Plant Circular RNA Database

Detail information of Zm00001d034823_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d034823_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006979
					
						Alias
						zma_circ_0000588
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 302962448-302976999  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d034823						
					
						Parent gene annotation
						
							ALBINO3-like protein 1 chloroplastic
							
						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  
						
							CT-AC							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
						Zm00001d034823_T002:8
Zm00001d034823_T003:2
Zm00001d034823_T001:8

General Information
CircRNA Name	Zm00001d034823_circ_g.1
ID in PlantcircBase	zma_circ_006979
Alias	zma_circ_0000588
Organism	Zea mays
Position	chr1: 302962448-302976999 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d034823
Parent gene annotation	ALBINO3-like protein 1 chloroplastic
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	CT-AC 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	Zm00001d034823_T002:8 Zm00001d034823_T003:2 Zm00001d034823_T001:8

			
						 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  
						
							GATATGAAAAACATCAAACATTGTAAATTCAGAGCTAACCTGCAAGTGGGTCAACACCAGATAA
TTTGTATAAGCGAGCAGTTTCGAGCTGTATCCTTTCctttccccacgttgcggtccagttggtt
tcagctcttggctgggctgggctttactaagtttgggcagaggtttgctctgaacagtggatcc
attcttct

									
								

					

						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: 2388
Transcript exons: 302962448-302962666,302967670-302967935,302968370-302968
435,302968493-302968586,302969533-302969640,302970268-30
2970372,302974454-302975922,302976939-302976999
CTTTCCCCACGTTGCGGTCCAGTTGGTTTCAGCTCTTGGCTGGGCTGGGCTTTACTAAGTTTGG
GCAGAGGTTTGCTCTGAACAGTGGATCCATTCTTCTGAACATTGGTGGATTCTTCTCTTGAAAG
TTTGTCAATATATTCTTTGACAGGATTTTTTGCACCTCCAAGCTTTTGAAGCCACACTTGTTGC
GCAGTACTGAGGATATTATTTGTAAGCCTTCCTCACTGCTCCTGTTGAGGGCTCTTAGTCATAG
CCTCCTGCCTGGTCATGTTGCTCCCTGTTTTCAGGTTAGTTGTAGCCTAGATTTGTTTTAATGG
AACTTTTTATTATCTCTGTTTCCGCCCTCTGTAAAGAGGATTGCATCTTGTAACTGGTCTATGT
TGAACCTCTCTTCTTCTCGGAAAAAAAAACCCATATTCCGACTTGTTAAAGGCAATACTGATAA
ATATTCTGATTATTTGGAGGAACTGTATCAATGGAGCATAGCAATTGGGATAGCGCGCCCAGCC
CATTTAGAAATGCCGCTGCAGAAGGGCAGTATCGGGACTCTAGTCCAGAAGGCACGGAAAGAGC
AAAATAACCAATTAGCAATGGTAAGAACTTTGTTACAGCCTGAGCACCTTGTTGGCTAGGATCA
TTGCTCTGTGGTGGCTGCATTACTTGAGAAGATATGTATTGTGAAATGACAAGAAGAACTGGTA
ACACGAGGTATGCCAAAGTGTCTGACCAGCCAAGAGGTGGATGACCATCAGTAAAAGGAAAAAG
CCAGGATATTCCCTGGCCATTTTGTTGAGCAGCAATTGTTGTAGGACCGGCCAAAGAAGGTATC
CAAAAAAAGCCTTCAGTCAGAAGTCCCACCCATCCAAAAAAGGACGCCAGCGCTTCAATATGTG
AAATAGGAAGTTCAGTGGAGAATACTTTCAGATAGTCTTCTTTGGCTTGCTGGGTGACTGCCCC
AGGATCCCCAATTACTTTCAAGGCCTGCATAACTTTCTTTGTGGTTCTTGAGGATAAATCCATG
TTGTCAAATTCAACTCCCACGCCAGCAATTCGACGGCTGCGGCGTGGGATAATTTCTGCAACTT
GGGCATTTTTAGACGTCATAAAAGGGGGATCTTCTGGTGTTGCAAGGAGGCCTGAAATCTTTTT
GGAGAGCTTGCTAAGGAATTGTTTGTTCTTGAGCTGCGTACTGCCTGTTTGGGTCTCTTGCGAA
GTTGACTGACTACCATCAGTAGTAACAGCTAGGCTGACCTCTCGCACCGTGGACACTGTATTTT
CATCAGTATCAATCCTCAGTACAGAAGCGATTGGCCCACTCCCTTCTTCATTCATATTTCCAGA
CTTGTCCCTACTGTTGAACCTTTTTCGTGAGTATACCATCAGCTTTTTGGATGATTGAAGGCCC
CTAATATGTAGCATCCCTGGCTGTTCAATGCCAGTAGTGCAGTGAATGGATTGGTGTAGCAAAT
TCCCGGTTGAGGACTTCCTTCCGCTGTCCGCAGCCACATGATCGCCCAGAGTCAAGGTCGTCCT
CTCAGTCTCAGAAATGCACATTTGATGGGTGAGGTCCGTCGTAGCCCAATCCACCGGTTCAGCC
ACAAGATCATCCTGGCGTGCTTCACCCGTAAATCCCAAAGGCCCAGTAGCTTGGGGCGAATCAG
TCCGGTCCCCCTCCAGCGGCCCAGCAGCTAAATGGTACTGGGGCGAGGCTGACCTCAACTGATT
CAGCGACCCAACAGCTAGTGGCACCTTGGTTCTTTCTTCATCATTAAAGGAGGCAGCTCGGACC
CCAAGGTCGCGTGCCTCATTAGCCAACTGTCTACACTGCTTCCATGAAGGGGAAGGCGACTCCT
GGGATCTCTCCACCGATATGAAGGAGCCGGCCCGAGCATCGAGCTGTGCGTTATTTAATTGGGC
AACGCAAGCATCAATGGACGGCTGGCCGCATATCCGCCTGGAAGGACCCAAGGCGCCACATATC
TGCCTGGAAGGACCCGAGGCGCCACAGACCAGCTGCATTCCCATCTCATCTCCCCAGGTCGGGC
AATCTTCAAGGGGCCGCATTGAATGTTGTGCATTAAGTCCCGAAGAGGCGCCTAAGCCCATCCT
TTCAGCTTCCTCAACCGAACACAGCGCCCTACTCCTTCCAGACACAAACTGGGCGCCTATCCGA
AGGTGAACAGATTCCCTAGGTGGCTGAGGTGGAAGGCGGCGCTGCTGGGAGTCAGCTGGATCAC
TGTCATTTCCTTCATCAAACTGACCATCGTCAGAGGAAGGGGATAGAGTTTCAGTGCTATTGGT
CATCTGAAAGGGCACCGATGACACTGCAAGTGGGTCAACACCAGATAATTTGTATAAGCGAGCA
GTTTCGAGCTGTATCCTTTC
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	GATATGAAAAACATCAAACATTGTAAATTCAGAGCTAACCTGCAAGTGGGTCAACACCAGATAA TTTGTATAAGCGAGCAGTTTCGAGCTGTATCCTTTCctttccccacgttgcggtccagttggtt tcagctcttggctgggctgggctttactaagtttgggcagaggtttgctctgaacagtggatcc attcttct
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: 2388 Transcript exons: 302962448-302962666,302967670-302967935,302968370-302968 435,302968493-302968586,302969533-302969640,302970268-30 2970372,302974454-302975922,302976939-302976999 CTTTCCCCACGTTGCGGTCCAGTTGGTTTCAGCTCTTGGCTGGGCTGGGCTTTACTAAGTTTGG GCAGAGGTTTGCTCTGAACAGTGGATCCATTCTTCTGAACATTGGTGGATTCTTCTCTTGAAAG TTTGTCAATATATTCTTTGACAGGATTTTTTGCACCTCCAAGCTTTTGAAGCCACACTTGTTGC GCAGTACTGAGGATATTATTTGTAAGCCTTCCTCACTGCTCCTGTTGAGGGCTCTTAGTCATAG CCTCCTGCCTGGTCATGTTGCTCCCTGTTTTCAGGTTAGTTGTAGCCTAGATTTGTTTTAATGG AACTTTTTATTATCTCTGTTTCCGCCCTCTGTAAAGAGGATTGCATCTTGTAACTGGTCTATGT TGAACCTCTCTTCTTCTCGGAAAAAAAAACCCATATTCCGACTTGTTAAAGGCAATACTGATAA ATATTCTGATTATTTGGAGGAACTGTATCAATGGAGCATAGCAATTGGGATAGCGCGCCCAGCC CATTTAGAAATGCCGCTGCAGAAGGGCAGTATCGGGACTCTAGTCCAGAAGGCACGGAAAGAGC AAAATAACCAATTAGCAATGGTAAGAACTTTGTTACAGCCTGAGCACCTTGTTGGCTAGGATCA TTGCTCTGTGGTGGCTGCATTACTTGAGAAGATATGTATTGTGAAATGACAAGAAGAACTGGTA ACACGAGGTATGCCAAAGTGTCTGACCAGCCAAGAGGTGGATGACCATCAGTAAAAGGAAAAAG CCAGGATATTCCCTGGCCATTTTGTTGAGCAGCAATTGTTGTAGGACCGGCCAAAGAAGGTATC CAAAAAAAGCCTTCAGTCAGAAGTCCCACCCATCCAAAAAAGGACGCCAGCGCTTCAATATGTG AAATAGGAAGTTCAGTGGAGAATACTTTCAGATAGTCTTCTTTGGCTTGCTGGGTGACTGCCCC AGGATCCCCAATTACTTTCAAGGCCTGCATAACTTTCTTTGTGGTTCTTGAGGATAAATCCATG TTGTCAAATTCAACTCCCACGCCAGCAATTCGACGGCTGCGGCGTGGGATAATTTCTGCAACTT GGGCATTTTTAGACGTCATAAAAGGGGGATCTTCTGGTGTTGCAAGGAGGCCTGAAATCTTTTT GGAGAGCTTGCTAAGGAATTGTTTGTTCTTGAGCTGCGTACTGCCTGTTTGGGTCTCTTGCGAA GTTGACTGACTACCATCAGTAGTAACAGCTAGGCTGACCTCTCGCACCGTGGACACTGTATTTT CATCAGTATCAATCCTCAGTACAGAAGCGATTGGCCCACTCCCTTCTTCATTCATATTTCCAGA CTTGTCCCTACTGTTGAACCTTTTTCGTGAGTATACCATCAGCTTTTTGGATGATTGAAGGCCC CTAATATGTAGCATCCCTGGCTGTTCAATGCCAGTAGTGCAGTGAATGGATTGGTGTAGCAAAT TCCCGGTTGAGGACTTCCTTCCGCTGTCCGCAGCCACATGATCGCCCAGAGTCAAGGTCGTCCT CTCAGTCTCAGAAATGCACATTTGATGGGTGAGGTCCGTCGTAGCCCAATCCACCGGTTCAGCC ACAAGATCATCCTGGCGTGCTTCACCCGTAAATCCCAAAGGCCCAGTAGCTTGGGGCGAATCAG TCCGGTCCCCCTCCAGCGGCCCAGCAGCTAAATGGTACTGGGGCGAGGCTGACCTCAACTGATT CAGCGACCCAACAGCTAGTGGCACCTTGGTTCTTTCTTCATCATTAAAGGAGGCAGCTCGGACC CCAAGGTCGCGTGCCTCATTAGCCAACTGTCTACACTGCTTCCATGAAGGGGAAGGCGACTCCT GGGATCTCTCCACCGATATGAAGGAGCCGGCCCGAGCATCGAGCTGTGCGTTATTTAATTGGGC AACGCAAGCATCAATGGACGGCTGGCCGCATATCCGCCTGGAAGGACCCAAGGCGCCACATATC TGCCTGGAAGGACCCGAGGCGCCACAGACCAGCTGCATTCCCATCTCATCTCCCCAGGTCGGGC AATCTTCAAGGGGCCGCATTGAATGTTGTGCATTAAGTCCCGAAGAGGCGCCTAAGCCCATCCT TTCAGCTTCCTCAACCGAACACAGCGCCCTACTCCTTCCAGACACAAACTGGGCGCCTATCCGA AGGTGAACAGATTCCCTAGGTGGCTGAGGTGGAAGGCGGCGCTGCTGGGAGTCAGCTGGATCAC TGTCATTTCCTTCATCAAACTGACCATCGTCAGAGGAAGGGGATAGAGTTTCAGTGCTATTGGT CATCTGAAAGGGCACCGATGACACTGCAAGTGGGTCAACACCAGATAATTTGTATAAGCGAGCA GTTTCGAGCTGTATCCTTTC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.075360693

Conservation Information
Conserved circRNAs	NA
PMCS	0.075360693

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							302975918-302962569(+)
						
						Potential amino acid sequence
						
							MTLQVGQHQIICISEQFRAVSFPFPTLRSSWFQLLAGLGFTKFGQRFALNSGSILLNIGGFFS*
(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	302975918-302962569(+)
Potential amino acid sequence	MTLQVGQHQIICISEQFRAVSFPFPTLRSSWFQLLAGLGFTKFGQRFALNSGSILLNIGGFFS* (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d034823_circ_g.1

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