Plant Circular RNA Database

Detail information of Zm00001d009424_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d009424_circ_g.6
					
						ID in PlantcircBase
						zma_circ_009615
					
						Alias
						Zm08circ00029, zma_circ_0002712, GRMZM2G109651_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 63800622-63813714  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d009424						
					
						Parent gene annotation
						
							Cyclin/Brf1-like TBP-binding protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d009424_circ_g.1 Zm00001d009424_circ_g.2 Zm00001d009424_circ_g.3 Zm00001d009424_circ_g.4 Zm00001d009424_circ_g.5 Zm00001d009424_circ_g.7 Zm00001d009424_circ_g.8 Zm00001d009424_circ_g.9 Zm00001d009424_circ_g.10 						
					
						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
						Zm00001d009424_T017:16
Zm00001d009424_T012:16
Zm00001d009424_T011:15
Zm00001d009424_T009:14
Zm00001d009424_T003:16
Zm00001d009424_T004:16
Zm00001d009424_T001:15
Zm00001d009424_T008:14
Zm00001d009424_T007:15
Zm00001d009424_T006:16
Zm00001d009424_T015:16
Zm00001d009424_T016:17
Zm00001d009424_T002:14
Zm00001d009424_T014:15
Zm00001d009424_T010:16
Zm00001d009424_T013:16
Zm00001d009424_T005:15

General Information
CircRNA Name	Zm00001d009424_circ_g.6
ID in PlantcircBase	zma_circ_009615
Alias	Zm08circ00029, zma_circ_0002712, GRMZM2G109651_C3
Organism	Zea mays
Position	chr8: 63800622-63813714 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d009424
Parent gene annotation	Cyclin/Brf1-like TBP-binding protein
Parent gene strand	+
Alternative splicing	Zm00001d009424_circ_g.1 Zm00001d009424_circ_g.2 Zm00001d009424_circ_g.3 Zm00001d009424_circ_g.4 Zm00001d009424_circ_g.5 Zm00001d009424_circ_g.7 Zm00001d009424_circ_g.8 Zm00001d009424_circ_g.9 Zm00001d009424_circ_g.10
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	Zm00001d009424_T017:16 Zm00001d009424_T012:16 Zm00001d009424_T011:15 Zm00001d009424_T009:14 Zm00001d009424_T003:16 Zm00001d009424_T004:16 Zm00001d009424_T001:15 Zm00001d009424_T008:14 Zm00001d009424_T007:15 Zm00001d009424_T006:16 Zm00001d009424_T015:16 Zm00001d009424_T016:17 Zm00001d009424_T002:14 Zm00001d009424_T014:15 Zm00001d009424_T010:16 Zm00001d009424_T013:16 Zm00001d009424_T005:15

			
						 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  
						
							TGCTACTACCTGCATTTTTATTTTACAGGAACAAGCAGCCAAGGAAGCTTTGGCAGCTGAATTG
GCAGCTAGAGGGATTGTTGTGGAAGAGGGAAAGAAAtttcacagattggtatgagctgatcacc
cctggttgtgtagttccttctgcaatgatttactgcactcactgtgctgattactgcccctcca
taaaggac

									
								

					

						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: 1450
Transcript exons: 63800622-63800738,63800928-63801009,63801099-63801174,63
801251-63801336,63801789-63801865,63803130-63803236,6380
3617-63803723,63803809-63803895,63804024-63804104,638111
43-63811289,63811375-63811560,63813122-63813206,63813303
-63813361,63813491-63813571,63813643-63813714
TTTCACAGATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTTACTGC
ACTCACTGTGCTGATTACTGCCCCTCCATAAAGGACCCTGACAAAGGATACATATGTTGTGGTA
CATGTGGGAAGGTTCTTGATCAGGAGGTATACACTGATGAGCCTACTTTTGTTAAGGATAACAC
AGGACAGAGTCGCTTAGCTGGAAGTATTCTTGCAAGCATTGAGTCTGGATATTCGATTTCTCAT
CAAAGAACCTTAGACAAAGGTAGGGATGAGATTAGGCAGATTGTCAATAACTTACATGTCAGCG
GTGGAGAAACTGTCGTTAGCAAGGCTTATCGCTTCTATGAGCTAGCTGTCGACCGTAATTTTAC
CAGGGGCCGTAGAACAAGCCATGTTGCAGCTGCTTGCCTTTACATTGCCTGCAGGCTAGGTGCT
GTTTTTCTCCAGCTCTGCCAAGTTTTGCTACTCGCGGATCATCCAGTTGTTCAGAAACTTGTAG
ATCCCAGCCTTTTCATCCATCGCTTTACCAAATGTTTGCTGGGAAGAAGAGATAATGCTGTCTC
AGACACAGCTTTTTCTCGAGAAGTCTCAGACACAGCTTTACGCATTGTAGCTAGCATGAAGAGA
GATTGGATGCAGACTGGGAGGAAACCAAGTGGATTATGTGGTGCAGCATTATACATTGCTGCAC
TCTCTCATGGGTGTAATTACACCAAGGCAGATATTGTCTCTGTTGTGCATGTGTGTGAGGCCAC
TCTAACGAAGCGATTGATAGAGTTTGAAAATACGGATTCTGGCAGCTTAACGATTGAAGAATTT
CTAGCAACAGCTGATGAATATAATGAAGCGTCTGTTTCAAAATATTCGCCTAAGTCTGGGGAAA
TCCTTTGCAAACACAAGGGTAAAGATTTTGAGCATTTTGCCCATGGACTTTGTGAAAAATGCTT
CAATAAGTTCACTAAACTGTCGGGTGGACTAGAAGGTGGTGCTAACCCTCCAGCATTCCAACGA
GCTGAAAACAAAAGACTTGAAGCTGCTAAAAGGGCTGAAGAAGCTGCTGCAGTTAAGGAGGCAG
CGCTGGAAGAATCTCTTTGCGACACACAGAATTCTGAGATTGAGAGTACCACAACTCCTAAAAA
GGCTTTAAGCGGGGATAAATCTTCAACAATTGGATCTGGGGGACTCATAAATGACTCTGTGCCA
CCGAAGGATCCTGAAGAGGGAGGTGAAAATTGTGAAGGCAATGCTGATCCAGAAAGCCTTTCTG
ACATCGACGATGTAGAGGTTGATTGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGAT
TATCTGGGAGGAAATGAACAAAGAGTACCTTGAGGAACAAGCAGCCAAGGAAGCTTTGGCAGCT
GAATTGGCAGCTAGAGGGATTGTTGTGGAAGAGGGAAAGAAA
						
					

						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	TGCTACTACCTGCATTTTTATTTTACAGGAACAAGCAGCCAAGGAAGCTTTGGCAGCTGAATTG GCAGCTAGAGGGATTGTTGTGGAAGAGGGAAAGAAAtttcacagattggtatgagctgatcacc cctggttgtgtagttccttctgcaatgatttactgcactcactgtgctgattactgcccctcca taaaggac
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: 1450 Transcript exons: 63800622-63800738,63800928-63801009,63801099-63801174,63 801251-63801336,63801789-63801865,63803130-63803236,6380 3617-63803723,63803809-63803895,63804024-63804104,638111 43-63811289,63811375-63811560,63813122-63813206,63813303 -63813361,63813491-63813571,63813643-63813714 TTTCACAGATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTTACTGC ACTCACTGTGCTGATTACTGCCCCTCCATAAAGGACCCTGACAAAGGATACATATGTTGTGGTA CATGTGGGAAGGTTCTTGATCAGGAGGTATACACTGATGAGCCTACTTTTGTTAAGGATAACAC AGGACAGAGTCGCTTAGCTGGAAGTATTCTTGCAAGCATTGAGTCTGGATATTCGATTTCTCAT CAAAGAACCTTAGACAAAGGTAGGGATGAGATTAGGCAGATTGTCAATAACTTACATGTCAGCG GTGGAGAAACTGTCGTTAGCAAGGCTTATCGCTTCTATGAGCTAGCTGTCGACCGTAATTTTAC CAGGGGCCGTAGAACAAGCCATGTTGCAGCTGCTTGCCTTTACATTGCCTGCAGGCTAGGTGCT GTTTTTCTCCAGCTCTGCCAAGTTTTGCTACTCGCGGATCATCCAGTTGTTCAGAAACTTGTAG ATCCCAGCCTTTTCATCCATCGCTTTACCAAATGTTTGCTGGGAAGAAGAGATAATGCTGTCTC AGACACAGCTTTTTCTCGAGAAGTCTCAGACACAGCTTTACGCATTGTAGCTAGCATGAAGAGA GATTGGATGCAGACTGGGAGGAAACCAAGTGGATTATGTGGTGCAGCATTATACATTGCTGCAC TCTCTCATGGGTGTAATTACACCAAGGCAGATATTGTCTCTGTTGTGCATGTGTGTGAGGCCAC TCTAACGAAGCGATTGATAGAGTTTGAAAATACGGATTCTGGCAGCTTAACGATTGAAGAATTT CTAGCAACAGCTGATGAATATAATGAAGCGTCTGTTTCAAAATATTCGCCTAAGTCTGGGGAAA TCCTTTGCAAACACAAGGGTAAAGATTTTGAGCATTTTGCCCATGGACTTTGTGAAAAATGCTT CAATAAGTTCACTAAACTGTCGGGTGGACTAGAAGGTGGTGCTAACCCTCCAGCATTCCAACGA GCTGAAAACAAAAGACTTGAAGCTGCTAAAAGGGCTGAAGAAGCTGCTGCAGTTAAGGAGGCAG CGCTGGAAGAATCTCTTTGCGACACACAGAATTCTGAGATTGAGAGTACCACAACTCCTAAAAA GGCTTTAAGCGGGGATAAATCTTCAACAATTGGATCTGGGGGACTCATAAATGACTCTGTGCCA CCGAAGGATCCTGAAGAGGGAGGTGAAAATTGTGAAGGCAATGCTGATCCAGAAAGCCTTTCTG ACATCGACGATGTAGAGGTTGATTGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGAT TATCTGGGAGGAAATGAACAAAGAGTACCTTGAGGAACAAGCAGCCAAGGAAGCTTTGGCAGCT GAATTGGCAGCTAGAGGGATTGTTGTGGAAGAGGGAAAGAAA
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
						0.147167555

Conservation Information
Conserved circRNAs	NA
PMCS	0.147167555

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							63800675-63800636(+)
						
						Potential amino acid sequence
						
							MIYCTHCADYCPSIKDPDKGYICCGTCGKVLDQEVYTDEPTFVKDNTGQSRLAGSILASIESGY
SISHQRTLDKGRDEIRQIVNNLHVSGGETVVSKAYRFYELAVDRNFTRGRRTSHVAAACLYIAC
RLGAVFLQLCQVLLLADHPVVQKLVDPSLFIHRFTKCLLGRRDNAVSDTAFSREVSDTALRIVA
SMKRDWMQTGRKPSGLCGAALYIAALSHGCNYTKADIVSVVHVCEATLTKRLIEFENTDSGSLT
IEEFLATADEYNEASVSKYSPKSGEILCKHKGKDFEHFAHGLCEKCFNKFTKLSGGLEGGANPP
AFQRAENKRLEAAKRAEEAAAVKEAALEESLCDTQNSEIESTTTPKKALSGDKSSTIGSGGLIN
DSVPPKDPEEGGENCEGNADPESLSDIDDVEVDWYLHNEEETQYKKIIWEEMNKEYLEEQAAKE
ALAAELAARGIVVEEGKKFHRLV*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	63800675-63800636(+)
Potential amino acid sequence	MIYCTHCADYCPSIKDPDKGYICCGTCGKVLDQEVYTDEPTFVKDNTGQSRLAGSILASIESGY SISHQRTLDKGRDEIRQIVNNLHVSGGETVVSKAYRFYELAVDRNFTRGRRTSHVAAACLYIAC RLGAVFLQLCQVLLLADHPVVQKLVDPSLFIHRFTKCLLGRRDNAVSDTAFSREVSDTALRIVA SMKRDWMQTGRKPSGLCGAALYIAALSHGCNYTKADIVSVVHVCEATLTKRLIEFENTDSGSLT IEEFLATADEYNEASVSKYSPKSGEILCKHKGKDFEHFAHGLCEKCFNKFTKLSGGLEGGANPP AFQRAENKRLEAAKRAEEAAAVKEAALEESLCDTQNSEIESTTTPKKALSGDKSSTIGSGGLIN DSVPPKDPEEGGENCEGNADPESLSDIDDVEVDWYLHNEEETQYKKIIWEEMNKEYLEEQAAKE ALAAELAARGIVVEEGKKFHRLV*(+)
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 Zm00001d009424_circ_g.6

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