATCGT
TATTTGCAGAAGCATTTCTTGATTTTAATGATGAATCTTTACTCTTTTCAAAACGCTTGGATCT
ATGCTCCCTACGTTTCTTTTCCTCAGGCGAGTTTGCTAGTGCAGTTGCACTGGCATAATGTTTG
GTTAGATCATGTTCCTTCTCACTGTCACTTGAAGCACTTCCATTCTGTATTTGACTCAAATTAC
TAGCCATTTTTTGCTTCTTGGCAGGCCTCTGATTGACTTTATTTGATGATGCTTGACAAGACTG
GAGAAACTTCCCACGATCCCAACTGCTACCCCGCACAGGATTTGGAATTCTATTTTTAGGGTCC
AAAGTACTGTGGACATTACTGCTGATCAATCCTTTTGCTATTTGTTCCACCTTATTGGTAACAT
TTTCATCCACAACAGGCTCCCATCTACTTTTCACACGTTTCCTTGGGGTAGATACTGACAAGAA
GGGACTTAAATCACTG
						
					

						Genomic sequence
						
							CTTTACAGTCAGTTCATTCTGGATTCTCTGAACTGTAAGATCTTGCCGGATAGATTTTAGTTGA
TCACACTTGTAAAGGTAATTCTTTTCTGATGTTTCAACCATTGCAAGGGCCTTCTCCAGAACAT
CTTCTGGCCTTACCTGCAAACAAAATACTCAGAAGAGTCAAGCAAACAGTAGAGTGATTAAGCA
GAAGCAATCAACCTAATGGGTCAACATCAGACCCTTTGAATCTAGAGTAAAGTAAGACAATTGG
TGAGTGTTGTTACTTTGGCAGGATCAGGTGCTTCTGTAAGTCGTAGATAGCGTTTCTCAATTTC
CTGACATGTTCCTTTGACTGTCAGTGCATCCCAATCCATATCCTCCACAGCCAAAGTGCCTTCT
TCATAGGTTCTAGTACGAAGAGACGAAATTGCCCTTCTTGCACGAAAACTAGCCATACCATCGT
TATTTGCAGAAGCATTTCTTGATTTTAATGATGAATCTTTACTCTTTTCAAAACGCTTGGATCT
ATGCTCCCTACGTTTCTTTTCCTCAGGCGAGTTTGCTAGTGCAGTTGCACTGGCATAATGTTTG
GTTAGATCATGTTCCTTCTCACTGTCACTTGAAGCACTTCCATTCTGTATTTGACTCAAATTAC
TAGCCATTTTTTGCTTCTTGGCAGGCCTCTGATTGACTTTATTTGATGATGCTTGACAAGACTG
GAGAAACTTCCCACGATCCCAACTGCTACCCCGCACAGGATTTGGCTAACATTACAAAGAGCAA
ACAAAAATAAGTTTGGAATACCAAATCTAGTGATAAAAGCATTTCATTGTGAAAACTTAGAAGC
AACAGCATGGAAGTCCATTCCACCAGTATGAGCAACAGATTAATGCTTACAATTCTATTTTTAG
GGTCCAAAGTACTGTGGACATTACTGCTGATCAATCCTTTTGCTATTTGTTCCACCTTATTGGT
AACATTTTCATCCACAACAGGCTCCCATCTACTTTTCACACGTTTCCTTGGGGTAGATACTGAC
AAGAAGGGACTTAAATCACTG
						
					

			
		

Sequences
Splice junction sequence	TTCCACCTTATTGGTAACATTTTCATCCACAACAGGCTCCCATCTACTTTTCACACGTTTCCTT GGGGTAGATACTGACAAGAAGGGACTTAAATCACTGctttacagtcagttcattctggattctc tgaactgtaagatcttgccggatagattttagttgatcacacttgtaaaggtaattcttttctg atgtttca
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: 784 Transcript exons: 120075635-120075775,120075904-120076383,120076517-120076 679 CTTTACAGTCAGTTCATTCTGGATTCTCTGAACTGTAAGATCTTGCCGGATAGATTTTAGTTGA TCACACTTGTAAAGGTAATTCTTTTCTGATGTTTCAACCATTGCAAGGGCCTTCTCCAGAACAT CTTCTGGCCTTACTTTGGCAGGATCAGGTGCTTCTGTAAGTCGTAGATAGCGTTTCTCAATTTC CTGACATGTTCCTTTGACTGTCAGTGCATCCCAATCCATATCCTCCACAGCCAAAGTGCCTTCT TCATAGGTTCTAGTACGAAGAGACGAAATTGCCCTTCTTGCACGAAAACTAGCCATACCATCGT TATTTGCAGAAGCATTTCTTGATTTTAATGATGAATCTTTACTCTTTTCAAAACGCTTGGATCT ATGCTCCCTACGTTTCTTTTCCTCAGGCGAGTTTGCTAGTGCAGTTGCACTGGCATAATGTTTG GTTAGATCATGTTCCTTCTCACTGTCACTTGAAGCACTTCCATTCTGTATTTGACTCAAATTAC TAGCCATTTTTTGCTTCTTGGCAGGCCTCTGATTGACTTTATTTGATGATGCTTGACAAGACTG GAGAAACTTCCCACGATCCCAACTGCTACCCCGCACAGGATTTGGAATTCTATTTTTAGGGTCC AAAGTACTGTGGACATTACTGCTGATCAATCCTTTTGCTATTTGTTCCACCTTATTGGTAACAT TTTCATCCACAACAGGCTCCCATCTACTTTTCACACGTTTCCTTGGGGTAGATACTGACAAGAA GGGACTTAAATCACTG
Genomic sequence	CTTTACAGTCAGTTCATTCTGGATTCTCTGAACTGTAAGATCTTGCCGGATAGATTTTAGTTGA TCACACTTGTAAAGGTAATTCTTTTCTGATGTTTCAACCATTGCAAGGGCCTTCTCCAGAACAT CTTCTGGCCTTACCTGCAAACAAAATACTCAGAAGAGTCAAGCAAACAGTAGAGTGATTAAGCA GAAGCAATCAACCTAATGGGTCAACATCAGACCCTTTGAATCTAGAGTAAAGTAAGACAATTGG TGAGTGTTGTTACTTTGGCAGGATCAGGTGCTTCTGTAAGTCGTAGATAGCGTTTCTCAATTTC CTGACATGTTCCTTTGACTGTCAGTGCATCCCAATCCATATCCTCCACAGCCAAAGTGCCTTCT TCATAGGTTCTAGTACGAAGAGACGAAATTGCCCTTCTTGCACGAAAACTAGCCATACCATCGT TATTTGCAGAAGCATTTCTTGATTTTAATGATGAATCTTTACTCTTTTCAAAACGCTTGGATCT ATGCTCCCTACGTTTCTTTTCCTCAGGCGAGTTTGCTAGTGCAGTTGCACTGGCATAATGTTTG GTTAGATCATGTTCCTTCTCACTGTCACTTGAAGCACTTCCATTCTGTATTTGACTCAAATTAC TAGCCATTTTTTGCTTCTTGGCAGGCCTCTGATTGACTTTATTTGATGATGCTTGACAAGACTG GAGAAACTTCCCACGATCCCAACTGCTACCCCGCACAGGATTTGGCTAACATTACAAAGAGCAA ACAAAAATAAGTTTGGAATACCAAATCTAGTGATAAAAGCATTTCATTGTGAAAACTTAGAAGC AACAGCATGGAAGTCCATTCCACCAGTATGAGCAACAGATTAATGCTTACAATTCTATTTTTAG GGTCCAAAGTACTGTGGACATTACTGCTGATCAATCCTTTTGCTATTTGTTCCACCTTATTGGT AACATTTTCATCCACAACAGGCTCCCATCTACTTTTCACACGTTTCCTTGGGGTAGATACTGAC AAGAAGGGACTTAAATCACTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.238530366

Conservation Information
Conserved circRNAs	NA
PMCS	0.238530366

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							120076283-120076676(-)
						
						Potential amino acid sequence
						
							MASNLSQIQNGSASSDSEKEHDLTKHYASATALANSPEEKKRREHRSKRFEKSKDSSLKSRNAS
ANNDGMASFRARRAISSLRTRTYEEGTLAVEDMDWDALTVKGTCQEIEKRYLRLTEAPDPAKVR
PEDVLEKALAMVETSEKNYLYKCDQLKSIRQDLTVQRIQNELTVKQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	120076283-120076676(-)
Potential amino acid sequence	MASNLSQIQNGSASSDSEKEHDLTKHYASATALANSPEEKKRREHRSKRFEKSKDSSLKSRNAS ANNDGMASFRARRAISSLRTRTYEEGTLAVEDMDWDALTVKGTCQEIEKRYLRLTEAPDPAKVR PEDVLEKALAMVETSEKNYLYKCDQLKSIRQDLTVQRIQNELTVKQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d010546_circ_g.3

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