Plant Circular RNA Database

Detail information of Zm00001d010523_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d010523_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009671
					
						Alias
						zma_circ_0002800
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 119147149-119148464  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d010523						
					
						Parent gene annotation
						
							Sucrose-phosphatase 1  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d010523_circ_g.1 Zm00001d010523_circ_g.2 Zm00001d010523_circ_g.4 						
					
						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
						Zm00001d010523_T012:5
Zm00001d010523_T008:5
Zm00001d010523_T002:5
Zm00001d010523_T001:5
Zm00001d010523_T004:5
Zm00001d010523_T006:5
Zm00001d010523_T011:5
Zm00001d010523_T009:5
Zm00001d010523_T003:5
Zm00001d010523_T007:5
Zm00001d010523_T005:4

General Information
CircRNA Name	Zm00001d010523_circ_g.3
ID in PlantcircBase	zma_circ_009671
Alias	zma_circ_0002800
Organism	Zea mays
Position	chr8: 119147149-119148464 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d010523
Parent gene annotation	Sucrose-phosphatase 1
Parent gene strand	-
Alternative splicing	Zm00001d010523_circ_g.1 Zm00001d010523_circ_g.2 Zm00001d010523_circ_g.4
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	Zm00001d010523_T012:5 Zm00001d010523_T008:5 Zm00001d010523_T002:5 Zm00001d010523_T001:5 Zm00001d010523_T004:5 Zm00001d010523_T006:5 Zm00001d010523_T011:5 Zm00001d010523_T009:5 Zm00001d010523_T003:5 Zm00001d010523_T007:5 Zm00001d010523_T005:4

			
						 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  
						
							CAGACCAAGATATGAGTTGGACGACATTCACCATTGTATGGTCAAGATCTGAAACAATCATAAG
ACGTGCAGAACCACTGAGCTTATCCATCTTGGGAGTagtgatgtttttgaagtactttataact
gaatcagactttggaacctcagccctgcgccacttctcatagagaacgtagaacttcactacag
catctgta

						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
						
							AGTGATGTTTTTGAAGTACTTTATAACTGAATCAGACTTTGGAACCTCAGCCCTGCGCCACTTC
TCATAGAGAACGTAGAACTTCACTACAGCATCTGTAGGTTTGAAAGAGGCTTCCTTTGCATAAG
GAAACTGCAGGTCTCTAGGAGAAATGTTAGGTCCTAGCTTGAAGTGTCCAATAGCTTGTATAAT
ACCAGCTGCACATCTCTCATTTGAATGAATTATCTTTGGGTTATCCTTCGCATTTTCTGTGTAC
CACTGAAGTAGTTCCTCTTGGGCATTGCTGACCTGAGCATTAGAAAATTTTGGAGTTGCAGTAA
CTATTCAGGCATTAACTTTGTTAGATACTTGATGCAATGTATTTTTCACTGACCATGACACCAT
GTACACCAGGGATGCTGAATAATTCTGCATCATTACCAGAGTCACCACAAACAAGAGTATTGTT
GGGCGGTTTTCCACATGAGCTTAGCTTTTTAAGCAAATATGCAAGTGCTTGGCCCTTTCCAGCT
CCTTGAGGTAATATATCAAGGTCCTGGCCACCACTATATATTATTTTGGCATCTAGCTGTTCAC
AAGAATTAAAGCAGTCAACCATAATGTGTCTCAACATAGATAGAGGAAATTATCCAAAACCAAA
TCACAACAATATAAGATGCATGCTGCCTCACCCCACATTTGTCCAATCTCTCGGCAACAGATTT
TATCACTTCCTGGGCATTCTTCTTATCAACAAAAAAGCTGACCTTGTGCGGGCGCTGTTCTGTC
TCTGGCTGTATCCATGCAAATGTAAAAGGCAAATTAGTATTAATTCCATGAATATAGATGAAGA
CACCAGCCATGCATGCAGCAGAACATACCTGAAGCTTCAGCTCAGAAAAGCTCACAGTTTCTGC
TACAACAATATTCCTGTCCCACTTATTGTTCAGATATTCTTCCCAGCCATCATCAGGAACCATT
GCCTCCCCATATGTTATCTCAGTGCCAACAGACATGATAGTGATGTCTGGAGTTAGCATAGGCT
TCTCTTTCCTTAATTCCTTGTAAAGAGTTGGTGATCTTCCAGTCGAGAAGACTAGTAGAGAATC
CTCACAGTAAACAGATTCCCACAGGGCACCAAACCTAAGCAAGGACAGGTTCTCCTCGTCATGA
TGATCAACCTGCAAGTTTTAGCCATCCCAAAAGAATGAAGAGTTTACATACAGATAGCTTAAGG
CAGACCAAGATATGAGTTGGACGACATTCACCATTGTATGGTCAAGATCTGAAACAATCATAAG
ACGTGCAGAACCACTGAGCTTATCCATCTTGGGAGT

Sequences
Splice junction sequence	CAGACCAAGATATGAGTTGGACGACATTCACCATTGTATGGTCAAGATCTGAAACAATCATAAG ACGTGCAGAACCACTGAGCTTATCCATCTTGGGAGTagtgatgtttttgaagtactttataact gaatcagactttggaacctcagccctgcgccacttctcatagagaacgtagaacttcactacag catctgta
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	AGTGATGTTTTTGAAGTACTTTATAACTGAATCAGACTTTGGAACCTCAGCCCTGCGCCACTTC TCATAGAGAACGTAGAACTTCACTACAGCATCTGTAGGTTTGAAAGAGGCTTCCTTTGCATAAG GAAACTGCAGGTCTCTAGGAGAAATGTTAGGTCCTAGCTTGAAGTGTCCAATAGCTTGTATAAT ACCAGCTGCACATCTCTCATTTGAATGAATTATCTTTGGGTTATCCTTCGCATTTTCTGTGTAC CACTGAAGTAGTTCCTCTTGGGCATTGCTGACCTGAGCATTAGAAAATTTTGGAGTTGCAGTAA CTATTCAGGCATTAACTTTGTTAGATACTTGATGCAATGTATTTTTCACTGACCATGACACCAT GTACACCAGGGATGCTGAATAATTCTGCATCATTACCAGAGTCACCACAAACAAGAGTATTGTT GGGCGGTTTTCCACATGAGCTTAGCTTTTTAAGCAAATATGCAAGTGCTTGGCCCTTTCCAGCT CCTTGAGGTAATATATCAAGGTCCTGGCCACCACTATATATTATTTTGGCATCTAGCTGTTCAC AAGAATTAAAGCAGTCAACCATAATGTGTCTCAACATAGATAGAGGAAATTATCCAAAACCAAA TCACAACAATATAAGATGCATGCTGCCTCACCCCACATTTGTCCAATCTCTCGGCAACAGATTT TATCACTTCCTGGGCATTCTTCTTATCAACAAAAAAGCTGACCTTGTGCGGGCGCTGTTCTGTC TCTGGCTGTATCCATGCAAATGTAAAAGGCAAATTAGTATTAATTCCATGAATATAGATGAAGA CACCAGCCATGCATGCAGCAGAACATACCTGAAGCTTCAGCTCAGAAAAGCTCACAGTTTCTGC TACAACAATATTCCTGTCCCACTTATTGTTCAGATATTCTTCCCAGCCATCATCAGGAACCATT GCCTCCCCATATGTTATCTCAGTGCCAACAGACATGATAGTGATGTCTGGAGTTAGCATAGGCT TCTCTTTCCTTAATTCCTTGTAAAGAGTTGGTGATCTTCCAGTCGAGAAGACTAGTAGAGAATC CTCACAGTAAACAGATTCCCACAGGGCACCAAACCTAAGCAAGGACAGGTTCTCCTCGTCATGA TGATCAACCTGCAAGTTTTAGCCATCCCAAAAGAATGAAGAGTTTACATACAGATAGCTTAAGG CAGACCAAGATATGAGTTGGACGACATTCACCATTGTATGGTCAAGATCTGAAACAATCATAAG ACGTGCAGAACCACTGAGCTTATCCATCTTGGGAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_001760* osa_circ_013109 						
					
						PMCS
						0.284904654

Conservation Information
Conserved circRNAs	osa_circ_001760* osa_circ_013109
PMCS	0.284904654

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							119148457-119147151(-)
						
						Potential amino acid sequence
						
							MDKLSGSARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRK
EKPMLTPDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPH
KVSFFVDKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGK
PPNNTLVCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAI
GHFKLGPNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNITTPKMD
KLSGSARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRKEK
PMLTPDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPHKV
SFFVDKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGKPP
NNTLVCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAIGH
FKLGPNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNITTPKMDKL
SGSARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRKEKPM
LTPDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPHKVSF
FVDKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGKPPNN
TLVCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAIGHFK
LGPNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNITTPKMDKLSG
SARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRKEKPMLT
PDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPHKVSFFV
DKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGKPPNNTL
VCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAIGHFKLG
PNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNIT(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	119148457-119147151(-)
Potential amino acid sequence	MDKLSGSARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRK EKPMLTPDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPH KVSFFVDKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGK PPNNTLVCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAI GHFKLGPNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNITTPKMD KLSGSARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRKEK PMLTPDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPHKV SFFVDKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGKPP NNTLVCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAIGH FKLGPNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNITTPKMDKL SGSARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRKEKPM LTPDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPHKVSF FVDKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGKPPNN TLVCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAIGHFK LGPNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNITTPKMDKLSG SARLMIVSDLDHTMVDHHDEENLSLLRFGALWESVYCEDSLLVFSTGRSPTLYKELRKEKPMLT PDITIMSVGTEITYGEAMVPDDGWEEYLNNKWDRNIVVAETVSFSELKLQPETEQRPHKVSFFV DKKNAQEVIKSVAERLDKCGLDAKIIYSGGQDLDILPQGAGKGQALAYLLKKLSSCGKPPNNTL VCGDSGNDAELFSIPGVHGVMVSNAQEELLQWYTENAKDNPKIIHSNERCAAGIIQAIGHFKLG PNISPRDLQFPYAKEASFKPTDAVVKFYVLYEKWRRAEVPKSDSVIKYFKNIT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d010523_circ_g.3

Address

Any questions?

Supported by