Plant Circular RNA Database

Detail information of Zm00001d011401_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d011401_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009728
					
						Alias
						Zm08circ00057, GRMZM2G149704_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 149531583-149534064  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d011401						
					
						Parent gene annotation
						
							Protein SGT1 homolog A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d011401_circ_g.1 Zm00001d011401_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d011401_T001:6
Zm00001d011401_T004:4
Zm00001d011401_T002:7
Zm00001d011401_T005:6
Zm00001d011401_T003:6

General Information
CircRNA Name	Zm00001d011401_circ_g.3
ID in PlantcircBase	zma_circ_009728
Alias	Zm08circ00057, GRMZM2G149704_C1
Organism	Zea mays
Position	chr8: 149531583-149534064 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d011401
Parent gene annotation	Protein SGT1 homolog A
Parent gene strand	+
Alternative splicing	Zm00001d011401_circ_g.1 Zm00001d011401_circ_g.2
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d011401_T001:6 Zm00001d011401_T004:4 Zm00001d011401_T002:7 Zm00001d011401_T005:6 Zm00001d011401_T003:6

			
						 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  
						
							AAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTGGAA
GACCAAAGGCTATTCCCCAGAAGATAAGCACGCCAGaggctgtggcagatgctaacaaagcaat
tggtcttgatcctacaatgcataaagcctactaccggaaagggttagcgttactcttcattttt
caattaaa

									
								

					

						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: 627
Transcript exons: 149531583-149531652,149531755-149531879,149532138-149532
267,149532499-149532595,149532676-149532741,149533926-14
9534064
AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCG
GAAAGGTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGT
TCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTG
CTGAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTACTGTTGAGGA
CAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAA
TATAGGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTC
CTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATGTTGAGTGTATCCATTGAAGTACCTGG
TGAAGAACCGTACCATTTTCAGCCCCGTCTGTTTTCTAAGATTATCCCTGAGAAATGCAAGTAT
CAAGTTTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCC
TGGATTATAGTGGAAGACCAAAGGCTATTCCCCAGAAGATAAGCACGCCAG
						
					

						Genomic sequence
						
							AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCG
GAAAGGGTTAGCGTTACTCTTCATTTTTCAATTAAAGTTATACATGAACACTTCCATAATCCCC
TCTGCTACATTTTATCTATGTAATAAGTAATTTATTGTTTACAGTGCTGCATGCATTAAGCTTG
AAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAG
GTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGGTGAGCAAAATTAACTTCAGAAG
TTAGTATATAATACAACAGTATGTGTGGGGGTATGTGGTGTGTGTGTGGGTGGGGTGGGGGGGT
GGGTGGGGGGATTGGGTATGCAGTGTGCCACATGCTATTTTCTGACTATTTATGTCCACTTAGC
TGCGTTGCCTGATAAATGTTCGCAGCAGCCTTGTAGACTGGAGAATGATTTTTTTTTTCAGTTT
AGTCGTCCCATACTATCTGCCCTGTCATTTGGTTTGTGTCCAGAGGAATCTAGCCAGGCACCAG
CAAAGAATGTCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGA
TAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGGTAATTAGGGTAAATTCCT
AGAACTCTTTGAACCACCTAGCTCAGATTGAATGCTATGTAATCAAACCACTTTATTTTGTCCC
AGTACAGATCTGTTTACTGATAAGCATATTCTTGTTTGTGGAGCCATACAAGGAGGAAAGAAAA
ATGCTTCTCTCTTACTGAAATTAATGTCAAGCATGAGTTGCTAGCTTTTTGCTAAAGTTTTCTC
CTAAATAATTTGTGATGCAGGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATAT
ATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATGGTGTGTTTTGC
TCATTATTATCATTGTTCTTTCATCTTTGTCTTTTTTACTGTATTCACTAATCTTGTTTCTCAT
TTTAGTTGAGTGTATCCATTGAAGTACCTGGTGAAGAACCGTACCATTTTCAGCCCCGTCTGTT
TTCTAAGGTAACCACTCTCCTTGTTATTTTGATGTTTTTACTAGTACTTGTGTTCTGTTACAAT
GGTGTAAGTTACACTGTGTAACCTATAGTTAGCACCTTGCCTTCAAGACAAGGGTCAGATACAA
AATAGAAATTTATTTATGACTTCTAGCTGCTGAACCTTGACCAAAGGATCAAGAGTGGAAAATT
TAAATAACCTTAGAAACTCGACCTGCCTGAGCATTGTATTAATGGGACCTTACGCAGGTCGAGA
AAACCCTCGAACCTTTGCTCTACCCGTACACAGCGGCACCATAGCTCATGTGAGAACGACTAGG
ACTAGGCCTTAGCCTTGTTCTTGTTGTGGGAGAAACGAGAGGATTTTTTTTAACTTCAGTCTAA
AATTCACTCCCATGGAGAGTCGAACTCGAGTTCTATCAAGGCACCTAACCAACTCAGCTAGAGG
CCCTTTCACAATAACCTTAGAAACAAAATAAAGCCACATATAAGCTTCATTTTACCTTTTTTCA
ACTTTATAAACACAGGCAATGGAGTTTTAAAGCAAGATGTTGTTTTTGTTAATTTAAAAGTATT
TAGCAGGCCATGTGCTCAATTGTGGATGTTTGTGGTTAATATTATACGCCGTGAAGTTCAACAA
CCTGAATTTTTTGTGATTTAGCTAAAATGGTTAGCTAATAACACATAATAGCGTTTCATTCAAA
GATTGGGTTTATACACATCACTGTCTTTTTTTTCTTCATGTATAATGCAGTCAATACATTTTTT
CGATAATTTCATCAATTTTTATAAGCATATGATGACTTAAATTCGTGAACTCCAAAAATTGCTT
CAACGACACTTGTTGACTTGTTTTTGGCTCTTCACTTGGTAAATAGTTTTGAATGCTAGTATAA
AATTTATATATATAGGTTTCAAAATGATCTTTCGGAAGTTCGTGAAAACTAAGGGGCTGTTTGG
TTTGTTGTCTAAGGCGCCACAATGTGGCTAACTTTTCTACCTAAGGTTAGTTCTTCAATTCGAG
CGACTAAGCTTAGGCAGATTGTAGTGCCTTAGGTAGGAAACCAAACAACCCCTAAATTAGTAGT
GCCAATACAATTATGTTTCTGGACTATTTGTAGTTATCTGATTAGCTTACTGAATATCGTTTAT
TTACGTGTTAATAAATGTTTTTATATCGTTGGAAATCAGATTATCCCTGAGAAATGCAAGTATC
AAGTTTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCT
GGATTATAGTGGAAGACCAAAGGCTATTCCCCAGAAGATAAGCACGCCAG
						
					

			
		

Sequences
Splice junction sequence	AAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTGGAA GACCAAAGGCTATTCCCCAGAAGATAAGCACGCCAGaggctgtggcagatgctaacaaagcaat tggtcttgatcctacaatgcataaagcctactaccggaaagggttagcgttactcttcattttt caattaaa
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: 627 Transcript exons: 149531583-149531652,149531755-149531879,149532138-149532 267,149532499-149532595,149532676-149532741,149533926-14 9534064 AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCG GAAAGGTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGT TCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTG CTGAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTACTGTTGAGGA CAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAA TATAGGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTC CTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATGTTGAGTGTATCCATTGAAGTACCTGG TGAAGAACCGTACCATTTTCAGCCCCGTCTGTTTTCTAAGATTATCCCTGAGAAATGCAAGTAT CAAGTTTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCC TGGATTATAGTGGAAGACCAAAGGCTATTCCCCAGAAGATAAGCACGCCAG
Genomic sequence	AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCG GAAAGGGTTAGCGTTACTCTTCATTTTTCAATTAAAGTTATACATGAACACTTCCATAATCCCC TCTGCTACATTTTATCTATGTAATAAGTAATTTATTGTTTACAGTGCTGCATGCATTAAGCTTG AAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAG GTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGGTGAGCAAAATTAACTTCAGAAG TTAGTATATAATACAACAGTATGTGTGGGGGTATGTGGTGTGTGTGTGGGTGGGGTGGGGGGGT GGGTGGGGGGATTGGGTATGCAGTGTGCCACATGCTATTTTCTGACTATTTATGTCCACTTAGC TGCGTTGCCTGATAAATGTTCGCAGCAGCCTTGTAGACTGGAGAATGATTTTTTTTTTCAGTTT AGTCGTCCCATACTATCTGCCCTGTCATTTGGTTTGTGTCCAGAGGAATCTAGCCAGGCACCAG CAAAGAATGTCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGA TAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGGTAATTAGGGTAAATTCCT AGAACTCTTTGAACCACCTAGCTCAGATTGAATGCTATGTAATCAAACCACTTTATTTTGTCCC AGTACAGATCTGTTTACTGATAAGCATATTCTTGTTTGTGGAGCCATACAAGGAGGAAAGAAAA ATGCTTCTCTCTTACTGAAATTAATGTCAAGCATGAGTTGCTAGCTTTTTGCTAAAGTTTTCTC CTAAATAATTTGTGATGCAGGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATAT ATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATGGTGTGTTTTGC TCATTATTATCATTGTTCTTTCATCTTTGTCTTTTTTACTGTATTCACTAATCTTGTTTCTCAT TTTAGTTGAGTGTATCCATTGAAGTACCTGGTGAAGAACCGTACCATTTTCAGCCCCGTCTGTT TTCTAAGGTAACCACTCTCCTTGTTATTTTGATGTTTTTACTAGTACTTGTGTTCTGTTACAAT GGTGTAAGTTACACTGTGTAACCTATAGTTAGCACCTTGCCTTCAAGACAAGGGTCAGATACAA AATAGAAATTTATTTATGACTTCTAGCTGCTGAACCTTGACCAAAGGATCAAGAGTGGAAAATT TAAATAACCTTAGAAACTCGACCTGCCTGAGCATTGTATTAATGGGACCTTACGCAGGTCGAGA AAACCCTCGAACCTTTGCTCTACCCGTACACAGCGGCACCATAGCTCATGTGAGAACGACTAGG ACTAGGCCTTAGCCTTGTTCTTGTTGTGGGAGAAACGAGAGGATTTTTTTTAACTTCAGTCTAA AATTCACTCCCATGGAGAGTCGAACTCGAGTTCTATCAAGGCACCTAACCAACTCAGCTAGAGG CCCTTTCACAATAACCTTAGAAACAAAATAAAGCCACATATAAGCTTCATTTTACCTTTTTTCA ACTTTATAAACACAGGCAATGGAGTTTTAAAGCAAGATGTTGTTTTTGTTAATTTAAAAGTATT TAGCAGGCCATGTGCTCAATTGTGGATGTTTGTGGTTAATATTATACGCCGTGAAGTTCAACAA CCTGAATTTTTTGTGATTTAGCTAAAATGGTTAGCTAATAACACATAATAGCGTTTCATTCAAA GATTGGGTTTATACACATCACTGTCTTTTTTTTCTTCATGTATAATGCAGTCAATACATTTTTT CGATAATTTCATCAATTTTTATAAGCATATGATGACTTAAATTCGTGAACTCCAAAAATTGCTT CAACGACACTTGTTGACTTGTTTTTGGCTCTTCACTTGGTAAATAGTTTTGAATGCTAGTATAA AATTTATATATATAGGTTTCAAAATGATCTTTCGGAAGTTCGTGAAAACTAAGGGGCTGTTTGG TTTGTTGTCTAAGGCGCCACAATGTGGCTAACTTTTCTACCTAAGGTTAGTTCTTCAATTCGAG CGACTAAGCTTAGGCAGATTGTAGTGCCTTAGGTAGGAAACCAAACAACCCCTAAATTAGTAGT GCCAATACAATTATGTTTCTGGACTATTTGTAGTTATCTGATTAGCTTACTGAATATCGTTTAT TTACGTGTTAATAAATGTTTTTATATCGTTGGAAATCAGATTATCCCTGAGAAATGCAAGTATC AAGTTTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCT GGATTATAGTGGAAGACCAAAGGCTATTCCCCAGAAGATAAGCACGCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.135736389

Conservation Information
Conserved circRNAs	NA
PMCS	0.135736389

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							149531628-149534061(+)
149531634-149533958(-)
						
						Potential amino acid sequence
						
							MHKAYYRKGAACIKLEEYQTAKAALELGSSYAPGDSRFTRLLKECDECIAEESSQAPAKNVEAP
VAATVEDKEDVANMDNTPPVVEPPSKPKYRHDYYNSATEVVLTIYAKGVPADSVVIDFGDQMLS
VSIEVPGEEPYHFQPRLFSKIIPEKCKYQVLSTKVEIRLAKAEQVTWTTLDYSGRPKAIPQKIS
TPEAVADANKAIGLDPTMHKAYYRKGAACIKLEEYQTAKAALELGSSYAPGDSRFTRLLKECDE
CIAEESSQAPAKNVEAPVAATVEDKEDVANMDNTPPVVEPPSKPKYRHDYYNSATEVVLTIYAK
GVPADSVVIDFGDQMLSVSIEVPGEEPYHFQPRLFSKIIPEKCKYQVLSTKVEIRLAKAEQVTW
TTLDYSGRPKAIPQKISTPEAVADANKAIGLDPTMHKAYYRKGAACIKLEEYQTAKAALELGSS
YAPGDSRFTRLLKECDECIAEESSQAPAKNVEAPVAATVEDKEDVANMDNTPPVVEPPSKPKYR
HDYYNSATEVVLTIYAKGVPADSVVIDFGDQMLSVSIEVPGEEPYHFQPRLFSKIIPEKCKYQV
LSTKVEIRLAKAEQVTWTTLDYSGRPKAIPQKISTPEAVADANKAIGLDPTMHKAYYRKGAACI
KLEEYQTAKAALELGSSYAPGDSRFTRLLKECDECIAEESSQAPAKNVEAPVAATVEDKEDVAN
MDNTPPVVEPPSKPKYRHDYYNSATEVVLTIYAKGVPADSVVIDFGDQMLSVSIEVPGEEPYHF
QPRLFSKIIPEKCKYQVLSTKVEIRLAKAEQVTWTTLDYSGRPKAIPQKISTP(+)
MHCRIKTNCFVSICHSLWRAYLLGNSLWSSTIIQGCPCHLLSFCKAYFDLGG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	149531628-149534061(+) 149531634-149533958(-)
Potential amino acid sequence	MHKAYYRKGAACIKLEEYQTAKAALELGSSYAPGDSRFTRLLKECDECIAEESSQAPAKNVEAP VAATVEDKEDVANMDNTPPVVEPPSKPKYRHDYYNSATEVVLTIYAKGVPADSVVIDFGDQMLS VSIEVPGEEPYHFQPRLFSKIIPEKCKYQVLSTKVEIRLAKAEQVTWTTLDYSGRPKAIPQKIS TPEAVADANKAIGLDPTMHKAYYRKGAACIKLEEYQTAKAALELGSSYAPGDSRFTRLLKECDE CIAEESSQAPAKNVEAPVAATVEDKEDVANMDNTPPVVEPPSKPKYRHDYYNSATEVVLTIYAK GVPADSVVIDFGDQMLSVSIEVPGEEPYHFQPRLFSKIIPEKCKYQVLSTKVEIRLAKAEQVTW TTLDYSGRPKAIPQKISTPEAVADANKAIGLDPTMHKAYYRKGAACIKLEEYQTAKAALELGSS YAPGDSRFTRLLKECDECIAEESSQAPAKNVEAPVAATVEDKEDVANMDNTPPVVEPPSKPKYR HDYYNSATEVVLTIYAKGVPADSVVIDFGDQMLSVSIEVPGEEPYHFQPRLFSKIIPEKCKYQV LSTKVEIRLAKAEQVTWTTLDYSGRPKAIPQKISTPEAVADANKAIGLDPTMHKAYYRKGAACI KLEEYQTAKAALELGSSYAPGDSRFTRLLKECDECIAEESSQAPAKNVEAPVAATVEDKEDVAN MDNTPPVVEPPSKPKYRHDYYNSATEVVLTIYAKGVPADSVVIDFGDQMLSVSIEVPGEEPYHF QPRLFSKIIPEKCKYQVLSTKVEIRLAKAEQVTWTTLDYSGRPKAIPQKISTP(+) MHCRIKTNCFVSICHSLWRAYLLGNSLWSSTIIQGCPCHLLSFCKAYFDLGG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d011401_circ_g.3

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