Plant Circular RNA Database

Detail information of Zm00001d027665_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d027665_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006404
					
						Alias
						Zm01circ00029, GRMZM2G439049_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 10524205-10527870  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d027665						
					
						Parent gene annotation
						
							Protein SHOOT GRAVITROPISM 6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027665_circ_g.2 Zm00001d027665_circ_g.4 Zm00001d027665_circ_g.5 Zm00001d027665_circ_g.6 Zm00001d027665_circ_g.7 Zm00001d027665_circ_g.8 Zm00001d027665_circ_g.9 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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_T010:7
Zm00001d027665_T026:3
Zm00001d027665_T012:7
Zm00001d027665_T017:7
Zm00001d027665_T004:7
Zm00001d027665_T001:7
Zm00001d027665_T009:7
Zm00001d027665_T024:7
Zm00001d027665_T013:7
Zm00001d027665_T008:7
Zm00001d027665_T005:7
Zm00001d027665_T014:7
Zm00001d027665_T023:7
Zm00001d027665_T015:7
Zm00001d027665_T018:7
Zm00001d027665_T007:7
Zm00001d027665_T019:7

General Information
CircRNA Name	Zm00001d027665_circ_g.3
ID in PlantcircBase	zma_circ_006404
Alias	Zm01circ00029, GRMZM2G439049_C1
Organism	Zea mays
Position	chr1: 10524205-10527870 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d027665
Parent gene annotation	Protein SHOOT GRAVITROPISM 6
Parent gene strand	+
Alternative splicing	Zm00001d027665_circ_g.2 Zm00001d027665_circ_g.4 Zm00001d027665_circ_g.5 Zm00001d027665_circ_g.6 Zm00001d027665_circ_g.7 Zm00001d027665_circ_g.8 Zm00001d027665_circ_g.9
Support reads	NA
Tissues	leaf, endosperm
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_T010:7 Zm00001d027665_T026:3 Zm00001d027665_T012:7 Zm00001d027665_T017:7 Zm00001d027665_T004:7 Zm00001d027665_T001:7 Zm00001d027665_T009:7 Zm00001d027665_T024:7 Zm00001d027665_T013:7 Zm00001d027665_T008:7 Zm00001d027665_T005:7 Zm00001d027665_T014:7 Zm00001d027665_T023:7 Zm00001d027665_T015:7 Zm00001d027665_T018:7 Zm00001d027665_T007:7 Zm00001d027665_T019:7

			
						 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  
						
							TCATTCTCTTGAACTCAGGGGAGTAATATGCTTGGAAGGTTGCTTCATGTTCAGCATCCTACTG
CAAAGCAAGCTGTGATTACTGCAATCGACCTTTTAGgttctgtgctacttgggtccacttttcc
ccagaaacctttctttattttggcaagatgaggtatagaacttaacacatccggtattgtttga
agatgaat

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GTTCTGTGCTACTTGGGTCCACTTTTCCCCAGAAACCTTTCTTTATTTTGGCAAGATGAGGTAT
AGAACTTAACACATCCGGTATTGTTTGAAGATGAATAGTACATGTTTTCAAGTTTTGATTCTTT
TTGCTTTTAGTTATTAATCCCCGAAATAAAGTTGCTGTATTGCATCTTGCAACTCTTGTGAATT
TCCGGTAATTCATATTGTACTTGCCCTGTGCTTGAGTTGTTTGTATAATGCACACTATTATGTG
ACTCTTGTGACAATTTACCCGAAAAATAAAGAGTTCATTTCCAGTCACCATGCTGTTAAAGTAG
CTTACAAAATGCATCTTTTGGCAAGTATTAGGTCCCTAAGATGAAAGCTTACATCAGTGATCCT
GAAGACCTAAAGCAAGATAGCACATACCAGGAAAAATGGGATGACATGATAATAAATGTAAGTA
TGTTATTGATGTTGATTATTAGTCCCTCCGTTTCAATTTATAATTTGTTTGATTTTTTACCCTA
AGTTTGACCGACTCGTCTTATTAAAAAAATCACAATTATTATAATTTTTTACTGTGATATTGTT
TAACATATAATATACTTTAATTTTGGCTTTGAATTTTTCAGTTTTTCGCGAAAATTTTGAATAA
GACGAGCCGGTCAAACTTGGTCTAAAAAAGTCAAACGAATTATAAATTGAGACAGAGGGAGTAT
TATTTTTTGAAATGAGTTCAGTCATTCAGGATTGTGTTCATGCCATAACAAGAGAGCCTGCAAC
TACGGTATTAGTAGTTACAATCATGATATGTTGTATTGATGTATACTTTAGTCAAATTGTGTTA
AGAGTTGAGCGAAACAAAAATATTAGGAAAAAAATGATGGCTTACCGTGTTAAAAATGTCCATT
TTTTCCTCTTGATTATTGTGTAGTATTTGTTATTCAAGGAGCATGTGGGTGGTGCATGTTTAAA
AGAACGTATTTCCCTATTGCTGCGTCCAGTCTTATGCTCATAGAGGTTGCAGCCCAGGCCTGTG
ATGGTTCCTTGTACACTGTAGGCCTTTTGTTTGTGTTTGATACTTCAGTTTGCTAGTTCCATAT
CAGTTTTTAAAGTACGGAGAATCTCTCTAAGTATATATTAAGAATTTTTTCTCTGTATTTTCTT
AGGTCAAGTATTTAGATGATGTACTATTTCCCTGAGAACTAATCTTGTGTTGTCCTTCAGTTTT
TGGCAGAATGTTTGGATGTTGTGAATGATACTGAGTGGGTCATTTCTTTGGGTGATGCATTTGC
ACGGCAGTATGATCTGTATTCTATATCTGACGGACACGCTGCTTTGCTGCACAGGTAAATATTA
ATAACCATTAAATTTGTGCTGTTCTTGGGCACTTTATCCATACTGCATGATACCCTGATACACC
TGGAAGGTCAATGAACCTGTACCTGATATGGCGGGATACGATGAGATGTAATGACATGTCCTTG
TTTTTTTGTGAGAAATGTTGTATCCTCGTATCAGTTACTTTTATTGCATATCAGTGAAACATAG
GTTACTAGATCAAAGCTAATGCTTTTGGTTCCATTGCATCCAAAATATTTTCTGAACATGTGCT
GCATGCTATTCATTTTGTTGTGACAACAGTCTTCCTTTCCTTCTTGTGTTACCTTTGGAGTGGC
AGCTATGTTATTACTCTAAATAATCCTAAGAAGTTTGTGCCGTTATATTTTTGGAGCTCAGTAG
CTTCTAGCTTGATTGTTTAGAGGTCTTATGTATTCTGTCAGAGTTTTTTTGGACAAAGGTTCAA
CAGTGCTTATATCAAAAGCAACAAACTGTTTTCGAGATGCTGGGGTTACTTGCTTACATAAGTG
CACCAACACCGCAAGAGGAAGCTAGGATACCAACACCAAAAAAACTAGGAAAGGCTAGCCTTCT
GTGAGATATTTGGCAGTATTTCTATATCAGAGTGAGCAAGGATACTATAAGTTGGCATCATCAT
TTCACATTAGCTTCTATACATTTATTTGTTAATCATTGTGCTAGATCTGTCAAAATCTGCCATA
ACAAGTGGATCATGCTTGTTTATTTCAAAAGCATGTTCATTCAGTGACATGTCTGATCGCCGGT
TATAGATTATACCCTTTGCTGTAGTTATTTTTGTTAAATGTTGCGGCCAAGACAATAAACTATT
GGTTTATGCTACCCTTCCTTGGTGATATTGAGTGACTTGTTATGGAAGCTACAAGAAAATGACT
CCATATATCGGCTTTGTTTTACCTTTTTAAATGTTGTGGAGCCAAGACAATAAACTATTGGTTT
ATGGAAGTTACATGAAAATGACTCCATATACTGGCTTTGTTTTACCTTTTTATTTGCAGATGCT
TGGGAATGCTTCTTCAGAAGGTTGATGATAGGATTTATGTCAGCGAGAAGATTGATTGGATGTG
TAGACACTCAAGTATGTCTATTCCTATTAATCGCCTTGGACTTGCTCAAGGCATCGGGCTGGTA
AGGTGCCATCAGTGAATCCTTCTATTTTGAGCTTATTTTGAATCCTTTTAGCACTAAAGTTCCC
ATTGCAGGTTGCGGCTTCTCATTTAGATACAGTGTTGGAGAAACTGAAGAACATACTAGATAGT
GCAGAGCAAAGTGCTTTCCAGAGGTACTTATATAATCTTTTGGCAGAAGACATCTATTTGTCAT
CTTACCGCCAGTCCTGTCTTGCAGCATTGCAGCAATATAACCTAAACCAAAACTTGGTTGTGTT
GCTTCACATGTACACTCCTTTGACCAATTTTGTGCCAAAATGGAATCCTGTACTTCATTCTTAA
CTTCAATGTACCAATTAGTTTCCCTTCTTTTCAGTTATTGGTTTGGCATATTTTGTGAAACTTC
ATTCCATATCCCATCTTGTATTTGGAAAAACAGAAATGGAGACTGGATCATTCAAAAGTGAATA
TCAAGCAACCACTACTTAGCTGGCGTATTTCATTTATGTAGGCCGTCTATCCTGTTATTTCAGT
ATTAATAAGTTTATGGCATCCAATTCTGCAGGTTCCTCTCATTTTTCTCATTCGGCCCAAAAGT
GGAAGATGTTGATGACACATATGCAGCATTGGCGTTGATGTATGGTTATGCCGCAAGATATGCT
CCATCAACTGTTATTGAAGCCAGAATTAATGCACTTGTGGTATGATATCCCATTTACAAACTAA
CTTTTGTTTCTTACATGAACAATTCCGATGAATAATAATATGTGTATGCATTTGAGACAAACTC
TTGCACTCCATAGACAAATTTATTTTGTTCAGTCTAATACTCAAGTTTGGTAGTTTACAAATAT
TGAAAACCAATCTGTCACCATTATTTCAATTTTAACCCAAAATTCTATCCCCTAATCTGTCCTT
CCCAACTGCCACATCTAGTACATTGCTGGCATTTATTTATTTTACATTATATTTATGTTGATCA
CATTTTACATTGTTGTATTTTGGGGCACTTACATTAAAACATCTCAGCGTCTTTGTACCTGGTC
AATGGAATATTCACAAACGGTTTATTACATTTTAGCTTGATGAATCTCATTCTCTTGAACTCAG
GGGAGTAATATGCTTGGAAGGTTGCTTCATGTTCAGCATCCTACTGCAAAGCAAGCTGTGATTA
CTGCAATCGACCTTTTAG
						
					

			
		

Sequences
Splice junction sequence	TCATTCTCTTGAACTCAGGGGAGTAATATGCTTGGAAGGTTGCTTCATGTTCAGCATCCTACTG CAAAGCAAGCTGTGATTACTGCAATCGACCTTTTAGgttctgtgctacttgggtccacttttcc ccagaaacctttctttattttggcaagatgaggtatagaacttaacacatccggtattgtttga agatgaat
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GTTCTGTGCTACTTGGGTCCACTTTTCCCCAGAAACCTTTCTTTATTTTGGCAAGATGAGGTAT AGAACTTAACACATCCGGTATTGTTTGAAGATGAATAGTACATGTTTTCAAGTTTTGATTCTTT TTGCTTTTAGTTATTAATCCCCGAAATAAAGTTGCTGTATTGCATCTTGCAACTCTTGTGAATT TCCGGTAATTCATATTGTACTTGCCCTGTGCTTGAGTTGTTTGTATAATGCACACTATTATGTG ACTCTTGTGACAATTTACCCGAAAAATAAAGAGTTCATTTCCAGTCACCATGCTGTTAAAGTAG CTTACAAAATGCATCTTTTGGCAAGTATTAGGTCCCTAAGATGAAAGCTTACATCAGTGATCCT GAAGACCTAAAGCAAGATAGCACATACCAGGAAAAATGGGATGACATGATAATAAATGTAAGTA TGTTATTGATGTTGATTATTAGTCCCTCCGTTTCAATTTATAATTTGTTTGATTTTTTACCCTA AGTTTGACCGACTCGTCTTATTAAAAAAATCACAATTATTATAATTTTTTACTGTGATATTGTT TAACATATAATATACTTTAATTTTGGCTTTGAATTTTTCAGTTTTTCGCGAAAATTTTGAATAA GACGAGCCGGTCAAACTTGGTCTAAAAAAGTCAAACGAATTATAAATTGAGACAGAGGGAGTAT TATTTTTTGAAATGAGTTCAGTCATTCAGGATTGTGTTCATGCCATAACAAGAGAGCCTGCAAC TACGGTATTAGTAGTTACAATCATGATATGTTGTATTGATGTATACTTTAGTCAAATTGTGTTA AGAGTTGAGCGAAACAAAAATATTAGGAAAAAAATGATGGCTTACCGTGTTAAAAATGTCCATT TTTTCCTCTTGATTATTGTGTAGTATTTGTTATTCAAGGAGCATGTGGGTGGTGCATGTTTAAA AGAACGTATTTCCCTATTGCTGCGTCCAGTCTTATGCTCATAGAGGTTGCAGCCCAGGCCTGTG ATGGTTCCTTGTACACTGTAGGCCTTTTGTTTGTGTTTGATACTTCAGTTTGCTAGTTCCATAT CAGTTTTTAAAGTACGGAGAATCTCTCTAAGTATATATTAAGAATTTTTTCTCTGTATTTTCTT AGGTCAAGTATTTAGATGATGTACTATTTCCCTGAGAACTAATCTTGTGTTGTCCTTCAGTTTT TGGCAGAATGTTTGGATGTTGTGAATGATACTGAGTGGGTCATTTCTTTGGGTGATGCATTTGC ACGGCAGTATGATCTGTATTCTATATCTGACGGACACGCTGCTTTGCTGCACAGGTAAATATTA ATAACCATTAAATTTGTGCTGTTCTTGGGCACTTTATCCATACTGCATGATACCCTGATACACC TGGAAGGTCAATGAACCTGTACCTGATATGGCGGGATACGATGAGATGTAATGACATGTCCTTG TTTTTTTGTGAGAAATGTTGTATCCTCGTATCAGTTACTTTTATTGCATATCAGTGAAACATAG GTTACTAGATCAAAGCTAATGCTTTTGGTTCCATTGCATCCAAAATATTTTCTGAACATGTGCT GCATGCTATTCATTTTGTTGTGACAACAGTCTTCCTTTCCTTCTTGTGTTACCTTTGGAGTGGC AGCTATGTTATTACTCTAAATAATCCTAAGAAGTTTGTGCCGTTATATTTTTGGAGCTCAGTAG CTTCTAGCTTGATTGTTTAGAGGTCTTATGTATTCTGTCAGAGTTTTTTTGGACAAAGGTTCAA CAGTGCTTATATCAAAAGCAACAAACTGTTTTCGAGATGCTGGGGTTACTTGCTTACATAAGTG CACCAACACCGCAAGAGGAAGCTAGGATACCAACACCAAAAAAACTAGGAAAGGCTAGCCTTCT GTGAGATATTTGGCAGTATTTCTATATCAGAGTGAGCAAGGATACTATAAGTTGGCATCATCAT TTCACATTAGCTTCTATACATTTATTTGTTAATCATTGTGCTAGATCTGTCAAAATCTGCCATA ACAAGTGGATCATGCTTGTTTATTTCAAAAGCATGTTCATTCAGTGACATGTCTGATCGCCGGT TATAGATTATACCCTTTGCTGTAGTTATTTTTGTTAAATGTTGCGGCCAAGACAATAAACTATT GGTTTATGCTACCCTTCCTTGGTGATATTGAGTGACTTGTTATGGAAGCTACAAGAAAATGACT CCATATATCGGCTTTGTTTTACCTTTTTAAATGTTGTGGAGCCAAGACAATAAACTATTGGTTT ATGGAAGTTACATGAAAATGACTCCATATACTGGCTTTGTTTTACCTTTTTATTTGCAGATGCT TGGGAATGCTTCTTCAGAAGGTTGATGATAGGATTTATGTCAGCGAGAAGATTGATTGGATGTG TAGACACTCAAGTATGTCTATTCCTATTAATCGCCTTGGACTTGCTCAAGGCATCGGGCTGGTA AGGTGCCATCAGTGAATCCTTCTATTTTGAGCTTATTTTGAATCCTTTTAGCACTAAAGTTCCC ATTGCAGGTTGCGGCTTCTCATTTAGATACAGTGTTGGAGAAACTGAAGAACATACTAGATAGT GCAGAGCAAAGTGCTTTCCAGAGGTACTTATATAATCTTTTGGCAGAAGACATCTATTTGTCAT CTTACCGCCAGTCCTGTCTTGCAGCATTGCAGCAATATAACCTAAACCAAAACTTGGTTGTGTT GCTTCACATGTACACTCCTTTGACCAATTTTGTGCCAAAATGGAATCCTGTACTTCATTCTTAA CTTCAATGTACCAATTAGTTTCCCTTCTTTTCAGTTATTGGTTTGGCATATTTTGTGAAACTTC ATTCCATATCCCATCTTGTATTTGGAAAAACAGAAATGGAGACTGGATCATTCAAAAGTGAATA TCAAGCAACCACTACTTAGCTGGCGTATTTCATTTATGTAGGCCGTCTATCCTGTTATTTCAGT ATTAATAAGTTTATGGCATCCAATTCTGCAGGTTCCTCTCATTTTTCTCATTCGGCCCAAAAGT GGAAGATGTTGATGACACATATGCAGCATTGGCGTTGATGTATGGTTATGCCGCAAGATATGCT CCATCAACTGTTATTGAAGCCAGAATTAATGCACTTGTGGTATGATATCCCATTTACAAACTAA CTTTTGTTTCTTACATGAACAATTCCGATGAATAATAATATGTGTATGCATTTGAGACAAACTC TTGCACTCCATAGACAAATTTATTTTGTTCAGTCTAATACTCAAGTTTGGTAGTTTACAAATAT TGAAAACCAATCTGTCACCATTATTTCAATTTTAACCCAAAATTCTATCCCCTAATCTGTCCTT CCCAACTGCCACATCTAGTACATTGCTGGCATTTATTTATTTTACATTATATTTATGTTGATCA CATTTTACATTGTTGTATTTTGGGGCACTTACATTAAAACATCTCAGCGTCTTTGTACCTGGTC AATGGAATATTCACAAACGGTTTATTACATTTTAGCTTGATGAATCTCATTCTCTTGAACTCAG GGGAGTAATATGCTTGGAAGGTTGCTTCATGTTCAGCATCCTACTGCAAAGCAAGCTGTGATTA CTGCAATCGACCTTTTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.023880685

Conservation Information
Conserved circRNAs	NA
PMCS	0.023880685

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10524566-10524260(+)
						
						Potential amino acid sequence
						
							MKAYISDPEDLKQDSTYQEKWDDMIINFLAECLDVVNDTEWVISLGDAFARQYDLYSISDGHAA
LLHRCLGMLLQKVDDRIYVSEKIDWMCRHSSMSIPINRLGLAQGIGLVAASHLDTVLEKLKNIL
DSAEQSAFQRFLSFFSFGPKVEDVDDTYAALALMYGYAARYAPSTVIEARINALVGSNMLGRLL
HVQHPTAKQAVITAIDLLGSVLLGSTFPQKPFFILAR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	10524566-10524260(+)
Potential amino acid sequence	MKAYISDPEDLKQDSTYQEKWDDMIINFLAECLDVVNDTEWVISLGDAFARQYDLYSISDGHAA LLHRCLGMLLQKVDDRIYVSEKIDWMCRHSSMSIPINRLGLAQGIGLVAASHLDTVLEKLKNIL DSAEQSAFQRFLSFFSFGPKVEDVDDTYAALALMYGYAARYAPSTVIEARINALVGSNMLGRLL HVQHPTAKQAVITAIDLLGSVLLGSTFPQKPFFILAR*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d027665_circ_g.3

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