Plant Circular RNA Database

Detail information of Zm00001d027665_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d027665_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006403
					
						Alias
						zma_circ_0000216
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 10510678-10551008  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d027665						
					
						Parent gene annotation
						
							Protein SHOOT GRAVITROPISM 6
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027665_circ_g.3 Zm00001d027665_circ_g.4 Zm00001d027665_circ_g.5 Zm00001d027665_circ_g.6 Zm00001d027665_circ_g.7 Zm00001d027665_circ_g.8 Zm00001d027665_circ_g.9 						
					
						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  
						
							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
						Zm00001d027665_T023:15
Zm00001d027665_T017:17
Zm00001d027665_T007:24
Zm00001d027665_T012:22
Zm00001d027665_T039:2
Zm00001d027665_T013:22
Zm00001d027665_T032:9
Zm00001d027665_T028:8
Zm00001d027665_T015:20
Zm00001d027665_T001:24
Zm00001d027665_T029:9
Zm00001d027665_T024:15
Zm00001d027665_T004:24
Zm00001d027665_T005:23
Zm00001d027665_T030:8
Zm00001d027665_T033:10
Zm00001d027665_T010:23
Zm00001d027665_T018:17
Zm00001d027665_T026:11
Zm00001d027665_T009:23
Zm00001d027665_T037:8
Zm00001d027665_T019:15
Zm00001d027665_T031:9
Zm00001d027665_T014:21
Zm00001d027665_T038:6
Zm00001d027665_T008:16

General Information
CircRNA Name	Zm00001d027665_circ_g.2
ID in PlantcircBase	zma_circ_006403
Alias	zma_circ_0000216
Organism	Zea mays
Position	chr1: 10510678-10551008 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d027665
Parent gene annotation	Protein SHOOT GRAVITROPISM 6
Parent gene strand	+
Alternative splicing	Zm00001d027665_circ_g.3 Zm00001d027665_circ_g.4 Zm00001d027665_circ_g.5 Zm00001d027665_circ_g.6 Zm00001d027665_circ_g.7 Zm00001d027665_circ_g.8 Zm00001d027665_circ_g.9
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	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	Zm00001d027665_T023:15 Zm00001d027665_T017:17 Zm00001d027665_T007:24 Zm00001d027665_T012:22 Zm00001d027665_T039:2 Zm00001d027665_T013:22 Zm00001d027665_T032:9 Zm00001d027665_T028:8 Zm00001d027665_T015:20 Zm00001d027665_T001:24 Zm00001d027665_T029:9 Zm00001d027665_T024:15 Zm00001d027665_T004:24 Zm00001d027665_T005:23 Zm00001d027665_T030:8 Zm00001d027665_T033:10 Zm00001d027665_T010:23 Zm00001d027665_T018:17 Zm00001d027665_T026:11 Zm00001d027665_T009:23 Zm00001d027665_T037:8 Zm00001d027665_T019:15 Zm00001d027665_T031:9 Zm00001d027665_T014:21 Zm00001d027665_T038:6 Zm00001d027665_T008:16

			
						 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  
						
							CATGTGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAG
AAGAGGCAAGGAGCTACGTGAAGCTGATGTCTCGAGgagcttactgttatcttagttacgcttc
ttcctttagtatctgccaataacaacaaagatgagcattatgtttcaaagggactgaaggtggc
tgcctcac

									
								

					

						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: 2528
Transcript exons: 10510678-10510764,10511096-10511173,10511266-10511333,10
511410-10511509,10511641-10511793,10511887-10511976,1051
2096-10512161,10522312-10522410,10522499-10522573,105242
05-10524264,10524556-10524645,10525417-10525538,10526568
-10526697,10526772-10526851,10527244-10527379,10527789-1
0527870,10537437-10537582,10537791-10537871,10537975-105
38075,10549889-10550124,10550205-10550314,10550521-10550
649,10550729-10550803,10550875-10551008
GAGCTTACTGTTATCTTAGTTACGCTTCTTCCTTTAGTATCTGCCAATAACAACAAAGATGAGC
ATTATGTTTCAAAGGGACTGAAGACATACAATGAGCTCCAGCATTGCTTTTTGGTAATTGGTTT
AGCATATCCTGAAGATCTTTGCATGTTCCTTTTGAGTAAATGCAAATCAAAAGATGAAGCATCT
ATTGTTGGAGCGCTTAGCACAATCAAACACCTATTGCCCAGATTGTTGGAATCATGGCATACTA
AACAAGCACCACTGGTTGAAATCATGAAATCACTTCTAGAGCAACAGAGCTTGGGTATTCGTAT
GGCGCTAGCTGAGCTAATTGTTGTTATGGCTTCACACTGCTATTTAAGTGGACATCCTGCTGAG
TTGGCAGTTGAGTTCCTGCTGCGGCATAGTGCTATAACTGATGCCGATCTAAATGACCTCGGCA
CTCTGAGAAATGAGTACTTCCAGGACAAAAGATTTGAGATGAAAGTAAGTCTTGCTGGCTTATC
AGAACTAAGAGCTGTGTGTGAAAAGGGTCTACTTTTGCTAGCAATCACCATTCCTGAAATGGAG
CTTGTTCTATGGCCGTTCATCTTGAAGTTGATAATCCCAAAGAAGTATACGGGTGCAGTAGCTA
CGGTCTGCAAATGCATAACTGAATTGTGCAGGCATAAATTTTCACATACAAACCCACTATATAC
TGAATTTAATGCCTCCAACGAAACCCCCAATCCTGAGGATTTGTTTGCTCGTTTGGTTGTGCTT
CTGCATAATCCACTTGCTAGGGGTCAACTGGCCACCCAGATCCTGACGGTTCTGTGCTACTTGG
GTCCACTTTTCCCCAGAAACCTTTCTTTATTTTGGCAAGATGAGGTCCCTAAGATGAAAGCTTA
CATCAGTGATCCTGAAGACCTAAAGCAAGATAGCACATACCAGGAAAAATGGGATGACATGATA
ATAAATTTTTTGGCAGAATGTTTGGATGTTGTGAATGATACTGAGTGGGTCATTTCTTTGGGTG
ATGCATTTGCACGGCAGTATGATCTGTATTCTATATCTGACGGACACGCTGCTTTGCTGCACAG
ATGCTTGGGAATGCTTCTTCAGAAGGTTGATGATAGGATTTATGTCAGCGAGAAGATTGATTGG
ATGTGTAGACACTCAAGTATGTCTATTCCTATTAATCGCCTTGGACTTGCTCAAGGCATCGGGC
TGGTTGCGGCTTCTCATTTAGATACAGTGTTGGAGAAACTGAAGAACATACTAGATAGTGCAGA
GCAAAGTGCTTTCCAGAGGTTCCTCTCATTTTTCTCATTCGGCCCAAAAGTGGAAGATGTTGAT
GACACATATGCAGCATTGGCGTTGATGTATGGTTATGCCGCAAGATATGCTCCATCAACTGTTA
TTGAAGCCAGAATTAATGCACTTGTGGGGAGTAATATGCTTGGAAGGTTGCTTCATGTTCAGCA
TCCTACTGCAAAGCAAGCTGTGATTACTGCAATCGACCTTTTAGGTCGAGCTGTTATTAGTGCT
GCTGAAATGGGAATCTCATTCCCACTGAAACGAAGAGATCAGTTACTGGAGTACGTTTTAACTC
TAATGGGTAGGGATCAAAGTAATGATCTCACTGATTTCAACACTGAGCTTTTGCACACACAGAG
CCTTGCTTTAAGTGCCTGTACTACTCTTGTCTCGCTAGAACCAAGATTGCCAATGGAAACAAGA
AACCGTGTCATGAAGGCAACATTAGGTTTTTTTGCTTTGCCAACAGAGCCCTCAAGCATTGTTG
AGAGTCTCGTAACAAACCTAATTATTCTGTTAGGTGCCATCCTGCTTACAAGTGGTGAAGATGG
TCGAAGTCGAGCAGAGCAGTTGCTGCATATTCTTAGGCAGCTTGATCCATATGTATCATCATCT
CTGGAACACCAAAGAAGAAGAGGATGTGTTGCTGTACAGGAGGTGTTAATAAAGTTTCGCAATC
TTTGTTCTGGTGGATTCGGTGCATTGGGCTCCTATCCAACTTTCACAATGAATAAACAAATCGA
TCGAGGGACTAGGAGCTTGTCAAGTTTGCCATCTGCATTTGTGTTGCCTAGTCGAGATTCTTTA
AGCTTGGGAGAGAGGACAATGGCATACCTTCCTCGTTGTGCTGATACAGACACGGAAGTTAGGA
AAGTTGCAATTCAGATCATTGCACTTTTCTTCGACATTTCATTGTCACTTCCAAAGCAGAAGGC
ATATCCTAATGATATTGATCTGGAATCCTCGTATAGTGCTTTGTCCTCCCTTGAGGAGTTAGTC
TCTATTGTCAGAAGGGAGGCATCTGTTGATCAAACTGAACTATTTCAGAGGGTTGTATCCTCAG
TGTGTATTCTATTATCAAAGGATGAGCTGGTCGTCTTGCTACACTCTTGTACGTTGGCAACATG
TGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAGAAGA
GGCAAGGAGCTACGTGAAGCTGATGTCTCGAG
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	CATGTGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAG AAGAGGCAAGGAGCTACGTGAAGCTGATGTCTCGAGgagcttactgttatcttagttacgcttc ttcctttagtatctgccaataacaacaaagatgagcattatgtttcaaagggactgaaggtggc tgcctcac
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: 2528 Transcript exons: 10510678-10510764,10511096-10511173,10511266-10511333,10 511410-10511509,10511641-10511793,10511887-10511976,1051 2096-10512161,10522312-10522410,10522499-10522573,105242 05-10524264,10524556-10524645,10525417-10525538,10526568 -10526697,10526772-10526851,10527244-10527379,10527789-1 0527870,10537437-10537582,10537791-10537871,10537975-105 38075,10549889-10550124,10550205-10550314,10550521-10550 649,10550729-10550803,10550875-10551008 GAGCTTACTGTTATCTTAGTTACGCTTCTTCCTTTAGTATCTGCCAATAACAACAAAGATGAGC ATTATGTTTCAAAGGGACTGAAGACATACAATGAGCTCCAGCATTGCTTTTTGGTAATTGGTTT AGCATATCCTGAAGATCTTTGCATGTTCCTTTTGAGTAAATGCAAATCAAAAGATGAAGCATCT ATTGTTGGAGCGCTTAGCACAATCAAACACCTATTGCCCAGATTGTTGGAATCATGGCATACTA AACAAGCACCACTGGTTGAAATCATGAAATCACTTCTAGAGCAACAGAGCTTGGGTATTCGTAT GGCGCTAGCTGAGCTAATTGTTGTTATGGCTTCACACTGCTATTTAAGTGGACATCCTGCTGAG TTGGCAGTTGAGTTCCTGCTGCGGCATAGTGCTATAACTGATGCCGATCTAAATGACCTCGGCA CTCTGAGAAATGAGTACTTCCAGGACAAAAGATTTGAGATGAAAGTAAGTCTTGCTGGCTTATC AGAACTAAGAGCTGTGTGTGAAAAGGGTCTACTTTTGCTAGCAATCACCATTCCTGAAATGGAG CTTGTTCTATGGCCGTTCATCTTGAAGTTGATAATCCCAAAGAAGTATACGGGTGCAGTAGCTA CGGTCTGCAAATGCATAACTGAATTGTGCAGGCATAAATTTTCACATACAAACCCACTATATAC TGAATTTAATGCCTCCAACGAAACCCCCAATCCTGAGGATTTGTTTGCTCGTTTGGTTGTGCTT CTGCATAATCCACTTGCTAGGGGTCAACTGGCCACCCAGATCCTGACGGTTCTGTGCTACTTGG GTCCACTTTTCCCCAGAAACCTTTCTTTATTTTGGCAAGATGAGGTCCCTAAGATGAAAGCTTA CATCAGTGATCCTGAAGACCTAAAGCAAGATAGCACATACCAGGAAAAATGGGATGACATGATA ATAAATTTTTTGGCAGAATGTTTGGATGTTGTGAATGATACTGAGTGGGTCATTTCTTTGGGTG ATGCATTTGCACGGCAGTATGATCTGTATTCTATATCTGACGGACACGCTGCTTTGCTGCACAG ATGCTTGGGAATGCTTCTTCAGAAGGTTGATGATAGGATTTATGTCAGCGAGAAGATTGATTGG ATGTGTAGACACTCAAGTATGTCTATTCCTATTAATCGCCTTGGACTTGCTCAAGGCATCGGGC TGGTTGCGGCTTCTCATTTAGATACAGTGTTGGAGAAACTGAAGAACATACTAGATAGTGCAGA GCAAAGTGCTTTCCAGAGGTTCCTCTCATTTTTCTCATTCGGCCCAAAAGTGGAAGATGTTGAT GACACATATGCAGCATTGGCGTTGATGTATGGTTATGCCGCAAGATATGCTCCATCAACTGTTA TTGAAGCCAGAATTAATGCACTTGTGGGGAGTAATATGCTTGGAAGGTTGCTTCATGTTCAGCA TCCTACTGCAAAGCAAGCTGTGATTACTGCAATCGACCTTTTAGGTCGAGCTGTTATTAGTGCT GCTGAAATGGGAATCTCATTCCCACTGAAACGAAGAGATCAGTTACTGGAGTACGTTTTAACTC TAATGGGTAGGGATCAAAGTAATGATCTCACTGATTTCAACACTGAGCTTTTGCACACACAGAG CCTTGCTTTAAGTGCCTGTACTACTCTTGTCTCGCTAGAACCAAGATTGCCAATGGAAACAAGA AACCGTGTCATGAAGGCAACATTAGGTTTTTTTGCTTTGCCAACAGAGCCCTCAAGCATTGTTG AGAGTCTCGTAACAAACCTAATTATTCTGTTAGGTGCCATCCTGCTTACAAGTGGTGAAGATGG TCGAAGTCGAGCAGAGCAGTTGCTGCATATTCTTAGGCAGCTTGATCCATATGTATCATCATCT CTGGAACACCAAAGAAGAAGAGGATGTGTTGCTGTACAGGAGGTGTTAATAAAGTTTCGCAATC TTTGTTCTGGTGGATTCGGTGCATTGGGCTCCTATCCAACTTTCACAATGAATAAACAAATCGA TCGAGGGACTAGGAGCTTGTCAAGTTTGCCATCTGCATTTGTGTTGCCTAGTCGAGATTCTTTA AGCTTGGGAGAGAGGACAATGGCATACCTTCCTCGTTGTGCTGATACAGACACGGAAGTTAGGA AAGTTGCAATTCAGATCATTGCACTTTTCTTCGACATTTCATTGTCACTTCCAAAGCAGAAGGC ATATCCTAATGATATTGATCTGGAATCCTCGTATAGTGCTTTGTCCTCCCTTGAGGAGTTAGTC TCTATTGTCAGAAGGGAGGCATCTGTTGATCAAACTGAACTATTTCAGAGGGTTGTATCCTCAG TGTGTATTCTATTATCAAAGGATGAGCTGGTCGTCTTGCTACACTCTTGTACGTTGGCAACATG TGATAAGATAAAACAGTCAGCAGATGCTTCAATTCAAGCTATTATCATGTTTATTATCAGAAGA GGCAAGGAGCTACGTGAAGCTGATGTCTCGAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.120833986

Conservation Information
Conserved circRNAs	NA
PMCS	0.120833986

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10511160-10510693(+)
10550937-10510724(+)
						
						Potential amino acid sequence
						
							MFLLSKCKSKDEASIVGALSTIKHLLPRLLESWHTKQAPLVEIMKSLLEQQSLGIRMALAELIV
VMASHCYLSGHPAELAVEFLLRHSAITDADLNDLGTLRNEYFQDKRFEMKVSLAGLSELRAVCE
KGLLLLAITIPEMELVLWPFILKLIIPKKYTGAVATVCKCITELCRHKFSHTNPLYTEFNASNE
TPNPEDLFARLVVLLHNPLARGQLATQILTVLCYLGPLFPRNLSLFWQDEVPKMKAYISDPEDL
KQDSTYQEKWDDMIINFLAECLDVVNDTEWVISLGDAFARQYDLYSISDGHAALLHRCLGMLLQ
KVDDRIYVSEKIDWMCRHSSMSIPINRLGLAQGIGLVAASHLDTVLEKLKNILDSAEQSAFQRF
LSFFSFGPKVEDVDDTYAALALMYGYAARYAPSTVIEARINALVGSNMLGRLLHVQHPTAKQAV
ITAIDLLGRAVISAAEMGISFPLKRRDQLLEYVLTLMGRDQSNDLTDFNTELLHTQSLALSACT
TLVSLEPRLPMETRNRVMKATLGFFALPTEPSSIVESLVTNLIILLGAILLTSGEDGRSRAEQL
LHILRQLDPYVSSSLEHQRRRGCVAVQEVLIKFRNLCSGGFGALGSYPTFTMNKQIDRGTRSLS
SLPSAFVLPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLSLPKQKAYPNDIDL
ESSYSALSSLEELVSIVRREASVDQTELFQRVVSSVCILLSKDELVVLLHSCTLATCDKIKQSA
DASIQAIIMFIIRRGKELREADVSRSLLLS*(+)
MLQFKLLSCLLSEEARSYVKLMSRGAYCYLSYASSFSICQ*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10511160-10510693(+) 10550937-10510724(+)
Potential amino acid sequence	MFLLSKCKSKDEASIVGALSTIKHLLPRLLESWHTKQAPLVEIMKSLLEQQSLGIRMALAELIV VMASHCYLSGHPAELAVEFLLRHSAITDADLNDLGTLRNEYFQDKRFEMKVSLAGLSELRAVCE KGLLLLAITIPEMELVLWPFILKLIIPKKYTGAVATVCKCITELCRHKFSHTNPLYTEFNASNE TPNPEDLFARLVVLLHNPLARGQLATQILTVLCYLGPLFPRNLSLFWQDEVPKMKAYISDPEDL KQDSTYQEKWDDMIINFLAECLDVVNDTEWVISLGDAFARQYDLYSISDGHAALLHRCLGMLLQ KVDDRIYVSEKIDWMCRHSSMSIPINRLGLAQGIGLVAASHLDTVLEKLKNILDSAEQSAFQRF LSFFSFGPKVEDVDDTYAALALMYGYAARYAPSTVIEARINALVGSNMLGRLLHVQHPTAKQAV ITAIDLLGRAVISAAEMGISFPLKRRDQLLEYVLTLMGRDQSNDLTDFNTELLHTQSLALSACT TLVSLEPRLPMETRNRVMKATLGFFALPTEPSSIVESLVTNLIILLGAILLTSGEDGRSRAEQL LHILRQLDPYVSSSLEHQRRRGCVAVQEVLIKFRNLCSGGFGALGSYPTFTMNKQIDRGTRSLS SLPSAFVLPSRDSLSLGERTMAYLPRCADTDTEVRKVAIQIIALFFDISLSLPKQKAYPNDIDL ESSYSALSSLEELVSIVRREASVDQTELFQRVVSSVCILLSKDELVVLLHSCTLATCDKIKQSA DASIQAIIMFIIRRGKELREADVSRSLLLS(+) MLQFKLLSCLLSEEARSYVKLMSRGAYCYLSYASSFSICQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d027665_circ_g.2

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