Plant Circular RNA Database

Detail information of Zm00001d027392_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d027392_circ_g.1
					
						ID in PlantcircBase
						zma_circ_006354
					
						Alias
						Zm01circ00007
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 4235011-4236877  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d027392						
					
						Parent gene annotation
						
							Callose synthase 9
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027392_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
						Zm00001d027392_T046:6
Zm00001d027392_T004:6
Zm00001d027392_T054:3
Zm00001d027392_T059:2
Zm00001d027392_T006:6
Zm00001d027392_T050:6
Zm00001d027392_T042:6
Zm00001d027392_T034:6
Zm00001d027392_T007:6
Zm00001d027392_T041:6
Zm00001d027392_T027:6
Zm00001d027392_T060:2
Zm00001d027392_T049:6
Zm00001d027392_T020:6
Zm00001d027392_T002:6
Zm00001d027392_T051:6
Zm00001d027392_T015:6
Zm00001d027392_T003:6
Zm00001d027392_T019:6
Zm00001d027392_T029:6
Zm00001d027392_T023:6
Zm00001d027392_T011:6
Zm00001d027392_T036:4
Zm00001d027392_T052:5
Zm00001d027392_T016:6
Zm00001d027392_T038:6
Zm00001d027392_T045:6
Zm00001d027392_T055:3
Zm00001d027392_T056:2
Zm00001d027392_T033:6
Zm00001d027392_T025:6
Zm00001d027392_T012:6
Zm00001d027392_T030:6

General Information
CircRNA Name	Zm00001d027392_circ_g.1
ID in PlantcircBase	zma_circ_006354
Alias	Zm01circ00007
Organism	Zea mays
Position	chr1: 4235011-4236877 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d027392
Parent gene annotation	Callose synthase 9
Parent gene strand	+
Alternative splicing	Zm00001d027392_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	Zm00001d027392_T046:6 Zm00001d027392_T004:6 Zm00001d027392_T054:3 Zm00001d027392_T059:2 Zm00001d027392_T006:6 Zm00001d027392_T050:6 Zm00001d027392_T042:6 Zm00001d027392_T034:6 Zm00001d027392_T007:6 Zm00001d027392_T041:6 Zm00001d027392_T027:6 Zm00001d027392_T060:2 Zm00001d027392_T049:6 Zm00001d027392_T020:6 Zm00001d027392_T002:6 Zm00001d027392_T051:6 Zm00001d027392_T015:6 Zm00001d027392_T003:6 Zm00001d027392_T019:6 Zm00001d027392_T029:6 Zm00001d027392_T023:6 Zm00001d027392_T011:6 Zm00001d027392_T036:4 Zm00001d027392_T052:5 Zm00001d027392_T016:6 Zm00001d027392_T038:6 Zm00001d027392_T045:6 Zm00001d027392_T055:3 Zm00001d027392_T056:2 Zm00001d027392_T033:6 Zm00001d027392_T025:6 Zm00001d027392_T012:6 Zm00001d027392_T030:6

			
						 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  
						
							TCATCACTACGGAAAGACATCTTTTGTGGAACATAGGACTTTTCTTCATCTTTACCACAGCTTT
CATCGCCTTTGGATGTTCCTTATTATGATGTTTCAGaaaattgatgagggtgccgtgcatgctg
tgttttctaaagcccttgataactatatcaaatggtgcaactatctgcctcttcgtcctgtctg
ggataagt

									
								

					

						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: 615
Transcript exons: 4235011-4235108,4235254-4235371,4236075-4236200,4236280-
4236356,4236433-4236511,4236761-4236877
AAAATTGATGAGGGTGCCGTGCATGCTGTGTTTTCTAAAGCCCTTGATAACTATATCAAATGGT
GCAACTATCTGCCTCTTCGTCCTGTCTGGGATAACAATGATTCGTTGACAAAGGAAAAGAAGTT
GCTATATGTGTGTTTATACTACTTGATGTGGGGAGAAGCTGCTAACGTGCGATTTATTCCAGAG
GGCTTATGCTACATATTTCATCATCTAGCAAGAGAATTAGGGGTGATTCTGCAGAAACAAACTG
CAGAGCCAGCTGAAAGCTGCAATTCTGGTGGTGGCGTATCGTTTCTTGACAATGTCATTTATCC
TTTCTATGAAATCATTGCAGCGGAAGCAGCCAATAATAAAAACGGGCGTGCACCACATTCTGAA
TGGAGAAATTATGATGATTTCAATGAGTTTTTCTGGTCTCATAAGTGCTTCCACCTACGATGGC
CTTGGAACCTGAGCGACCCGTTTTTCTCGAAGCCCAGTAGGAAATATAAGGGCTTGCTCAGTAG
GAATCATCACTACGGAAAGACATCTTTTGTGGAACATAGGACTTTTCTTCATCTTTACCACAGC
TTTCATCGCCTTTGGATGTTCCTTATTATGATGTTTCAG
						
					

						Genomic sequence
						
							AAAATTGATGAGGGTGCCGTGCATGCTGTGTTTTCTAAAGCCCTTGATAACTATATCAAATGGT
GCAACTATCTGCCTCTTCGTCCTGTCTGGGATAAGTATGTTCTTTTTTAAAAAATATACTTTGG
TCTCATCTACTTAATTCCTTAGTATGGTTTCTTTTTATATATACTTTGGTCTTATCTACTTAAC
TCCTTATGATCGCCTCATTTGGTTTTAAGATATTGCATGGTTTTCTTTTAGCAATGATTCGTTG
ACAAAGGAAAAGAAGTTGCTATATGTGTGTTTATACTACTTGATGTGGGGAGAAGCTGCTAACG
TGCGATTTATTCCAGAGGGCTTATGCTACATATTTCATCATGTAAGTCTGTATGATTTTAATGA
AGCTACCTATTATGGTTTTTGATGCTGCACGATTTTCCTTTATTTTTCTGTTTTTGTGTGAAAA
TATTTCGTAATCACAATGATTGGTTGGTCCATGAGCTTCCTTTTTTCAGCGACACACACCAGTA
TATCATATATGTCCCTTTCTCATGTCTCTGTGGCTAGATTTATGCTTATGACTCATGGTTTAAC
AGACATAACTTTGAAACTATTTTTGTTGTGTGTATGTGTGTGTGTGCTACTGTGCTTTAGCAGG
GTCCTTATCCCTTTTCTTTTTCTTAAAATAATGATACCCAGCTCTCCTGCATGTTCAAGATTTT
TTTGCCTTGTCAATTTGTGTCCTGGTGTTGGCGTTTGTCACACGTGAAGTGACTCTATCCTACT
ACCTTCCTGGGATGGGAGCAGCCTCAATGCTATGTGATCTGGTGATGCACATGATATGTGAGGA
TTGTAGGAGATAGTTTATGTGAGGGGGAGGAACTAGTTAGTATGCTTCAGACCCAAATAGAATT
TGATAAAGAGCTATTCCATCATGGTTAATCCATGTTCACAGTATGAAATCAAAATGATGAACCC
AAATCTCATTTTTGAAGATTGCGTGCCAATGTCTGGATTGGATTTCAATACGTGCTGGATGGTA
CTCATATTGTTAACATTTGTTTTCGGTTTCAATTTTGCAGCTAGCAAGAGAATTAGGGGTGATT
CTGCAGAAACAAACTGCAGAGCCAGCTGAAAGCTGCAATTCTGGTGGTGGCGTATCGTTTCTTG
ACAATGTCATTTATCCTTTCTATGAAATCATTGCAGCGGTAAGTGTGCCTGCTGGTGAGCTAAT
ACCAGTCATTATTTTTGGTCCTATATGGTTTTCTTAATGTTGAATGTCCGCAGGAAGCAGCCAA
TAATAAAAACGGGCGTGCACCACATTCTGAATGGAGAAATTATGATGATTTCAATGAGTTTTTC
TGGTAAGCGAATCAATCCAATTACTTTTGTTTGTCAATTTGTTTCTATTTTTTATAATCTTTTG
ATGTTTCCTTCTAGGTCTCATAAGTGCTTCCACCTACGATGGCCTTGGAACCTGAGCGACCCGT
TTTTCTCGAAGCCCAGTAGGAAATATAAGGTTTGTTTTTATATTAAATCATAATCACAATTATT
TTGATCTTTCTGTAGCTGTAACCAAATCAGTATTTGTATATCTGTAAGTCAATAAATATGTTTT
GTGCTTCTTGACCATCATAGGAAGTCGTCAATAATGAGATATGATCCATTTTCACTTTAACCAA
GCTTAAGTACAGGCTTACAAAAATGCTTCTATTTCTTGTGAATTGTTTGCCTGCTTCGCTTACA
AGATGCACATTTGGTTTTGCAGGGCTTGCTCAGTAGGAATCATCACTACGGAAAGACATCTTTT
GTGGAACATAGGACTTTTCTTCATCTTTACCACAGCTTTCATCGCCTTTGGATGTTCCTTATTA
TGATGTTTCAG
						
					

			
		

Sequences
Splice junction sequence	TCATCACTACGGAAAGACATCTTTTGTGGAACATAGGACTTTTCTTCATCTTTACCACAGCTTT CATCGCCTTTGGATGTTCCTTATTATGATGTTTCAGaaaattgatgagggtgccgtgcatgctg tgttttctaaagcccttgataactatatcaaatggtgcaactatctgcctcttcgtcctgtctg ggataagt
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: 615 Transcript exons: 4235011-4235108,4235254-4235371,4236075-4236200,4236280- 4236356,4236433-4236511,4236761-4236877 AAAATTGATGAGGGTGCCGTGCATGCTGTGTTTTCTAAAGCCCTTGATAACTATATCAAATGGT GCAACTATCTGCCTCTTCGTCCTGTCTGGGATAACAATGATTCGTTGACAAAGGAAAAGAAGTT GCTATATGTGTGTTTATACTACTTGATGTGGGGAGAAGCTGCTAACGTGCGATTTATTCCAGAG GGCTTATGCTACATATTTCATCATCTAGCAAGAGAATTAGGGGTGATTCTGCAGAAACAAACTG CAGAGCCAGCTGAAAGCTGCAATTCTGGTGGTGGCGTATCGTTTCTTGACAATGTCATTTATCC TTTCTATGAAATCATTGCAGCGGAAGCAGCCAATAATAAAAACGGGCGTGCACCACATTCTGAA TGGAGAAATTATGATGATTTCAATGAGTTTTTCTGGTCTCATAAGTGCTTCCACCTACGATGGC CTTGGAACCTGAGCGACCCGTTTTTCTCGAAGCCCAGTAGGAAATATAAGGGCTTGCTCAGTAG GAATCATCACTACGGAAAGACATCTTTTGTGGAACATAGGACTTTTCTTCATCTTTACCACAGC TTTCATCGCCTTTGGATGTTCCTTATTATGATGTTTCAG
Genomic sequence	AAAATTGATGAGGGTGCCGTGCATGCTGTGTTTTCTAAAGCCCTTGATAACTATATCAAATGGT GCAACTATCTGCCTCTTCGTCCTGTCTGGGATAAGTATGTTCTTTTTTAAAAAATATACTTTGG TCTCATCTACTTAATTCCTTAGTATGGTTTCTTTTTATATATACTTTGGTCTTATCTACTTAAC TCCTTATGATCGCCTCATTTGGTTTTAAGATATTGCATGGTTTTCTTTTAGCAATGATTCGTTG ACAAAGGAAAAGAAGTTGCTATATGTGTGTTTATACTACTTGATGTGGGGAGAAGCTGCTAACG TGCGATTTATTCCAGAGGGCTTATGCTACATATTTCATCATGTAAGTCTGTATGATTTTAATGA AGCTACCTATTATGGTTTTTGATGCTGCACGATTTTCCTTTATTTTTCTGTTTTTGTGTGAAAA TATTTCGTAATCACAATGATTGGTTGGTCCATGAGCTTCCTTTTTTCAGCGACACACACCAGTA TATCATATATGTCCCTTTCTCATGTCTCTGTGGCTAGATTTATGCTTATGACTCATGGTTTAAC AGACATAACTTTGAAACTATTTTTGTTGTGTGTATGTGTGTGTGTGCTACTGTGCTTTAGCAGG GTCCTTATCCCTTTTCTTTTTCTTAAAATAATGATACCCAGCTCTCCTGCATGTTCAAGATTTT TTTGCCTTGTCAATTTGTGTCCTGGTGTTGGCGTTTGTCACACGTGAAGTGACTCTATCCTACT ACCTTCCTGGGATGGGAGCAGCCTCAATGCTATGTGATCTGGTGATGCACATGATATGTGAGGA TTGTAGGAGATAGTTTATGTGAGGGGGAGGAACTAGTTAGTATGCTTCAGACCCAAATAGAATT TGATAAAGAGCTATTCCATCATGGTTAATCCATGTTCACAGTATGAAATCAAAATGATGAACCC AAATCTCATTTTTGAAGATTGCGTGCCAATGTCTGGATTGGATTTCAATACGTGCTGGATGGTA CTCATATTGTTAACATTTGTTTTCGGTTTCAATTTTGCAGCTAGCAAGAGAATTAGGGGTGATT CTGCAGAAACAAACTGCAGAGCCAGCTGAAAGCTGCAATTCTGGTGGTGGCGTATCGTTTCTTG ACAATGTCATTTATCCTTTCTATGAAATCATTGCAGCGGTAAGTGTGCCTGCTGGTGAGCTAAT ACCAGTCATTATTTTTGGTCCTATATGGTTTTCTTAATGTTGAATGTCCGCAGGAAGCAGCCAA TAATAAAAACGGGCGTGCACCACATTCTGAATGGAGAAATTATGATGATTTCAATGAGTTTTTC TGGTAAGCGAATCAATCCAATTACTTTTGTTTGTCAATTTGTTTCTATTTTTTATAATCTTTTG ATGTTTCCTTCTAGGTCTCATAAGTGCTTCCACCTACGATGGCCTTGGAACCTGAGCGACCCGT TTTTCTCGAAGCCCAGTAGGAAATATAAGGTTTGTTTTTATATTAAATCATAATCACAATTATT TTGATCTTTCTGTAGCTGTAACCAAATCAGTATTTGTATATCTGTAAGTCAATAAATATGTTTT GTGCTTCTTGACCATCATAGGAAGTCGTCAATAATGAGATATGATCCATTTTCACTTTAACCAA GCTTAAGTACAGGCTTACAAAAATGCTTCTATTTCTTGTGAATTGTTTGCCTGCTTCGCTTACA AGATGCACATTTGGTTTTGCAGGGCTTGCTCAGTAGGAATCATCACTACGGAAAGACATCTTTT GTGGAACATAGGACTTTTCTTCATCTTTACCACAGCTTTCATCGCCTTTGGATGTTCCTTATTA TGATGTTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.072089502

Conservation Information
Conserved circRNAs	NA
PMCS	0.072089502

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4235310-4236874(+)
4235036-4236454(-)
						
						Potential amino acid sequence
						
							MWGEAANVRFIPEGLCYIFHHLARELGVILQKQTAEPAESCNSGGGVSFLDNVIYPFYEIIAAE
AANNKNGRAPHSEWRNYDDFNEFFWSHKCFHLRWPWNLSDPFFSKPSRKYKGLLSRNHHYGKTS
FVEHRTFLHLYHSFHRLWMFLIMMFQKIDEGAVHAVFSKALDNYIKWCNYLPLRPVWDNNDSLT
KEKKLLYVCLYYLMWGEAANVRFIPEGLCYIFHHLARELGVILQKQTAEPAESCNSGGGVSFLD
NVIYPFYEIIAAEAANNKNGRAPHSEWRNYDDFNEFFWSHKCFHLRWPWNLSDPFFSKPSRKYK
GLLSRNHHYGKTSFVEHRTFLHLYHSFHRLWMFLIMMFQKIDEGAVHAVFSKALDNYIKWCNYL
PLRPVWDNNDSLTKEKKLLYVCLYYLMWGEAANVRFIPEGLCYIFHHLARELGVILQKQTAEPA
ESCNSGGGVSFLDNVIYPFYEIIAAEAANNKNGRAPHSEWRNYDDFNEFFWSHKCFHLRWPWNL
SDPFFSKPSRKYKGLLSRNHHYGKTSFVEHRTFLHLYHSFHRLWMFLIMMFQKIDEGAVHAVFS
KALDNYIKWCNYLPLRPVWDNNDSLTKEKKLLYVCLYYLMWGEAANVRFIPEGLCYIFHHLARE
LGVILQKQTAEPAESCNSGGGVSFLDNVIYPFYEIIAAEAANNKNGRAPHSEWRNYDDFNEFFW
SHKCFHLRWPWNLSDPFFSKPSRKYKGLLSRNHHYGKTSFVEHRTFLHLYHSFHRLWMFLIMMF
Q(+)
MHGTLINFLKHHNKEHPKAMKAVVKMKKSPMFHKRCLSVVMIPTEQALIFPTGLREKRVAQVPR
PS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4235310-4236874(+) 4235036-4236454(-)
Potential amino acid sequence	MWGEAANVRFIPEGLCYIFHHLARELGVILQKQTAEPAESCNSGGGVSFLDNVIYPFYEIIAAE AANNKNGRAPHSEWRNYDDFNEFFWSHKCFHLRWPWNLSDPFFSKPSRKYKGLLSRNHHYGKTS FVEHRTFLHLYHSFHRLWMFLIMMFQKIDEGAVHAVFSKALDNYIKWCNYLPLRPVWDNNDSLT KEKKLLYVCLYYLMWGEAANVRFIPEGLCYIFHHLARELGVILQKQTAEPAESCNSGGGVSFLD NVIYPFYEIIAAEAANNKNGRAPHSEWRNYDDFNEFFWSHKCFHLRWPWNLSDPFFSKPSRKYK GLLSRNHHYGKTSFVEHRTFLHLYHSFHRLWMFLIMMFQKIDEGAVHAVFSKALDNYIKWCNYL PLRPVWDNNDSLTKEKKLLYVCLYYLMWGEAANVRFIPEGLCYIFHHLARELGVILQKQTAEPA ESCNSGGGVSFLDNVIYPFYEIIAAEAANNKNGRAPHSEWRNYDDFNEFFWSHKCFHLRWPWNL SDPFFSKPSRKYKGLLSRNHHYGKTSFVEHRTFLHLYHSFHRLWMFLIMMFQKIDEGAVHAVFS KALDNYIKWCNYLPLRPVWDNNDSLTKEKKLLYVCLYYLMWGEAANVRFIPEGLCYIFHHLARE LGVILQKQTAEPAESCNSGGGVSFLDNVIYPFYEIIAAEAANNKNGRAPHSEWRNYDDFNEFFW SHKCFHLRWPWNLSDPFFSKPSRKYKGLLSRNHHYGKTSFVEHRTFLHLYHSFHRLWMFLIMMF Q(+) MHGTLINFLKHHNKEHPKAMKAVVKMKKSPMFHKRCLSVVMIPTEQALIFPTGLREKRVAQVPR PS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d027392_circ_g.1

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