Plant Circular RNA Database

Detail information of Zm00001d038849_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d038849_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009164
					
						Alias
						Zm06circ00101, zma_circ_0002307, GRMZM2G016503_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 165825412-165831692  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d038849						
					
						Parent gene annotation
						
							alpha/beta-Hydrolases superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d038849_circ_g.1 Zm00001d038849_circ_g.2 Zm00001d038849_circ_g.3 Zm00001d038849_circ_g.5 Zm00001d038849_circ_g.6 Zm00001d038849_circ_g.7 						
					
						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
						Zm00001d038849_T002:4
Zm00001d038849_T003:3
Zm00001d038849_T001:3
Zm00001d038849_T004:3
Zm00001d038849_T005:4

General Information
CircRNA Name	Zm00001d038849_circ_g.4
ID in PlantcircBase	zma_circ_009164
Alias	Zm06circ00101, zma_circ_0002307, GRMZM2G016503_C2
Organism	Zea mays
Position	chr6: 165825412-165831692 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d038849
Parent gene annotation	alpha/beta-Hydrolases superfamily protein
Parent gene strand	+
Alternative splicing	Zm00001d038849_circ_g.1 Zm00001d038849_circ_g.2 Zm00001d038849_circ_g.3 Zm00001d038849_circ_g.5 Zm00001d038849_circ_g.6 Zm00001d038849_circ_g.7
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	Zm00001d038849_T002:4 Zm00001d038849_T003:3 Zm00001d038849_T001:3 Zm00001d038849_T004:3 Zm00001d038849_T005:4

			
						 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  
						
							GGCCGCTTTGCATTAGAGCGAGGTATGGAGGGACGCCTTGGGAAGAATTTCATGAGGAGAATAA
ACGAAGATGGATACATTGATGTGAAGAATAAAAAAGttatttgcgaacaaagagttataattcc
aaacgggcatggggagaagcttgttggtttattacatcgaacaagttcaaagaatcttgtgatc
ctttgtca

									
								

					

						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: 1966
Transcript exons: 165825412-165827090,165827330-165827451,165831528-165831
692
TTATTTGCGAACAAAGAGTTATAATTCCAAACGGGCATGGGGAGAAGCTTGTTGGTTTATTACA
TCGAACAAGTTCAAAGAATCTTGTGATCCTTTGTCATGGATTCCAAGCCACAAAGGCAAGTCCG
TACCATCCATGGATTTTTTTTTTTTTTTTGCATTTAGGTACGTTAGATTGGATATTGAGTTTTG
CCCTATGGTTATAGTCTCCCACCCTACTTATAATATACACTAGGAACAAAATCGTTTAATTGGT
ATCTGATCCTCCTTGGTACTAATTCCCTGTGCATGTACTTATGAGAATGTTGAGTGAAGTGATA
AGTAGGTGTATAGCTATTTAAACATCAAAGATCTGAAGATACTTGTATGTCTCCATATTTGGTC
TGCTAAATTATTCTTTTGAGTGGGGATGGAACATGGTTTTGCTTTGTTTATATTCTTTCATTCG
AGATGTAAAACTTCCAAGATGCTTCAATATCTTGCTCTCTCTCTCTCTCTCTTATCGAACGCAC
AGGAGGACTGCGTATCTTTTATATATCAGAGAGGAAGAAACGGGTCAAGTCTCAAGTACACAAT
CTTTTATATATTAGAGAGGAAGAAACAGGATAAGTCCCAAGTACACAGAGAACCCTGCTACAGG
GCCAAAGCATCCTGATATAAACCTATTAAAGATGAAATATGAAACTCAACCCAACCCTCCTAAG
ATCATCCTCAACCCTTTGCAGGTGACGAGCCCTCACCAAAACCCAGCAGCTGAGCTCTTGAAGA
AAGCTTTGCTGCACCTTCCCAAGGGCCGGTTGATCCCCATCAAACACACACCTGTTGCGCTGAA
GCCATATGCACCAAGCACCCAGGATGATGGCGCTGTTTATGCCTTTCCTTTTATCCTTTTGAAC
AAACTCGATCACTTTCCTCCATTCTGCAAAGGATGCCTCCTCTACCTCTGGAGTCAGTGTTTCA
ATCCAAGGGGACCCAATAGACTAAACCAGAATTGTCGTGCCAAGACACAGGAGGTCAAGATATG
TTTGGACGGTTTCGTCTTGATCACGAAGTGGATAGGTCTCAGGATGGTTTGATCCTTTCTGTTG
CAATCTATCGGCTGTCCAACATTTGTTCCGAATTGCTAACCAACCATAAGAATACTTTCCTTTC
TCCCTTTCTTTTTTGTAGACTTTTGCTTGTGCAAAGTTGTTCCACTTCTGATGCAAATTCAATT
GAGATCTTGCTAGTCTTATTATAAAGAAATGAGCAATAGTAAGACACTTGTACCTGTCACAACA
AGGATATGTACATTCTCAATGTATGGCAACAATAACGAGGACAAAGATCTTGCTAGTCTTATTA
TAAAGAAATGAGCAATAGCAAGACACTTGTACCTGTCACAACAAGGATATGTACATTCTCAATG
TATGGCAACAATAACGAGGACAGAGCCTTTTTAACCCCGAGCAAGTTGGGGTAAGATGGAGAAA
AAATGCACAGAATTCACAAAGTAGAGAAGAAAGGATTAAGGATAAAGAGTTAATATGTTTCTAC
TTGAGTTCTATACTGTTATGGTCACTATTAATGATCTGCACTTTTGAACAAAACTTGTAGGATG
ACAGCATCTTGGTTGACCTTGCTGATGCCATCACAAAGGAAGGAATTAGTGCTTTTCGGTTTGA
TTTTTCTGGAAATGGGGAAAGTGATGGTGAATTCCAGTATGGAAGCTACAGAAAAGAGGCAGCT
GATTTGCGCTCTGTAGTATTACATTTCTCAGAACAGAAATATGACATAATTGCTCTTATCGGGC
ATAGCAAAGGAGGAAATGCTGTTCTTCTTTATGCTTCCAAGTACCATGATGTCCCTGCCATTGT
GAACATTTCTGGCCGCTTTGCATTAGAGCGAGGTATGGAGGGACGCCTTGGGAAGAATTTCATG
AGGAGAATAAACGAAGATGGATACATTGATGTGAAGAATAAAAAAG
						
					

						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	GGCCGCTTTGCATTAGAGCGAGGTATGGAGGGACGCCTTGGGAAGAATTTCATGAGGAGAATAA ACGAAGATGGATACATTGATGTGAAGAATAAAAAAGttatttgcgaacaaagagttataattcc aaacgggcatggggagaagcttgttggtttattacatcgaacaagttcaaagaatcttgtgatc ctttgtca
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: 1966 Transcript exons: 165825412-165827090,165827330-165827451,165831528-165831 692 TTATTTGCGAACAAAGAGTTATAATTCCAAACGGGCATGGGGAGAAGCTTGTTGGTTTATTACA TCGAACAAGTTCAAAGAATCTTGTGATCCTTTGTCATGGATTCCAAGCCACAAAGGCAAGTCCG TACCATCCATGGATTTTTTTTTTTTTTTTGCATTTAGGTACGTTAGATTGGATATTGAGTTTTG CCCTATGGTTATAGTCTCCCACCCTACTTATAATATACACTAGGAACAAAATCGTTTAATTGGT ATCTGATCCTCCTTGGTACTAATTCCCTGTGCATGTACTTATGAGAATGTTGAGTGAAGTGATA AGTAGGTGTATAGCTATTTAAACATCAAAGATCTGAAGATACTTGTATGTCTCCATATTTGGTC TGCTAAATTATTCTTTTGAGTGGGGATGGAACATGGTTTTGCTTTGTTTATATTCTTTCATTCG AGATGTAAAACTTCCAAGATGCTTCAATATCTTGCTCTCTCTCTCTCTCTCTTATCGAACGCAC AGGAGGACTGCGTATCTTTTATATATCAGAGAGGAAGAAACGGGTCAAGTCTCAAGTACACAAT CTTTTATATATTAGAGAGGAAGAAACAGGATAAGTCCCAAGTACACAGAGAACCCTGCTACAGG GCCAAAGCATCCTGATATAAACCTATTAAAGATGAAATATGAAACTCAACCCAACCCTCCTAAG ATCATCCTCAACCCTTTGCAGGTGACGAGCCCTCACCAAAACCCAGCAGCTGAGCTCTTGAAGA AAGCTTTGCTGCACCTTCCCAAGGGCCGGTTGATCCCCATCAAACACACACCTGTTGCGCTGAA GCCATATGCACCAAGCACCCAGGATGATGGCGCTGTTTATGCCTTTCCTTTTATCCTTTTGAAC AAACTCGATCACTTTCCTCCATTCTGCAAAGGATGCCTCCTCTACCTCTGGAGTCAGTGTTTCA ATCCAAGGGGACCCAATAGACTAAACCAGAATTGTCGTGCCAAGACACAGGAGGTCAAGATATG TTTGGACGGTTTCGTCTTGATCACGAAGTGGATAGGTCTCAGGATGGTTTGATCCTTTCTGTTG CAATCTATCGGCTGTCCAACATTTGTTCCGAATTGCTAACCAACCATAAGAATACTTTCCTTTC TCCCTTTCTTTTTTGTAGACTTTTGCTTGTGCAAAGTTGTTCCACTTCTGATGCAAATTCAATT GAGATCTTGCTAGTCTTATTATAAAGAAATGAGCAATAGTAAGACACTTGTACCTGTCACAACA AGGATATGTACATTCTCAATGTATGGCAACAATAACGAGGACAAAGATCTTGCTAGTCTTATTA TAAAGAAATGAGCAATAGCAAGACACTTGTACCTGTCACAACAAGGATATGTACATTCTCAATG TATGGCAACAATAACGAGGACAGAGCCTTTTTAACCCCGAGCAAGTTGGGGTAAGATGGAGAAA AAATGCACAGAATTCACAAAGTAGAGAAGAAAGGATTAAGGATAAAGAGTTAATATGTTTCTAC TTGAGTTCTATACTGTTATGGTCACTATTAATGATCTGCACTTTTGAACAAAACTTGTAGGATG ACAGCATCTTGGTTGACCTTGCTGATGCCATCACAAAGGAAGGAATTAGTGCTTTTCGGTTTGA TTTTTCTGGAAATGGGGAAAGTGATGGTGAATTCCAGTATGGAAGCTACAGAAAAGAGGCAGCT GATTTGCGCTCTGTAGTATTACATTTCTCAGAACAGAAATATGACATAATTGCTCTTATCGGGC ATAGCAAAGGAGGAAATGCTGTTCTTCTTTATGCTTCCAAGTACCATGATGTCCCTGCCATTGT GAACATTTCTGGCCGCTTTGCATTAGAGCGAGGTATGGAGGGACGCCTTGGGAAGAATTTCATG AGGAGAATAAACGAAGATGGATACATTGATGTGAAGAATAAAAAAG
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
						0.127165847

Conservation Information
Conserved circRNAs	NA
PMCS	0.127165847

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							165831618-165825614(+)
165825451-165831607(-)
						
						Potential amino acid sequence
						
							MEGRLGKNFMRRINEDGYIDVKNKKVICEQRVIIPNGHGEKLVGLLHRTSSKNLVILCHGFQAT
KASPYHPWIFFFFLHLGTLDWILSFALWL*(+)
MPVWNYNSLFANNFFILHINVSIFVYSPHEILPKASLHTSL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	165831618-165825614(+) 165825451-165831607(-)
Potential amino acid sequence	MEGRLGKNFMRRINEDGYIDVKNKKVICEQRVIIPNGHGEKLVGLLHRTSSKNLVILCHGFQAT KASPYHPWIFFFFLHLGTLDWILSFALWL(+) MPVWNYNSLFANNFFILHINVSIFVYSPHEILPKASLHTSL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d038849_circ_g.4

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