Plant Circular RNA Database

Detail information of Zm00001d033927_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d033927_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006921
					
						Alias
						Zm01circ00178, zma_circ_0000540
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 278727421-278729166  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.2 						
					
						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_T010:3
Zm00001d033927_T018:1
Zm00001d033927_T019:3
Zm00001d033927_T002:2
Zm00001d033927_T026:2
Zm00001d033927_T005:2
Zm00001d033927_T011:2
Zm00001d033927_T013:3
Zm00001d033927_T001:2
Zm00001d033927_T014:2
Zm00001d033927_T023:2
Zm00001d033927_T007:2
Zm00001d033927_T015:3
Zm00001d033927_T004:2
Zm00001d033927_T021:2
Zm00001d033927_T027:2

General Information
CircRNA Name	Zm00001d033927_circ_g.1
ID in PlantcircBase	zma_circ_006921
Alias	Zm01circ00178, zma_circ_0000540
Organism	Zea mays
Position	chr1: 278727421-278729166 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.2
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_T010:3 Zm00001d033927_T018:1 Zm00001d033927_T019:3 Zm00001d033927_T002:2 Zm00001d033927_T026:2 Zm00001d033927_T005:2 Zm00001d033927_T011:2 Zm00001d033927_T013:3 Zm00001d033927_T001:2 Zm00001d033927_T014:2 Zm00001d033927_T023:2 Zm00001d033927_T007:2 Zm00001d033927_T015:3 Zm00001d033927_T004:2 Zm00001d033927_T021:2 Zm00001d033927_T027:2

			
						 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  
						
							GAAACCATAACTTCAAGTACACTGTAAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGG
ATAACTTAGATCTCATCATTTCTAATCCAAACTTATaatagcttgttttgcaatcaccatgtct
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: 587
Transcript exons: 278727421-278727831,278728991-278729166
AATAGCTTGTTTTGCAATCACCATGTCTGATGCTCCGTGTAGAAAGAGTACATCAACTGCCTCA
CGCAAATTCTTAAAAGGGTATCTGTCAATACTAAAATGATCGGTTGTAATTGTGGAACAGAACA
TAGATGATGATTGTTCATTCTGTAAACATGTGATTGCTATTTCTTCCTCCTTATCCATATAACT
TTGTTCAATCCCAAGGTTTTGTAGGGCCTGCTCAATGAATAGTGTACTCTTACTGGCTTGATTT
ACATCTGACACTTCATCAGAAAATCCAGGCCATTTTGTTTCTGCATATGCTTTCCTTTGAATCA
CATCAGAACTCCATGATGTATGATCAGCGTACCTTGAGCAGATATCCTGAATAAAGCTATGCCT
GATACACCAGATCATAGCCTCCAAATGCTGCTTTGCCTTCAATGTGTTCTCAATGAGTTGATGC
AGGTCATTAACATGCGCTGAAACCGCTTCGGTGAAAGATGAAACCATAACTTCAAGTACACTGT
AAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGGATAACTTAGATCTCATCATTTCTAA
TCCAAACTTAT
						
					

						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
TTTCTAATCCAAACTTAT
						
					

			
		

Sequences
Splice junction sequence	GAAACCATAACTTCAAGTACACTGTAAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGG ATAACTTAGATCTCATCATTTCTAATCCAAACTTATaatagcttgttttgcaatcaccatgtct 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: 587 Transcript exons: 278727421-278727831,278728991-278729166 AATAGCTTGTTTTGCAATCACCATGTCTGATGCTCCGTGTAGAAAGAGTACATCAACTGCCTCA CGCAAATTCTTAAAAGGGTATCTGTCAATACTAAAATGATCGGTTGTAATTGTGGAACAGAACA TAGATGATGATTGTTCATTCTGTAAACATGTGATTGCTATTTCTTCCTCCTTATCCATATAACT TTGTTCAATCCCAAGGTTTTGTAGGGCCTGCTCAATGAATAGTGTACTCTTACTGGCTTGATTT ACATCTGACACTTCATCAGAAAATCCAGGCCATTTTGTTTCTGCATATGCTTTCCTTTGAATCA CATCAGAACTCCATGATGTATGATCAGCGTACCTTGAGCAGATATCCTGAATAAAGCTATGCCT GATACACCAGATCATAGCCTCCAAATGCTGCTTTGCCTTCAATGTGTTCTCAATGAGTTGATGC AGGTCATTAACATGCGCTGAAACCGCTTCGGTGAAAGATGAAACCATAACTTCAAGTACACTGT AAATTCCTGCCAACTGTGTGGCAAACTTTTGCAGTTGGGATAACTTAGATCTCATCATTTCTAA TCCAAACTTAT
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 TTTCTAATCCAAACTTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.199272573

Conservation Information
Conserved circRNAs	NA
PMCS	0.199272573

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							278729151-278729154(-)
						
						Potential amino acid sequence
						
							MMRSKLSQLQKFATQLAGIYSVLEVMVSSFTEAVSAHVNDLHQLIENTLKAKQHLEAMIWCIRH
SFIQDICSRYADHTSWSSDVIQRKAYAETKWPGFSDEVSDVNQASKSTLFIEQALQNLGIEQSY
MDKEEEIAITCLQNEQSSSMFCSTITTDHFSIDRYPFKNLREAVDVLFLHGASDMVIAKQAIIS
LD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	278729151-278729154(-)
Potential amino acid sequence	MMRSKLSQLQKFATQLAGIYSVLEVMVSSFTEAVSAHVNDLHQLIENTLKAKQHLEAMIWCIRH SFIQDICSRYADHTSWSSDVIQRKAYAETKWPGFSDEVSDVNQASKSTLFIEQALQNLGIEQSY MDKEEEIAITCLQNEQSSSMFCSTITTDHFSIDRYPFKNLREAVDVLFLHGASDMVIAKQAIIS LD*(-)
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.1

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