Plant Circular RNA Database

Detail information of Zm00001d028238_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d028238_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006438
					
						Alias
						zma_circ_0000534, GRMZM2G407287_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 27589725-27592187  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d028238						
					
						Parent gene annotation
						
							CCAAT-binding factor
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d028238_circ_g.1 Zm00001d028238_circ_g.2 Zm00001d028238_circ_g.4 Zm00001d028238_circ_g.5 						
					
						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
						Zm00001d028238_T007:7
Zm00001d028238_T006:7
Zm00001d028238_T011:7
Zm00001d028238_T005:7
Zm00001d028238_T002:7
Zm00001d028238_T012:7
Zm00001d028238_T004:7
Zm00001d028238_T008:7
Zm00001d028238_T001:7
Zm00001d028238_T003:7

General Information
CircRNA Name	Zm00001d028238_circ_g.3
ID in PlantcircBase	zma_circ_006438
Alias	zma_circ_0000534, GRMZM2G407287_C2
Organism	Zea mays
Position	chr1: 27589725-27592187 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d028238
Parent gene annotation	CCAAT-binding factor
Parent gene strand	-
Alternative splicing	Zm00001d028238_circ_g.1 Zm00001d028238_circ_g.2 Zm00001d028238_circ_g.4 Zm00001d028238_circ_g.5
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	Zm00001d028238_T007:7 Zm00001d028238_T006:7 Zm00001d028238_T011:7 Zm00001d028238_T005:7 Zm00001d028238_T002:7 Zm00001d028238_T012:7 Zm00001d028238_T004:7 Zm00001d028238_T008:7 Zm00001d028238_T001:7 Zm00001d028238_T003:7

			
						 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  
						
							AAGAGAGATATGATAGAGTTGCATAACTCACTTTGTTAACAAGAGCTGTGAGCAAACGACGTTC
CTGTTCTGACTTACTTTTCAAAAGCATGAAAACTGTctttgaggaagtaacagcagaaggactc
aagagttttgagtataatgcacggtacaaacgatcacttgctatattattctttatagatattt
ggaacaaa

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTTTGAGGAAGTAACAGCAGAAGGACTCAAGAGTTTTGAGTATAATGCACGGTACAAACGATCA
CTTGCTATATTATTCTTTATAGATATTTGGAACAAAAGCATCAATGCCTGAACACCAACATTGA
AATTTTCAGCGTGAACCTACACAAAGCCAAAATGATAAGTTTCGGAAAGCTGTCCAAAAAATAC
AAACTTAGCAAGGTACTTCATAACATTATCTAAAAAAATCACCAATCTGAAAAGAATAGGTGTC
TGCACTTCCACAATATCGTCAACTTCTGAGCTTGCAACATATGGTAATGCCCTATTTACACCCT
GCAAGTGATGAGAGAATTAATAAATGAACTGCAGAAACAAACCAAACACCAGTTTGAACAAAAA
TAAGCAAAGACAAGGTGTACAAGCAAGGTGCTGATGGGACATAAATAAGAAACAAATCCAGGGA
TCTGCAGAGTGGTTACATACAGTTAAAAGCGCAGAAAGGATTCTGGAGTCCAGCTCCAAATCTG
ATCCTGCTGTTGAACCCACTTCATTGTTTCCCTTGGATCTGGAGTCCATCTTGTTATTTCCTCC
CTCTATTTTTCCTACCTTTTTCTTGCTGTCCTTGCTATATGTATCTCCTTTGGTATCACCAGAG
CTCATTAGTACCTAACATAATTGTGCAACAGAACAAAAAAAGTTGAGTTATCGTTTCTATCAAA
CCTTGGAAGTAGTACAGCAAAAGATGTCAAAATGAAACAAACCAAATGGCAAAAAAGAAATGAA
GTGCAGTGTGTGTTCCAGAAAAAACATCTTAACAAAAAATGGGAAAATATCTATGGCACACTGA
CAGAGTGGTTTTAGCTCTTGGACACTAGAAATGGCACTATTTATCAGGAACACACAGGGAAACG
TTGATTATCATCAACCGCACACCAGAGATTAAAAATTTTCATTTTAGGAAAAATATTGTACACA
AAGTCTTGCCGGAAATGGAGTGTGCCCAGATAATGAACAATGTTTCTTAATGTTTTCCTGATAA
TACCATTTCCAATGTCTAAGAGCTAAAGACACTCTTTGTCAGTGTGACACAGATAATTTCCCCT
AGAGAAATAGTACATGGCAAATACATGTGACCAAAAAGCAATAAAATCAAAAGATGACAAGATC
AAGCCCAAATTACATATGACGGCTGGACATCATAATTACTAGTGAAACACACCAAATTGATGGC
TGGCAATGTTCCCAGCACCAAAACGAAGCACAACCACATGCTCAAAGATTACAATATAGTATTG
TCACAACCGCCACTGATAGAGGGAGAATAGTTGATACATCAGTGAACTGGAGATAGGGTTACAC
ATATATGTTGGTAGCCTAGGGTTACAGCCCTAACAGGCCTCTCGAGTTGGGCTCACAACCCACC
ACACCTGAGTGACGCTTTTTACCAGTGTGTTCCCCTCCATCGAGGATCATGCCCATCTCTGTAC
AAACTTGAAGTGACACAATAGCACCTTCCATGTGCCACAAAGCCCCATTGACTAAACCACAAAA
TGCTCCTAAAGGTAATTCATACAAGAGATGCCCATGTGATGGGTAATAGAACTTAAAATAATGG
AGAACAAAGGCTAACAAATTTTTCACAGTAAGCATAAATAATTATACAAAGTTGAAACACATCC
AAACCTTGAAAAGTGCAATGTAGACATCCACCAACCGTTTTGCAATTTTAGGCCCATCTCCCTT
GTTTGTAAGAAGAATCTGGCTCAAGAAATTGACCTGTAAAGATGATACCAATTAAAGGCTAAAA
ATCATGATGTAAATCATATTTCATATAATCACATGGCAGTTTTGGTACATAATTCAGTAAAAAT
ACAATATTAATGAAGATGCTATCTACGAAAATTCTAAAACAATACTAGCATAGAAAGTGTTATT
AATAATTACATACAGCCTGGTACTTGGCCCTAAGTCCAACATGTGGTCTGAAGAGAAAAGAATC
CACCTCATCTATCACCACCATCTGCAAATTGAAACATTTAATGAGCTCAAGGGATATGAATTTA
TGTGCAATTTTGCATGCAAAATATTAAATAATTAGATTAAAACAAACACTCTGTGTCATACCAG
AATCTCACAGCATTTACCTTCATATTAGGGTGAGCAGCCAAGAGACATGTTAACAGATATGCAG
CACTTGATGCTGCTCTCCTTTCAGGATCACCAAGCTGCAATACATATTTTTTAACAAAATATGA
GCAAAAATGCAACTCATAGTAAGGCTTTAGGCAATGTTGCTCATAAATAATATAATGTATTCTT
ATTTCTCGTTGTTTTCAATCTAGATCATAACAGTTCTTCATATATTGAATTAAAAAAGGAAGAG
AGATATGATAGAGTTGCATAACTCACTTTGTTAACAAGAGCTGTGAGCAAACGACGTTCCTGTT
CTGACTTACTTTTCAAAAGCATGAAAACTGT
						
					

			
		

Sequences
Splice junction sequence	AAGAGAGATATGATAGAGTTGCATAACTCACTTTGTTAACAAGAGCTGTGAGCAAACGACGTTC CTGTTCTGACTTACTTTTCAAAAGCATGAAAACTGTctttgaggaagtaacagcagaaggactc aagagttttgagtataatgcacggtacaaacgatcacttgctatattattctttatagatattt ggaacaaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTTTGAGGAAGTAACAGCAGAAGGACTCAAGAGTTTTGAGTATAATGCACGGTACAAACGATCA CTTGCTATATTATTCTTTATAGATATTTGGAACAAAAGCATCAATGCCTGAACACCAACATTGA AATTTTCAGCGTGAACCTACACAAAGCCAAAATGATAAGTTTCGGAAAGCTGTCCAAAAAATAC AAACTTAGCAAGGTACTTCATAACATTATCTAAAAAAATCACCAATCTGAAAAGAATAGGTGTC TGCACTTCCACAATATCGTCAACTTCTGAGCTTGCAACATATGGTAATGCCCTATTTACACCCT GCAAGTGATGAGAGAATTAATAAATGAACTGCAGAAACAAACCAAACACCAGTTTGAACAAAAA TAAGCAAAGACAAGGTGTACAAGCAAGGTGCTGATGGGACATAAATAAGAAACAAATCCAGGGA TCTGCAGAGTGGTTACATACAGTTAAAAGCGCAGAAAGGATTCTGGAGTCCAGCTCCAAATCTG ATCCTGCTGTTGAACCCACTTCATTGTTTCCCTTGGATCTGGAGTCCATCTTGTTATTTCCTCC CTCTATTTTTCCTACCTTTTTCTTGCTGTCCTTGCTATATGTATCTCCTTTGGTATCACCAGAG CTCATTAGTACCTAACATAATTGTGCAACAGAACAAAAAAAGTTGAGTTATCGTTTCTATCAAA CCTTGGAAGTAGTACAGCAAAAGATGTCAAAATGAAACAAACCAAATGGCAAAAAAGAAATGAA GTGCAGTGTGTGTTCCAGAAAAAACATCTTAACAAAAAATGGGAAAATATCTATGGCACACTGA CAGAGTGGTTTTAGCTCTTGGACACTAGAAATGGCACTATTTATCAGGAACACACAGGGAAACG TTGATTATCATCAACCGCACACCAGAGATTAAAAATTTTCATTTTAGGAAAAATATTGTACACA AAGTCTTGCCGGAAATGGAGTGTGCCCAGATAATGAACAATGTTTCTTAATGTTTTCCTGATAA TACCATTTCCAATGTCTAAGAGCTAAAGACACTCTTTGTCAGTGTGACACAGATAATTTCCCCT AGAGAAATAGTACATGGCAAATACATGTGACCAAAAAGCAATAAAATCAAAAGATGACAAGATC AAGCCCAAATTACATATGACGGCTGGACATCATAATTACTAGTGAAACACACCAAATTGATGGC TGGCAATGTTCCCAGCACCAAAACGAAGCACAACCACATGCTCAAAGATTACAATATAGTATTG TCACAACCGCCACTGATAGAGGGAGAATAGTTGATACATCAGTGAACTGGAGATAGGGTTACAC ATATATGTTGGTAGCCTAGGGTTACAGCCCTAACAGGCCTCTCGAGTTGGGCTCACAACCCACC ACACCTGAGTGACGCTTTTTACCAGTGTGTTCCCCTCCATCGAGGATCATGCCCATCTCTGTAC AAACTTGAAGTGACACAATAGCACCTTCCATGTGCCACAAAGCCCCATTGACTAAACCACAAAA TGCTCCTAAAGGTAATTCATACAAGAGATGCCCATGTGATGGGTAATAGAACTTAAAATAATGG AGAACAAAGGCTAACAAATTTTTCACAGTAAGCATAAATAATTATACAAAGTTGAAACACATCC AAACCTTGAAAAGTGCAATGTAGACATCCACCAACCGTTTTGCAATTTTAGGCCCATCTCCCTT GTTTGTAAGAAGAATCTGGCTCAAGAAATTGACCTGTAAAGATGATACCAATTAAAGGCTAAAA ATCATGATGTAAATCATATTTCATATAATCACATGGCAGTTTTGGTACATAATTCAGTAAAAAT ACAATATTAATGAAGATGCTATCTACGAAAATTCTAAAACAATACTAGCATAGAAAGTGTTATT AATAATTACATACAGCCTGGTACTTGGCCCTAAGTCCAACATGTGGTCTGAAGAGAAAAGAATC CACCTCATCTATCACCACCATCTGCAAATTGAAACATTTAATGAGCTCAAGGGATATGAATTTA TGTGCAATTTTGCATGCAAAATATTAAATAATTAGATTAAAACAAACACTCTGTGTCATACCAG AATCTCACAGCATTTACCTTCATATTAGGGTGAGCAGCCAAGAGACATGTTAACAGATATGCAG CACTTGATGCTGCTCTCCTTTCAGGATCACCAAGCTGCAATACATATTTTTTAACAAAATATGA GCAAAAATGCAACTCATAGTAAGGCTTTAGGCAATGTTGCTCATAAATAATATAATGTATTCTT ATTTCTCGTTGTTTTCAATCTAGATCATAACAGTTCTTCATATATTGAATTAAAAAAGGAAGAG AGATATGATAGAGTTGCATAACTCACTTTGTTAACAAGAGCTGTGAGCAAACGACGTTCCTGTT CTGACTTACTTTTCAAAAGCATGAAAACTGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.077856977

Conservation Information
Conserved circRNAs	NA
PMCS	0.077856977

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27592178-27589836(+)
27592180-27589727(-)
						
						Potential amino acid sequence
						
							MKTVFEEVTAEGLKSFEYNARYKRSLAILFFIDIWNKSINA*(+)
MLLKSKSEQERRLLTALVNKLGDPERRAASSAAYLLTCLLAAHPNMKMVVIDEVDSFLFRPHVG
LRAKYQAVNFLSQILLTNKGDGPKIAKRLVDVYIALFKVLMSSGDTKGDTYSKDSKKKVGKIEG
GNNKMDSRSKGNNEVGSTAGSDLELDSRILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLV
HAENFNVGVQALMLLFQISIKNNIASDRLYRALYSKLLSPSAVTSSKTVFMLLKSKSEQERRLL
TALVNKLGDPERRAASSAAYLLTCLLAAHPNMKMVVIDEVDSFLFRPHVGLRAKYQAVNFLSQI
LLTNKGDGPKIAKRLVDVYIALFKVLMSSGDTKGDTYSKDSKKKVGKIEGGNNKMDSRSKGNNE
VGSTAGSDLELDSRILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHAENFNVGVQALML
LFQISIKNNIASDRLYRALYSKLLSPSAVTSSKTVFMLLKSKSEQERRLLTALVNKLGDPERRA
ASSAAYLLTCLLAAHPNMKMVVIDEVDSFLFRPHVGLRAKYQAVNFLSQILLTNKGDGPKIAKR
LVDVYIALFKVLMSSGDTKGDTYSKDSKKKVGKIEGGNNKMDSRSKGNNEVGSTAGSDLELDSR
ILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHAENFNVGVQALMLLFQISIKNNIASDR
LYRALYSKLLSPSAVTSSKTVFMLLKSKSEQERRLLTALVNKLGDPERRAASSAAYLLTCLLAA
HPNMKMVVIDEVDSFLFRPHVGLRAKYQAVNFLSQILLTNKGDGPKIAKRLVDVYIALFKVLMS
SGDTKGDTYSKDSKKKVGKIEGGNNKMDSRSKGNNEVGSTAGSDLELDSRILSALLTGVNRALP
YVASSEVDDIVEVQTPILFRLVHAENFNVGVQALMLLFQISIKNNIASDRLYRALYSKLLSPSA
VTSSK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	27592178-27589836(+) 27592180-27589727(-)
Potential amino acid sequence	MKTVFEEVTAEGLKSFEYNARYKRSLAILFFIDIWNKSINA*(+) MLLKSKSEQERRLLTALVNKLGDPERRAASSAAYLLTCLLAAHPNMKMVVIDEVDSFLFRPHVG LRAKYQAVNFLSQILLTNKGDGPKIAKRLVDVYIALFKVLMSSGDTKGDTYSKDSKKKVGKIEG GNNKMDSRSKGNNEVGSTAGSDLELDSRILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLV HAENFNVGVQALMLLFQISIKNNIASDRLYRALYSKLLSPSAVTSSKTVFMLLKSKSEQERRLL TALVNKLGDPERRAASSAAYLLTCLLAAHPNMKMVVIDEVDSFLFRPHVGLRAKYQAVNFLSQI LLTNKGDGPKIAKRLVDVYIALFKVLMSSGDTKGDTYSKDSKKKVGKIEGGNNKMDSRSKGNNE VGSTAGSDLELDSRILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHAENFNVGVQALML LFQISIKNNIASDRLYRALYSKLLSPSAVTSSKTVFMLLKSKSEQERRLLTALVNKLGDPERRA ASSAAYLLTCLLAAHPNMKMVVIDEVDSFLFRPHVGLRAKYQAVNFLSQILLTNKGDGPKIAKR LVDVYIALFKVLMSSGDTKGDTYSKDSKKKVGKIEGGNNKMDSRSKGNNEVGSTAGSDLELDSR ILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHAENFNVGVQALMLLFQISIKNNIASDR LYRALYSKLLSPSAVTSSKTVFMLLKSKSEQERRLLTALVNKLGDPERRAASSAAYLLTCLLAA HPNMKMVVIDEVDSFLFRPHVGLRAKYQAVNFLSQILLTNKGDGPKIAKRLVDVYIALFKVLMS SGDTKGDTYSKDSKKKVGKIEGGNNKMDSRSKGNNEVGSTAGSDLELDSRILSALLTGVNRALP YVASSEVDDIVEVQTPILFRLVHAENFNVGVQALMLLFQISIKNNIASDRLYRALYSKLLSPSA VTSSK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d028238_circ_g.3

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