Plant Circular RNA Database

Detail information of Os12g0407500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os12g0407500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_011288
					
						Alias
						Os12circ05237
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 12325480-12327527  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Os12g0407500						
					
						Parent gene annotation
						
							Tensin phosphatase, C2 domain domain containing protein. (Os12t0
407500-01);Similar to PTEN-like protein. (Os12t0407500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os12g0407200_circ_ag.1 Os12g0407500_circ_igg.1 Os12g0407500_circ_g.1 Os12g0407500_circ_g.2 Os12g0407500_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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
						Os12t0407500-02:4
Os12t0407500-01:7

General Information
CircRNA Name	Os12g0407500_circ_g.3
ID in PlantcircBase	osa_circ_011288
Alias	Os12circ05237
Organism	Oryza sativa
Position	chr12: 12325480-12327527 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl
Parent gene	Os12g0407500
Parent gene annotation	Tensin phosphatase, C2 domain domain containing protein. (Os12t0 407500-01);Similar to PTEN-like protein. (Os12t0407500-02)
Parent gene strand	-
Alternative splicing	Os12g0407200_circ_ag.1 Os12g0407500_circ_igg.1 Os12g0407500_circ_g.1 Os12g0407500_circ_g.2 Os12g0407500_circ_g.4
Support reads	2
Tissues	leaf
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	Os12t0407500-02:4 Os12t0407500-01:7

			
						 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  
						
							CAAAATATCCAAAAAGCCCTGAGCTCAAATCTCCAGCAGGGAAACCCATAGCAATGATGTTCTC
TGTAATATATGTCATATCTAAATCAAAGCCGCCTTCcattgtgattagacacagtgattgatgg
tctaatccaataagggcatctatgaaggcgaaatcccctgagcatgcacctgcaaaataaaatt
gcatatta

									
								

					

						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: 631
Transcript exons: 12325480-12325556,12325640-12325704,12325782-12325868,12
325977-12326153,12326649-12326714,12327285-12327341,1232
7426-12327527
CATTGTGATTAGACACAGTGATTGATGGTCTAATCCAATAAGGGCATCTATGAAGGCGAAATCC
CCTGAGCATGCACCTGCGTGGAGGCTGATTTTCACCATTGAAGTAAGTTAAGATGCGCTCAAAA
TATTTCACATATCTAATCTGACTTGGGAGAATAAGCCCTTTTCCATCTACACATCTTTTCTGAT
TGTAGTATTCAATGGACTCTTCCGCAGTTGGAAAGAACTTCAGGTATAGTAGCAGACTGGAGAT
CATCAATCCTGTCCTCGCCTTTCCAGCTTTGCAATGAACAACCACTACATTTTCTATATCTTCC
TTCAACCAAGAGTAAGCACTATGGCAGAACGATATGACAAGTTGTATCGGAGGGCAATTGTGAT
CATCAAAAGGGAAGCATGCAACCTTTCCCTCAAAAAGAGATGCATCATATAGCCTTTCCGAGCA
AAGGTTGTACACCTTATACTTTCCCTTGTGGTGCATTTCAAAGAACCTGATGACTTCCTCCATG
TGGTTGCGGTAGAAGCCCTCAAAATATCCAAAAAGCCCTGAGCTCAAATCTCCAGCAGGGAAAC
CCATAGCAATGATGTTCTCTGTAATATATGTCATATCTAAATCAAAGCCGCCTTC
						
					

						Genomic sequence
						
							CATTGTGATTAGACACAGTGATTGATGGTCTAATCCAATAAGGGCATCTATGAAGGCGAAATCC
CCTGAGCATGCACCTGCAAAATAAAATTGCATATTAATAAGATATACATGTAGCGCATATCCTC
ATACTGAAACCATGGTAGAACTAGATGAATACCTGCGTGGAGGCTGATTTTCACCATTGAAGTA
AGTTAAGATGCGCTCAAAATATTTCACATATCTCTGTAATTTTGGAACACATTCAGAACAACCA
CTGTTAAGTTGTATGAATAAATTTGAATAATTTTGGAGTTACTTACAATCTGACTTGGGAGAAT
AAGCCCTTTTCCATCTACACATCTTTTCTGATTGTAGTATTCAATGGACTCTTCCGCAGTTGGA
AAGAACTGTCAATTGTATAATACACAGGCTTCAAATATTAAGAAAATTTGATGAAGATTCTCTT
GGGCAATGTATCATAATTATCATTTAATTTAATGTGAAACCAATTTTACCTTCAGGTATAGTAG
CAGACTGGAGATCATCAATCCTGTCCTCGCCTTTCCAGCTTTGCAATGAACAACCACTACATTT
TCTATATCTTCCTTCAACCAAGAGTAAGCACTATGGCAGAACGATATGACAAGTTGTATCGGAG
GGCAATTGTGATCATCAAAAGGGAAGCATGCAACCTGAAACATGGCTACTAAATTTGACCACTA
TGTGCAATATGCAATTAAATCGATTATTACACACCATTTAAAATACTGATACAAATGAAGGAAT
ATTCAATATACCACCGGATGAACTGCGGACATTAAAATTTTCGGCAAGTCTTTTTCTAGCCTTG
ATAAGCTTGAGTGCTAGACTAGTCACTTGGAACTTAGAAATAAAACAAGATTTTGGATGCCACC
TAGCCTAGGTGACCTAGATTAACGATTACTCCATCCTAATCGTGTCCCACTCCTCTTCAAACTC
TAATGGTTGCTGCCGAGGTGAATAACTGAACACGCAGCCAAGTCAAACATGGCAAACAATCTAG
ATAGCTCAGCTAAGCTATAGCTCATCTTAGCAAAGAACCAAGCGTACCCTTTGTTGTATTCCCA
TTTTTGGTGGTTCATACGTGTATCACATGGTATGGAAATGACAGAACAGAGGACCTAGACAAAA
TTATAAGCTTCCCATACCTTTCCCTCAAAAAGAGATGCATCATATAGCCTTTCCGAGCAAAGGT
TGTACACCTTATACTTTCCCTGTAACACAATATGATAAGGGGTTGAAAAACACAAATAGATTAT
ATAACACCTCTAAATAATGCACCAATCAAGTGATTTTACTACAATGATATTTCTTCAAATGTAA
CAGAAAAAATCACATATCAACAATGTAAATAACATGTGTGCGGTATGTGCATCACATATAAAAC
CCTCATGCCAATGCAGAACATGTACTAGTACCAAAAAATTATTGCCCCATGCTCATAATCTTAT
GAAAAAATACATCTATATAGACGATGACAAAGTTAACCAGCATAATCATCAATGATAGAAAATA
TTAGACTTCTTCAATAGTTATACTAAGTCATGGTTTTAACACAGAAAATAATACCCTTTATATG
TGATGTTGAAGCTGATTCATTCCATGAAAAGTCAATTTAAACATACTAATAAGTCAAGGCAGCA
TGATCAAGGTATCCAAGACCATAAAGATGCATCAACAAGCAAAAGGAACCAGATATCTGTGAAA
AAAAGTTATAACAACGGCCTGAGATGAGTTGTCAGGTGGCATATACATCAACAAACTCAAGAGT
GAGTCAAAGCTACCTTGTGGTGCATTTCAAAGAACCTGATGACTTCCTCCATGTGGTTGCGGTA
GAAGCCCTGCAATAGAAGTATTACCCTGTTTTTGTCTACAGAGAAACGAAAAGGTGCCATAAGT
AATTTGTGTCTTGTCATTATACTGACCTCAAAATATCCAAAAAGCCCTGAGCTCAAATCTCCAG
CAGGGAAACCCATAGCAATGATGTTCTCTGTAATATATGTCATATCTAAATCAAAGCCGCCTTC
						
					

			
		

Sequences
Splice junction sequence	CAAAATATCCAAAAAGCCCTGAGCTCAAATCTCCAGCAGGGAAACCCATAGCAATGATGTTCTC TGTAATATATGTCATATCTAAATCAAAGCCGCCTTCcattgtgattagacacagtgattgatgg tctaatccaataagggcatctatgaaggcgaaatcccctgagcatgcacctgcaaaataaaatt gcatatta
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: 631 Transcript exons: 12325480-12325556,12325640-12325704,12325782-12325868,12 325977-12326153,12326649-12326714,12327285-12327341,1232 7426-12327527 CATTGTGATTAGACACAGTGATTGATGGTCTAATCCAATAAGGGCATCTATGAAGGCGAAATCC CCTGAGCATGCACCTGCGTGGAGGCTGATTTTCACCATTGAAGTAAGTTAAGATGCGCTCAAAA TATTTCACATATCTAATCTGACTTGGGAGAATAAGCCCTTTTCCATCTACACATCTTTTCTGAT TGTAGTATTCAATGGACTCTTCCGCAGTTGGAAAGAACTTCAGGTATAGTAGCAGACTGGAGAT CATCAATCCTGTCCTCGCCTTTCCAGCTTTGCAATGAACAACCACTACATTTTCTATATCTTCC TTCAACCAAGAGTAAGCACTATGGCAGAACGATATGACAAGTTGTATCGGAGGGCAATTGTGAT CATCAAAAGGGAAGCATGCAACCTTTCCCTCAAAAAGAGATGCATCATATAGCCTTTCCGAGCA AAGGTTGTACACCTTATACTTTCCCTTGTGGTGCATTTCAAAGAACCTGATGACTTCCTCCATG TGGTTGCGGTAGAAGCCCTCAAAATATCCAAAAAGCCCTGAGCTCAAATCTCCAGCAGGGAAAC CCATAGCAATGATGTTCTCTGTAATATATGTCATATCTAAATCAAAGCCGCCTTC
Genomic sequence	CATTGTGATTAGACACAGTGATTGATGGTCTAATCCAATAAGGGCATCTATGAAGGCGAAATCC CCTGAGCATGCACCTGCAAAATAAAATTGCATATTAATAAGATATACATGTAGCGCATATCCTC ATACTGAAACCATGGTAGAACTAGATGAATACCTGCGTGGAGGCTGATTTTCACCATTGAAGTA AGTTAAGATGCGCTCAAAATATTTCACATATCTCTGTAATTTTGGAACACATTCAGAACAACCA CTGTTAAGTTGTATGAATAAATTTGAATAATTTTGGAGTTACTTACAATCTGACTTGGGAGAAT AAGCCCTTTTCCATCTACACATCTTTTCTGATTGTAGTATTCAATGGACTCTTCCGCAGTTGGA AAGAACTGTCAATTGTATAATACACAGGCTTCAAATATTAAGAAAATTTGATGAAGATTCTCTT GGGCAATGTATCATAATTATCATTTAATTTAATGTGAAACCAATTTTACCTTCAGGTATAGTAG CAGACTGGAGATCATCAATCCTGTCCTCGCCTTTCCAGCTTTGCAATGAACAACCACTACATTT TCTATATCTTCCTTCAACCAAGAGTAAGCACTATGGCAGAACGATATGACAAGTTGTATCGGAG GGCAATTGTGATCATCAAAAGGGAAGCATGCAACCTGAAACATGGCTACTAAATTTGACCACTA TGTGCAATATGCAATTAAATCGATTATTACACACCATTTAAAATACTGATACAAATGAAGGAAT ATTCAATATACCACCGGATGAACTGCGGACATTAAAATTTTCGGCAAGTCTTTTTCTAGCCTTG ATAAGCTTGAGTGCTAGACTAGTCACTTGGAACTTAGAAATAAAACAAGATTTTGGATGCCACC TAGCCTAGGTGACCTAGATTAACGATTACTCCATCCTAATCGTGTCCCACTCCTCTTCAAACTC TAATGGTTGCTGCCGAGGTGAATAACTGAACACGCAGCCAAGTCAAACATGGCAAACAATCTAG ATAGCTCAGCTAAGCTATAGCTCATCTTAGCAAAGAACCAAGCGTACCCTTTGTTGTATTCCCA TTTTTGGTGGTTCATACGTGTATCACATGGTATGGAAATGACAGAACAGAGGACCTAGACAAAA TTATAAGCTTCCCATACCTTTCCCTCAAAAAGAGATGCATCATATAGCCTTTCCGAGCAAAGGT TGTACACCTTATACTTTCCCTGTAACACAATATGATAAGGGGTTGAAAAACACAAATAGATTAT ATAACACCTCTAAATAATGCACCAATCAAGTGATTTTACTACAATGATATTTCTTCAAATGTAA CAGAAAAAATCACATATCAACAATGTAAATAACATGTGTGCGGTATGTGCATCACATATAAAAC CCTCATGCCAATGCAGAACATGTACTAGTACCAAAAAATTATTGCCCCATGCTCATAATCTTAT GAAAAAATACATCTATATAGACGATGACAAAGTTAACCAGCATAATCATCAATGATAGAAAATA TTAGACTTCTTCAATAGTTATACTAAGTCATGGTTTTAACACAGAAAATAATACCCTTTATATG TGATGTTGAAGCTGATTCATTCCATGAAAAGTCAATTTAAACATACTAATAAGTCAAGGCAGCA TGATCAAGGTATCCAAGACCATAAAGATGCATCAACAAGCAAAAGGAACCAGATATCTGTGAAA AAAAGTTATAACAACGGCCTGAGATGAGTTGTCAGGTGGCATATACATCAACAAACTCAAGAGT GAGTCAAAGCTACCTTGTGGTGCATTTCAAAGAACCTGATGACTTCCTCCATGTGGTTGCGGTA GAAGCCCTGCAATAGAAGTATTACCCTGTTTTTGTCTACAGAGAAACGAAAAGGTGCCATAAGT AATTTGTGTCTTGTCATTATACTGACCTCAAAATATCCAAAAAGCCCTGAGCTCAAATCTCCAG CAGGGAAACCCATAGCAATGATGTTCTCTGTAATATATGTCATATCTAAATCAAAGCCGCCTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010452 						
					
						PMCS
						0.264088346

Conservation Information
Conserved circRNAs	osi_circ_010452
PMCS	0.264088346

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12327482-12325501(+)
12327508-12327516(-)
12325666-12327516(-)
						
						Potential amino acid sequence
						
							MMFSVIYVISKSKPPSIVIRHSD*(+)
MTYITENIIAMGFPAGDLSSGLFGYFEGFYRNHMEEVIRFFEMHHKGKYKVYNLCSERLYDASL
FEGKVACFPFDDHNCPPIQLVISFCHSAYSWLKEDIENVVVVHCKAGKARTGLMISSLLLYLKF
FPTAEESIEYYNQKRCVDGKGLILPSQIRYVKYFERILTYFNGENQPPRRCMLRGFRLHRCPYW
IRPSITVSNHNGRRL*(-)
MVKISLHAGACSGDFAFIDALIGLDHQSLCLITMEGGFDLDMTYITENIIAMGFPAGDLSSGLF
GYFEGFYRNHMEEVIRFFEMHHKGKYKVYNLCSERLYDASLFEGKVACFPFDDHNCPPIQLVIS
FCHSAYSWLKEDIENVVVVHCKAGKARTGLMISSLLLYLKFFPTAEESIEYYNQKRCVDGKGLI
LPSQIRYVKYFERILTYFNGENQPPRRCMLRGFRLHRCPYWIRPSITVSNHNGRRL*(-)
						
						Sponge-miRNAs
						
							osa-miR2105 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12327482-12325501(+) 12327508-12327516(-) 12325666-12327516(-)
Potential amino acid sequence	MMFSVIYVISKSKPPSIVIRHSD(+) MTYITENIIAMGFPAGDLSSGLFGYFEGFYRNHMEEVIRFFEMHHKGKYKVYNLCSERLYDASL FEGKVACFPFDDHNCPPIQLVISFCHSAYSWLKEDIENVVVVHCKAGKARTGLMISSLLLYLKF FPTAEESIEYYNQKRCVDGKGLILPSQIRYVKYFERILTYFNGENQPPRRCMLRGFRLHRCPYW IRPSITVSNHNGRRL(-) MVKISLHAGACSGDFAFIDALIGLDHQSLCLITMEGGFDLDMTYITENIIAMGFPAGDLSSGLF GYFEGFYRNHMEEVIRFFEMHHKGKYKVYNLCSERLYDASLFEGKVACFPFDDHNCPPIQLVIS FCHSAYSWLKEDIENVVVVHCKAGKARTGLMISSLLLYLKFFPTAEESIEYYNQKRCVDGKGLI LPSQIRYVKYFERILTYFNGENQPPRRCMLRGFRLHRCPYWIRPSITVSNHNGRRL*(-)
Sponge-miRNAs	osa-miR2105
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Os12g0407500_circ_g.3

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