SustainPineDB

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Assembly info
Unigenes
SNPs
SSRs
Descriptions
GOs
ECs
KEGGs
InterPros
miRNAs

Assembly Name: uagpf v2.0

UniGene Name: uagpf_v2_unigene35945

Length: 432 nt

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

UniGene Fasta (sense)

>uagpf_v2_unigene35945
GCGAAGGGCTGTGATGCTAAACAACAAGCTGATTTAGAAAAAGTTGTTTCAGAATATGATATCTTGTTTCAAGAACCTAAAGGTCTACCACCCAAAAAAGAAATAGTGCATGATATTAATTTGCAACAAGATGCTCTATTGCCTAACATCAGAATGTACAGGTTGTCCGCTTTAGAGAATGCAGAAATCAAGAAGCAGGTACAAGAGTGCTCGAGAAGGGGTTCATCAGACCTAGCACATCACCATGTGGATCTCCAATCGTTTTGGTGAAAAATAAAGATGGCTTGTGGATAATTCACATTGATTACCGAGCACTGAATAAGACAACGATAAAAAATTGTTATCCCGTTCCTCGCATAGATGATCTATTAGATCAGTTAAAAGAAGTTGTTTATTTTTCCAAGTTAGTGAGTGACAGCCAAGGTCACGACG

Ace file of the UniGene uagpf_v2_unigene35945 (antisense)

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

To watch this ACE file you will need an ACE viewer program as Tablet:

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Annotations

Parent Assembly	Parent UniGene	Reads (related/total)
SustainPine v2.0	sp_v2.0_unigene59420	1/3
SustainPine v2.0	sp_v2.0_unigene59999	2/3

Source	Descriptions	Term	Type	e value	Identity
AutoFact	putative reverse-transcriptase-like protein [Arabidopsis thaliana] emb\|CAB78181.1\| putative reverse-transcriptase-like protein [Arabidopsis thaliana]	-	-	5.0e-25	46%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	0.0	40%
Blast2go	reverse-transcriptase-like protein	-	-	3.63293e-32	65%

Source	InterPros	Term	Type	Identity
Sma3	Reverse transcriptase	IPR000477	-	-
Sma3	Chromo domain/shadow	IPR000953	-	-
Sma3	O-methyltransferase, family 2	IPR001077	-	-
Sma3	Integrase, catalytic core	IPR001584	-	-
Sma3	Zinc finger, CCHC-type	IPR001878	-	-
Sma3	Peptidase aspartic, active site	IPR001969	-	-
Sma3	Peptidase A2A, retrovirus, catalytic	IPR001995	-	-
Sma3	Putative S-adenosyl-L-methionine-dependent methyltransferase	IPR004159	-	-
Sma3	Retrotransposon gag protein	IPR005162	-	-
Sma3	Domain of unknown function DUF834	IPR008552	-	-
Sma3	Peptidase aspartic, catalytic	IPR009007	-	-
Sma3	TonB box, conserved site	IPR010916	-	-
Sma3	Winged helix-turn-helix transcription repressor DNA-binding	IPR011991	-	-
Sma3	Plant methyltransferase dimerisation	IPR012967	-	-
Sma3		IPR013084	-	-
Sma3	Retroviral aspartyl protease	IPR013242	-	-
Sma3	Zinc finger, H2C2-type, histone UAS binding	IPR015416	-	-

Full-Lengther Next Prediction

Fln status: Putative Complete

Fln database: coniferopsida.fasta

Fln subject: A9NWN2

Fln msg: STOP codon was not found. Distance to subject end: 3 aas, W1: There is no M at the beginning,

Fln protein: HQNVQVVRFRECRNQEAGTRVLEKGFIRPSTSPCGSPIVLVKNKDGLWIIHIDYRALNKTTIKNCYPVPRIDDLLDQLKEVVYFSKLVSDSQGHD

Protein Length: 96

Fln nts: GCGAAGGGCTGTGATGCTAAACAACAAGCTGATTTAGAAAAAGTTGTTTCAGAATATGATATCTTGTTTCAAGAACCTAAAGGTCTACCACCCAAAAAAGAAATAGTGCATGATATTAATTTGCAACAAGATGCTCTATTGCCTAACATCAGAATGTACAGGTTGTCCGCTTTAGAGAATGCAGAAATCAAGAAGCAGGTACAAGAGTGCTCGAGAAGGGGTTCATCAGACCTAGCACATCACCATGTGGATCTCCAATCGTTTTGGTGAAAAATAAAGATGGCTTGTGGATAATTCACATTGATTACCGAGCACTGAATAAGACAACGATAAAAAATTGTTATCCCGTTCCTCGCATAGATGATCTATTAGATCAGTTAAAAGAAGTTGTTTATTTTTCCAAGTTAGTGAGTGACAGCCAAGGTCACGACG

Fln Alignment:

uagpf_mira_c23653___SPIVLVKNKDGLWIIHIDYRALNKTTIKNCYPVPRIDDLLDQLKEVVYFSKL
A9NWN2________________TPIILVRINDGSYILCNNCRVLNEITIKDKFHISIVDELLDELYGTMYFLEL

SNPs (tot: 30)

Position	A %	C %	G %	T %	Probability
196		33		66	0.997452
200	66			33	0.997452
203		33		66	0.997452
204		66		33	0.997452
206			66	33	0.997452
215		66		33	0.997453
218		66	33		0.997452
220		66		33	0.997453
226	33		33		0.997753
230		33		66	0.997455
233		33		66	0.997467
238	33		66		0.997452
239	33	66			0.997452
242		66		33	0.997452
248		33		66	0.997452
269		66		33	0.997452
273		66		33	0.997452
275	33		66		0.997453
293		66		33	0.997452
297	66		33		0.997452
305	33			66	0.997452
308		33		66	0.997452
316			33	66	0.997452
326		66		33	0.997452
335		33	33	33	0.997733
351		66		33	0.997452
368		66		33	0.997452
370	66		33		0.997453
371			66	33	0.997452
382		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