Plant Circular RNA Database

Detail information of Zm00001d054070_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d054070_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008329
					
						Alias
						Zm04circ00110, zma_circ_0001637, GRMZM2G054162_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 245873085-245874585  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d054070						
					
						Parent gene annotation
						
							Putative jumonji-like transcription factor family protein  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d054070_circ_g.1 						
					
						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
						Zm00001d054070_T009:5
Zm00001d054070_T015:5
Zm00001d054070_T018:1
Zm00001d054070_T014:5
Zm00001d054070_T012:5
Zm00001d054070_T010:5
Zm00001d054070_T002:5
Zm00001d054070_T007:5
Zm00001d054070_T013:5
Zm00001d054070_T005:5

General Information
CircRNA Name	Zm00001d054070_circ_g.2
ID in PlantcircBase	zma_circ_008329
Alias	Zm04circ00110, zma_circ_0001637, GRMZM2G054162_C1
Organism	Zea mays
Position	chr4: 245873085-245874585 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d054070
Parent gene annotation	Putative jumonji-like transcription factor family protein
Parent gene strand	+
Alternative splicing	Zm00001d054070_circ_g.1
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	Zm00001d054070_T009:5 Zm00001d054070_T015:5 Zm00001d054070_T018:1 Zm00001d054070_T014:5 Zm00001d054070_T012:5 Zm00001d054070_T010:5 Zm00001d054070_T002:5 Zm00001d054070_T007:5 Zm00001d054070_T013:5 Zm00001d054070_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  
						
							AAATTATGTGTCTTGTTTGCCAGGTTAAGAAGATAGCTCTTCATGCATTCAATCAAGCTATTAA
AGATATCACTGATGAATCATCTAATAGCAATGAAAGgtcaatatcctcacacatactgatgaaa
taaaactcaaagcaaaaaggattgccgcggtggaaaagaagaagcggtgtttaggaatgaagat
tctatcta

									
								

					

						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: 1040
Transcript exons: 245873085-245873768,245873857-245873929,245874007-245874
092,245874194-245874313,245874509-245874585
GTCAATATCCTCACACATACTGATGAAATAAAACTCAAAGCAAAAAGGATTGCCGCGGTGGAAA
AGAAGAAGCGGTGTTTAGGAATGAAGATTCTATCTACCAAGGAAGCAAGTGGAGGCCTTCAACG
GTGTGCAGATTATTTTGGTATGCCAACAGCTCCCAGTGAATCTAACAAGGAGCCAAGGCCTGAA
GAGTGTGTAAATGAACTGGGCATTAAACAACCAGTACAGCATGTTGCTTCCGAGGAGCAGGAAG
GAGTTCAAGATGATGCCAAGGCAGATGCAAATGTTATGAATGTTTCTTTTGGTAAGGGAAAATC
AGAAGATTCTTTTGGTACAATTAATGGTACCAACAGTGGAGATAAAATAGAATCTCCTAGTGGT
TTAGCAGAAAGAACATTGACTCAGCCTACCACTAAGGGTTGCAGTAAGCAGCGTGGCCGTAGTT
CTAATGGTAGAGGAAACAGGACTAAAAAAATAGAAGAGGGGAATGCGTCTGGACTAATTGCTGT
GGCTCCCGAGTCAGAAGATGATGATGATGATGCCGCATTTATAGATGGAAACCAAGCAGAGGGT
GGTGCACTGTGGGATATTTTTCGACGGGAAGATGTGAGCAAACTGCATGATTATCTAATGAAGC
ATGCACATGAGTTTAGACATTGCAACTTTGAGCCAGTGAAGCAGGTTACTCATCCTATACATGA
TCAGTGTTTTTATCTAACAATTGAGCACAAGAGAAAGCTTAAGGAAGAATATGGAGTCGAGCCT
TGGACATTTGAACAGAAGCTAGGTGAGGCAGTATTTATCCCGGCAGGATGTCCCCACCAGGTTA
GAAATTTGAAGTCTTGCATAAAGGTTGCACTAGATTTTGTTTCTCCGGAAAATGTCCGAGAGTG
CATCAGGTTAACAGAAGGTTTCCGTCTGCTGCCGAAGTGGCATAAGGTGAATGAAGATAAACTG
GAGGTTAAGAAGATAGCTCTTCATGCATTCAATCAAGCTATTAAAGATATCACTGATGAATCAT
CTAATAGCAATGAAAG
						
					

						Genomic sequence
						
							GTCAATATCCTCACACATACTGATGAAATAAAACTCAAAGCAAAAAGGATTGCCGCGGTGGAAA
AGAAGAAGCGGTGTTTAGGAATGAAGATTCTATCTACCAAGGAAGCAAGTGGAGGCCTTCAACG
GTGTGCAGATTATTTTGGTATGCCAACAGCTCCCAGTGAATCTAACAAGGAGCCAAGGCCTGAA
GAGTGTGTAAATGAACTGGGCATTAAACAACCAGTACAGCATGTTGCTTCCGAGGAGCAGGAAG
GAGTTCAAGATGATGCCAAGGCAGATGCAAATGTTATGAATGTTTCTTTTGGTAAGGGAAAATC
AGAAGATTCTTTTGGTACAATTAATGGTACCAACAGTGGAGATAAAATAGAATCTCCTAGTGGT
TTAGCAGAAAGAACATTGACTCAGCCTACCACTAAGGGTTGCAGTAAGCAGCGTGGCCGTAGTT
CTAATGGTAGAGGAAACAGGACTAAAAAAATAGAAGAGGGGAATGCGTCTGGACTAATTGCTGT
GGCTCCCGAGTCAGAAGATGATGATGATGATGCCGCATTTATAGATGGAAACCAAGCAGAGGGT
GGTGCACTGTGGGATATTTTTCGACGGGAAGATGTGAGCAAACTGCATGATTATCTAATGAAGC
ATGCACATGAGTTTAGACATTGCAACTTTGAGCCAGTGAAGCAGGTAACCAGTACTTTTTGTTT
GGCCACTAAAGTATGTCGTACCATATGACATCCAATTTCATGTGGAAGAGCTATCCCATATTTG
GCAGGTTACTCATCCTATACATGATCAGTGTTTTTATCTAACAATTGAGCACAAGAGAAAGCTT
AAGGAAGAATATGGTTAGTTAATAACCTTTATGTCTTTAAACTTGAACTTCACCCTAGTGATAT
TCCCTGGTTTCATGCTTCTTTTGCAGGAGTCGAGCCTTGGACATTTGAACAGAAGCTAGGTGAG
GCAGTATTTATCCCGGCAGGATGTCCCCACCAGGTTAGAAATTTGAAGGTATGACATGACATGG
AAATAGCTGTTTGTCCCCACTGTCATCAGTGACATGCTCCTTAATCAAATTAGCTGCTAATCAC
TTGTACCTTTTTATTGGGCAGTCTTGCATAAAGGTTGCACTAGATTTTGTTTCTCCGGAAAATG
TCCGAGAGTGCATCAGGTTAACAGAAGGTTTCCGTCTGCTGCCGAAGTGGCATAAGGTGAATGA
AGATAAACTGGAGGTTTGTCACTCACTCTGTTCATACTAATGTAACATTTGCTAATTCTTTTTT
ATGATTGTAAATGAAGTATTCTTGTGTATATTATGCCATTTTTTTGTCTGCCCTAGCTTCTATA
TCGTCTCTATTAGGCATTCTTATCTTTCTGTCCGCATGAATCTAGATATTTAAATTTAAATTAT
GTGTCTTGTTTGCCAGGTTAAGAAGATAGCTCTTCATGCATTCAATCAAGCTATTAAAGATATC
ACTGATGAATCATCTAATAGCAATGAAAG
						
					

			
		

Sequences
Splice junction sequence	AAATTATGTGTCTTGTTTGCCAGGTTAAGAAGATAGCTCTTCATGCATTCAATCAAGCTATTAA AGATATCACTGATGAATCATCTAATAGCAATGAAAGgtcaatatcctcacacatactgatgaaa taaaactcaaagcaaaaaggattgccgcggtggaaaagaagaagcggtgtttaggaatgaagat tctatcta
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: 1040 Transcript exons: 245873085-245873768,245873857-245873929,245874007-245874 092,245874194-245874313,245874509-245874585 GTCAATATCCTCACACATACTGATGAAATAAAACTCAAAGCAAAAAGGATTGCCGCGGTGGAAA AGAAGAAGCGGTGTTTAGGAATGAAGATTCTATCTACCAAGGAAGCAAGTGGAGGCCTTCAACG GTGTGCAGATTATTTTGGTATGCCAACAGCTCCCAGTGAATCTAACAAGGAGCCAAGGCCTGAA GAGTGTGTAAATGAACTGGGCATTAAACAACCAGTACAGCATGTTGCTTCCGAGGAGCAGGAAG GAGTTCAAGATGATGCCAAGGCAGATGCAAATGTTATGAATGTTTCTTTTGGTAAGGGAAAATC AGAAGATTCTTTTGGTACAATTAATGGTACCAACAGTGGAGATAAAATAGAATCTCCTAGTGGT TTAGCAGAAAGAACATTGACTCAGCCTACCACTAAGGGTTGCAGTAAGCAGCGTGGCCGTAGTT CTAATGGTAGAGGAAACAGGACTAAAAAAATAGAAGAGGGGAATGCGTCTGGACTAATTGCTGT GGCTCCCGAGTCAGAAGATGATGATGATGATGCCGCATTTATAGATGGAAACCAAGCAGAGGGT GGTGCACTGTGGGATATTTTTCGACGGGAAGATGTGAGCAAACTGCATGATTATCTAATGAAGC ATGCACATGAGTTTAGACATTGCAACTTTGAGCCAGTGAAGCAGGTTACTCATCCTATACATGA TCAGTGTTTTTATCTAACAATTGAGCACAAGAGAAAGCTTAAGGAAGAATATGGAGTCGAGCCT TGGACATTTGAACAGAAGCTAGGTGAGGCAGTATTTATCCCGGCAGGATGTCCCCACCAGGTTA GAAATTTGAAGTCTTGCATAAAGGTTGCACTAGATTTTGTTTCTCCGGAAAATGTCCGAGAGTG CATCAGGTTAACAGAAGGTTTCCGTCTGCTGCCGAAGTGGCATAAGGTGAATGAAGATAAACTG GAGGTTAAGAAGATAGCTCTTCATGCATTCAATCAAGCTATTAAAGATATCACTGATGAATCAT CTAATAGCAATGAAAG
Genomic sequence	GTCAATATCCTCACACATACTGATGAAATAAAACTCAAAGCAAAAAGGATTGCCGCGGTGGAAA AGAAGAAGCGGTGTTTAGGAATGAAGATTCTATCTACCAAGGAAGCAAGTGGAGGCCTTCAACG GTGTGCAGATTATTTTGGTATGCCAACAGCTCCCAGTGAATCTAACAAGGAGCCAAGGCCTGAA GAGTGTGTAAATGAACTGGGCATTAAACAACCAGTACAGCATGTTGCTTCCGAGGAGCAGGAAG GAGTTCAAGATGATGCCAAGGCAGATGCAAATGTTATGAATGTTTCTTTTGGTAAGGGAAAATC AGAAGATTCTTTTGGTACAATTAATGGTACCAACAGTGGAGATAAAATAGAATCTCCTAGTGGT TTAGCAGAAAGAACATTGACTCAGCCTACCACTAAGGGTTGCAGTAAGCAGCGTGGCCGTAGTT CTAATGGTAGAGGAAACAGGACTAAAAAAATAGAAGAGGGGAATGCGTCTGGACTAATTGCTGT GGCTCCCGAGTCAGAAGATGATGATGATGATGCCGCATTTATAGATGGAAACCAAGCAGAGGGT GGTGCACTGTGGGATATTTTTCGACGGGAAGATGTGAGCAAACTGCATGATTATCTAATGAAGC ATGCACATGAGTTTAGACATTGCAACTTTGAGCCAGTGAAGCAGGTAACCAGTACTTTTTGTTT GGCCACTAAAGTATGTCGTACCATATGACATCCAATTTCATGTGGAAGAGCTATCCCATATTTG GCAGGTTACTCATCCTATACATGATCAGTGTTTTTATCTAACAATTGAGCACAAGAGAAAGCTT AAGGAAGAATATGGTTAGTTAATAACCTTTATGTCTTTAAACTTGAACTTCACCCTAGTGATAT TCCCTGGTTTCATGCTTCTTTTGCAGGAGTCGAGCCTTGGACATTTGAACAGAAGCTAGGTGAG GCAGTATTTATCCCGGCAGGATGTCCCCACCAGGTTAGAAATTTGAAGGTATGACATGACATGG AAATAGCTGTTTGTCCCCACTGTCATCAGTGACATGCTCCTTAATCAAATTAGCTGCTAATCAC TTGTACCTTTTTATTGGGCAGTCTTGCATAAAGGTTGCACTAGATTTTGTTTCTCCGGAAAATG TCCGAGAGTGCATCAGGTTAACAGAAGGTTTCCGTCTGCTGCCGAAGTGGCATAAGGTGAATGA AGATAAACTGGAGGTTTGTCACTCACTCTGTTCATACTAATGTAACATTTGCTAATTCTTTTTT ATGATTGTAAATGAAGTATTCTTGTGTATATTATGCCATTTTTTTGTCTGCCCTAGCTTCTATA TCGTCTCTATTAGGCATTCTTATCTTTCTGTCCGCATGAATCTAGATATTTAAATTTAAATTAT GTGTCTTGTTTGCCAGGTTAAGAAGATAGCTCTTCATGCATTCAATCAAGCTATTAAAGATATC ACTGATGAATCATCTAATAGCAATGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.150210213

Conservation Information
Conserved circRNAs	NA
PMCS	0.150210213

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							245873170-245873112(+)
245874529-245873104(+)
245873104-245874540(-)
						
						Potential amino acid sequence
						
							MKILSTKEASGGLQRCADYFGMPTAPSESNKEPRPEECVNELGIKQPVQHVASEEQEGVQDDAK
ADANVMNVSFGKGKSEDSFGTINGTNSGDKIESPSGLAERTLTQPTTKGCSKQRGRSSNGRGNR
TKKIEEGNASGLIAVAPESEDDDDDAAFIDGNQAEGGALWDIFRREDVSKLHDYLMKHAHEFRH
CNFEPVKQVTHPIHDQCFYLTIEHKRKLKEEYGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCI
KVALDFVSPENVRECIRLTEGFRLLPKWHKVNEDKLEVKKIALHAFNQAIKDITDESSNSNERS
ISSHILMK*(+)
MHSIKLLKISLMNHLIAMKGQYPHTY*(+)
MCEDIDLSLLLDDSSVISLIA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	245873170-245873112(+) 245874529-245873104(+) 245873104-245874540(-)
Potential amino acid sequence	MKILSTKEASGGLQRCADYFGMPTAPSESNKEPRPEECVNELGIKQPVQHVASEEQEGVQDDAK ADANVMNVSFGKGKSEDSFGTINGTNSGDKIESPSGLAERTLTQPTTKGCSKQRGRSSNGRGNR TKKIEEGNASGLIAVAPESEDDDDDAAFIDGNQAEGGALWDIFRREDVSKLHDYLMKHAHEFRH CNFEPVKQVTHPIHDQCFYLTIEHKRKLKEEYGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCI KVALDFVSPENVRECIRLTEGFRLLPKWHKVNEDKLEVKKIALHAFNQAIKDITDESSNSNERS ISSHILMK(+) MHSIKLLKISLMNHLIAMKGQYPHTY(+) MCEDIDLSLLLDDSSVISLIA*(-)
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 Zm00001d054070_circ_g.2

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