SustainPineDB

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Assembly info
Unigenes
SNPs
SSRs
Descriptions
GOs
ECs
KEGGs
InterPros
miRNAs

Assembly Name: SustainPine v3.0

UniGene Name: sp_v3.0_unigene35000

Length: 523 nt

This UniGene was originaly assembled in antisense
ACE File: antisense
Fasta: sense

UniGene Fasta (sense)

>sp_v3.0_unigene35000
ATGGGATGATTCTCAAGTTATTTTAAAGGGAATTTCCACAGACCGTATTCTTGATTTACGCCGATTATTAGCTGTGAATGTGGAGACATGCCATCTGACCAACTATTCTTTATCCCATGAGGTAAGAAAATCAGTAGTTCAGAAGCTCATTAAATAATGGGATTGTTTGACAGGTTGGTGGATTGCATCTGACCAACTATTCTTTATCTCATGAGGTTCGTGGCAACAGGTTGAGGGATTCATCAGATGTTGCAACGTTGAAGCCCTGTGCCCTTACTATTGTAGAAGAGGACTACACTGAAGAGCATGCAGTTGCACACGTTAGAAGATTACTGGACATTGTTGCCTGTACAACATGCTTTGGTTCTTCAGGAAAGCAAGGGGAACCTCGGTCTGGGCAGGGAGGTGGAAAAGAATCAGCTCACTCAATCACAGAGAATGTGGCTGAACAAAACAACGATGTTGCTCTAAAGAAATCTTCTAGACAATAAAGAAAGAAAAGAAGCAAACAAAGATGGACATT

Ace file of the UniGene sp_v3.0_unigene35000 (antisense)

If you push the Download ace button, you will download an ace file of this UniGene.

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Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	Tetratricopeptide repeat-containing protein n=4 Tax=Arabidopsis RepID=F4HS99_ARATH	-	-	4.0e-23	65%
FL-Next	tr=Tetratricopeptide repeat-containing protein; Arabidopsis lyrata subsp. lyrata (Lyre-leaved rock-cress).	-	-	0.0	72%
Sma3	Eukaryotic translation initiation factor 3 subunit, putative	-	-	2.82e-07	-

Source	Gene names
Sma3	B1123E10.126; GSVIVT00000280001; GSVIVT00017134001; GSVIVT00027051001; OSJNBa0052K15.22-1; OSJNBa0070O11.2; OSJNBa0084P08.1; Os02g0255700; Os04g0645100; OsI_06619; OsI_17662; OsI_25780; OsJ_06127; OsJ_16398; OsJ_24005; P0613F08.4-1; PHYPADRAFT_40106; POPT

Source	GOs	Term	Type	Identity
Sma3	RNA binding	GO:0003723	Molecular Function	-
Sma3	RNA-directed DNA polymerase activity	GO:0003964	Molecular Function	-
Sma3	binding	GO:0005488	Molecular Function	-
Sma3	RNA-dependent DNA replication	GO:0006278	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	Reverse transcriptase	IPR000477	-	-
Sma3	Tetratricopeptide-like helical	IPR011990	-	-
Sma3	Tetratricopeptide repeat-containing domain	IPR013026	-	-
Sma3	Tetratricopeptide TPR2	IPR013105	-	-
Sma3	DNA ligase, ATP-dependent, conserved site	IPR016059	-	-
Sma3	Tetratricopeptide repeat	IPR019734	-	-

Source	Species	ID	Description	e value	Identity
ATG	Arabidoptis thaliana	AT1G01320.1	Tetratricopeptide repeat (TPR)-like superfamily protein chr1:121582-130099 REVERSE LENGTH=1797	1.0e-27	65%
RefSeq	Arabidopsis thaliana	NP_001184884.1	tetratricopeptide repeat-containing protein [Arabidopsis thaliana]	2.0e-27	65%
RefSeq	Populus trichocarpa	XP_002325116.1	predicted protein [Populus trichocarpa]	9.0e-16	84%

Full-Lengther Next Prediction

Fln status: Internal

Fln database: tr_plants

Fln subject: D7KQ88

Fln msg: Separated hits, possible frame ERROR between 133 and 186, Unexpected STOP codon at 3' end. Distance to subject end: 1615 aas, your sequence is shorter than subject: 164 - 1793

Fln protein: WDDSQVILKGISTDRILDLRRLLAVNVETCHLTNYSLSHEVRKxxxxxxxxxxxxxxxxxxxHLTNYSLSHEVRGNRLRDSSDVATLKPCALTIVEEDYTEEHAVAHVRRLLDIVACTTCFGSSGKQGEPRSGQGGGKESAHSITENVAEQNNDVALKKSSRQ*

Protein Length: 165

Fln nts: ATGGGATGATTCTCAAGTTATTTTAAAGGGAATTTCCACAGACCGTATTCTTGATTTACGCCGATTATTAGCTGTGAATGTGGAGACATGCCATCTGACCAACTATTCTTTATCCCATGAGGTAAGAAAATCxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGCATCTGACCAACTATTCTTTATCTCATGAGGTTCGTGGCAACAGGTTGAGGGATTCATCAGATGTTGCAACGTTGAAGCCCTGTGCCCTTACTATTGTAGAAGAGGACTACACTGAAGAGCATGCAGTTGCACACGTTAGAAGATTACTGGACATTGTTGCCTGTACAACATGCTTTGGTTCTTCAGGAAAGCAAGGGGAACCTCGGTCTGGGCAGGGAGGTGGAAAAGAATCAGCTCACTCAATCACAGAGAATGTGGCTGAACAAAACAACGATGTTGCTCTAAAGAAATCTTCTAGACAATAAAGAAAGAAAAGAAGCAAACAAAGATGGACATT

Fln Alignment:

Contig35000___DDSQVILKGISTDRILDLRRLLAVNVETCHLTNYSLSHEVRKSxxxxxxxxxxxxxxxxxxHLTNYSLSHEVRGNRLRDSSDVATLKPCALTIVEEDYTEEHAVAHVRRLLDIVACTTCFGSSGKQGEP-RSGQ--GGGKESAHSIT
D7KQ88_______________DETEAILKGISTDRIIDVRRLLSVNFDTCHVTNYSLSHEIRGSxxxxxxxxxxxxxxxxxxHVTNYSLSHEIRGSRLKDTVDVSALKPCVLTLTEEDYNEGTAVAHVRRLLDIVACTTCFGPSPEKSDSVKSAQVKGGGKNSKHSET

SNPs (tot: 18)

Position	A %	C %	G %	T %	Probability
158	11		88		0.923564
159	88	11			0.923564
161		88		11	0.923564
162		88		11	0.923564
210	11	88			0.923564
211	88	11			0.923564
213		88		11	0.923564
316	50		50		1.0
317		25	50	25	0.995533
320	50	25		25	0.995533
321	66			33	0.997452
322	66			33	0.997452
326		33		66	0.997452
329	33			66	0.997452
330	33			66	0.997452
331		33	66		0.997452
338	33		66		0.997452
339	66			33	0.997452

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Biología Molecular y Biotecnología de Plantas, Facultad de Ciencias y Plataforma Andaluza de Bioinformática, Universidad de Málaga, E-29071 Málaga, Spain