Plant Circular RNA Database

Detail information of Zm00001d027665_circ_g.9

			
						 General Information
					
						CircRNA Name
						Zm00001d027665_circ_g.9
					
						ID in PlantcircBase
						zma_circ_006409
					
						Alias
						Zm01circ00033, zma_circ_0000043, GRMZM2G086093_C3
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 10549889-10551008  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d027665						
					
						Parent gene annotation
						
							Protein SHOOT GRAVITROPISM 6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027665_circ_g.2 Zm00001d027665_circ_g.3 Zm00001d027665_circ_g.4 Zm00001d027665_circ_g.5 Zm00001d027665_circ_g.6 Zm00001d027665_circ_g.7 Zm00001d027665_circ_g.8 						
					
						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
						Zm00001d027665_T037:5
Zm00001d027665_T007:5
Zm00001d027665_T028:5
Zm00001d027665_T029:5
Zm00001d027665_T010:5
Zm00001d027665_T001:5
Zm00001d027665_T033:5
Zm00001d027665_T014:5
Zm00001d027665_T031:5
Zm00001d027665_T012:5
Zm00001d027665_T004:5
Zm00001d027665_T026:5
Zm00001d027665_T019:4
Zm00001d027665_T023:5
Zm00001d027665_T015:5
Zm00001d027665_T038:5
Zm00001d027665_T017:5
Zm00001d027665_T009:5
Zm00001d027665_T024:5
Zm00001d027665_T030:5
Zm00001d027665_T018:5
Zm00001d027665_T032:5
Zm00001d027665_T039:2
Zm00001d027665_T013:5
Zm00001d027665_T005:5

General Information
CircRNA Name	Zm00001d027665_circ_g.9
ID in PlantcircBase	zma_circ_006409
Alias	Zm01circ00033, zma_circ_0000043, GRMZM2G086093_C3
Organism	Zea mays
Position	chr1: 10549889-10551008 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d027665
Parent gene annotation	Protein SHOOT GRAVITROPISM 6
Parent gene strand	+
Alternative splicing	Zm00001d027665_circ_g.2 Zm00001d027665_circ_g.3 Zm00001d027665_circ_g.4 Zm00001d027665_circ_g.5 Zm00001d027665_circ_g.6 Zm00001d027665_circ_g.7 Zm00001d027665_circ_g.8
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	Zm00001d027665_T037:5 Zm00001d027665_T007:5 Zm00001d027665_T028:5 Zm00001d027665_T029:5 Zm00001d027665_T010:5 Zm00001d027665_T001:5 Zm00001d027665_T033:5 Zm00001d027665_T014:5 Zm00001d027665_T031:5 Zm00001d027665_T012:5 Zm00001d027665_T004:5 Zm00001d027665_T026:5 Zm00001d027665_T019:4 Zm00001d027665_T023:5 Zm00001d027665_T015:5 Zm00001d027665_T038:5 Zm00001d027665_T017:5 Zm00001d027665_T009:5 Zm00001d027665_T024:5 Zm00001d027665_T030:5 Zm00001d027665_T018:5 Zm00001d027665_T032:5 Zm00001d027665_T039:2 Zm00001d027665_T013:5 Zm00001d027665_T005:5

			
						 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  
						
							CATGTGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAG
AAGAGGCAAGGAGCTACGTGAAGCTGATGTCTCGAGtggtgaagatggtcgaagtcgagcagag
cagttgctgcatattcttaggcagcttgatccatatgtatcatcatctctggaacaccaaagaa
gaagagga

									
								

					

						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: 684
Transcript exons: 10549889-10550124,10550205-10550314,10550521-10550649,10
550729-10550803,10550875-10551008
TGGTGAAGATGGTCGAAGTCGAGCAGAGCAGTTGCTGCATATTCTTAGGCAGCTTGATCCATAT
GTATCATCATCTCTGGAACACCAAAGAAGAAGAGGATGTGTTGCTGTACAGGAGGTGTTAATAA
AGTTTCGCAATCTTTGTTCTGGTGGATTCGGTGCATTGGGCTCCTATCCAACTTTCACAATGAA
TAAACAAATCGATCGAGGGACTAGGAGCTTGTCAAGTTTGCCATCTGCATTTGTGTTGCCTAGT
CGAGATTCTTTAAGCTTGGGAGAGAGGACAATGGCATACCTTCCTCGTTGTGCTGATACAGACA
CGGAAGTTAGGAAAGTTGCAATTCAGATCATTGCACTTTTCTTCGACATTTCATTGTCACTTCC
AAAGCAGAAGGCATATCCTAATGATATTGATCTGGAATCCTCGTATAGTGCTTTGTCCTCCCTT
GAGGAGTTAGTCTCTATTGTCAGAAGGGAGGCATCTGTTGATCAAACTGAACTATTTCAGAGGG
TTGTATCCTCAGTGTGTATTCTATTATCAAAGGATGAGCTGGTCGTCTTGCTACACTCTTGTAC
GTTGGCAACATGTGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTT
ATTATCAGAAGAGGCAAGGAGCTACGTGAAGCTGATGTCTCGAG
						
					

						Genomic sequence
						
							TGGTGAAGATGGTCGAAGTCGAGCAGAGCAGTTGCTGCATATTCTTAGGCAGCTTGATCCATAT
GTATCATCATCTCTGGAACACCAAAGAAGAAGAGGATGTGTTGCTGTACAGGAGGTGTTAATAA
AGTTTCGCAATCTTTGTTCTGGTGGATTCGGTGCATTGGGCTCCTATCCAACTTTCACAATGAA
TAAACAAATCGATCGAGGGACTAGGAGCTTGTCAAGTTTGCCATGTATGCTTAATGATTTCCTT
AGAATGCTTTAGTAAGTGTAGGGATCAACCCTGTATAAGATGACTTTTATTTTATCACAGCTGC
ATTTGTGTTGCCTAGTCGAGATTCTTTAAGCTTGGGAGAGAGGACAATGGCATACCTTCCTCGT
TGTGCTGATACAGACACGGAAGTTAGGAAAGTTGCAATTCAGGTTTGTGCAAAAAGGACTGCTT
TGCATTATTTTGTTTGTTACATCATGTTTCTGCCTTTTTATCTAATATGCAATTTCTGTTTCCA
CATGTGCTGTATGATTGTGCTGTAAAATAGTTATGGTTTGCAGAATTATTTAAAGTTTTCATCT
TATGTTGTAACTGATTTCACCAAGTTATTTTGATTATATGTTTTTTATTCTTCTAGATCATTGC
ACTTTTCTTCGACATTTCATTGTCACTTCCAAAGCAGAAGGCATATCCTAATGATATTGATCTG
GAATCCTCGTATAGTGCTTTGTCCTCCCTTGAGGAGTTAGTCTCTATTGTCAGAAGGGTGAGTA
TGATGTCTTGGTTTACTATCCGTTTGACCCATTTAGTCCAACTTATGGAGGGTATGTTTGTATT
GTTCTCAGGAGGCATCTGTTGATCAAACTGAACTATTTCAGAGGGTTGTATCCTCAGTGTGTAT
TCTATTATCAAAGGATGAGGTAACTAATTCAATTTAACTTTGGAAATTGTACATTGGCATGATT
GTATTAACATTTGTATACTTGGATAGCTGGTCGTCTTGCTACACTCTTGTACGTTGGCAACATG
TGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAGAAGA
GGCAAGGAGCTACGTGAAGCTGATGTCTCGAG
						
					

			
		

Sequences
Splice junction sequence	CATGTGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAG AAGAGGCAAGGAGCTACGTGAAGCTGATGTCTCGAGtggtgaagatggtcgaagtcgagcagag cagttgctgcatattcttaggcagcttgatccatatgtatcatcatctctggaacaccaaagaa gaagagga
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: 684 Transcript exons: 10549889-10550124,10550205-10550314,10550521-10550649,10 550729-10550803,10550875-10551008 TGGTGAAGATGGTCGAAGTCGAGCAGAGCAGTTGCTGCATATTCTTAGGCAGCTTGATCCATAT GTATCATCATCTCTGGAACACCAAAGAAGAAGAGGATGTGTTGCTGTACAGGAGGTGTTAATAA AGTTTCGCAATCTTTGTTCTGGTGGATTCGGTGCATTGGGCTCCTATCCAACTTTCACAATGAA TAAACAAATCGATCGAGGGACTAGGAGCTTGTCAAGTTTGCCATCTGCATTTGTGTTGCCTAGT CGAGATTCTTTAAGCTTGGGAGAGAGGACAATGGCATACCTTCCTCGTTGTGCTGATACAGACA CGGAAGTTAGGAAAGTTGCAATTCAGATCATTGCACTTTTCTTCGACATTTCATTGTCACTTCC AAAGCAGAAGGCATATCCTAATGATATTGATCTGGAATCCTCGTATAGTGCTTTGTCCTCCCTT GAGGAGTTAGTCTCTATTGTCAGAAGGGAGGCATCTGTTGATCAAACTGAACTATTTCAGAGGG TTGTATCCTCAGTGTGTATTCTATTATCAAAGGATGAGCTGGTCGTCTTGCTACACTCTTGTAC GTTGGCAACATGTGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTT ATTATCAGAAGAGGCAAGGAGCTACGTGAAGCTGATGTCTCGAG
Genomic sequence	TGGTGAAGATGGTCGAAGTCGAGCAGAGCAGTTGCTGCATATTCTTAGGCAGCTTGATCCATAT GTATCATCATCTCTGGAACACCAAAGAAGAAGAGGATGTGTTGCTGTACAGGAGGTGTTAATAA AGTTTCGCAATCTTTGTTCTGGTGGATTCGGTGCATTGGGCTCCTATCCAACTTTCACAATGAA TAAACAAATCGATCGAGGGACTAGGAGCTTGTCAAGTTTGCCATGTATGCTTAATGATTTCCTT AGAATGCTTTAGTAAGTGTAGGGATCAACCCTGTATAAGATGACTTTTATTTTATCACAGCTGC ATTTGTGTTGCCTAGTCGAGATTCTTTAAGCTTGGGAGAGAGGACAATGGCATACCTTCCTCGT TGTGCTGATACAGACACGGAAGTTAGGAAAGTTGCAATTCAGGTTTGTGCAAAAAGGACTGCTT TGCATTATTTTGTTTGTTACATCATGTTTCTGCCTTTTTATCTAATATGCAATTTCTGTTTCCA CATGTGCTGTATGATTGTGCTGTAAAATAGTTATGGTTTGCAGAATTATTTAAAGTTTTCATCT TATGTTGTAACTGATTTCACCAAGTTATTTTGATTATATGTTTTTTATTCTTCTAGATCATTGC ACTTTTCTTCGACATTTCATTGTCACTTCCAAAGCAGAAGGCATATCCTAATGATATTGATCTG GAATCCTCGTATAGTGCTTTGTCCTCCCTTGAGGAGTTAGTCTCTATTGTCAGAAGGGTGAGTA TGATGTCTTGGTTTACTATCCGTTTGACCCATTTAGTCCAACTTATGGAGGGTATGTTTGTATT GTTCTCAGGAGGCATCTGTTGATCAAACTGAACTATTTCAGAGGGTTGTATCCTCAGTGTGTAT TCTATTATCAAAGGATGAGGTAACTAATTCAATTTAACTTTGGAAATTGTACATTGGCATGATT GTATTAACATTTGTATACTTGGATAGCTGGTCGTCTTGCTACACTCTTGTACGTTGGCAACATG TGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAGAAGA GGCAAGGAGCTACGTGAAGCTGATGTCTCGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.169475109

Conservation Information
Conserved circRNAs	NA
PMCS	0.169475109

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10550077-10551005(+)
10550937-10550010(+)
10549930-10550988(-)
						
						Potential amino acid sequence
						
							MNKQIDRGTRSLSSLPSAFVLPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLS
LPKQKAYPNDIDLESSYSALSSLEELVSIVRREASVDQTELFQRVVSSVCILLSKDELVVLLHS
CTLATCDKIKQSADASIQAIIMFIIRRGKELREADVSSGEDGRSRAEQLLHILRQLDPYVSSSL
EHQRRRGCVAVQEVLIKFRNLCSGGFGALGSYPTFTMNKQIDRGTRSLSSLPSAFVLPSRDSLS
LGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLSLPKQKAYPNDIDLESSYSALSSLEELVS
IVRREASVDQTELFQRVVSSVCILLSKDELVVLLHSCTLATCDKIKQSADASIQAIIMFIIRRG
KELREADVSSGEDGRSRAEQLLHILRQLDPYVSSSLEHQRRRGCVAVQEVLIKFRNLCSGGFGA
LGSYPTFTMNKQIDRGTRSLSSLPSAFVLPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIA
LFFDISLSLPKQKAYPNDIDLESSYSALSSLEELVSIVRREASVDQTELFQRVVSSVCILLSKD
ELVVLLHSCTLATCDKIKQSADASIQAIIMFIIRRGKELREADVSSGEDGRSRAEQLLHILRQL
DPYVSSSLEHQRRRGCVAVQEVLIKFRNLCSGGFGALGSYPTFTMNKQIDRGTRSLSSLPSAFV
LPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLSLPKQKAYPNDIDLESSYSAL
SSLEELVSIVRREASVDQTELFQRVVSSVCILLSKDELVVLLHSCTLATCDKIKQSADASIQAI
IMFIIRRGKELREADVS(+)
MLQFKLLSCLLSEEARSYVKLMSRVVKMVEVEQSSCCIFLGSLIHMYHHLWNTKEEEDVLLYRR
C*(+)
MQQLLCSTSTIFTTRDISFT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	10550077-10551005(+) 10550937-10550010(+) 10549930-10550988(-)
Potential amino acid sequence	MNKQIDRGTRSLSSLPSAFVLPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLS LPKQKAYPNDIDLESSYSALSSLEELVSIVRREASVDQTELFQRVVSSVCILLSKDELVVLLHS CTLATCDKIKQSADASIQAIIMFIIRRGKELREADVSSGEDGRSRAEQLLHILRQLDPYVSSSL EHQRRRGCVAVQEVLIKFRNLCSGGFGALGSYPTFTMNKQIDRGTRSLSSLPSAFVLPSRDSLS LGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLSLPKQKAYPNDIDLESSYSALSSLEELVS IVRREASVDQTELFQRVVSSVCILLSKDELVVLLHSCTLATCDKIKQSADASIQAIIMFIIRRG KELREADVSSGEDGRSRAEQLLHILRQLDPYVSSSLEHQRRRGCVAVQEVLIKFRNLCSGGFGA LGSYPTFTMNKQIDRGTRSLSSLPSAFVLPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIA LFFDISLSLPKQKAYPNDIDLESSYSALSSLEELVSIVRREASVDQTELFQRVVSSVCILLSKD ELVVLLHSCTLATCDKIKQSADASIQAIIMFIIRRGKELREADVSSGEDGRSRAEQLLHILRQL DPYVSSSLEHQRRRGCVAVQEVLIKFRNLCSGGFGALGSYPTFTMNKQIDRGTRSLSSLPSAFV LPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLSLPKQKAYPNDIDLESSYSAL SSLEELVSIVRREASVDQTELFQRVVSSVCILLSKDELVVLLHSCTLATCDKIKQSADASIQAI IMFIIRRGKELREADVS(+) MLQFKLLSCLLSEEARSYVKLMSRVVKMVEVEQSSCCIFLGSLIHMYHHLWNTKEEEDVLLYRR C(+) MQQLLCSTSTIFTTRDISFT(-)
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 Zm00001d027665_circ_g.9

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