Plant Circular RNA Database

Detail information of Zm00001d053022_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d053022_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008240
					
						Alias
						Zm04circ00088, GRMZM2G317652_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 209728828-209730723  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d053022						
					
						Parent gene annotation
						
							Transcription factor GTE12
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d053022_circ_g.3 						
					
						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  
						
							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
						Zm00001d053022_T007:7
Zm00001d053022_T003:6
Zm00001d053022_T005:7
Zm00001d053022_T006:7
Zm00001d053022_T001:7
Zm00001d053022_T002:7
Zm00001d053022_T004:7

General Information
CircRNA Name	Zm00001d053022_circ_g.4
ID in PlantcircBase	zma_circ_008240
Alias	Zm04circ00088, GRMZM2G317652_C1
Organism	Zea mays
Position	chr4: 209728828-209730723 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d053022
Parent gene annotation	Transcription factor GTE12
Parent gene strand	-
Alternative splicing	Zm00001d053022_circ_g.3
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	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	Zm00001d053022_T007:7 Zm00001d053022_T003:6 Zm00001d053022_T005:7 Zm00001d053022_T006:7 Zm00001d053022_T001:7 Zm00001d053022_T002:7 Zm00001d053022_T004:7

			
						 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  
						
							AGTTTGATTTCTTGTCTAACAACGGAGCAATAACTCAAGACTTGGTAAATGGTGAAGCAGTGTC
CAAGACCCACAGAGCACGGGTCTTCCTCAGCCAAGCcttcttgctgcctcttttccagcctctc
cttttccaattgcaatttcacagggtctatattcttcccctggggcatcaaaacggcatgtcag
caacagct

									
								

					

						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: 1262
Transcript exons: 209728828-209728894,209729012-209729133,209729286-209729
345,209729414-209729468,209729572-209729675,209729783-20
9729831,209729919-209730723
CTTCTTGCTGCCTCTTTTCCAGCCTCTCCTTTTCCAATTGCAATTTCACAGGGTCTATATTCTT
CCCATGATCCAGAAGTGCCTTCTGTTGAGCCTTCACTATAGTCCCAGCAAAACGACTCCTGAGC
ATTGCTGCACGAAGAGCCCTGCTTGGTGATAAAGGTTCATCACAAAGGTAACTTTCCTCACCTT
GTACAGAGGAGGCGATAGGCGAAGTAGAAATGTCATTGCAAGACCATGAATCATTTCCAGTTGA
ACCAGAGCTGCGCTCAGTTTCTCGTGTACTTGAAATTTTAGCATTCTCCTTAGCAAAAGGAAAA
GTGCAATTTAAATATGCCTCTTTGTTGCCGGTAGGAAAAGAGTGGTTTAATGACCCCTCTTTGA
CACCAGCTGTTTGAACAGGTATATCTTTGGAAGAGGTATGTGCAGAGCTGCGCACGGAAAATTT
GATTTTTACTTTGGAGGATAATGCATCTGTCAGTGTCTTCTTTGCAAACGAATTTGAGCAAGGT
ACTGGCCCTCTTGCAGCCAAAGATTTAGGATTTGAGCAGGCAACCTGCCCTCTAGCAACTGTAG
ACTTCGAATCCACGATAGCTCGAACTTTTATGGCCTTTGTCTTCTGCTCTTGAACAAGGTTTCG
GCCTCTAAATTTCCTTTCTACTGATTCCCATTCTGAGTCAAATATTTCATTCAATTCTCTAGCG
AAAGCATGTACATCATTGCCTGGAGGATTATACTTCATAGCATTTGAAAATGTTAGCCTCACAT
CTGCTGCGAACTCCTCAATGCTTACATACTTCTTTTTTGTGAGTTTATTCTTAACAGTACCCAA
ATCCATTGGGTTGCGGATAACATCAAAGTAGTCAGGAATCTTATATAGATCTGGATCAACAGGA
TCTTTGAAAAGCCAACCACCTTTGTGATCGATGAGCTTCCTTACAATATTTCCACACAGCCTTA
TCATCCTGCTACTTTTCATACTTGCAGCCTTGAGATTATAAGATGACTGATGCTCGCATGTAGA
AATTGATGTCACCCCAGATTTTTTAGAGGGTTTGCTTCCCTCAACATCAGAATCTGTATCAGAG
CCTCCCAATTCAGTGCTTATATAAACTCCTCTCCTCTTCTTACAGGCTTGTGCCATCATTGTGT
TTGGCCAGAGAGTTTGATTTCTTGTCTAACAACGGAGCAATAACTCAAGACTTGGTAAATGGTG
AAGCAGTGTCCAAGACCCACAGAGCACGGGTCTTCCTCAGCCAAGC
						
					

						Genomic sequence
						
							CTTCTTGCTGCCTCTTTTCCAGCCTCTCCTTTTCCAATTGCAATTTCACAGGGTCTATATTCTT
CCCCTGGGGCATCAAAACGGCATGTCAGCAACAGCTGCATCACTGCACAGAGATAAGCTTTGTC
CTCTGCAAAGCCAAATAGAAGATCACAAAGTTCAGCATATATTTTTGGAATATTACATGATCCA
GAAGTGCCTTCTGTTGAGCCTTCACTATAGTCCCAGCAAAACGACTCCTGAGCATTGCTGCACG
AAGAGCCCTGCTTGGTGATAAAGGTTCATCACAAAGGTAACTTTCCTCACCTGGAACTCACATG
AGAGCAAGCAGTACATTAGCCAAGAATTATATGGACAAAATCAAGTACACTAAGCTCCTAAATG
TTAAATTTTCATTGATTCCAGTAATAGGAATTAAAAAATAAGCAGATAAATTAAGGGAGAACAT
GTGAAATAACCTTGTACAGAGGAGGCGATAGGCGAAGTAGAAATGTCATTGCAAGACCATGAAT
CATTTCCTAGGATTTCAAGTATATTAGCAACACAGAAACCCTGGAATAACATTGTGCAGAAATG
CTCAACATACCAGTTGAACCAGAGCTGCGCTCAGTTTCTCGTGTACTTGAAATTTTAGCATTCT
CCTAAAGTTAGAAAATATAGCTTTAGATGAGTTACAAATTTGTTTATACTGTGAACAGATAATA
ATGAGTCAAAAAGATTGAGAAGGTAACTCATGCCCAATACCTTAGCAAAAGGAAAAGTGCAATT
TAAATATGCCTCTTTGTTGCCGGTAGGAAAAGAGTGGTTTAATGACCCCTCTTTGACACCAGCT
GTTTGAACAGGTATATCTGAATGAAAAAGAAAGCATTAACAATTACAACAATGAGTTCTAATTA
ACCTTAGGGTAAAAGCATGTCATGTAATGCATATAAGTAAGAAATTATGACATTGACACCTTTG
GAAGAGGTATGTGCAGAGCTGCGCACGGAAAATTTGATTTTTACCTGTACAAATAATAGATAGC
AGTACTTTTAAAATCACATTACCACCAGAGAAACAAATCAAGTGAATAAGAACATGTGTGGTCT
CACTTTGGAGGATAATGCATCTGTCAGTGTCTTCTTTGCAAACGAATTTGAGCAAGGTACTGGC
CCTCTTGCAGCCAAAGATTTAGGATTTGAGCAGGCAACCTGCCCTCTAGCAACTGTAGACTTCG
AATCCACGATAGCTCGAACTTTTATGGCCTTTGTCTTCTGCTCTTGAACAAGGTTTCGGCCTCT
AAATTTCCTTTCTACTGATTCCCATTCTGAGTCAAATATTTCATTCAATTCTCTAGCGAAAGCA
TGTACATCATTGCCTGGAGGATTATACTTCATAGCATTTGAAAATGTTAGCCTCACATCTGCTG
CGAACTCCTCAATGCTTACATACTTCTTTTTTGTGAGTTTATTCTTAACAGTACCCAAATCCAT
TGGGTTGCGGATAACATCAAAGTAGTCAGGAATCTTATATAGATCTGGATCAACAGGATCTTTG
AAAAGCCAACCACCTTTGTGATCGATGAGCTTCCTTACAATATTTCCACACAGCCTTATCATCC
TGCTACTTTTCATACTTGCAGCCTTGAGATTATAAGATGACTGATGCTCGCATGTAGAAATTGA
TGTCACCCCAGATTTTTTAGAGGGTTTGCTTCCCTCAACATCAGAATCTGTATCAGAGCCTCCC
AATTCAGTGCTTATATAAACTCCTCTCCTCTTCTTACAGGCTTGTGCCATCATTGTGTTTGGCC
AGAGAGTTTGATTTCTTGTCTAACAACGGAGCAATAACTCAAGACTTGGTAAATGGTGAAGCAG
TGTCCAAGACCCACAGAGCACGGGTCTTCCTCAGCCAAGC
						
					

			
		

Sequences
Splice junction sequence	AGTTTGATTTCTTGTCTAACAACGGAGCAATAACTCAAGACTTGGTAAATGGTGAAGCAGTGTC CAAGACCCACAGAGCACGGGTCTTCCTCAGCCAAGCcttcttgctgcctcttttccagcctctc cttttccaattgcaatttcacagggtctatattcttcccctggggcatcaaaacggcatgtcag caacagct
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: 1262 Transcript exons: 209728828-209728894,209729012-209729133,209729286-209729 345,209729414-209729468,209729572-209729675,209729783-20 9729831,209729919-209730723 CTTCTTGCTGCCTCTTTTCCAGCCTCTCCTTTTCCAATTGCAATTTCACAGGGTCTATATTCTT CCCATGATCCAGAAGTGCCTTCTGTTGAGCCTTCACTATAGTCCCAGCAAAACGACTCCTGAGC ATTGCTGCACGAAGAGCCCTGCTTGGTGATAAAGGTTCATCACAAAGGTAACTTTCCTCACCTT GTACAGAGGAGGCGATAGGCGAAGTAGAAATGTCATTGCAAGACCATGAATCATTTCCAGTTGA ACCAGAGCTGCGCTCAGTTTCTCGTGTACTTGAAATTTTAGCATTCTCCTTAGCAAAAGGAAAA GTGCAATTTAAATATGCCTCTTTGTTGCCGGTAGGAAAAGAGTGGTTTAATGACCCCTCTTTGA CACCAGCTGTTTGAACAGGTATATCTTTGGAAGAGGTATGTGCAGAGCTGCGCACGGAAAATTT GATTTTTACTTTGGAGGATAATGCATCTGTCAGTGTCTTCTTTGCAAACGAATTTGAGCAAGGT ACTGGCCCTCTTGCAGCCAAAGATTTAGGATTTGAGCAGGCAACCTGCCCTCTAGCAACTGTAG ACTTCGAATCCACGATAGCTCGAACTTTTATGGCCTTTGTCTTCTGCTCTTGAACAAGGTTTCG GCCTCTAAATTTCCTTTCTACTGATTCCCATTCTGAGTCAAATATTTCATTCAATTCTCTAGCG AAAGCATGTACATCATTGCCTGGAGGATTATACTTCATAGCATTTGAAAATGTTAGCCTCACAT CTGCTGCGAACTCCTCAATGCTTACATACTTCTTTTTTGTGAGTTTATTCTTAACAGTACCCAA ATCCATTGGGTTGCGGATAACATCAAAGTAGTCAGGAATCTTATATAGATCTGGATCAACAGGA TCTTTGAAAAGCCAACCACCTTTGTGATCGATGAGCTTCCTTACAATATTTCCACACAGCCTTA TCATCCTGCTACTTTTCATACTTGCAGCCTTGAGATTATAAGATGACTGATGCTCGCATGTAGA AATTGATGTCACCCCAGATTTTTTAGAGGGTTTGCTTCCCTCAACATCAGAATCTGTATCAGAG CCTCCCAATTCAGTGCTTATATAAACTCCTCTCCTCTTCTTACAGGCTTGTGCCATCATTGTGT TTGGCCAGAGAGTTTGATTTCTTGTCTAACAACGGAGCAATAACTCAAGACTTGGTAAATGGTG AAGCAGTGTCCAAGACCCACAGAGCACGGGTCTTCCTCAGCCAAGC
Genomic sequence	CTTCTTGCTGCCTCTTTTCCAGCCTCTCCTTTTCCAATTGCAATTTCACAGGGTCTATATTCTT CCCCTGGGGCATCAAAACGGCATGTCAGCAACAGCTGCATCACTGCACAGAGATAAGCTTTGTC CTCTGCAAAGCCAAATAGAAGATCACAAAGTTCAGCATATATTTTTGGAATATTACATGATCCA GAAGTGCCTTCTGTTGAGCCTTCACTATAGTCCCAGCAAAACGACTCCTGAGCATTGCTGCACG AAGAGCCCTGCTTGGTGATAAAGGTTCATCACAAAGGTAACTTTCCTCACCTGGAACTCACATG AGAGCAAGCAGTACATTAGCCAAGAATTATATGGACAAAATCAAGTACACTAAGCTCCTAAATG TTAAATTTTCATTGATTCCAGTAATAGGAATTAAAAAATAAGCAGATAAATTAAGGGAGAACAT GTGAAATAACCTTGTACAGAGGAGGCGATAGGCGAAGTAGAAATGTCATTGCAAGACCATGAAT CATTTCCTAGGATTTCAAGTATATTAGCAACACAGAAACCCTGGAATAACATTGTGCAGAAATG CTCAACATACCAGTTGAACCAGAGCTGCGCTCAGTTTCTCGTGTACTTGAAATTTTAGCATTCT CCTAAAGTTAGAAAATATAGCTTTAGATGAGTTACAAATTTGTTTATACTGTGAACAGATAATA ATGAGTCAAAAAGATTGAGAAGGTAACTCATGCCCAATACCTTAGCAAAAGGAAAAGTGCAATT TAAATATGCCTCTTTGTTGCCGGTAGGAAAAGAGTGGTTTAATGACCCCTCTTTGACACCAGCT GTTTGAACAGGTATATCTGAATGAAAAAGAAAGCATTAACAATTACAACAATGAGTTCTAATTA ACCTTAGGGTAAAAGCATGTCATGTAATGCATATAAGTAAGAAATTATGACATTGACACCTTTG GAAGAGGTATGTGCAGAGCTGCGCACGGAAAATTTGATTTTTACCTGTACAAATAATAGATAGC AGTACTTTTAAAATCACATTACCACCAGAGAAACAAATCAAGTGAATAAGAACATGTGTGGTCT CACTTTGGAGGATAATGCATCTGTCAGTGTCTTCTTTGCAAACGAATTTGAGCAAGGTACTGGC CCTCTTGCAGCCAAAGATTTAGGATTTGAGCAGGCAACCTGCCCTCTAGCAACTGTAGACTTCG AATCCACGATAGCTCGAACTTTTATGGCCTTTGTCTTCTGCTCTTGAACAAGGTTTCGGCCTCT AAATTTCCTTTCTACTGATTCCCATTCTGAGTCAAATATTTCATTCAATTCTCTAGCGAAAGCA TGTACATCATTGCCTGGAGGATTATACTTCATAGCATTTGAAAATGTTAGCCTCACATCTGCTG CGAACTCCTCAATGCTTACATACTTCTTTTTTGTGAGTTTATTCTTAACAGTACCCAAATCCAT TGGGTTGCGGATAACATCAAAGTAGTCAGGAATCTTATATAGATCTGGATCAACAGGATCTTTG AAAAGCCAACCACCTTTGTGATCGATGAGCTTCCTTACAATATTTCCACACAGCCTTATCATCC TGCTACTTTTCATACTTGCAGCCTTGAGATTATAAGATGACTGATGCTCGCATGTAGAAATTGA TGTCACCCCAGATTTTTTAGAGGGTTTGCTTCCCTCAACATCAGAATCTGTATCAGAGCCTCCC AATTCAGTGCTTATATAAACTCCTCTCCTCTTCTTACAGGCTTGTGCCATCATTGTGTTTGGCC AGAGAGTTTGATTTCTTGTCTAACAACGGAGCAATAACTCAAGACTTGGTAAATGGTGAAGCAG TGTCCAAGACCCACAGAGCACGGGTCTTCCTCAGCCAAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.12831839

Conservation Information
Conserved circRNAs	NA
PMCS	0.12831839

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							209730673-209729012(+)
209730610-209730607(-)
						
						Potential amino acid sequence
						
							MVKQCPRPTEHGSSSAKPSCCLFSSLSFSNCNFTGSIFFP*(+)
MMAQACKKRRGVYISTELGGSDTDSDVEGSKPSKKSGVTSISTCEHQSSYNLKAASMKSSRMIR
LCGNIVRKLIDHKGGWLFKDPVDPDLYKIPDYFDVIRNPMDLGTVKNKLTKKKYVSIEEFAADV
RLTFSNAMKYNPPGNDVHAFARELNEIFDSEWESVERKFRGRNLVQEQKTKAIKVRAIVDSKST
VARGQVACSNPKSLAARGPVPCSNSFAKKTLTDALSSKVKIKFSVRSSAHTSSKDIPVQTAGVK
EGSLNHSFPTGNKEAYLNCTFPFAKENAKISSTRETERSSGSTGNDSWSCNDISTSPIASSVQG
EESYLCDEPLSPSRALRAAMLRSRFAGTIVKAQQKALLDHGKNIDPVKLQLEKERLEKRQQEGL
AEEDPCSVGLGHCFTIYQVLSYCSVVRQEIKLSGQTQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	209730673-209729012(+) 209730610-209730607(-)
Potential amino acid sequence	MVKQCPRPTEHGSSSAKPSCCLFSSLSFSNCNFTGSIFFP(+) MMAQACKKRRGVYISTELGGSDTDSDVEGSKPSKKSGVTSISTCEHQSSYNLKAASMKSSRMIR LCGNIVRKLIDHKGGWLFKDPVDPDLYKIPDYFDVIRNPMDLGTVKNKLTKKKYVSIEEFAADV RLTFSNAMKYNPPGNDVHAFARELNEIFDSEWESVERKFRGRNLVQEQKTKAIKVRAIVDSKST VARGQVACSNPKSLAARGPVPCSNSFAKKTLTDALSSKVKIKFSVRSSAHTSSKDIPVQTAGVK EGSLNHSFPTGNKEAYLNCTFPFAKENAKISSTRETERSSGSTGNDSWSCNDISTSPIASSVQG EESYLCDEPLSPSRALRAAMLRSRFAGTIVKAQQKALLDHGKNIDPVKLQLEKERLEKRQQEGL AEEDPCSVGLGHCFTIYQVLSYCSVVRQEIKLSGQTQ(-)
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 Zm00001d053022_circ_g.4

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