SustainPineDB

Assembly Name: SustainPine v3.0

UniGene Name: sp_v3.0_unigene24027

Length: 1357 nt

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

UniGene Fasta (sense)

Ace file of the UniGene sp_v3.0_unigene24027 (antisense)

Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 [Arabidopsis thaliana] gb\|AAL67014.1\| putative RNA helicase [Arabidopsis thaliana] gb\|AAM91806.1\| putative RNA helicase [Arabidopsis thaliana] gb\|AEE31492.1\| pre-mRNA-splicing factor ATP-dependent	-	-	0.0	79%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	0.0	41%
Sma3	ATP-dependent RNA helicase, putative	-	-	6.004e-20	-

Source	Gene names
Sma3	AT4g16680; ATH1; At1g32490; At2g35340; At2g47250; At3g26560; At3g62310; At4g16680; At5g13010; At5g14900; F2G14_20; F5D14.27; GSVIVT00002999001; GSVIVT00016254001; GSVIVT00028144001; GSVIVT00033641001; LOC_Os03g19960; MFE16.8; MICPUCDRAFT_24785; MICPUCDRAF

Source	GOs	Term	Type	Identity
Sma3	nucleus	GO:0005634	Cellular Component	-
Sma3	nucleolus	GO:0005730	Cellular Component	-
Sma3	mitochondrion	GO:0005739	Cellular Component	-
Sma3	chloroplast envelope	GO:0009941	Cellular Component	-
Sma3	membrane	GO:0016020	Cellular Component	-
Sma3	nucleic acid binding	GO:0003676	Molecular Function	-
Sma3	RNA binding	GO:0003723	Molecular Function	-
Sma3	helicase activity	GO:0004386	Molecular Function	-
Sma3	ATP binding	GO:0005524	Molecular Function	-
Sma3	ATP-dependent helicase activity	GO:0008026	Molecular Function	-
Sma3	mRNA processing	GO:0006397	Biological Process	-
Sma3	RNA splicing	GO:0008380	Biological Process	-
Sma3	embryo development ending in seed dormancy	GO:0009793	Biological Process	-
Sma3	posttranscriptional gene silencing by RNA	GO:0035194	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	Helicase, C-terminal	IPR001650	-	-
Sma3	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	IPR002464	-	-
Sma3	Pentatricopeptide repeat	IPR002885	-	-
Sma3	Ribosomal protein S1, RNA-binding domain	IPR003029	-	-
Sma3	AAA+ ATPase domain	IPR003593	-	-
Sma3	Helicase-associated domain	IPR007502	-	-
Sma3	Domain of unknown function DUF1605	IPR011709	-	-
Sma3	Nucleic acid-binding, OB-fold	IPR012340	-	-
Sma3	Helicase, superfamily 1/2, ATP-binding domain	IPR014001	-	-
Sma3		IPR014021	-	-

Source	Species	ID	Description	Identity
ATG	Arabidoptis thaliana	AT1G32490.1	EMB2733, ESP3 RNA helicase family protein chr1:11742356-11749286 REVERSE LENGTH=1044	79%
RefSeq	Arabidopsis thaliana	NP_001185127.1	pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 [Arabidopsis thaliana]	79%
RefSeq	Populus trichocarpa	XP_002331832.1	predicted protein [Populus trichocarpa]	49%

Full-Lengther Next Prediction

Fln status: Putative C-terminus

Fln database: coniferopsida.fasta

Fln subject: D5ADJ5

Fln msg: query STOP codon too far from subject stop. Distance to subject end: 51 aas, putative chimeric sequence, your sequence is shorter than subject: 265 - 348

Fln protein: FMDPPPAETLMRALEQLYALGALNDRGELTKLGRRMAEFPLDPMLSKMIVSSDKYKCSEEIITISAMLSVGSAIFYRPKDKQVHADNARMNFHAGNVGDHIALLKVYETWKETNFSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEPSTNLNDLESIKKAITSGYFYHTSKLQKNGSYRTVKNPQIVHIHPSSGLAQVLPRWVVYYELVYTTKEYMRQAIEIKPDWLVEIAPHYYKLNDVEDAGSQKLPKGKGRAVMDKF*

Protein Length: 266

Fln nts: TTTCATGGATCCTCCTCCAGCAGAAACATTAATGAGAGCATTGGAGCAGCTTTATGCTCTTGGTGCCTTGAATGACCGGGGTGAGTTAACAAAATTAGGGAGGCGGATGGCAGAATTTCCACTAGATCCAATGCTTTCCAAAATGATAGTTTCATCAGACAAATATAAATGTTCAGAAGAAATCATCACAATTTCTGCTATGCTATCAGTTGGAAGTGCCATATTTTATCGTCCAAAGGATAAGCAAGTTCATGCTGATAATGCTAGGATGAACTTCCATGCTGGCAATGTGGGAGATCATATTGCATTGCTGAAGGTCTATGAGACGTGGAAGGAAACAAACTTTTCAACGCAGTGGTGTTATGAAAACTACATTCAGGTGAGGAGTATGAAACGAGCACGAGACATCAGAGATCAATTAGAGGGACTGTTAGAAAGGGTTGAGATAGAGCCTTCAACCAATTTAAATGATCTTGAGTCAATAAAGAAGGCTATAACGTCAGGATATTTTTACCACACTTCCAAGCTGCAGAAAAATGGATCCTATCGCACAGTCAAGAACCCGCAAATTGTACATATACATCCAAGTTCTGGCCTTGCTCAGGTCCTACCACGCTGGGTTGTTTATTACGAGTTAGTTTATACAACGAAAGAATACATGCGACAAGCTATTGAAATTAAACCTGATTGGCTGGTCGAGATTGCTCCGCACTACTACAAGCTAAATGATGTGGAAGATGCTGGGTCCCAGAAACTGCCAAAGGGTAAAGGCAGAGCAGTAATGGATAAGTTCTGA___TTCCAAGGCTTTAGAAAGTTATGTGTTCTGCAATGGTTTTACCGGATAACACAATGAGGAGTATAGAGCACAATTTATGTATAACTGATTCGATGGCTTGTTACTGAAGATGAAGTCAATAAAGAATGGAGTTATTTCCCCTAATGAAAAGAGTAATTTTTTGTGAGAATATGTGAATAATTTATTGCGCTCTAAATATAAGGTGTATTACTCAAATTTCAGTGATAATTTTTGTGCTGCAAACTTGCAGCTCGAGAATCAATTTTTTAAATAAGTTTCTATTAGCAATTTATACATTGCGAGGTGAAAGTTCCCATTTTTGTATGGTTGGACGAAAGGGTGTAACACCCTCGAGTACGGTACGTTGAGCTGTAATATAAGCCATTCAAGAATCTGAAAATGAACTGCTTGAATTCTGATAAAAGATATGTAGGATAGGTAAAAACATATACATCTCTCATGTAAATATATAAAGCGTTATTGACATACCCACATTGTTATTTGAATTGTTTGACATGGAGCCATGTTTGTTATATTCAATAATAATTTGTTGTTAAGTGC

Fln Alignment:

Contig24027___FMDPPPAETLMRALEQLYALGALNDRGELTKLGRRMAEFPLDPMLSKMIVSSDKYKCSEEIITISAMLSVGSAIFYRPKDKQVHADNARMNFHAGNVGDHIALLKVYETWKETNFSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEPSTNLNDLESIKKAITSGYFYHTSKLQKNGSYRTVKNPQIVHIHPSSGLAQV--LPRWVVYYELVYTTKEYMRQAIEIKPDWLVEIAPHYYKLND
D5ADJ5_______________FMDPPPQDNILNSMYQLWVLGALDNVGRLTALGRKMVEFPLDPPLAKMLLIGEQLGCVNEVLTIVSMLSVPS-VFFRPKDRAEESDAAREKFFVPE-SDHLTLLNVYQQWKSNQYRGDWCNDHFLQVKGLRKAREVRSQLLDILKMQKITLTTCGHDWDVIRKAICSAYFHNAARLKGIGEYANSRTGMPCHLHPSSALYGLGYTPDYVVYHELVLTTKEYMQCVTAVEPQWLAELGPMFFSIKD

SNPs (tot: 19)

Position	A %	C %	G %	T %	Probability
313		88		11	0.923564
373	11		88		0.923564
403	85		14		0.993533
404	85		14		0.993533
483	85		14		0.993533
681	90		10		0.90298
683			10	90	0.90298
684	10			90	0.90298
687	90		10		0.90298
688		10		90	0.90298
689	90	10			0.90298
690	10		90		0.90298
691	10	90			0.90298
692			10	90	0.90298
697	11		88		0.923564
700		11		88	0.923564
816		20	80		0.995493
817		20	80		0.995493
853	33		66		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