Plant Circular RNA Database

Detail information of AT4G29900_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G29900_circ_g.4
					
						ID in PlantcircBase
						ath_circ_033544
					
						Alias
						At_ciR5112
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 14613637-14615833  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT4G29900						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 10, plasma membrane-type
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G29900_circ_g.1 AT4G29900_circ_g.2 AT4G29900_circ_g.3 AT4G29900_circ_g.5 AT4G29900_circ_g.6 AT4G29900_circ_g.7 AT4G29900_circ_g.8 AT4G29900_circ_g.9 AT4G29900_circ_g.10 AT4G29900_circ_g.11 AT4G29900_circ_g.12 AT4G29900_circ_g.13 AT4G29900_circ_g.14 						
					
						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
						AT4G29900.1:11
AT4G29900.2:11

General Information
CircRNA Name	AT4G29900_circ_g.4
ID in PlantcircBase	ath_circ_033544
Alias	At_ciR5112
Organism	Arabidpsis thaliana
Position	chr4: 14613637-14615833 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT4G29900
Parent gene annotation	Calcium-transporting ATPase 10, plasma membrane-type
Parent gene strand	-
Alternative splicing	AT4G29900_circ_g.1 AT4G29900_circ_g.2 AT4G29900_circ_g.3 AT4G29900_circ_g.5 AT4G29900_circ_g.6 AT4G29900_circ_g.7 AT4G29900_circ_g.8 AT4G29900_circ_g.9 AT4G29900_circ_g.10 AT4G29900_circ_g.11 AT4G29900_circ_g.12 AT4G29900_circ_g.13 AT4G29900_circ_g.14
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	AT4G29900.1:11 AT4G29900.2:11

			
						 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  
						
							AAAAGTTGATACTCACCTGCAATGGTGTTTCTCCACCATTGTCCTCTGAGACGCTAGCCATTAG
TAAGCCCCATTCAGTGTTGACCCCTACCCCAGTAACcttaataccaacgatagccaacaatata
agatcatcctcaggtaattcccatctagagagttgctcttcatcagttggaatcttatccgctt
caaatgtt

									
								

					

						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
						
							CTTAATACCAACGATAGCCAACAATATAAGATCATCCTCAGGTAATTCCCATCTAGAGAGTTGC
TCTTCATCAGTTGGAATCTTATCCGCTTCAAATGTTCGGAAGGCAATTGCAACACAGCGCAGAC
TCCTTGCAGCCATATCATCGATAGCATCTTTTAACCCACCCATCTGAAACAACAAGACTTATAC
TCAGAATAAAAAACAAGTATTTCTATCAAGACTCTCATTACCAAATCTGGCACTGATTTGGACT
TGCAGTATGACATGGTCTTGAGTCAAGACACAATGATAAGTTCAACATTCAGACAAACTCTATC
ATGATAAAGAGAAACATAGTTACTGACCTTATCTTCACTCATATCTACAAAACTCTCACTCTCA
TCCATATAGTGCGTGCAGGATCCCAAAACAATTTCGGCAGCACCTTTCCAGTGAATATGGACAC
TCGAATCTGGCTGAAAATGAATTAGAAAGTCGTTAGGATGCTGATTGACAAGTAGAAACAACGA
TAAGAGAAAAATCAAAAACAAAGCAAAAGATCTACAAAAACTATGGGAGGAAATGAAAAGAAAA
AACATTACTGATTTCACTGCTACACCTCCTCGTTTCTTCTCTGAGTTGAATGGAAAAAATTGTA
CAGCAGAAGACTCAGACTTAAGAGCATCAAAATCCATACCCAACTGCAGTGTATAAGAAATTAA
AAGATTAGTTCTTCTCACGGCTATATATACGGGAACCAGAAAATGTAGCTAAAGAATAAACCTT
TATCGCCCAATTGAGAATTGCTCTTTCTGTAGGAGATCCAGAAACCTGAATCTCACCACTCTGT
CATCAGTAAAGACATAGGCATTATTACATTAAATCAGCTGAAGTAGAAACCAAACGGGAAATCA
GTAAAGTTCCAAAGAATTTTAATCCTACTTCAGATCGGAACACACTGCCGGTTGTATTGTGAGC
AATACCCTCAACAAGTATGGATGTAAAAGCAGATGGCAATTTTGAGCTGCTGTCGGGAGAATCC
ATCTTTTGTAACCCAGCATAACACTCAACAACGGTCATCTGAGAAAAAAGAAAGTCGTAGGGGA
CCCGCTTGTTGGGTACACAATTCAAAATAGCAAAAGCTCATAACTAGGAAAGCACATACCAAAA
CTGGTAAGTGTTAAGTGTGTTAGCAAATACAAAAAGAAGGCAGAGCACCAAGATTCACCTCGTT
TAAGGTCAAAGTTCCAGTCTTATCACTGCAAATTGTTGTTGCAGACCCCATGGTTTCACAGGCT
GAAAGCCTACGCACCTGAAATTAAAATTCGTTTAAGTTGCAAAAGACATTCACGTATAAGAATT
TTGCATTTATGTTCATTCAAACTTATTGAGTCCCAAAAATTAAAATATACATACCAAAGCTTTA
TCTGCCATCATTTTTCTCATGGAATACGCAAGACTGCCAGTAAGAAGTAGAAAAGATCAGTGAC
AAAAAGACTATTCAATTTTACAGCAGATCCATCATTTTCTTTAAAGTTTGACTCTGACCATGTA
ATAACTAAATTCTTTCCAACTCTAAAGGCCAAAGCAATTGCTATTAAAATATGTATATAGAAGA
CAATAGACTTACGTCAAGGTAACAGCTAAAGGAAGCCCTTCAGGCACTGCCACTACAACAATTG
TAACCTATTCGACAAGTTGAGCAGAACAGCCAGAGATGTAAATAAGAAGATGACAACCGTATTA
GCCATGCTAATTTCTTCTAAAGAAACACTTACTGCAACAGTGAAGATTTCAACAAGATCATCTA
GCACGTGCTCAAATTTTGTCTTCCCTCCAATAAACTGTGGGCCTCCCTGTTCATTCTTCGTGTG
ACCGGTAAAGTAACTGCATAGAACAAAGATTCGTTCAATAATCACTGACATCCACTCCACACGG
TACTTTAGTTGTCATAAAGAAATTTAAACGCACCGGACAACTAGGACAAATAATACAACGCCAG
CAACTGTGAGCCCGACAATCCCGATAAATGTTGCTACACCATTCAAGCGCACCTGAAGAAAGCA
TAGTACGGATGACTATTGAGCAACAAAAACCACGAATATATGAACAGAGAAAAGTTGATACTCA
CCTGCAATGGTGTTTCTCCACCATTGTCCTCTGAGACGCTAGCCATTAGTAAGCCCCATTCAGT
GTTGACCCCTACCCCAGTAAC
						
					

			
		

Sequences
Splice junction sequence	AAAAGTTGATACTCACCTGCAATGGTGTTTCTCCACCATTGTCCTCTGAGACGCTAGCCATTAG TAAGCCCCATTCAGTGTTGACCCCTACCCCAGTAACcttaataccaacgatagccaacaatata agatcatcctcaggtaattcccatctagagagttgctcttcatcagttggaatcttatccgctt caaatgtt
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	CTTAATACCAACGATAGCCAACAATATAAGATCATCCTCAGGTAATTCCCATCTAGAGAGTTGC TCTTCATCAGTTGGAATCTTATCCGCTTCAAATGTTCGGAAGGCAATTGCAACACAGCGCAGAC TCCTTGCAGCCATATCATCGATAGCATCTTTTAACCCACCCATCTGAAACAACAAGACTTATAC TCAGAATAAAAAACAAGTATTTCTATCAAGACTCTCATTACCAAATCTGGCACTGATTTGGACT TGCAGTATGACATGGTCTTGAGTCAAGACACAATGATAAGTTCAACATTCAGACAAACTCTATC ATGATAAAGAGAAACATAGTTACTGACCTTATCTTCACTCATATCTACAAAACTCTCACTCTCA TCCATATAGTGCGTGCAGGATCCCAAAACAATTTCGGCAGCACCTTTCCAGTGAATATGGACAC TCGAATCTGGCTGAAAATGAATTAGAAAGTCGTTAGGATGCTGATTGACAAGTAGAAACAACGA TAAGAGAAAAATCAAAAACAAAGCAAAAGATCTACAAAAACTATGGGAGGAAATGAAAAGAAAA AACATTACTGATTTCACTGCTACACCTCCTCGTTTCTTCTCTGAGTTGAATGGAAAAAATTGTA CAGCAGAAGACTCAGACTTAAGAGCATCAAAATCCATACCCAACTGCAGTGTATAAGAAATTAA AAGATTAGTTCTTCTCACGGCTATATATACGGGAACCAGAAAATGTAGCTAAAGAATAAACCTT TATCGCCCAATTGAGAATTGCTCTTTCTGTAGGAGATCCAGAAACCTGAATCTCACCACTCTGT CATCAGTAAAGACATAGGCATTATTACATTAAATCAGCTGAAGTAGAAACCAAACGGGAAATCA GTAAAGTTCCAAAGAATTTTAATCCTACTTCAGATCGGAACACACTGCCGGTTGTATTGTGAGC AATACCCTCAACAAGTATGGATGTAAAAGCAGATGGCAATTTTGAGCTGCTGTCGGGAGAATCC ATCTTTTGTAACCCAGCATAACACTCAACAACGGTCATCTGAGAAAAAAGAAAGTCGTAGGGGA CCCGCTTGTTGGGTACACAATTCAAAATAGCAAAAGCTCATAACTAGGAAAGCACATACCAAAA CTGGTAAGTGTTAAGTGTGTTAGCAAATACAAAAAGAAGGCAGAGCACCAAGATTCACCTCGTT TAAGGTCAAAGTTCCAGTCTTATCACTGCAAATTGTTGTTGCAGACCCCATGGTTTCACAGGCT GAAAGCCTACGCACCTGAAATTAAAATTCGTTTAAGTTGCAAAAGACATTCACGTATAAGAATT TTGCATTTATGTTCATTCAAACTTATTGAGTCCCAAAAATTAAAATATACATACCAAAGCTTTA TCTGCCATCATTTTTCTCATGGAATACGCAAGACTGCCAGTAAGAAGTAGAAAAGATCAGTGAC AAAAAGACTATTCAATTTTACAGCAGATCCATCATTTTCTTTAAAGTTTGACTCTGACCATGTA ATAACTAAATTCTTTCCAACTCTAAAGGCCAAAGCAATTGCTATTAAAATATGTATATAGAAGA CAATAGACTTACGTCAAGGTAACAGCTAAAGGAAGCCCTTCAGGCACTGCCACTACAACAATTG TAACCTATTCGACAAGTTGAGCAGAACAGCCAGAGATGTAAATAAGAAGATGACAACCGTATTA GCCATGCTAATTTCTTCTAAAGAAACACTTACTGCAACAGTGAAGATTTCAACAAGATCATCTA GCACGTGCTCAAATTTTGTCTTCCCTCCAATAAACTGTGGGCCTCCCTGTTCATTCTTCGTGTG ACCGGTAAAGTAACTGCATAGAACAAAGATTCGTTCAATAATCACTGACATCCACTCCACACGG TACTTTAGTTGTCATAAAGAAATTTAAACGCACCGGACAACTAGGACAAATAATACAACGCCAG CAACTGTGAGCCCGACAATCCCGATAAATGTTGCTACACCATTCAAGCGCACCTGAAGAAAGCA TAGTACGGATGACTATTGAGCAACAAAAACCACGAATATATGAACAGAGAAAAGTTGATACTCA CCTGCAATGGTGTTTCTCCACCATTGTCCTCTGAGACGCTAGCCATTAGTAAGCCCCATTCAGT GTTGACCCCTACCCCAGTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.167583292

Conservation Information
Conserved circRNAs	NA
PMCS	0.167583292

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14615795-14613639(-)
						
						Potential amino acid sequence
						
							MASVSEDNGGETPLQVRLNGVATFIGIVGLTVAGVVLFVLVVRYFTGHTKNEQGGPQFIGGKTK
FEHVLDDLVEIFTVAVTIVVVAVPEGLPLAVTLTLAYSMRKMMADKALVRRLSACETMGSATTI
CSDKTGTLTLNEMTVVECYAGLQKMDSPDSSSKLPSAFTSILVEGIAHNTTGSVFRSESGEIQV
SGSPTERAILNWAIKLGMDFDALKSESSAVQFFPFNSEKKRGGVAVKSPDSSVHIHWKGAAEIV
LGSCTHYMDESESFVDMSEDKMGGLKDAIDDMAARSLRCVAIAFRTFEADKIPTDEEQLSRWEL
PEDDLILLAIVGIKVTGVGVNTEWGLLMASVSEDNGGETPLQVRLNGVATFIGIVGLTVAGVVL
FVLVVRYFTGHTKNEQGGPQFIGGKTKFEHVLDDLVEIFTVAVTIVVVAVPEGLPLAVTLTLAY
SMRKMMADKALVRRLSACETMGSATTICSDKTGTLTLNEMTVVECYAGLQKMDSPDSSSKLPSA
FTSILVEGIAHNTTGSVFRSESGEIQVSGSPTERAILNWAIKLGMDFDALKSESSAVQFFPFNS
EKKRGGVAVKSPDSSVHIHWKGAAEIVLGSCTHYMDESESFVDMSEDKMGGLKDAIDDMAARSL
RCVAIAFRTFEADKIPTDEEQLSRWELPEDDLILLAIVGIKVTGVGVNTEWGLLMASVSEDNGG
ETPLQVRLNGVATFIGIVGLTVAGVVLFVLVVRYFTGHTKNEQGGPQFIGGKTKFEHVLDDLVE
IFTVAVTIVVVAVPEGLPLAVTLTLAYSMRKMMADKALVRRLSACETMGSATTICSDKTGTLTL
NEMTVVECYAGLQKMDSPDSSSKLPSAFTSILVEGIAHNTTGSVFRSESGEIQVSGSPTERAIL
NWAIKLGMDFDALKSESSAVQFFPFNSEKKRGGVAVKSPDSSVHIHWKGAAEIVLGSCTHYMDE
SESFVDMSEDKMGGLKDAIDDMAARSLRCVAIAFRTFEADKIPTDEEQLSRWELPEDDLILLAI
VGIKVTGVGVNTEWGLLMASVSEDNGGETPLQVRLNGVATFIGIVGLTVAGVVLFVLVVRYFTG
HTKNEQGGPQFIGGKTKFEHVLDDLVEIFTVAVTIVVVAVPEGLPLAVTLTLAYSMRKMMADKA
LVRRLSACETMGSATTICSDKTGTLTLNEMTVVECYAGLQKMDSPDSSSKLPSAFTSILVEGIA
HNTTGSVFRSESGEIQVSGSPTERAILNWAIKLGMDFDALKSESSAVQFFPFNSEKKRGGVAVK
SPDSSVHIHWKGAAEIVLGSCTHYMDESESFVDMSEDKMGGLKDAIDDMAARSLRCVAIAFRTF
EADKIPTDEEQLSRWELPEDDLILLAIVGIK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	14615795-14613639(-)
Potential amino acid sequence	MASVSEDNGGETPLQVRLNGVATFIGIVGLTVAGVVLFVLVVRYFTGHTKNEQGGPQFIGGKTK FEHVLDDLVEIFTVAVTIVVVAVPEGLPLAVTLTLAYSMRKMMADKALVRRLSACETMGSATTI CSDKTGTLTLNEMTVVECYAGLQKMDSPDSSSKLPSAFTSILVEGIAHNTTGSVFRSESGEIQV SGSPTERAILNWAIKLGMDFDALKSESSAVQFFPFNSEKKRGGVAVKSPDSSVHIHWKGAAEIV LGSCTHYMDESESFVDMSEDKMGGLKDAIDDMAARSLRCVAIAFRTFEADKIPTDEEQLSRWEL PEDDLILLAIVGIKVTGVGVNTEWGLLMASVSEDNGGETPLQVRLNGVATFIGIVGLTVAGVVL FVLVVRYFTGHTKNEQGGPQFIGGKTKFEHVLDDLVEIFTVAVTIVVVAVPEGLPLAVTLTLAY SMRKMMADKALVRRLSACETMGSATTICSDKTGTLTLNEMTVVECYAGLQKMDSPDSSSKLPSA FTSILVEGIAHNTTGSVFRSESGEIQVSGSPTERAILNWAIKLGMDFDALKSESSAVQFFPFNS EKKRGGVAVKSPDSSVHIHWKGAAEIVLGSCTHYMDESESFVDMSEDKMGGLKDAIDDMAARSL RCVAIAFRTFEADKIPTDEEQLSRWELPEDDLILLAIVGIKVTGVGVNTEWGLLMASVSEDNGG ETPLQVRLNGVATFIGIVGLTVAGVVLFVLVVRYFTGHTKNEQGGPQFIGGKTKFEHVLDDLVE IFTVAVTIVVVAVPEGLPLAVTLTLAYSMRKMMADKALVRRLSACETMGSATTICSDKTGTLTL NEMTVVECYAGLQKMDSPDSSSKLPSAFTSILVEGIAHNTTGSVFRSESGEIQVSGSPTERAIL NWAIKLGMDFDALKSESSAVQFFPFNSEKKRGGVAVKSPDSSVHIHWKGAAEIVLGSCTHYMDE SESFVDMSEDKMGGLKDAIDDMAARSLRCVAIAFRTFEADKIPTDEEQLSRWELPEDDLILLAI VGIKVTGVGVNTEWGLLMASVSEDNGGETPLQVRLNGVATFIGIVGLTVAGVVLFVLVVRYFTG HTKNEQGGPQFIGGKTKFEHVLDDLVEIFTVAVTIVVVAVPEGLPLAVTLTLAYSMRKMMADKA LVRRLSACETMGSATTICSDKTGTLTLNEMTVVECYAGLQKMDSPDSSSKLPSAFTSILVEGIA HNTTGSVFRSESGEIQVSGSPTERAILNWAIKLGMDFDALKSESSAVQFFPFNSEKKRGGVAVK SPDSSVHIHWKGAAEIVLGSCTHYMDESESFVDMSEDKMGGLKDAIDDMAARSLRCVAIAFRTF EADKIPTDEEQLSRWELPEDDLILLAIVGIK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT4G29900_circ_g.4

Address

Any questions?

Supported by