Plant Circular RNA Database

Detail information of Zm00001d043439_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d043439_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007795
					
						Alias
						zma_circ_0001304
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 199915818-199918771  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d043439						
					
						Parent gene annotation
						
							Nuclear pore complex protein NUP85
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d043439_T007:7
Zm00001d043439_T006:8
Zm00001d043439_T004:7
Zm00001d043439_T008:6
Zm00001d043439_T005:7
Zm00001d043439_T002:7
Zm00001d043439_T003:8
Zm00001d043439_T009:7
Zm00001d043439_T010:7
Zm00001d043439_T011:8

General Information
CircRNA Name	Zm00001d043439_circ_g.1
ID in PlantcircBase	zma_circ_007795
Alias	zma_circ_0001304
Organism	Zea mays
Position	chr3: 199915818-199918771 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d043439
Parent gene annotation	Nuclear pore complex protein NUP85
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, 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	Zm00001d043439_T007:7 Zm00001d043439_T006:8 Zm00001d043439_T004:7 Zm00001d043439_T008:6 Zm00001d043439_T005:7 Zm00001d043439_T002:7 Zm00001d043439_T003:8 Zm00001d043439_T009:7 Zm00001d043439_T010:7 Zm00001d043439_T011:8

			
						 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  
						
							AATTGTGCCAAGGTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGT
GAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGggttttgaagggatgcaccatttagcac
agaaatgcatacagcttatgccatcctctggcactaatggattaacaggcctcattatcggtgt
tatgtcag

									
								

					

						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
						
							GGTTTTGAAGGGATGCACCATTTAGCACAGAAATGCATACAGCTTATGCCATCCTCTGGCACTA
ATGGATTAACAGGCCTCATTATCGGTGTTATGTCAGAAAATCCAGAGGTTAGAGCATGAAGTCG
TCCTCTATCTGTGTCCTTGGACTTCTTATACATTCTTATTTATTGTTTTTATAACATCTTTTCC
ATGATTAGGTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGGTAAGAGTAACAATTTGC
TAATTTCTATTCACTGAAGCACTGTCCTAACTGATTTTGGCATTTGTACCTGCAGGCTGGTCAC
ACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGATATTATGTTGCATGAAGAGCGA
CCTAACTTAGGCGGTATAAGCATAGAGGAACTTCACCGATTAGTCTATGCTCAAGTTTTATGTT
GTCATCCTTTAACTTGGCAGGTTAGTTATGTAACATAGTAACCCTAGTACATCACCAACTAATT
TTATGTATTTTTATTAGGCATTAGCCACACACTTCTTGAACTAGCAAATGCACAAATTGCATGT
TGCATTATTTAATTGGGTTATTTCCAGTGGCGGAGCTGGTGAATTTCCAAGCCTAGGGCCAATA
GTTAAGGATCTAAATATTTGAGACCTGATCCGCATATCAATTTCTTCACAAAGGCGAACAATAA
AATACATAGATCTAAATATTTGAGACCTGATCCGCATATCAATTTCTTCACAAAGGCGAACAAT
AAAATACATACATATAATTGTACAACAAACTGATTCTGGTTGCATGACATTTCCATTACTAGTT
CTCATTGCATATTTGTACTTATACATAAACACAAGATTGGCTTGGTTGTATAATAGGCGTAGGA
GTCTAGGACCAAGAGAAAAACAGATTTTCGATGTCTTTGTCCTCTCCATTGTGTAAGTTTACGG
AATGCAAAAGGAAAACAAAGTAAACAACCTGGCTGCTAGTTGCTACATCATACAAAAACACAAA
TATTGAACAATGGAACCATGGAAAATTGGAACAAGAGATTGGATTATTTCATATTTGGTTGGAG
GCTTGGATCAATCGAATTAGAGAACAACCTGCTGTAGTGTATTAATGTGCTTGTGTGGTGTACG
GTGTACCCCTATTGCTCTGCAGTCTTGCAGAAGGGAAGGGGCCACTTAGCACAGGGGCACGCCA
GTTGCCGGCTCGCTGGCTAGGCGGCCGCTCAATGTGCCTCCGACCATGGAGTGCGGAGCCGTGG
ACAGCCTCTAGTGGCTAGCATAGAGGACCTTTGGGCGATGGGCTGCCGCAACCCCTCTTGTCAA
GTTGGTGGTGACGTGATTGGCGGCGTGGCAAGCAGGGTTAATCAAAGCAGCACTGCAGCAGCCA
GCTGGACAGAGAGGAACAGGGATGGGAGTCGAGTTGCCAAGTCGGATTGTGGCGCTAGCGCACG
AAGCCACACCCTGACTTCCCGAGTCAGGGTCAGATGTCAAGGAGATCCTGCTTTCTCATCTGTC
TGGACCGGCTGGGAGTAAGAGTTTGTCCCAAGAGCCCAGGGTTACTTCAGATTGGGCCAAAAAA
TCACATGTAATATAAGAAATATTCTGGGTCAAGCCTAGGGCTATGATCCTAGGCCCATATCCAC
CCCTGATTATTTCCTTTCTCTCATTTCAGTTCTTAATGCCTTTTTCTCTCATTTTGAGATCTCG
TTTCCCTTTTACCTGTTGGGTGGCTTATTGCAGCATGGATCCATCCAATGATAAATAGGAAATA
GGTTCCAACCGAGTGGTGAGTAGGAACTATTTCATATGTTTTGCTGAACATTTATATGTGCATA
TGAGGATATGCCTTTGATTTGCTATATCGATCTGTTTTGCTTTTTAGTATGAGAAGCTTTTGGA
TTTCTGTTGTTGTTTGTTTTGATAGCAAAAATATCTTCTTTTGACAACATTTATCTTGGCTTTC
TTGCATGTTTGGTTCTCAGATCGCGCCGACTTATCTGTCCTCATGTCTAAACCAAGGCCTAGGA
CTCTTGGAGATTCTACTTCTTAAGCAACCCATACAAGATAATTGCCTAGTACTCAAGGTACCAT
GCATTTTAATCAATTATAAATTTCAGCGTCTCAGACCCACTTTTATTCTCTAATCCTCATTTCT
GTGGGCAGACTTTGGAAATTTGCCGATTGTACGAACTGGAGAATGTTAGTACAATCATCATGAA
GGTAAACCGTAAACATGGATTCAAGTGCTGCACAACTTTTTTGTTACAAATAAAAATTTGGGAC
ATGGCATAGTGATCATCTTGTGTTTTGGATGTTGCTTATTCAAACTTCCACATGTAGCTTGCAT
TTTCCATGGTTCTCAACTGAACTCAACGTTAGCTTAAACTAAGGATTCATATCTAATAACTGCT
TGTTTCTTTTTTTAGATTGCTGGCATTTATCGTTGGAAGCATGGACGAAAAGGAACTGGTGTAT
ACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACA
CATTGGGAAGTCAGTGACAGACGATAGTTTTAAGGTTCTTTTTTCTTTCTAAATTCCTCAGATG
TAACTGGCAACTAGTTCTCTGCACAATAGTAATCTAGGAACATTGATCATAAGGAAGAGTAATC
CCCTTGAACTAATAACGATTTTGCATTTCAGCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCT
GACATTGGTAGTGCAGGCGGTCTTGAGTTCCTTCACAGGTATTTTCTTTGCCCATAAAATTTGT
CTCTCTACATGACAATGTTGAATGCCAGCTTAGTATATAATTGTGCCAAGGTACCGGGATTTCA
AGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTT
TTTAATACAG
						
					

			
		

Sequences
Splice junction sequence	AATTGTGCCAAGGTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGT GAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGggttttgaagggatgcaccatttagcac agaaatgcatacagcttatgccatcctctggcactaatggattaacaggcctcattatcggtgt tatgtcag
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	GGTTTTGAAGGGATGCACCATTTAGCACAGAAATGCATACAGCTTATGCCATCCTCTGGCACTA ATGGATTAACAGGCCTCATTATCGGTGTTATGTCAGAAAATCCAGAGGTTAGAGCATGAAGTCG TCCTCTATCTGTGTCCTTGGACTTCTTATACATTCTTATTTATTGTTTTTATAACATCTTTTCC ATGATTAGGTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGGTAAGAGTAACAATTTGC TAATTTCTATTCACTGAAGCACTGTCCTAACTGATTTTGGCATTTGTACCTGCAGGCTGGTCAC ACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGATATTATGTTGCATGAAGAGCGA CCTAACTTAGGCGGTATAAGCATAGAGGAACTTCACCGATTAGTCTATGCTCAAGTTTTATGTT GTCATCCTTTAACTTGGCAGGTTAGTTATGTAACATAGTAACCCTAGTACATCACCAACTAATT TTATGTATTTTTATTAGGCATTAGCCACACACTTCTTGAACTAGCAAATGCACAAATTGCATGT TGCATTATTTAATTGGGTTATTTCCAGTGGCGGAGCTGGTGAATTTCCAAGCCTAGGGCCAATA GTTAAGGATCTAAATATTTGAGACCTGATCCGCATATCAATTTCTTCACAAAGGCGAACAATAA AATACATAGATCTAAATATTTGAGACCTGATCCGCATATCAATTTCTTCACAAAGGCGAACAAT AAAATACATACATATAATTGTACAACAAACTGATTCTGGTTGCATGACATTTCCATTACTAGTT CTCATTGCATATTTGTACTTATACATAAACACAAGATTGGCTTGGTTGTATAATAGGCGTAGGA GTCTAGGACCAAGAGAAAAACAGATTTTCGATGTCTTTGTCCTCTCCATTGTGTAAGTTTACGG AATGCAAAAGGAAAACAAAGTAAACAACCTGGCTGCTAGTTGCTACATCATACAAAAACACAAA TATTGAACAATGGAACCATGGAAAATTGGAACAAGAGATTGGATTATTTCATATTTGGTTGGAG GCTTGGATCAATCGAATTAGAGAACAACCTGCTGTAGTGTATTAATGTGCTTGTGTGGTGTACG GTGTACCCCTATTGCTCTGCAGTCTTGCAGAAGGGAAGGGGCCACTTAGCACAGGGGCACGCCA GTTGCCGGCTCGCTGGCTAGGCGGCCGCTCAATGTGCCTCCGACCATGGAGTGCGGAGCCGTGG ACAGCCTCTAGTGGCTAGCATAGAGGACCTTTGGGCGATGGGCTGCCGCAACCCCTCTTGTCAA GTTGGTGGTGACGTGATTGGCGGCGTGGCAAGCAGGGTTAATCAAAGCAGCACTGCAGCAGCCA GCTGGACAGAGAGGAACAGGGATGGGAGTCGAGTTGCCAAGTCGGATTGTGGCGCTAGCGCACG AAGCCACACCCTGACTTCCCGAGTCAGGGTCAGATGTCAAGGAGATCCTGCTTTCTCATCTGTC TGGACCGGCTGGGAGTAAGAGTTTGTCCCAAGAGCCCAGGGTTACTTCAGATTGGGCCAAAAAA TCACATGTAATATAAGAAATATTCTGGGTCAAGCCTAGGGCTATGATCCTAGGCCCATATCCAC CCCTGATTATTTCCTTTCTCTCATTTCAGTTCTTAATGCCTTTTTCTCTCATTTTGAGATCTCG TTTCCCTTTTACCTGTTGGGTGGCTTATTGCAGCATGGATCCATCCAATGATAAATAGGAAATA GGTTCCAACCGAGTGGTGAGTAGGAACTATTTCATATGTTTTGCTGAACATTTATATGTGCATA TGAGGATATGCCTTTGATTTGCTATATCGATCTGTTTTGCTTTTTAGTATGAGAAGCTTTTGGA TTTCTGTTGTTGTTTGTTTTGATAGCAAAAATATCTTCTTTTGACAACATTTATCTTGGCTTTC TTGCATGTTTGGTTCTCAGATCGCGCCGACTTATCTGTCCTCATGTCTAAACCAAGGCCTAGGA CTCTTGGAGATTCTACTTCTTAAGCAACCCATACAAGATAATTGCCTAGTACTCAAGGTACCAT GCATTTTAATCAATTATAAATTTCAGCGTCTCAGACCCACTTTTATTCTCTAATCCTCATTTCT GTGGGCAGACTTTGGAAATTTGCCGATTGTACGAACTGGAGAATGTTAGTACAATCATCATGAA GGTAAACCGTAAACATGGATTCAAGTGCTGCACAACTTTTTTGTTACAAATAAAAATTTGGGAC ATGGCATAGTGATCATCTTGTGTTTTGGATGTTGCTTATTCAAACTTCCACATGTAGCTTGCAT TTTCCATGGTTCTCAACTGAACTCAACGTTAGCTTAAACTAAGGATTCATATCTAATAACTGCT TGTTTCTTTTTTTAGATTGCTGGCATTTATCGTTGGAAGCATGGACGAAAAGGAACTGGTGTAT ACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACA CATTGGGAAGTCAGTGACAGACGATAGTTTTAAGGTTCTTTTTTCTTTCTAAATTCCTCAGATG TAACTGGCAACTAGTTCTCTGCACAATAGTAATCTAGGAACATTGATCATAAGGAAGAGTAATC CCCTTGAACTAATAACGATTTTGCATTTCAGCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCT GACATTGGTAGTGCAGGCGGTCTTGAGTTCCTTCACAGGTATTTTCTTTGCCCATAAAATTTGT CTCTCTACATGACAATGTTGAATGCCAGCTTAGTATATAATTGTGCCAAGGTACCGGGATTTCA AGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTT TTTAATACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.023025609

Conservation Information
Conserved circRNAs	NA
PMCS	0.023025609

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							199915831-199918768(+)
199915902-199918604(-)
						
						Potential amino acid sequence
						
							MHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDYADI
MLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQDNC
LVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEHIGK
SVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQGFE
GMHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDYAD
IMLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQDN
CLVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEHIG
KSVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQGF
EGMHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDYA
DIMLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQD
NCLVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEHI
GKSVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQG
FEGMHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDY
ADIMLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQ
DNCLVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEH
IGKSVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQ
(+)
MRPVNPLVPEDGISCMHFCAKWCIPSKPCIKKSTVCRAASPHLLSRACCRDLLKSRYL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	199915831-199918768(+) 199915902-199918604(-)
Potential amino acid sequence	MHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDYADI MLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQDNC LVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEHIGK SVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQGFE GMHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDYAD IMLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQDN CLVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEHIG KSVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQGF EGMHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDYA DIMLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQD NCLVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEHI GKSVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQG FEGMHHLAQKCIQLMPSSGTNGLTGLIIGVMSENPEVVLAECTKNFGPWLVTHAMELLTADNDY ADIMLHEERPNLGGISIEELHRLVYAQVLCCHPLTWQIAPTYLSSCLNQGLGLLEILLLKQPIQ DNCLVLKTLEICRLYELENVSTIIMKIAGIYRWKHGRKGTGVYWFQQARDKVCLDRIAQQLFEH IGKSVTDDSFKQWEGLLELLGSDIGSAGGLEFLHRYRDFKRSLQQALDRRCGEAARQTVDFLIQ (+) MRPVNPLVPEDGISCMHFCAKWCIPSKPCIKKSTVCRAASPHLLSRACCRDLLKSRYL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d043439_circ_g.1

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