Plant Circular RNA Database

Detail information of Zm00001d033927_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d033927_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006922
					
						Alias
						Zm01circ00177, zma_circ_0000539
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 278727421-278729521  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d033927						
					
						Parent gene annotation
						
							 low phytic acid3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d033927_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  
						
							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
						Zm00001d033927_T015:4
Zm00001d033927_T026:3
Zm00001d033927_T010:3
Zm00001d033927_T004:3
Zm00001d033927_T013:4
Zm00001d033927_T002:3
Zm00001d033927_T019:4
Zm00001d033927_T014:3
Zm00001d033927_T018:1
Zm00001d033927_T011:3
Zm00001d033927_T001:3
Zm00001d033927_T021:3
Zm00001d033927_T027:3
Zm00001d033927_T023:3
Zm00001d033927_T007:3
Zm00001d033927_T005:3

General Information
CircRNA Name	Zm00001d033927_circ_g.2
ID in PlantcircBase	zma_circ_006922
Alias	Zm01circ00177, zma_circ_0000539
Organism	Zea mays
Position	chr1: 278727421-278729521 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d033927
Parent gene annotation	low phytic acid3
Parent gene strand	-
Alternative splicing	Zm00001d033927_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	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	Zm00001d033927_T015:4 Zm00001d033927_T026:3 Zm00001d033927_T010:3 Zm00001d033927_T004:3 Zm00001d033927_T013:4 Zm00001d033927_T002:3 Zm00001d033927_T019:4 Zm00001d033927_T014:3 Zm00001d033927_T018:1 Zm00001d033927_T011:3 Zm00001d033927_T001:3 Zm00001d033927_T021:3 Zm00001d033927_T027:3 Zm00001d033927_T023:3 Zm00001d033927_T007:3 Zm00001d033927_T005:3

			
						 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  
						
							GCCTTCTTGCACCAGTCCTTGATGACCACCTCATCCAAAAGAAAAGCCAGAAGTGGATCACTTG
ACACAGCATTCTCATCCAAACAAACATCTGTGATATaatagcttgttttgcaatcaccatgtct
gatgctccgtgtagaaagagtacatcaactgcctcacgcaaattcttaaaagggtatctgtcaa
tactaaaa

									
								

					

						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: 818
Transcript exons: 278727421-278727831,278728991-278729215,278729340-278729
521
AATAGCTTGTTTTGCAATCACCATGTCTGATGCTCCGTGTAGAAAGAGTACATCAACTGCCTCA
CGCAAATTCTTAAAAGGGTATCTGTCAATACTAAAATGATCGGTTGTAATTGTGGAACAGAACA
TAGATGATGATTGTTCATTCTGTAAACATGTGATTGCTATTTCTTCCTCCTTATCCATATAACT
TTGTTCAATCCCAAGGTTTTGTAGGGCCTGCTCAATGAATAGTGTACTCTTACTGGCTTGATTT
ACATCTGACACTTCATCAGAAAATCCAGGCCATTTTGTTTCTGCATATGCTTTCCTTTGAATCA
CATCAGAACTCCATGATGTATGATCAGCGTACCTTGAGCAGATATCCTGAATAAAGCTATGCCT
GATACACCAGATCATAGCCTCCAAATGCTGCTTTGCCTTCAATGTGTTCTCAATGAGTTGATGC
AGGTCATTAACATGCGCTGAAACCGCTTCGGTGAAAGATGAAACCATAACTTCAAGTACACTGT
AAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGGATAACTTAGATCTCATCATTTCTAA
TCCAAACTTATCTAAGGCGTCGTTAAGGTTAGTTACTTAAGACTGTCTCCAGCGGGTCGCTAAA
AATGTATATAAACCACGTAACTGAATCTAGAGTTTTTGGATACAGATCACGCCAATCTCAGTAA
TGAGCGCATTAACAGCCTTCTTGCACCAGTCCTTGATGACCACCTCATCCAAAAGAAAAGCCAG
AAGTGGATCACTTGACACAGCATTCTCATCCAAACAAACATCTGTGATAT
						
					

						Genomic sequence
						
							AATAGCTTGTTTTGCAATCACCATGTCTGATGCTCCGTGTAGAAAGAGTACATCAACTGCCTCA
CGCAAATTCTTAAAAGGGTATCTGTCAATACTAAAATGATCGGTTGTAATTGTGGAACAGAACA
TAGATGATGATTGTTCATTCTGTAAACATGTGATTGCTATTTCTTCCTCCTTATCCATATAACT
TTGTTCAATCCCAAGGTTTTGTAGGGCCTGCTCAATGAATAGTGTACTCTTACTGGCTTGATTT
ACATCTGACACTTCATCAGAAAATCCAGGCCATTTTGTTTCTGCATATGCTTTCCTTTGAATCA
CATCAGAACTCCATGATGTATGATCAGCGTACCTTGAGCAGATATCCTGAATAAAGCTATGCCT
GATACACCAGATCATAGCCTCCAAATGCTGTAGAAAAAGGTACAATTAATACTTTACCAAGATA
ATGATTATTCTGAAAGAAGTGTATCCTTTCCACTGTTCGCCTAAACAGCCATTTAGCCCATTTA
AACACCGTGTAAACACTACCCGGTGGTGCACTGTTTCCATTTAATCATCCATTTACCCCGTTTA
GTTGGCCGAAACCCGTTCAATGGATCGTTTAGCCCTAATAACCACTAAATAGAAGGTGACCGAC
TGTTTACCACACTGATCCTTTCAAGCATTTCAGTGATGTACAAGTGGATATACATGGCCCTAAG
ATACAGATTGTTTAAAAGATTGGAGTTTATTGAGGCGTTATGCACAGCATTAGTGTAGTGATAG
GGGGGATTGGGAATCATAGGACATCGCCAATTGGAGTGAGTGACTCCTTAAATTAAAGATTATA
TATCAACTAAAGCAATGCTACAAAAAACTAAAAGGATTGTTGATGTACATGCATCTTTAACAGA
TGAGCTAGAAGCTTTCATAACACATACTAGGAAAAACCTATGGTACAGAATTGTTCTATGATCT
AATGCCATAACACTACATCACTAGCAACCATCAAAGTGTAAGAAAGCACAAGGTTTCATAAACA
AGAAAAGTTCTAGAGATATACTCCATCTGATTGTACATATAGTCGTCTCAGGATTCTTGGCGGT
CTAATTTTTTTCTAGTATGATGCATAAAGAATTAGGTAGATTGAGAACATAAGGTCGATGTTTG
TAGATTTAACATGAAGCTAGTTTCATAATACACAACCCTCTTATTTTAAATATATGACATTTTT
ATGAAAATTGCTAGTCAAAGCTCAACATAGTAGGTTGTATCAATGTACAAATGACTTATATTCA
CAGTTGGAGGGAGTACTTATTAGTTATTACAAAAATGAACCAGAAACTATCTTGAGCAGTTATA
TCAATACTTGTCCAGGATCAGGATGAGACCAAGGCAAAAAGGAGATAAAAAGGTTTTATTCCAA
TGTGCGCACAAAATTTTATAATGAAAAAGGAGCCCCGTGGGACACTCATCTTATAGAAATTCCA
GCAATGCATAGACAAATTGAAGTACCTAGACCAGTTCAGTGTTAGTTCTTAGTAGTGATCGAAA
ATCCTTAGCAATAGAGGGGTTAAGAAAGAAAGACCTGCTTTGCCTTCAATGTGTTCTCAATGAG
TTGATGCAGGTCATTAACATGCGCTGAAACCGCTTCGGTGAAAGATGAAACCATAACTTCAAGT
ACACTGTAAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGGATAACTTAGATCTCATCA
TTTCTAATCCAAACTTATCTAAGGCGTCGTTAAGGTTAGTTACTTAAGACTGTCTCCAGCGGGT
CGCCTAAAATAGGGGACGTGGAACTGTAGATGACACTGTTTGCAAAGTGGAGTTTGAAATAGGG
GATGGAATAGGAGATCTGTCCCTCAACATGTGTGGCCTTGAACACATGAAAAGCGAAACATAAT
AAAAATGTATATAAACCACGTAACTGAATCTAGAGTTTTTGGATACAGATCACGCCAATCTCAG
TAATGAGCGCATTAACAGCCTTCTTGCACCAGTCCTTGATGACCACCTCATCCAAAAGAAAAGC
CAGAAGTGGATCACTTGACACAGCATTCTCATCCAAACAAACATCTGTGATAT
						
					

			
		

Sequences
Splice junction sequence	GCCTTCTTGCACCAGTCCTTGATGACCACCTCATCCAAAAGAAAAGCCAGAAGTGGATCACTTG ACACAGCATTCTCATCCAAACAAACATCTGTGATATaatagcttgttttgcaatcaccatgtct gatgctccgtgtagaaagagtacatcaactgcctcacgcaaattcttaaaagggtatctgtcaa tactaaaa
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: 818 Transcript exons: 278727421-278727831,278728991-278729215,278729340-278729 521 AATAGCTTGTTTTGCAATCACCATGTCTGATGCTCCGTGTAGAAAGAGTACATCAACTGCCTCA CGCAAATTCTTAAAAGGGTATCTGTCAATACTAAAATGATCGGTTGTAATTGTGGAACAGAACA TAGATGATGATTGTTCATTCTGTAAACATGTGATTGCTATTTCTTCCTCCTTATCCATATAACT TTGTTCAATCCCAAGGTTTTGTAGGGCCTGCTCAATGAATAGTGTACTCTTACTGGCTTGATTT ACATCTGACACTTCATCAGAAAATCCAGGCCATTTTGTTTCTGCATATGCTTTCCTTTGAATCA CATCAGAACTCCATGATGTATGATCAGCGTACCTTGAGCAGATATCCTGAATAAAGCTATGCCT GATACACCAGATCATAGCCTCCAAATGCTGCTTTGCCTTCAATGTGTTCTCAATGAGTTGATGC AGGTCATTAACATGCGCTGAAACCGCTTCGGTGAAAGATGAAACCATAACTTCAAGTACACTGT AAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGGATAACTTAGATCTCATCATTTCTAA TCCAAACTTATCTAAGGCGTCGTTAAGGTTAGTTACTTAAGACTGTCTCCAGCGGGTCGCTAAA AATGTATATAAACCACGTAACTGAATCTAGAGTTTTTGGATACAGATCACGCCAATCTCAGTAA TGAGCGCATTAACAGCCTTCTTGCACCAGTCCTTGATGACCACCTCATCCAAAAGAAAAGCCAG AAGTGGATCACTTGACACAGCATTCTCATCCAAACAAACATCTGTGATAT
Genomic sequence	AATAGCTTGTTTTGCAATCACCATGTCTGATGCTCCGTGTAGAAAGAGTACATCAACTGCCTCA CGCAAATTCTTAAAAGGGTATCTGTCAATACTAAAATGATCGGTTGTAATTGTGGAACAGAACA TAGATGATGATTGTTCATTCTGTAAACATGTGATTGCTATTTCTTCCTCCTTATCCATATAACT TTGTTCAATCCCAAGGTTTTGTAGGGCCTGCTCAATGAATAGTGTACTCTTACTGGCTTGATTT ACATCTGACACTTCATCAGAAAATCCAGGCCATTTTGTTTCTGCATATGCTTTCCTTTGAATCA CATCAGAACTCCATGATGTATGATCAGCGTACCTTGAGCAGATATCCTGAATAAAGCTATGCCT GATACACCAGATCATAGCCTCCAAATGCTGTAGAAAAAGGTACAATTAATACTTTACCAAGATA ATGATTATTCTGAAAGAAGTGTATCCTTTCCACTGTTCGCCTAAACAGCCATTTAGCCCATTTA AACACCGTGTAAACACTACCCGGTGGTGCACTGTTTCCATTTAATCATCCATTTACCCCGTTTA GTTGGCCGAAACCCGTTCAATGGATCGTTTAGCCCTAATAACCACTAAATAGAAGGTGACCGAC TGTTTACCACACTGATCCTTTCAAGCATTTCAGTGATGTACAAGTGGATATACATGGCCCTAAG ATACAGATTGTTTAAAAGATTGGAGTTTATTGAGGCGTTATGCACAGCATTAGTGTAGTGATAG GGGGGATTGGGAATCATAGGACATCGCCAATTGGAGTGAGTGACTCCTTAAATTAAAGATTATA TATCAACTAAAGCAATGCTACAAAAAACTAAAAGGATTGTTGATGTACATGCATCTTTAACAGA TGAGCTAGAAGCTTTCATAACACATACTAGGAAAAACCTATGGTACAGAATTGTTCTATGATCT AATGCCATAACACTACATCACTAGCAACCATCAAAGTGTAAGAAAGCACAAGGTTTCATAAACA AGAAAAGTTCTAGAGATATACTCCATCTGATTGTACATATAGTCGTCTCAGGATTCTTGGCGGT CTAATTTTTTTCTAGTATGATGCATAAAGAATTAGGTAGATTGAGAACATAAGGTCGATGTTTG TAGATTTAACATGAAGCTAGTTTCATAATACACAACCCTCTTATTTTAAATATATGACATTTTT ATGAAAATTGCTAGTCAAAGCTCAACATAGTAGGTTGTATCAATGTACAAATGACTTATATTCA CAGTTGGAGGGAGTACTTATTAGTTATTACAAAAATGAACCAGAAACTATCTTGAGCAGTTATA TCAATACTTGTCCAGGATCAGGATGAGACCAAGGCAAAAAGGAGATAAAAAGGTTTTATTCCAA TGTGCGCACAAAATTTTATAATGAAAAAGGAGCCCCGTGGGACACTCATCTTATAGAAATTCCA GCAATGCATAGACAAATTGAAGTACCTAGACCAGTTCAGTGTTAGTTCTTAGTAGTGATCGAAA ATCCTTAGCAATAGAGGGGTTAAGAAAGAAAGACCTGCTTTGCCTTCAATGTGTTCTCAATGAG TTGATGCAGGTCATTAACATGCGCTGAAACCGCTTCGGTGAAAGATGAAACCATAACTTCAAGT ACACTGTAAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGGATAACTTAGATCTCATCA TTTCTAATCCAAACTTATCTAAGGCGTCGTTAAGGTTAGTTACTTAAGACTGTCTCCAGCGGGT CGCCTAAAATAGGGGACGTGGAACTGTAGATGACACTGTTTGCAAAGTGGAGTTTGAAATAGGG GATGGAATAGGAGATCTGTCCCTCAACATGTGTGGCCTTGAACACATGAAAAGCGAAACATAAT AAAAATGTATATAAACCACGTAACTGAATCTAGAGTTTTTGGATACAGATCACGCCAATCTCAG TAATGAGCGCATTAACAGCCTTCTTGCACCAGTCCTTGATGACCACCTCATCCAAAAGAAAAGC CAGAAGTGGATCACTTGACACAGCATTCTCATCCAAACAAACATCTGTGATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							tae_circ_000060 osa_circ_021746* osi_circ_005087* osi_circ_013609 
						
						PMCS
						0.223861307

Conservation Information
Conserved circRNAs	tae_circ_000060 osa_circ_021746* osi_circ_005087* osi_circ_013609
PMCS	0.223861307

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							278729151-278729392(-)
						
						Potential amino acid sequence
						
							MMRSKLSQLQKFATQLAGIYSVLEVMVSSFTEAVSAHVNDLHQLIENTLKAKQHLEAMIWCIRH
SFIQDICSRYADHTSWSSDVIQRKAYAETKWPGFSDEVSDVNQASKSTLFIEQALQNLGIEQSY
MDKEEEIAITCLQNEQSSSMFCSTITTDHFSIDRYPFKNLREAVDVLFLHGASDMVIAKQAIIS
QMFVWMRMLCQVIHFWLFFWMRWSSRTGARRLLMRSLLRLA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	278729151-278729392(-)
Potential amino acid sequence	MMRSKLSQLQKFATQLAGIYSVLEVMVSSFTEAVSAHVNDLHQLIENTLKAKQHLEAMIWCIRH SFIQDICSRYADHTSWSSDVIQRKAYAETKWPGFSDEVSDVNQASKSTLFIEQALQNLGIEQSY MDKEEEIAITCLQNEQSSSMFCSTITTDHFSIDRYPFKNLREAVDVLFLHGASDMVIAKQAIIS QMFVWMRMLCQVIHFWLFFWMRWSSRTGARRLLMRSLLRLA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d033927_circ_g.2

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