Plant Circular RNA Database

Detail information of Zm00001d012661_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d012661_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009819
					
						Alias
						Zm08circ00085, zma_circ_0002872
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 178189030-178195735  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d012661						
					
						Parent gene annotation
						
							DExH-box ATP-dependent RNA helicase DExH6
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d012661_circ_g.1 Zm00001d012661_circ_g.2 Zm00001d012661_circ_g.4 Zm00001d012661_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  
						
							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
						Zm00001d012661_T015:6
Zm00001d012661_T004:6
Zm00001d012661_T003:5
Zm00001d012661_T001:5
Zm00001d012661_T002:5
Zm00001d012661_T012:6
Zm00001d012661_T010:6
Zm00001d012661_T008:1
Zm00001d012661_T018:6
Zm00001d012661_T016:7
Zm00001d012661_T013:4
Zm00001d012661_T005:6
Zm00001d012661_T007:6

General Information
CircRNA Name	Zm00001d012661_circ_g.3
ID in PlantcircBase	zma_circ_009819
Alias	Zm08circ00085, zma_circ_0002872
Organism	Zea mays
Position	chr8: 178189030-178195735 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d012661
Parent gene annotation	DExH-box ATP-dependent RNA helicase DExH6
Parent gene strand	-
Alternative splicing	Zm00001d012661_circ_g.1 Zm00001d012661_circ_g.2 Zm00001d012661_circ_g.4 Zm00001d012661_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	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	Zm00001d012661_T015:6 Zm00001d012661_T004:6 Zm00001d012661_T003:5 Zm00001d012661_T001:5 Zm00001d012661_T002:5 Zm00001d012661_T012:6 Zm00001d012661_T010:6 Zm00001d012661_T008:1 Zm00001d012661_T018:6 Zm00001d012661_T016:7 Zm00001d012661_T013:4 Zm00001d012661_T005:6 Zm00001d012661_T007:6

			
						 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  
						
							TTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAACACCATTTGTGCAGAACAAGAC
TGATGAATTCTTCCCGCCTTTTGACTCCAAACGTATctggatctttagagtttaagctgcaggc
agatgcatctgcagggacaaaccctctttgagacagttcattctgaagttgtttcctcatgctt
gatagcat

									
								

					

						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: 1969
Transcript exons: 178189030-178189588,178189730-178190890,178194130-178194
163,178194255-178194307,178195574-178195735
CTGGATCTTTAGAGTTTAAGCTGCAGGCAGATGCATCTGCAGGGACAAACCCTCTTTGAGACAG
TTCATTCTGAAGTTGTTTCCTCATGCTTGATAGCATATTCATGATGTTTGAAGAGACAAAGTAC
TTCGCACAAAATTGAGAATCTTGGCCTCTATCTTTGGCATGCCTCCAGAAGTCAAATGCCGCGA
CAACAGCAAGTTGGTCGCTGAACCCACCATACAACGAAGCAAGCTCAACTTTCGCTGCAGCTGC
CCTTTTCCTCTCATCAGGCGCTACTGGAAGGACAAATGGATCTCTATAATCAGCTGCACATGCC
AATGTCAATGCTGGATCCAGGCAGTTCATTAATATAGCAAACAGGAGCATCTTGGTGGTGGATG
GATGGACTGGCAGGGAACCCAGCTTTTCTCCTAATTCTGTTAGTTGTTCGTCTTGTGTTAAAGC
ACCAAGATCCTGAAGCACAGCAATAGCATTTCTTACAGTTTCTGGAATTGGAGGGTCCAAGGTT
TTCTTCAGAAAGTCTGCTATTCTGCAGTTTGAATCAAGCAGTTTGACCTGCAAACAAAGTTCCT
CAATGGGCATTCTTTTTATTTCAGGAATTTGGTAGTCTGGCAAGGATGAAGCTCTAAACCTTGA
GTAAAGATGATAGCAAGTTCCTGGCTGACATCGGCCAGCACGCCCTTCGCGTTGTCTTGCACTG
GCTTTTGAAACCCAAGAAGCATGAAGTGTGGACACATTATTGTATGGATCATAACTTTTCTCTT
TCATTCTCCCACTATCTATGACAAACACAACATCATCAATTGTCACAGCAGTCTCTGCAATATT
AGTTGAGAGAATAATTTTACGAACCCCCACTGGTGGACGTTTGAAAACCTTTTTCTGCTCTGAG
GACGGGATCATAGAATGAAGAGACAACACAAGAAATCTTGATGAATCCTGAAAGAATGGAGAAG
CAAATAATCTTTCACGTGTTTGACTGATATCTTCCCAGCCAGGAAGGAATACCAAGATGGCTCC
TTCATTGGAATCCACACAAATTTTTCGAAGCAGCCGTTCAATTAGCAGAGTATCAATGTGCTCT
GGATTAATAGATGCCAAGTACTTGTTAAGCAGCTCGTTATCTTCAGTTGATTTTTCTGAACTAC
ACTCCATATGTTTCTTTATTACTTCACAGACCTCTTGTTGATTCTCTTGTTGTGCCCAATCTAA
TGCGGATTTTCCATCATGATCCTGTGCTGAACAATCCACACCAAAAGATAAAAGCATACAGACG
TCCCCAAGCTGACCCTTCATAGCAAAAACCATTAAAGGAGTTATACCAGTCTCTGAATGCTGGT
AATTGTAGACTTCTGTGTTCTGCTCTGCAGAAATAAGCTCAAGAAGAGGATCAAATTCATCATT
GACCAAAGCCAGATTAATTGAATCATCCATTGAGCTTTTGAAATCGTGAGTTAAAACGCTGCCC
TCTGTTTTATGACTGGTAAGATGGTTATCACCTGCAGACTGCAGAATAGAAAGCACATCCTCCA
AATAGAAAGTTTTGACCTGAGGGGGGAAAAAGTTATAACTTCCAAAAATAATTTCAGATCGCTT
AATGTATTCAATCTGAGAGAGTTTACTAACAGGATAGGTAAAACCAGGGACTTGTATGACCGAA
CATCCATTGAAATATTGCGAAAAACGCTCAGCATCAATTGTTGCACTCATGAGTACCATACGAA
GATGAGGATACAAAGGCAACAAGTCTCTTAGAATAGTCAGCATGAAATCAGAAAACCTATCCCT
TTCATGGATTTCATCCACAATGATGTGCGTTATTCCCAAAACTGCATCATCTAATGAGCGCTTC
TGGTTTCGTGCTTTTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAACACCATTTG
TGCAGAACAAGACTGATGAATTCTTCCCGCCTTTTGACTCCAAACGTAT
						
					

						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	TTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAACACCATTTGTGCAGAACAAGAC TGATGAATTCTTCCCGCCTTTTGACTCCAAACGTATctggatctttagagtttaagctgcaggc agatgcatctgcagggacaaaccctctttgagacagttcattctgaagttgtttcctcatgctt gatagcat
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: 1969 Transcript exons: 178189030-178189588,178189730-178190890,178194130-178194 163,178194255-178194307,178195574-178195735 CTGGATCTTTAGAGTTTAAGCTGCAGGCAGATGCATCTGCAGGGACAAACCCTCTTTGAGACAG TTCATTCTGAAGTTGTTTCCTCATGCTTGATAGCATATTCATGATGTTTGAAGAGACAAAGTAC TTCGCACAAAATTGAGAATCTTGGCCTCTATCTTTGGCATGCCTCCAGAAGTCAAATGCCGCGA CAACAGCAAGTTGGTCGCTGAACCCACCATACAACGAAGCAAGCTCAACTTTCGCTGCAGCTGC CCTTTTCCTCTCATCAGGCGCTACTGGAAGGACAAATGGATCTCTATAATCAGCTGCACATGCC AATGTCAATGCTGGATCCAGGCAGTTCATTAATATAGCAAACAGGAGCATCTTGGTGGTGGATG GATGGACTGGCAGGGAACCCAGCTTTTCTCCTAATTCTGTTAGTTGTTCGTCTTGTGTTAAAGC ACCAAGATCCTGAAGCACAGCAATAGCATTTCTTACAGTTTCTGGAATTGGAGGGTCCAAGGTT TTCTTCAGAAAGTCTGCTATTCTGCAGTTTGAATCAAGCAGTTTGACCTGCAAACAAAGTTCCT CAATGGGCATTCTTTTTATTTCAGGAATTTGGTAGTCTGGCAAGGATGAAGCTCTAAACCTTGA GTAAAGATGATAGCAAGTTCCTGGCTGACATCGGCCAGCACGCCCTTCGCGTTGTCTTGCACTG GCTTTTGAAACCCAAGAAGCATGAAGTGTGGACACATTATTGTATGGATCATAACTTTTCTCTT TCATTCTCCCACTATCTATGACAAACACAACATCATCAATTGTCACAGCAGTCTCTGCAATATT AGTTGAGAGAATAATTTTACGAACCCCCACTGGTGGACGTTTGAAAACCTTTTTCTGCTCTGAG GACGGGATCATAGAATGAAGAGACAACACAAGAAATCTTGATGAATCCTGAAAGAATGGAGAAG CAAATAATCTTTCACGTGTTTGACTGATATCTTCCCAGCCAGGAAGGAATACCAAGATGGCTCC TTCATTGGAATCCACACAAATTTTTCGAAGCAGCCGTTCAATTAGCAGAGTATCAATGTGCTCT GGATTAATAGATGCCAAGTACTTGTTAAGCAGCTCGTTATCTTCAGTTGATTTTTCTGAACTAC ACTCCATATGTTTCTTTATTACTTCACAGACCTCTTGTTGATTCTCTTGTTGTGCCCAATCTAA TGCGGATTTTCCATCATGATCCTGTGCTGAACAATCCACACCAAAAGATAAAAGCATACAGACG TCCCCAAGCTGACCCTTCATAGCAAAAACCATTAAAGGAGTTATACCAGTCTCTGAATGCTGGT AATTGTAGACTTCTGTGTTCTGCTCTGCAGAAATAAGCTCAAGAAGAGGATCAAATTCATCATT GACCAAAGCCAGATTAATTGAATCATCCATTGAGCTTTTGAAATCGTGAGTTAAAACGCTGCCC TCTGTTTTATGACTGGTAAGATGGTTATCACCTGCAGACTGCAGAATAGAAAGCACATCCTCCA AATAGAAAGTTTTGACCTGAGGGGGGAAAAAGTTATAACTTCCAAAAATAATTTCAGATCGCTT AATGTATTCAATCTGAGAGAGTTTACTAACAGGATAGGTAAAACCAGGGACTTGTATGACCGAA CATCCATTGAAATATTGCGAAAAACGCTCAGCATCAATTGTTGCACTCATGAGTACCATACGAA GATGAGGATACAAAGGCAACAAGTCTCTTAGAATAGTCAGCATGAAATCAGAAAACCTATCCCT TTCATGGATTTCATCCACAATGATGTGCGTTATTCCCAAAACTGCATCATCTAATGAGCGCTTC TGGTTTCGTGCTTTTGAAGCGTTAGTTCCTCTTCCTATCAATAATCTCAAAAGAACACCATTTG TGCAGAACAAGACTGATGAATTCTTCCCGCCTTTTGACTCCAAACGTAT
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
						0.164017806

Conservation Information
Conserved circRNAs	NA
PMCS	0.164017806

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							178195703-178189085(+)
178194271-178189045(+)
178194273-178195646(-)
						
						Potential amino acid sequence
						
							MNSSRLLTPNVSGSLEFKLQADASAGTNPL*(+)
MKSENLSLSWISSTMMCVIPKTASSNERFWFRAFEALVPLPINNLKRTPFVQNKTDEFFPPFDS
KRIWIFRV*(+)
MLTILRDLLPLYPHLRMVLMSATIDAERFSQYFNGCSVIQVPGFTYPVKTFYLEDVLSILQSAG
DNHLTSHKTEGSVLTHDFKSSMDDSINLALVNDEFDPLLELISAEQNTEVYNYQHSETGITPLM
VFAMKGQLGDVCMLLSFGVDCSAQDHDGKSALDWAQQENQQEVCEVIKKHMECSSEKSTEDNEL
LNKYLASINPEHIDTLLIERLLRKICVDSNEGAILVFLPGWEDISQTRERLFASPFFQDSSRFL
VLSLHSMIPSSEQKKVFKRPPVGVRKIILSTNIAETAVTIDDVVFVIDSGRMKEKSYDPYNNVS
TLHASWVSKASARQREGRAGRCQPGTCYHLYSRFRASSLPDYQIPEIKRMPIEELCLQVKLLDS
NCRIADFLKKTLDPPIPETVRNAIAVLQDLGALTQDEQLTELGEKLGSLPVHPSTTKMLLFAIL
MNCLDPALTLACAADYRDPFVLPVAPDERKRAAAAKVELASLYGGFSDQLAVVAAFDFWRHAKD
RGQDSQFCAKYFVSSNIMNMLSSMRKQLQNELSQRGFVPADASACSLNSKDPDTFGVKRREEFI
SLVLHKWCSFEIIDRKRN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	178195703-178189085(+) 178194271-178189045(+) 178194273-178195646(-)
Potential amino acid sequence	MNSSRLLTPNVSGSLEFKLQADASAGTNPL(+) MKSENLSLSWISSTMMCVIPKTASSNERFWFRAFEALVPLPINNLKRTPFVQNKTDEFFPPFDS KRIWIFRV(+) MLTILRDLLPLYPHLRMVLMSATIDAERFSQYFNGCSVIQVPGFTYPVKTFYLEDVLSILQSAG DNHLTSHKTEGSVLTHDFKSSMDDSINLALVNDEFDPLLELISAEQNTEVYNYQHSETGITPLM VFAMKGQLGDVCMLLSFGVDCSAQDHDGKSALDWAQQENQQEVCEVIKKHMECSSEKSTEDNEL LNKYLASINPEHIDTLLIERLLRKICVDSNEGAILVFLPGWEDISQTRERLFASPFFQDSSRFL VLSLHSMIPSSEQKKVFKRPPVGVRKIILSTNIAETAVTIDDVVFVIDSGRMKEKSYDPYNNVS TLHASWVSKASARQREGRAGRCQPGTCYHLYSRFRASSLPDYQIPEIKRMPIEELCLQVKLLDS NCRIADFLKKTLDPPIPETVRNAIAVLQDLGALTQDEQLTELGEKLGSLPVHPSTTKMLLFAIL MNCLDPALTLACAADYRDPFVLPVAPDERKRAAAAKVELASLYGGFSDQLAVVAAFDFWRHAKD RGQDSQFCAKYFVSSNIMNMLSSMRKQLQNELSQRGFVPADASACSLNSKDPDTFGVKRREEFI SLVLHKWCSFEIIDRKRN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d012661_circ_g.3

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