Plant Circular RNA Database

Detail information of Zm00001d038689_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d038689_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009151
					
						Alias
						Zm06circ00098
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 162607320-162610537  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d038689						
					
						Parent gene annotation
						
							Proline iminopeptidase  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d038689_circ_g.1 Zm00001d038689_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
						Zm00001d038689_T003:8
Zm00001d038689_T005:8
Zm00001d038689_T001:9
Zm00001d038689_T002:7
Zm00001d038689_T004:9

General Information
CircRNA Name	Zm00001d038689_circ_g.2
ID in PlantcircBase	zma_circ_009151
Alias	Zm06circ00098
Organism	Zea mays
Position	chr6: 162607320-162610537 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d038689
Parent gene annotation	Proline iminopeptidase
Parent gene strand	-
Alternative splicing	Zm00001d038689_circ_g.1 Zm00001d038689_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	Zm00001d038689_T003:8 Zm00001d038689_T005:8 Zm00001d038689_T001:9 Zm00001d038689_T002:7 Zm00001d038689_T004:9

			
						 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  
						
							TCCGACGACGGATCCATCTGCGCGGCGATGGGGACGGAGAGGCTCGCGCGGCAGCGGCGGCGCG
TGCCTTTCGCCTGTACGCAACCCAGACCCCCTTCCCcttgaattctgcttcaggccaagcctta
tgaagatcccaagcagacatcatagggcaacaaacatcataacgtccctgcaccacaaagtgtt
caggcaca

									
								

					

						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
						
							CTTGAATTCTGCTTCAGGCCAAGCCTTATGAAGATCCCAAGCAGACATCATAGGGCAACAAACA
TCATAACGTCCCTGCACCACAAAGTGTTCAGGCACAAGCACACTTATATTTATCGATTTGATAT
CTGCCACTGATTTGAGTTCCAGATTATCCAAGCAATCATGCAAGACAATAACAAAGAAAACATG
CTTGACCAGAAGTTCAATGACAACTAAAGGTAGACAGGCATGAAGAGCTAAAGGCAATGCACAA
CTTGACTTGTCAAATATAATATCTACTCCATCCGTTCCAAATTATAAGCCGTTTTGCCTTCTAG
CAGACACACATGGACATTGTGAAAACAGCAAAACTCATTGACAAGCATACCTGTACAATAAAAC
CTTTAATATGTCGGATCTTATCAACATTGTCCAATAGGAATGAGTCCGAGGGTAAAAATCCCTT
ATTCACAAAGTAGTGGTTTTCAATCCTTGCAAATGCCTGAAAAATCATAGAACCTTGCATCAGA
AAATATAAGAGAAAATGTAATTTGACCACATAAATCATAAAACTGTCGACTAAAAAAATGTCTT
ATCAAAATTATGTTGCTCTTTGTAGCTTTAGGCATGTTATCTGTGGGAAGTGATTCAATAAGAG
AAGTAATTTGATGGTTGAAAGCGTTTCAATAGGATAAATTATATGTAGAAAGTGATTATGTGAC
GGAAGTGAAAGAGAAGCTACTTTTTTTTCAACTCCTAGCCTTCTAGTTCATTTCAGAAATCCCT
TCACGAAATAAGCAAGCAATCACTTCTCTGCAAAACAAACTGTTTGGTGGATTCAGCCTGGAAA
CTGCTCTAGGACTCGATGCAGATTTCTACAGCCATTGGTGGCAACAGTTTACTAACACTAAAAA
CTCCACCTGCGAGGGGTAAGACAGCCCCCGGCATTACAATAAGAAGACCTTCTCATCCAAGTCG
AGAAAACCCCCAAACCTCTGCCCCAACCATATACAGCGGCACCGTAGTCTATGTGATAACACGA
CCGCGACCGGGTCTTAGACCTGTGCTTTGGCGTGGGACAGACGAGGGGATTTTTTAACCATAGC
TCCCACGGAGAGTCGAACTCAGGATCTGAGGAGTGCTATTCAGACCACCTAACCAACTCGGCTA
GAGGCCCTTTTGCAACAGTTTACTAACACTAAGATGTATTTTTTCCAAATTGTGCTTACAATGA
TTGCTTATTGTTTCTATTTCAAGTCCAGAGTAATATTGAGGATATAATGATTTAAAGAAAAAAC
ATTGCATGTCCCTTGCAAGGCATTCTTCTTTCAATTCTGTATAGAGATAACCAGAATGAAAAGA
AAAAAAAAGTGGCTAAGCAGGAGGGGGAGAAACTGAAATGGTGTTAGTGTTACAAAGAAAAGTA
GAGATGCTTGTGTGAGAGGACTTGCCAGTGAAAATTCATCATCTTCTCCTCGTTTAATGTTATC
ATTGTTTTGGATAAGTTGCGCAGTCATCATCTCCCACATCGTCCAGCGCTTAGCAGCTTCAACC
TAATTTGAAAAGGAAAATGTCTGTTTATTAAAAAAATAAACATAAAACAAAGGCTATGACAAGG
CACCAGATATATAACATAATGTATTTACTTCCAAAAGGAAATATGTGGGGCTACCTGAACAATA
GGATCAGAGGAAGTTAACCTTTTGTTATAAGCATCTACGAAACAATTCCTTTCATCCTCAGGAA
TAAAATCTCTAAATGGTTCCCATGCTGCAGATTTAAAACTAAAGTTATCAATGTACTCCAAACA
AAAAAGGCGCATATGTGGGTTTTCTTTCATAAAACCAGAAAATAAAATGTTTTTTATTAGAGAA
AAAATATAACAAAATGCATTAACAAACATCATTTAAATACAACTATAATTGCTGAAACAGATTT
AACATAGTTAATATAAGTTGCCAGTACCATTATGGAACATTGAAGATTGGAAATGTGTTTAAGA
AAAGTTTTTTCGGTTTATAGAACGTAAAATCAAAAATACAAACCATCTGGGAAAATGGCTGCTG
CACCACCCTCATAGAACCAATCAAACTCCTTTTTCCTAAGCAAGAAAATTCCTCTCAGAACAAG
GCCAGTGACCTAGTGAGCATACAGGGAGTGTTAGTGAGGTCTACAACATGGTTATTTATTTGCT
TAAGAGCTTCATGCTCAAATACAGAATACATCAGACAAAAAAAAATCCATCACCTTATCAGGGT
GCTCCTGGCTGTAGGCAAGTGCCAAGGTGCTTCCCCATGAACCACCAAACACCTACATTGTCTG
GCAGCATTGAGTTCCAGCACTGAAGAGTGAGTAATCAGTGTTGTTGAAAAAGAAGATAATTGCC
TGCCATTCAGGGATGCCAAGATGCTCCCTGAGCTTCTCAATGTCAGCTACCAAGTCCCAAGTAG
TGTTCTGCTCTAAACAAGCATGGGGAGTGCTTCTGCCTGCACCCCTCTGCAATCGAACCATAAC
ACATATCAGGAACAACACACAGCCCCCAAGGCCCCAAGCAGTGTTTTTAAGGCGTTGCCTAGGC
GTCGCCTAGGCGTCGAGGCGCTCGGAGAATTCTTGGCGCCTTGCCCGCCTAGGTGCTAAGGCAG
TGATCATGTTTACTTGCTCGCTTTAACGCCTTAAGAACACTGCCCCAAGGCCCTTTGGTTGCGT
TTAATAAGAAAAGAAAAGAAAGAGACGAGTCGCCGAAATAACCTGGTCAAACAGAACGATCCTG
TAGAACTGCGGGTCAAAGAACCTCCTGTTGCCGGGCGACGTGCCGGCTCCGGGACCGCCGTGGA
GAAACACCGCCGCCTGCAAAATTGACAGGACGATAAGCTTATCTCATAAGGGCAGAACAACCAT
GCAGTTCTAGCAAGTTATTCGCTGCGTGTACGAGGCTCAGCGAGCTGGGTTATCAAAATCCCAC
GATCTACCAAATTCAACAGAGAGACAGGATTGTATGAAATTCAACAGAAAGAGATAGAGGAATT
AGACCCTCACATGGCCCTGCGGGTTCCCGGACTGCTCGTAGTAGATGGTGTGGACATCGGAGAC
CTTGAGGAACCCGGAGTCGTACGGCTCGACCTGCGCGTACAGGGGCTCCGACGACGGATCCATC
TGCGCGGCGATGGGGACGGAGAGGCTCGCGCGGCAGCGGCGGCGCGTGCCTTTCGCCTGTACGC
AACCCAGACCCCCTTCCC
						
					

			
		

Sequences
Splice junction sequence	TCCGACGACGGATCCATCTGCGCGGCGATGGGGACGGAGAGGCTCGCGCGGCAGCGGCGGCGCG TGCCTTTCGCCTGTACGCAACCCAGACCCCCTTCCCcttgaattctgcttcaggccaagcctta tgaagatcccaagcagacatcatagggcaacaaacatcataacgtccctgcaccacaaagtgtt caggcaca
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	CTTGAATTCTGCTTCAGGCCAAGCCTTATGAAGATCCCAAGCAGACATCATAGGGCAACAAACA TCATAACGTCCCTGCACCACAAAGTGTTCAGGCACAAGCACACTTATATTTATCGATTTGATAT CTGCCACTGATTTGAGTTCCAGATTATCCAAGCAATCATGCAAGACAATAACAAAGAAAACATG CTTGACCAGAAGTTCAATGACAACTAAAGGTAGACAGGCATGAAGAGCTAAAGGCAATGCACAA CTTGACTTGTCAAATATAATATCTACTCCATCCGTTCCAAATTATAAGCCGTTTTGCCTTCTAG CAGACACACATGGACATTGTGAAAACAGCAAAACTCATTGACAAGCATACCTGTACAATAAAAC CTTTAATATGTCGGATCTTATCAACATTGTCCAATAGGAATGAGTCCGAGGGTAAAAATCCCTT ATTCACAAAGTAGTGGTTTTCAATCCTTGCAAATGCCTGAAAAATCATAGAACCTTGCATCAGA AAATATAAGAGAAAATGTAATTTGACCACATAAATCATAAAACTGTCGACTAAAAAAATGTCTT ATCAAAATTATGTTGCTCTTTGTAGCTTTAGGCATGTTATCTGTGGGAAGTGATTCAATAAGAG AAGTAATTTGATGGTTGAAAGCGTTTCAATAGGATAAATTATATGTAGAAAGTGATTATGTGAC GGAAGTGAAAGAGAAGCTACTTTTTTTTCAACTCCTAGCCTTCTAGTTCATTTCAGAAATCCCT TCACGAAATAAGCAAGCAATCACTTCTCTGCAAAACAAACTGTTTGGTGGATTCAGCCTGGAAA CTGCTCTAGGACTCGATGCAGATTTCTACAGCCATTGGTGGCAACAGTTTACTAACACTAAAAA CTCCACCTGCGAGGGGTAAGACAGCCCCCGGCATTACAATAAGAAGACCTTCTCATCCAAGTCG AGAAAACCCCCAAACCTCTGCCCCAACCATATACAGCGGCACCGTAGTCTATGTGATAACACGA CCGCGACCGGGTCTTAGACCTGTGCTTTGGCGTGGGACAGACGAGGGGATTTTTTAACCATAGC TCCCACGGAGAGTCGAACTCAGGATCTGAGGAGTGCTATTCAGACCACCTAACCAACTCGGCTA GAGGCCCTTTTGCAACAGTTTACTAACACTAAGATGTATTTTTTCCAAATTGTGCTTACAATGA TTGCTTATTGTTTCTATTTCAAGTCCAGAGTAATATTGAGGATATAATGATTTAAAGAAAAAAC ATTGCATGTCCCTTGCAAGGCATTCTTCTTTCAATTCTGTATAGAGATAACCAGAATGAAAAGA AAAAAAAAGTGGCTAAGCAGGAGGGGGAGAAACTGAAATGGTGTTAGTGTTACAAAGAAAAGTA GAGATGCTTGTGTGAGAGGACTTGCCAGTGAAAATTCATCATCTTCTCCTCGTTTAATGTTATC ATTGTTTTGGATAAGTTGCGCAGTCATCATCTCCCACATCGTCCAGCGCTTAGCAGCTTCAACC TAATTTGAAAAGGAAAATGTCTGTTTATTAAAAAAATAAACATAAAACAAAGGCTATGACAAGG CACCAGATATATAACATAATGTATTTACTTCCAAAAGGAAATATGTGGGGCTACCTGAACAATA GGATCAGAGGAAGTTAACCTTTTGTTATAAGCATCTACGAAACAATTCCTTTCATCCTCAGGAA TAAAATCTCTAAATGGTTCCCATGCTGCAGATTTAAAACTAAAGTTATCAATGTACTCCAAACA AAAAAGGCGCATATGTGGGTTTTCTTTCATAAAACCAGAAAATAAAATGTTTTTTATTAGAGAA AAAATATAACAAAATGCATTAACAAACATCATTTAAATACAACTATAATTGCTGAAACAGATTT AACATAGTTAATATAAGTTGCCAGTACCATTATGGAACATTGAAGATTGGAAATGTGTTTAAGA AAAGTTTTTTCGGTTTATAGAACGTAAAATCAAAAATACAAACCATCTGGGAAAATGGCTGCTG CACCACCCTCATAGAACCAATCAAACTCCTTTTTCCTAAGCAAGAAAATTCCTCTCAGAACAAG GCCAGTGACCTAGTGAGCATACAGGGAGTGTTAGTGAGGTCTACAACATGGTTATTTATTTGCT TAAGAGCTTCATGCTCAAATACAGAATACATCAGACAAAAAAAAATCCATCACCTTATCAGGGT GCTCCTGGCTGTAGGCAAGTGCCAAGGTGCTTCCCCATGAACCACCAAACACCTACATTGTCTG GCAGCATTGAGTTCCAGCACTGAAGAGTGAGTAATCAGTGTTGTTGAAAAAGAAGATAATTGCC TGCCATTCAGGGATGCCAAGATGCTCCCTGAGCTTCTCAATGTCAGCTACCAAGTCCCAAGTAG TGTTCTGCTCTAAACAAGCATGGGGAGTGCTTCTGCCTGCACCCCTCTGCAATCGAACCATAAC ACATATCAGGAACAACACACAGCCCCCAAGGCCCCAAGCAGTGTTTTTAAGGCGTTGCCTAGGC GTCGCCTAGGCGTCGAGGCGCTCGGAGAATTCTTGGCGCCTTGCCCGCCTAGGTGCTAAGGCAG TGATCATGTTTACTTGCTCGCTTTAACGCCTTAAGAACACTGCCCCAAGGCCCTTTGGTTGCGT TTAATAAGAAAAGAAAAGAAAGAGACGAGTCGCCGAAATAACCTGGTCAAACAGAACGATCCTG TAGAACTGCGGGTCAAAGAACCTCCTGTTGCCGGGCGACGTGCCGGCTCCGGGACCGCCGTGGA GAAACACCGCCGCCTGCAAAATTGACAGGACGATAAGCTTATCTCATAAGGGCAGAACAACCAT GCAGTTCTAGCAAGTTATTCGCTGCGTGTACGAGGCTCAGCGAGCTGGGTTATCAAAATCCCAC GATCTACCAAATTCAACAGAGAGACAGGATTGTATGAAATTCAACAGAAAGAGATAGAGGAATT AGACCCTCACATGGCCCTGCGGGTTCCCGGACTGCTCGTAGTAGATGGTGTGGACATCGGAGAC CTTGAGGAACCCGGAGTCGTACGGCTCGACCTGCGCGTACAGGGGCTCCGACGACGGATCCATC TGCGCGGCGATGGGGACGGAGAGGCTCGCGCGGCAGCGGCGGCGCGTGCCTTTCGCCTGTACGC AACCCAGACCCCCTTCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.124502903

Conservation Information
Conserved circRNAs	NA
PMCS	0.124502903

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							162609772-162607347(+)
162610373-162607321(+)
162610456-162609763(-)
						
						Potential amino acid sequence
						
							MGSASACTPLVKQNDPVELRVKEPPVAGRRAGSGTAVEKHRRMALRVPGLLVVDGVDIGDLEEP
GVVRLDLRVQGLRRRIHLRGDGDGEARAAAAARAFRLYATQTPFPLNSASGQAL*(+)
MVWTSETLRNPESYGSTCAYRGSDDGSICAAMGTERLARQRRRVPFACTQPRPPSP*(+)
MDPSSEPLYAQVEPYDSGFLKVSDVHTIYYEQSGNPQGHAAVFLHGGPGAGTSPGNRRFFDPQF
YRIVLFDQRGAGRSTPHACLEQNTTWDLVADIEKLREHLGIPEWQVFGGSWGSTLALAYSQEHP
DKVTGLVLRGIFLLRKKEFDWFYEGGAAAIFPDAWEPFRDFIPEDERNCFVDAYNKRLTSSDPI
VQVEAAKRWTMWEMMTAQLIQNNDNIKRGEDDEFSLAFARIENHYFVNKGFLPSDSFLLDNVDK
IRHIKGFIVQGRYDVCCPMMSAWDLHKAWPEAEFKGKGVWVAYRRKARAAAAARASPSPSPRRW
IRRRSPCTRRSSRTTPGSSRSPMSTPSTTSSPGTRRAMRRCFSTAVPEPARRPATGGSLTRSST
GSFCLTRGVQAEALPMLV*(-)
						
						Sponge-miRNAs
						
							zma-miR156j-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	162609772-162607347(+) 162610373-162607321(+) 162610456-162609763(-)
Potential amino acid sequence	MGSASACTPLVKQNDPVELRVKEPPVAGRRAGSGTAVEKHRRMALRVPGLLVVDGVDIGDLEEP GVVRLDLRVQGLRRRIHLRGDGDGEARAAAAARAFRLYATQTPFPLNSASGQAL(+) MVWTSETLRNPESYGSTCAYRGSDDGSICAAMGTERLARQRRRVPFACTQPRPPSP(+) MDPSSEPLYAQVEPYDSGFLKVSDVHTIYYEQSGNPQGHAAVFLHGGPGAGTSPGNRRFFDPQF YRIVLFDQRGAGRSTPHACLEQNTTWDLVADIEKLREHLGIPEWQVFGGSWGSTLALAYSQEHP DKVTGLVLRGIFLLRKKEFDWFYEGGAAAIFPDAWEPFRDFIPEDERNCFVDAYNKRLTSSDPI VQVEAAKRWTMWEMMTAQLIQNNDNIKRGEDDEFSLAFARIENHYFVNKGFLPSDSFLLDNVDK IRHIKGFIVQGRYDVCCPMMSAWDLHKAWPEAEFKGKGVWVAYRRKARAAAAARASPSPSPRRW IRRRSPCTRRSSRTTPGSSRSPMSTPSTTSSPGTRRAMRRCFSTAVPEPARRPATGGSLTRSST GSFCLTRGVQAEALPMLV*(-)
Sponge-miRNAs	zma-miR156j-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d038689_circ_g.2

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