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_unigene13534

Length: 471 nt

UniGene Fasta

>sp_v3.0_unigene13534
ATGTGGGTGGCTGTGGATCCAAGTTCCTCCTACAAGCTCTCCTTGCGCCCGAGTATGCGGAAGTACACCTCAGATAATAGGAGTCTGGACGTCCTTAATTGGACAAAATACAGGCCTTGTTTCTTAAATCGGCAAATCATTACGCTTTTGTCTACTTTGGGTGTTGCAGGTCATCACTTCGAGACGCTTCAGAAAGAAGCAATAGAACTCATAAATCAAGTCTTAACAAGCAGAGATGAGGCTCTTGACGTGCTACAAACTTTGTACACAGGTGAAAATCATAATGCTCTTACGGATATGCTTTCATGTGGCTACTCCCCAAAATCGGAGCCTTACCTATCAATGATGCTTCAGGCATTTCGAGCATCTAAACTTGTGGAGTTAAGAAACAAGGCACGCATTTTTTGTTCCTAAGGGGCGATGTTTAATCGGGATGCCTTGACGAAACTAAAACTCTGAATTATGGTGAAG

Ace file of the UniGene sp_v3.0_unigene13534

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Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	RNA-dependent RNA polymerase n=2 Tax=Gossypium hirsutum RepID=B2B9K0_GOSHI	-	-	3.9937e-43	60%
FL-Next	sp=RNA-dependent RNA polymerase 1; Arabidopsis thaliana (Mouse-ear cress).	-	-	0.0	57%
Sma3	Rna-dependent RNA polymerase	-	-	1.429e-19	-

Source	Gene names
Sma3	AT4g11130; At1g14790; At4g11130; F2P3.11; GSVIVT00016129001; GSVIVT00030600001; GSVIVT00030602001; GSVIVT00032651001; NtRDR6; Os02g0736200; OsI_08849; OsJ_08301; PHYPADRAFT_219654; POPTRDRAFT_231683; POPTRDRAFT_561891; POPTRDRAFT_564678; POPTRDRAFT_575133

Source	GOs	Term	Type	Identity
Sma3	nucleolus	GO:0005730	Cellular Component	-
Sma3	nucleotide binding	GO:0000166	Molecular Function	-
Sma3	nucleic acid binding	GO:0003676	Molecular Function	-
Sma3	RNA-directed RNA polymerase activity	GO:0003968	Molecular Function	-
Sma3	cell-cell signaling	GO:0007267	Biological Process	-
Sma3	long-distance posttranscriptional gene silencing	GO:0010495	Biological Process	-
Sma3	production of siRNA involved in RNA interference	GO:0030422	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	RNA recognition motif domain	IPR000504	-	-
Sma3	RNA-dependent RNA polymerase, eukaryotic-type	IPR007855	-	-
Sma3	Nucleotide-binding, alpha-beta plait	IPR012677	-	-

Source	Species	ID	Description	e value	Identity
ATG	Arabidoptis thaliana	AT1G14790.1	RDR1, ATRDRP1 RNA-dependent RNA polymerase 1 chr1:5094317-5097817 REVERSE LENGTH=1107	9.94922e-44	57%
RefSeq	Arabidopsis thaliana	NP_172932.1	RNA-dependent RNA polymerase 1 [Arabidopsis thaliana]	2.00386e-43	57%
RefSeq	Populus trichocarpa	XP_002311536.1	rna-dependent RNA polymerase [Populus trichocarpa]	0.0	62%

Full-Lengther Next Prediction

Fln status: Internal

Fln database: sp_plants

Fln subject: Q9LQV2

Fln msg: Unexpected STOP codon at 3' end. Distance to subject end: 379 aas, your sequence is shorter than subject: 138 - 1107

Fln protein: MWVAVDPSSSYKLSLRPSMRKYTSDNRSLDVLNWTKYRPCFLNRQIITLLSTLGVAGHHFETLQKEAIELINQVLTSRDEALDVLQTLYTGENHNALTDMLSCGYSPKSEPYLSMMLQAFRASKLVELRNKARIFCS*

Protein Length: 139

Fln nts: ATGTGGGTGGCTGTGGATCCAAGTTCCTCCTACAAGCTCTCCTTGCGCCCGAGTATGCGGAAGTACACCTCAGATAATAGGAGTCTGGACGTCCTTAATTGGACAAAATACAGGCCTTGTTTCTTAAATCGGCAAATCATTACGCTTTTGTCTACTTTGGGTGTTGCAGGTCATCACTTCGAGACGCTTCAGAAAGAAGCAATAGAACTCATAAATCAAGTCTTAACAAGCAGAGATGAGGCTCTTGACGTGCTACAAACTTTGTACACAGGTGAAAATCATAATGCTCTTACGGATATGCTTTCATGTGGCTACTCCCCAAAATCGGAGCCTTACCTATCAATGATGCTTCAGGCATTTCGAGCATCTAAACTTGTGGAGTTAAGAAACAAGGCACGCATTTTTTGTTCCTAAGGGGCGATGTTTAATCGGGATGCCTTGACGAAACTAAAACTCTGAATTATGGTGAAG

Fln Alignment:

Contig13534___VAVDPSSSYKLSLRPSMRKYTSDNRSLDVLNWTKYRPCFLNRQIITLLSTLGVAGHHFETLQKEAIELINQVLTSRDEALDVLQTLYTGENHNALTDMLSCGYSPKSEPYLSMMLQAFRASKLVELRNKARIFCS*G
Q9LQV2_______________VAVDPNSSKKLSLRKSMSKFESENTKLDVLAWSKYQPCYMNRQLITLLSTLGVTDSVFEKKQREVVDRLDAILTHPLEAHEALGLMAPGENTNILKALILCGYKPDAEPFLSMMLQNFRASKLLELRTKTRIFISGG

SNPs (tot: 1)

Position	A %	C %	G %	T %	Probability
305	12	87			0.992554

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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