Plant Circular RNA Database

Detail information of Zm00001d012400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d012400_circ_g.1
					
						ID in PlantcircBase
						zma_circ_002867
					
						Alias
						circ1347
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 173695442-173699334  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d012400						
					
						Parent gene annotation
						
							Probable methyltransferase PMT10
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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-CA							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
						Zm00001d012400_T008:7
Zm00001d012400_T001:7
Zm00001d012400_T006:6
Zm00001d012400_T004:6
Zm00001d012400_T007:7
Zm00001d012400_T002:7
Zm00001d012400_T003:5
Zm00001d012400_T009:5
Zm00001d012400_T005:7

General Information
CircRNA Name	Zm00001d012400_circ_g.1
ID in PlantcircBase	zma_circ_002867
Alias	circ1347
Organism	Zea mays
Position	chr8: 173695442-173699334 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRI
Parent gene	Zm00001d012400
Parent gene annotation	Probable methyltransferase PMT10
Parent gene strand	+
Alternative splicing	NA
Support reads	2
Tissues	seedling leaves
Exon boundary	No-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-CA 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	Zm00001d012400_T008:7 Zm00001d012400_T001:7 Zm00001d012400_T006:6 Zm00001d012400_T004:6 Zm00001d012400_T007:7 Zm00001d012400_T002:7 Zm00001d012400_T003:5 Zm00001d012400_T009:5 Zm00001d012400_T005:7

			
						 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  
						
							ATGTTGCCTTCTCCATGGGTAGGTGTGAACCCTTTGATACATACCCTAGGACGTACGATCTACT
TCATGCATCTGGTCTTTTCTCAAAGGAGCAGAACAGggtctggtttagcaacgtgcctcacaca
agattgattgatgacaaaggaggacagaattggatcaccaaggtcaaagataaattcagatttc
ctggaggc

									
								

					

						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
						
							GGTCTGGTTTAGCAACGTGCCTCACACAAGATTGATTGATGACAAAGGAGGACAGAATTGGATC
ACCAAGGTCAAAGATAAATTCAGATTTCCTGGAGGCGGAACTCAATTCATTCATGGAGCAAATC
AATACCTAGACCAGATCTCCCAGGTTCGATGTCAAATATTCTTCAAAACTGCTTGGAATTTAAT
CCTTACTCTGACTAGAGCAACCTGTTCCCTCTGTTCGTCCAGATGGTACCAAATGTTGCATTTG
GATCTCATACTAGAGTTGTCTTGGATGTTGGCTGTGGAGTAGCAAGTTTTGGTGCATATTTACT
TTCACGTGATGTCCTGACATTGTCCATAGCTCCAAAAGATGTTCATGAAAATCAGATTCAGTTT
GCTCTTGAACGTGGTGTGCCTGCAATGGCAGCAGCATTTGCAACGCGCCGGTTGTTATATACAA
GCCAAGCGTTTGATATAATACATTGCTCACGCTGCCGAATAAATTGGACCCGTGATGGTGAGCT
GTGATTACTATATAATTATTTTTAATTAACATTGCACACTTAGTTTGTCACCATGCTGTATCTT
GATATCTTCATAGTTAGGCTGAATGCTCACTTAACTCTTCTCTCCCAGTTTTCCTAGTCTTCCC
CCTTAGATCTGTAGGGATGATATTTTTATTTGTCTTAGACGTCGAATTTATTTCACGATTCTCA
AAGAAAATAAATACTTTTAACCAATGGATAGAAAACGAGGTGAGTTATTGTGAAGAAGCTAAAG
GTTGTTATTGATTGTATACTTTTCATTTAAACTTGATCTCAAAGGTATGTGCACTTATCTATGT
ACTTTCCAAATTTGCCTAAGTTTTGTACTTTTGTTATCATATTTGTTTATTTGAAGATGGTATC
CTGCTCCTGGAGGTTAATAGATTGCTTAGAGCTGGAGGCTACTTTGCTTGGGCAGCCCAACCTG
TTTATAAGCATGAAGAGGCCCAACAAGAGGCATGGAAAGGTATGTTCTACTTATTCTGTTGTAC
CTTCTCTTTTGTTAGTGTGATAACATACAGCTCATGTATGAGTTTGGTAGTTCTTTAATGCTAG
AGATTTGTCATAATCAAATCCATTCTTTTATTCGCTACTATCCTGCATACTTATAGCTGGCAAG
TTGTGTAGTTTGTGTTTGTTGATGCCAAATAGCCAGTGTTCCTGTATACACGTATCTAACATTT
ATTTAAAACACCTTGCCTTATCAGTTCAACTTTATGTATTTTGACTTGAATTTGTCCTTGTCAC
AACATGCTAAGTGCCCTCACATAAGTTAACTTGCATGATAGGTGTTACCATTTTAGGCATCATC
TTGACTATCCGCTGACCCGTTAATGGTGACTGAACTTCGAGAATGATTTCATAATAATATATCC
ATGCAGAACTATATGTCTATATTGATATGAAATGAAAAGGCTACCTTATCAGATTGCTATTATA
ACTGAGAACTCCTTTAATGCTAAGTTGTTTAGAGAAGTTGCTCTTGATTTTATTTAAAATCTGA
AAACACTTTATGGAAACTCAGAGATAAGTATCTCTTTTTTGGATTTTTTTGCATCATCAGTTTG
ATATACATTCAATAACTTGTGTTTTTTGCTTTTGTTTTTATGAAACTATTGCTCATATACAAAA
TCATGTGTAGAGATGGAGAACCTCACTGCCCGACTTTGCTGGGAGTTTGTGAAGAAAGAGGGAT
ACATCGCTATGTGGAGGAAACCCTTAAATAACTCTTGCTACATTAACCGAGGTCCTGAAGGAAA
ACCTCCACTTTGTGATGCTGATGATAACCCGGATGATGTCTGGTACTCATTTAGCCTGTTGCCA
TAATTATTGAAATGCATATCAATTTAGTATTCTCTTCTGTAAGCTGGGTCCAGCCTTTCTTACT
GCTGCTGAGTTGTATTTGATGAGATTATGTATTCTTTATATCAGATCTCATTGCGCCATAGATT
TCTGTGGATTTATCCGATCAGCTTTTCATTTGTCACATTGGCTGTCATCCCTGTACACATATCT
TTGCTGCAAAACCCTTTTTTATTACTCTTTACATTCTATTTTATCTCAGGTATGTTGGTCTGAA
AGCATGTATTAGTCGGCTTCCAGAGAATGGCGAAGCACCAACTCCTGTTCAATGGCCTGCACGC
TTAATGGAGCCACCAAAGAGGCTTCAAGGCGTCGAAATGGATGCCTACTCATCAAAGAATGAGC
TTTTCAAAGCAGAAACAAAATTTTGGGACGACATAATTGACGGTTATATCCGTATCTTTAAGTG
GAGGAAGTTCAAAGTCCGGAATGTAATGGACATGAGGGCTGGATTTGGAGGGTATTTTTCTCAA
ATCTCTTCCTTTCATTTGCTTCATTGGATGTATGATTGCAAGTACAAAGTCCATTAGAACTTCT
ACATGTTCTCTAGCATGACACCTTGACTAGTAATATCTATGAATATACTATCTGAAACAAAGAG
TTATTTAAGCCATTCTTGTGCTGTCAACCTGTATGAAATTTAAGATATTGATAGTCAAATCTAA
AAATTTGGCTTCAGATAAACCTAAATGGACTTCTATCTGGGGAAGTATTTCGTTTTTATTAATA
AGATCTTGCACAGTTGGATGGATGGCTAGAGTCTGCAACTAAAACAAAGATTAGCTGAACAAGC
CAACAAGAACATCTCTGAATGGGAAGAATAAGGTTTTTTTAGGGAACTGTTTCAGGATGTTGTG
CTATATTTAGTACTACCTCCGTTCTCGTATATTTGTCGTCCGCTAGTTCATTTTTGAACTAAAC
TGCGACAAATAAAAAAGAACGGAGGGAGTACAAATAAATGTGTGCTCAAGTCACTTTTTTCACC
CACTTAGTTCATAACAATCTATTCACATCCACAACAACAAAAAAGCCTTTCAGTAACAAGCAAT
TTAGGGTATGCTAAAGTTGAAACCCAACATGAGACCCTAATCACGGTTCAGGCATGTCAATAGC
TGCTTTCCAAGCACTCTATTAAAGCATAACACTTTAGGTGTATCCCAATCTTTCAAGTCTCCTT
ATATTGCCTCCTTCATGTCAATTTTGGTCTTCCCCTACCTCTCCTATCATTTTATCTTGACTTA
GCACCTAATTGTTGAATATTTTTAATTGTGATGGTTGTAGTGAAACCTTATTCTTTGTGGGAAA
TGTATTCTTGTTTCTATTTTGCTTGTTGGTGGTTAGCTACTCTTTGTAGATAAAAGAATATAGA
AAACAGAATCTTATGTGCTTATAAATGGAGATGAGGCCATCATGCTTATTTTTGTCAGTCTAGT
TTTTTACTCCCACTTTGTATGTAGGTTTGCAGCTGCTTTGATCCGCCAGAAACTGGATTGGTGG
GTGATGAATGTTGTTCCTATTAGTGAGCCAAATACACTACCTGTAATTTTTGATCGGGGGCTTC
TTGGAGTAGCTCATGACTGGTACACTTTTGTACATTCTTGGTTCTTCAAATATTATTTCTATTT
TTTCTAGATTCAAAATGGTTTACTTGAAATTTTATATAGTGCAATTGATAATGTTCTGGATAGA
GTACACGGATCGCTTGCACCAGTTCCTGATTGTCTCTTGTATTCCTGGACCCCTATGAATTTTC
TTTATCAGAATTCACAAGTCAGAATGAATGGCCATAGATTAGTTTTAACCGGTGTGTCTGATTA
TAATGACCAGCAAGCTTTTTTCGTTTTGATGTAATTTTATGAAACTTATAGCATCAAAATTTCT
GCCCTGATTTGAATATTATGTTGCCTTCTCCATGGGTAGGTGTGAACCCTTTGATACATACCCT
AGGACGTACGATCTACTTCATGCATCTGGTCTTTTCTCAAAGGAGCAGAACAG
						
					

			
		

Sequences
Splice junction sequence	ATGTTGCCTTCTCCATGGGTAGGTGTGAACCCTTTGATACATACCCTAGGACGTACGATCTACT TCATGCATCTGGTCTTTTCTCAAAGGAGCAGAACAGggtctggtttagcaacgtgcctcacaca agattgattgatgacaaaggaggacagaattggatcaccaaggtcaaagataaattcagatttc ctggaggc
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	GGTCTGGTTTAGCAACGTGCCTCACACAAGATTGATTGATGACAAAGGAGGACAGAATTGGATC ACCAAGGTCAAAGATAAATTCAGATTTCCTGGAGGCGGAACTCAATTCATTCATGGAGCAAATC AATACCTAGACCAGATCTCCCAGGTTCGATGTCAAATATTCTTCAAAACTGCTTGGAATTTAAT CCTTACTCTGACTAGAGCAACCTGTTCCCTCTGTTCGTCCAGATGGTACCAAATGTTGCATTTG GATCTCATACTAGAGTTGTCTTGGATGTTGGCTGTGGAGTAGCAAGTTTTGGTGCATATTTACT TTCACGTGATGTCCTGACATTGTCCATAGCTCCAAAAGATGTTCATGAAAATCAGATTCAGTTT GCTCTTGAACGTGGTGTGCCTGCAATGGCAGCAGCATTTGCAACGCGCCGGTTGTTATATACAA GCCAAGCGTTTGATATAATACATTGCTCACGCTGCCGAATAAATTGGACCCGTGATGGTGAGCT GTGATTACTATATAATTATTTTTAATTAACATTGCACACTTAGTTTGTCACCATGCTGTATCTT GATATCTTCATAGTTAGGCTGAATGCTCACTTAACTCTTCTCTCCCAGTTTTCCTAGTCTTCCC CCTTAGATCTGTAGGGATGATATTTTTATTTGTCTTAGACGTCGAATTTATTTCACGATTCTCA AAGAAAATAAATACTTTTAACCAATGGATAGAAAACGAGGTGAGTTATTGTGAAGAAGCTAAAG GTTGTTATTGATTGTATACTTTTCATTTAAACTTGATCTCAAAGGTATGTGCACTTATCTATGT ACTTTCCAAATTTGCCTAAGTTTTGTACTTTTGTTATCATATTTGTTTATTTGAAGATGGTATC CTGCTCCTGGAGGTTAATAGATTGCTTAGAGCTGGAGGCTACTTTGCTTGGGCAGCCCAACCTG TTTATAAGCATGAAGAGGCCCAACAAGAGGCATGGAAAGGTATGTTCTACTTATTCTGTTGTAC CTTCTCTTTTGTTAGTGTGATAACATACAGCTCATGTATGAGTTTGGTAGTTCTTTAATGCTAG AGATTTGTCATAATCAAATCCATTCTTTTATTCGCTACTATCCTGCATACTTATAGCTGGCAAG TTGTGTAGTTTGTGTTTGTTGATGCCAAATAGCCAGTGTTCCTGTATACACGTATCTAACATTT ATTTAAAACACCTTGCCTTATCAGTTCAACTTTATGTATTTTGACTTGAATTTGTCCTTGTCAC AACATGCTAAGTGCCCTCACATAAGTTAACTTGCATGATAGGTGTTACCATTTTAGGCATCATC TTGACTATCCGCTGACCCGTTAATGGTGACTGAACTTCGAGAATGATTTCATAATAATATATCC ATGCAGAACTATATGTCTATATTGATATGAAATGAAAAGGCTACCTTATCAGATTGCTATTATA ACTGAGAACTCCTTTAATGCTAAGTTGTTTAGAGAAGTTGCTCTTGATTTTATTTAAAATCTGA AAACACTTTATGGAAACTCAGAGATAAGTATCTCTTTTTTGGATTTTTTTGCATCATCAGTTTG ATATACATTCAATAACTTGTGTTTTTTGCTTTTGTTTTTATGAAACTATTGCTCATATACAAAA TCATGTGTAGAGATGGAGAACCTCACTGCCCGACTTTGCTGGGAGTTTGTGAAGAAAGAGGGAT ACATCGCTATGTGGAGGAAACCCTTAAATAACTCTTGCTACATTAACCGAGGTCCTGAAGGAAA ACCTCCACTTTGTGATGCTGATGATAACCCGGATGATGTCTGGTACTCATTTAGCCTGTTGCCA TAATTATTGAAATGCATATCAATTTAGTATTCTCTTCTGTAAGCTGGGTCCAGCCTTTCTTACT GCTGCTGAGTTGTATTTGATGAGATTATGTATTCTTTATATCAGATCTCATTGCGCCATAGATT TCTGTGGATTTATCCGATCAGCTTTTCATTTGTCACATTGGCTGTCATCCCTGTACACATATCT TTGCTGCAAAACCCTTTTTTATTACTCTTTACATTCTATTTTATCTCAGGTATGTTGGTCTGAA AGCATGTATTAGTCGGCTTCCAGAGAATGGCGAAGCACCAACTCCTGTTCAATGGCCTGCACGC TTAATGGAGCCACCAAAGAGGCTTCAAGGCGTCGAAATGGATGCCTACTCATCAAAGAATGAGC TTTTCAAAGCAGAAACAAAATTTTGGGACGACATAATTGACGGTTATATCCGTATCTTTAAGTG GAGGAAGTTCAAAGTCCGGAATGTAATGGACATGAGGGCTGGATTTGGAGGGTATTTTTCTCAA ATCTCTTCCTTTCATTTGCTTCATTGGATGTATGATTGCAAGTACAAAGTCCATTAGAACTTCT ACATGTTCTCTAGCATGACACCTTGACTAGTAATATCTATGAATATACTATCTGAAACAAAGAG TTATTTAAGCCATTCTTGTGCTGTCAACCTGTATGAAATTTAAGATATTGATAGTCAAATCTAA AAATTTGGCTTCAGATAAACCTAAATGGACTTCTATCTGGGGAAGTATTTCGTTTTTATTAATA AGATCTTGCACAGTTGGATGGATGGCTAGAGTCTGCAACTAAAACAAAGATTAGCTGAACAAGC CAACAAGAACATCTCTGAATGGGAAGAATAAGGTTTTTTTAGGGAACTGTTTCAGGATGTTGTG CTATATTTAGTACTACCTCCGTTCTCGTATATTTGTCGTCCGCTAGTTCATTTTTGAACTAAAC TGCGACAAATAAAAAAGAACGGAGGGAGTACAAATAAATGTGTGCTCAAGTCACTTTTTTCACC CACTTAGTTCATAACAATCTATTCACATCCACAACAACAAAAAAGCCTTTCAGTAACAAGCAAT TTAGGGTATGCTAAAGTTGAAACCCAACATGAGACCCTAATCACGGTTCAGGCATGTCAATAGC TGCTTTCCAAGCACTCTATTAAAGCATAACACTTTAGGTGTATCCCAATCTTTCAAGTCTCCTT ATATTGCCTCCTTCATGTCAATTTTGGTCTTCCCCTACCTCTCCTATCATTTTATCTTGACTTA GCACCTAATTGTTGAATATTTTTAATTGTGATGGTTGTAGTGAAACCTTATTCTTTGTGGGAAA TGTATTCTTGTTTCTATTTTGCTTGTTGGTGGTTAGCTACTCTTTGTAGATAAAAGAATATAGA AAACAGAATCTTATGTGCTTATAAATGGAGATGAGGCCATCATGCTTATTTTTGTCAGTCTAGT TTTTTACTCCCACTTTGTATGTAGGTTTGCAGCTGCTTTGATCCGCCAGAAACTGGATTGGTGG GTGATGAATGTTGTTCCTATTAGTGAGCCAAATACACTACCTGTAATTTTTGATCGGGGGCTTC TTGGAGTAGCTCATGACTGGTACACTTTTGTACATTCTTGGTTCTTCAAATATTATTTCTATTT TTTCTAGATTCAAAATGGTTTACTTGAAATTTTATATAGTGCAATTGATAATGTTCTGGATAGA GTACACGGATCGCTTGCACCAGTTCCTGATTGTCTCTTGTATTCCTGGACCCCTATGAATTTTC TTTATCAGAATTCACAAGTCAGAATGAATGGCCATAGATTAGTTTTAACCGGTGTGTCTGATTA TAATGACCAGCAAGCTTTTTTCGTTTTGATGTAATTTTATGAAACTTATAGCATCAAAATTTCT GCCCTGATTTGAATATTATGTTGCCTTCTCCATGGGTAGGTGTGAACCCTTTGATACATACCCT AGGACGTACGATCTACTTCATGCATCTGGTCTTTTCTCAAAGGAGCAGAACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.018918272

Conservation Information
Conserved circRNAs	NA
PMCS	0.018918272

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							zma-miR156a-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	zma-miR156a-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d012400_circ_g.1

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