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_unigene102649

Length: 555 nt

UniGene Fasta

>sp_v3.0_unigene102649
CTACAATCCCATGCAAGGAATGATGGATTTTCGTCAATACTGGCAAGGATAGAAGGGGTCTGCTGCACCAGTTAAGACTCAAGAAATGAAAAGAACCAGAATGGATCGTGGTGAATTAGAGAACATTCTTTTCAAGCTATTTGAGCGGCAGTCAAACTGGACATTAAAACAACTTGTGATGGAAACAGATCAGCCTCAGCAATTTATAAAGGAAATATTGAATGATCTTGGCATTTACAACAAACGGGGTACAAATCAAGGAACTTATGAGCTTAAGCCTGAATATAAGAAAACTGCTGAAGACATTGAGGGTGAATAGATGGATTAAGACGTTTGGTGAGTACTTGTGTACTAATACAACTTGTGATACCGTTAAGCACATTTTTGTTCCACGTTGTAGTTTCAGTGTTGTCAATGAGGCAAAGGAAAAGCTGTTTCTTCTTATGGTGGAGGAGTTGGTCAATATATACATGAAGAAATAAGTTGCATATGCCATTTATTTTTTCTAGTGGCAAATTACATTCTTACAGTAACTATTGTTTTTTCTCTGCTACT

Ace file of the UniGene sp_v3.0_unigene102649

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Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	transcription initiation factor TFIIF beta subunit [Arabidopsis thaliana] gb\|AAF87120.1\|AC006434_16 F10A5.27 [Arabidopsis thaliana] gb\|AAG40024.1\|AF324673_1 At1g75700 [Arabidopsis thaliana] gb\|AAG42013.1\|AF327423_1 putative transcription initiation factor	-	-	3.0e-31	67%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	0.0	85%
Sma3	Transcription initiation factor IIF subunit beta, putative	-	-	5.167e-09	-

Source	Gene names
Sma3	At1g75510; At1g75700/F1B16.4; GSVIVT00014517001; GSVIVT00018227001; GSVIVT00033877001; OSJNBb0108E17.21; Os01g0772200; Os05g0509900; OsI_03910; OsI_20575; OsJ_03621; OsJ_19152; P0695H10.13-1; PHYPADRAFT_138652; POPTRDRAFT_652001; POPTRDRAFT_830044; POPTRD

Source	GOs	Term	Type	Identity
Sma3	transcription factor TFIIF complex	GO:0005674	Cellular Component	-
Sma3	mitochondrion	GO:0005739	Cellular Component	-
Sma3	RNA polymerase II transcription factor activity	GO:0003702	Molecular Function	-
Sma3	translation initiation factor activity	GO:0003743	Molecular Function	-
Sma3	catalytic activity	GO:0003824	Molecular Function	-
Sma3	ATP binding	GO:0005524	Molecular Function	-
Sma3	ATP-dependent helicase activity	GO:0008026	Molecular Function	-
Sma3	general RNA polymerase II transcription factor activity	GO:0016251	Molecular Function	-
Sma3	transcription initiation from RNA polymerase II promoter	GO:0006367	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	Transcription initiation factor IIF, beta subunit	IPR003196	-	-
Sma3	Winged helix-turn-helix transcription repressor DNA-binding	IPR011991	-	-
Sma3	Transcription initiation factor IIF, beta subunit, subgroup	IPR016640	-	-
Sma3	Beta-ketoacyl synthase, active site	IPR018201	-	-

Source	Species	ID	Description	e value	Identity
ATG	Arabidoptis thaliana	AT1G75510.1	Transcription initiation factor IIF, beta subunit chr1:28347254-28348629 REVERSE LENGTH=261	2.0e-39	67%
RefSeq	Arabidopsis thaliana	NP_177683.1	transcription initiation factor TFIIF beta subunit [Arabidopsis thaliana]	3.0e-39	67%
RefSeq	Populus trichocarpa	XP_002300734.1	predicted protein [Populus trichocarpa]	8.00001e-41	69%

Full-Lengther Next Prediction

Fln status: C-terminus

Fln database: coniferopsida.fasta

Fln subject: D5ADM8

Fln msg: your sequence is shorter than subject: 106 - 293

Fln protein: YNPMQGMMDFRQYWQG*KGSAAPVKTQEMKRTRMDRGELENILFKLFERQSNWTLKQLVMETDQPQQFIKEILNDLGIYNKRGTNQGTYELKPEYKKTAEDIEGE*

Protein Length: 107

Fln nts: CTACAATCCCATGCAAGGAATGATGGATTTTCGTCAATACTGGCAAGGATAGAAGGGGTCTGCTGCACCAGTTAAGACTCAAGAAATGAAAAGAACCAGAATGGATCGTGGTGAATTAGAGAACATTCTTTTCAAGCTATTTGAGCGGCAGTCAAACTGGACATTAAAACAACTTGTGATGGAAACAGATCAGCCTCAGCAATTTATAAAGGAAATATTGAATGATCTTGGCATTTACAACAAACGGGGTACAAATCAAGGAACTTATGAGCTTAAGCCTGAATATAAGAAAACTGCTGAAGACATTGAGGGTGAATAG___ATGGATTAAGACGTTTGGTGAGTACTTGTGTACTAATACAACTTGTGATACCGTTAAGCACATTTTTGTTCCACGTTGTAGTTTCAGTGTTGTCAATGAGGCAAAGGAAAAGCTGTTTCTTCTTATGGTGGAGGAGTTGGTCAATATATACATGAAGAAATAAGTTGCATATGCCATTTATTTTTTCTAGTGGCAAATTACATTCTTACAGTAACTATTGTTTTTTCTCTGCTACT

Fln Alignment:

AllPine_a_c32276___YNPMQGMMDFRQYW-QG*KGSAAPVKTQEMKRTRMDRGELENILFKLFERQSNWTLKQLVMETDQPQQFIKEILNDLGIYNKRGTNQGTYELKPEYKKTAEDIEGE
D5ADM8________________YNPMQGMMDFSTILSKDKKGSAAPVKAQEMKRTRMDRGELENILFKLFERQSNWTLKQLVTETDQPQQFIKEILNDLGLYNKRGTNQGTYELKPEYKKSTEDMEAE

SNPs (tot: 2)

Position	A %	C %	G %	T %	Probability
353			14	85	0.993533
478	80		20		0.995493

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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