Plant Circular RNA Database

Detail information of AT5G23490_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G23490_circ_g.2
					
						ID in PlantcircBase
						ath_circ_040038
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7920544-7922014  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT5G23490						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G23490_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						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
						AT5G23490.3:5
AT5G23490.4:5
AT5G23490.2:5
AT5G23490.1:5

General Information
CircRNA Name	AT5G23490_circ_g.2
ID in PlantcircBase	ath_circ_040038
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 7920544-7922014 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT5G23490
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	AT5G23490_circ_g.1
Support reads	1
Tissues	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	AT5G23490.3:5 AT5G23490.4:5 AT5G23490.2:5 AT5G23490.1:5

			
						 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  
						
							TGATCAACAGCAACAAGATCTTGTTGATGCTTCATCAAAAGCTCTCTCTTACAGACAAGAGATA
ATTGAAGAAAATATACGCCTAACATATGCCTTACAGaaatcagatgaatccttgccccaaactt
ctaatatcggagatcacacaaattctaccactgtgtcccgcctggttcaccagccagttgactg
gaagccag

									
								

					

						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: 639
Transcript exons: 7920544-7920839,7920956-7921055,7921135-7921212,7921748-
7921807,7921910-7922014
AAATCAGATGAATCCTTGCCCCAAACTTCTAATATCGGAGATCACACAAATTCTACCACTGTGT
CCCGCCTGGTTCACCAGCCAGTTGACTGGAAGCCAGTTGTGATCAAAGCTTCAGATGCTGATTC
ATCAGGCTTGCTGGTTGTTCACCCCCATGTGAATGCTAATGGTGAAGAAGCTACTGTGAGTAAT
CGTTTTGAAAGCCATTCTGAAGAAACTATAAGTAATGGCACTGTTAAAAGAGCTATAGATGGTA
CTGGTCCCTCTCAATTCGATTCGTCAATATCTCCTATGAGAATGCGATTGGAGGGAGAGCATGA
CGCACACTTCAGTTCGTCTACTCATGGATCTATGCCAGTTGGTGAAGTAAATCATTCAGGCAAT
GCATGGAAGCAGGACCTCATTCACAAGGTCCAGGAGCAGGAACAAGAAATTTCGCAGTTGAGAA
GATATCTTACTGACTGTTCTGTTAAGGAAGCCCAAATTCGCAATGAAAAATATGTTCTGGAAAA
GAGAATTGCCTACATGCGTCTGGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCA
AAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCTTACAG
						
					

						Genomic sequence
						
							AAATCAGATGAATCCTTGCCCCAAACTTCTAATATCGGAGATCACACAAATTCTACCACTGTGT
CCCGCCTGGTTCACCAGCCAGTTGACTGGAAGCCAGTTGTGATCAAAGCTTCAGATGCTGATTC
ATCAGGCTTGCTGGTTGTTCACCCCCATGTGAATGCTAATGGTGAAGAAGCTACTGTGAGTAAT
CGTTTTGAAAGCCATTCTGAAGAAACTATAAGTAATGGCACTGTTAAAAGAGCTATAGATGGTA
CTGGTCCCTCTCAATTCGATTCGTCAATATCTCCTATGAGGTACTGAAACAGAAACTACCACTC
TTGCGTGTGCTGAGTCTATTTGTAAATCTTATGGCTTAGATGAATTTCCATGAACGAAATGCCT
ATAATTTTCAAGATCTGATATCTGCTAGAATGCGATTGGAGGGAGAGCATGACGCACACTTCAG
TTCGTCTACTCATGGATCTATGCCAGTTGGTGAAGTAAATCATTCAGGCAATGCATGGAAGCAG
GTCTCTATCATACTTACTCTACGTCTTGGTTTTATTGGTGTAAATGAAAAACTGTTTACCGGAC
TATGTACCTATTCAGGACCTCATTCACAAGGTCCAGGAGCAGGAACAAGAAATTTCGCAGTTGA
GAAGATATCTTACTGACTGTTCTGTTAAGGTGAGTCTTGTTCGACATGGGAGATTTCTAGTCAC
TATTGGGGTTTTGTGTTACTAACTTTTGTGGTTCCTTGGGATTTGTTTGTGATTGAGTCAGGTT
TCTTTGGTTGCATATGGGTTTTCTCTTCTTTTTTGTCCTTTAGAAGTGAGCAGAACAAGAAATG
AAAATCATCTATGGTTTGGATCAATAAAAGGTTGTCATAAACAGAGTATAATATTCATGGGAAA
AGATAGATTTTCTGCTACTTAGAAGGACCTGCAAATATCTTACTCCGTTTCATCGGAGAAACAG
CAAACTCTCTATTGATCCAAACCAAAGATAATCTCTTCAATGGTTTTTATGTTCACTTCGAAAG
GGCACAAAACAAGAGCAAAACCCTAAACAATCAGCTCAACCACAAATAAAGCCCATGCGACCAT
AAGCGTAAATGACATAATAAACTATGTAGTCATTAATGCTTTCTGTTGGTTCATCCCTTGCATT
CTTTGTTAATTTTATGCTAAATCAGATGACTAACATTTTAGTTATCTTATAGGAAGCCCAAATT
CGCAATGAAAAATATGTTCTGGAAAAGAGAATTGCCTACATGCGTCTGGTAGGCCTTTCCTTTT
TTTTACTTATCTGTTTTATTCATCTCGTATTAAATGTATTTAATTTAATTGTTTGGAAGCTGAA
AGATTGTTGCTGTTGTAACCAGGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCA
AAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCTTACAG
						
					

			
		

Sequences
Splice junction sequence	TGATCAACAGCAACAAGATCTTGTTGATGCTTCATCAAAAGCTCTCTCTTACAGACAAGAGATA ATTGAAGAAAATATACGCCTAACATATGCCTTACAGaaatcagatgaatccttgccccaaactt ctaatatcggagatcacacaaattctaccactgtgtcccgcctggttcaccagccagttgactg gaagccag
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: 639 Transcript exons: 7920544-7920839,7920956-7921055,7921135-7921212,7921748- 7921807,7921910-7922014 AAATCAGATGAATCCTTGCCCCAAACTTCTAATATCGGAGATCACACAAATTCTACCACTGTGT CCCGCCTGGTTCACCAGCCAGTTGACTGGAAGCCAGTTGTGATCAAAGCTTCAGATGCTGATTC ATCAGGCTTGCTGGTTGTTCACCCCCATGTGAATGCTAATGGTGAAGAAGCTACTGTGAGTAAT CGTTTTGAAAGCCATTCTGAAGAAACTATAAGTAATGGCACTGTTAAAAGAGCTATAGATGGTA CTGGTCCCTCTCAATTCGATTCGTCAATATCTCCTATGAGAATGCGATTGGAGGGAGAGCATGA CGCACACTTCAGTTCGTCTACTCATGGATCTATGCCAGTTGGTGAAGTAAATCATTCAGGCAAT GCATGGAAGCAGGACCTCATTCACAAGGTCCAGGAGCAGGAACAAGAAATTTCGCAGTTGAGAA GATATCTTACTGACTGTTCTGTTAAGGAAGCCCAAATTCGCAATGAAAAATATGTTCTGGAAAA GAGAATTGCCTACATGCGTCTGGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCA AAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCTTACAG
Genomic sequence	AAATCAGATGAATCCTTGCCCCAAACTTCTAATATCGGAGATCACACAAATTCTACCACTGTGT CCCGCCTGGTTCACCAGCCAGTTGACTGGAAGCCAGTTGTGATCAAAGCTTCAGATGCTGATTC ATCAGGCTTGCTGGTTGTTCACCCCCATGTGAATGCTAATGGTGAAGAAGCTACTGTGAGTAAT CGTTTTGAAAGCCATTCTGAAGAAACTATAAGTAATGGCACTGTTAAAAGAGCTATAGATGGTA CTGGTCCCTCTCAATTCGATTCGTCAATATCTCCTATGAGGTACTGAAACAGAAACTACCACTC TTGCGTGTGCTGAGTCTATTTGTAAATCTTATGGCTTAGATGAATTTCCATGAACGAAATGCCT ATAATTTTCAAGATCTGATATCTGCTAGAATGCGATTGGAGGGAGAGCATGACGCACACTTCAG TTCGTCTACTCATGGATCTATGCCAGTTGGTGAAGTAAATCATTCAGGCAATGCATGGAAGCAG GTCTCTATCATACTTACTCTACGTCTTGGTTTTATTGGTGTAAATGAAAAACTGTTTACCGGAC TATGTACCTATTCAGGACCTCATTCACAAGGTCCAGGAGCAGGAACAAGAAATTTCGCAGTTGA GAAGATATCTTACTGACTGTTCTGTTAAGGTGAGTCTTGTTCGACATGGGAGATTTCTAGTCAC TATTGGGGTTTTGTGTTACTAACTTTTGTGGTTCCTTGGGATTTGTTTGTGATTGAGTCAGGTT TCTTTGGTTGCATATGGGTTTTCTCTTCTTTTTTGTCCTTTAGAAGTGAGCAGAACAAGAAATG AAAATCATCTATGGTTTGGATCAATAAAAGGTTGTCATAAACAGAGTATAATATTCATGGGAAA AGATAGATTTTCTGCTACTTAGAAGGACCTGCAAATATCTTACTCCGTTTCATCGGAGAAACAG CAAACTCTCTATTGATCCAAACCAAAGATAATCTCTTCAATGGTTTTTATGTTCACTTCGAAAG GGCACAAAACAAGAGCAAAACCCTAAACAATCAGCTCAACCACAAATAAAGCCCATGCGACCAT AAGCGTAAATGACATAATAAACTATGTAGTCATTAATGCTTTCTGTTGGTTCATCCCTTGCATT CTTTGTTAATTTTATGCTAAATCAGATGACTAACATTTTAGTTATCTTATAGGAAGCCCAAATT CGCAATGAAAAATATGTTCTGGAAAAGAGAATTGCCTACATGCGTCTGGTAGGCCTTTCCTTTT TTTTACTTATCTGTTTTATTCATCTCGTATTAAATGTATTTAATTTAATTGTTTGGAAGCTGAA AGATTGTTGCTGTTGTAACCAGGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCA AAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCTTACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.20021148

Conservation Information
Conserved circRNAs	NA
PMCS	0.20021148

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7920835-7922011(+)
						
						Potential amino acid sequence
						
							MRMRLEGEHDAHFSSSTHGSMPVGEVNHSGNAWKQDLIHKVQEQEQEISQLRRYLTDCSVKEAQ
IRNEKYVLEKRIAYMRLAFDQQQQDLVDASSKALSYRQEIIEENIRLTYALQKSDESLPQTSNI
GDHTNSTTVSRLVHQPVDWKPVVIKASDADSSGLLVVHPHVNANGEEATVSNRFESHSEETISN
GTVKRAIDGTGPSQFDSSISPMRMRLEGEHDAHFSSSTHGSMPVGEVNHSGNAWKQDLIHKVQE
QEQEISQLRRYLTDCSVKEAQIRNEKYVLEKRIAYMRLAFDQQQQDLVDASSKALSYRQEIIEE
NIRLTYALQKSDESLPQTSNIGDHTNSTTVSRLVHQPVDWKPVVIKASDADSSGLLVVHPHVNA
NGEEATVSNRFESHSEETISNGTVKRAIDGTGPSQFDSSISPMRMRLEGEHDAHFSSSTHGSMP
VGEVNHSGNAWKQDLIHKVQEQEQEISQLRRYLTDCSVKEAQIRNEKYVLEKRIAYMRLAFDQQ
QQDLVDASSKALSYRQEIIEENIRLTYALQKSDESLPQTSNIGDHTNSTTVSRLVHQPVDWKPV
VIKASDADSSGLLVVHPHVNANGEEATVSNRFESHSEETISNGTVKRAIDGTGPSQFDSSISPM
RMRLEGEHDAHFSSSTHGSMPVGEVNHSGNAWKQDLIHKVQEQEQEISQLRRYLTDCSVKEAQI
RNEKYVLEKRIAYMRLAFDQQQQDLVDASSKALSYRQEIIEENIRLTYALQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7920835-7922011(+)
Potential amino acid sequence	MRMRLEGEHDAHFSSSTHGSMPVGEVNHSGNAWKQDLIHKVQEQEQEISQLRRYLTDCSVKEAQ IRNEKYVLEKRIAYMRLAFDQQQQDLVDASSKALSYRQEIIEENIRLTYALQKSDESLPQTSNI GDHTNSTTVSRLVHQPVDWKPVVIKASDADSSGLLVVHPHVNANGEEATVSNRFESHSEETISN GTVKRAIDGTGPSQFDSSISPMRMRLEGEHDAHFSSSTHGSMPVGEVNHSGNAWKQDLIHKVQE QEQEISQLRRYLTDCSVKEAQIRNEKYVLEKRIAYMRLAFDQQQQDLVDASSKALSYRQEIIEE NIRLTYALQKSDESLPQTSNIGDHTNSTTVSRLVHQPVDWKPVVIKASDADSSGLLVVHPHVNA NGEEATVSNRFESHSEETISNGTVKRAIDGTGPSQFDSSISPMRMRLEGEHDAHFSSSTHGSMP VGEVNHSGNAWKQDLIHKVQEQEQEISQLRRYLTDCSVKEAQIRNEKYVLEKRIAYMRLAFDQQ QQDLVDASSKALSYRQEIIEENIRLTYALQKSDESLPQTSNIGDHTNSTTVSRLVHQPVDWKPV VIKASDADSSGLLVVHPHVNANGEEATVSNRFESHSEETISNGTVKRAIDGTGPSQFDSSISPM RMRLEGEHDAHFSSSTHGSMPVGEVNHSGNAWKQDLIHKVQEQEQEISQLRRYLTDCSVKEAQI RNEKYVLEKRIAYMRLAFDQQQQDLVDASSKALSYRQEIIEENIRLTYALQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G23490_circ_g.2

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