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_unigene55893

Length: 300 nt

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

UniGene Fasta (sense)

>uagpf_v2_unigene55893
CGTCGTGACCTTGGCTGTCACTCATTTTTTTTGATGTAGGTGATTGGGTATTTTTATGATACATCTCAAGCAAGCTATTTATGAGAAGGAAATGTTGGCAATACTACATGCACTTAAGAAATGGCGACCTTACCCAATGGGAAGACACTTCAAGGTAAAAATGGATCATGATAGTCTTAAATACATTTTAGAACAAATATTATCATTAGAAGAAAACAAAATGGGTCACAAAGATGTTGGGTTATGACTTCGAAATCATCTACAAAAAAGGGAAGCTGAGTGACAGCCAAGGTCACGACG

Ace file of the UniGene uagpf_v2_unigene55893 (antisense)

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

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Annotations

Parent Assembly	Parent UniGene	Reads (related/total)
SustainPine v2.0	sp_v2.0_unigene24573	1/5
SustainPine v2.0	sp_v2.0_unigene83535	1/5

Source	Descriptions	Term	Type	Identity
AutoFact	Gypsy/Ty-3 retroelement polyprotein; 69905-74404 n=1 Tax=Arabidopsis thaliana RepID=Q9LHM4_ARATH	-	-	45%
FL-Next	tr=Putative polyprotein; Zea mays (Maize).	-	-	56%
Blast2go	retrotransposon unclassified	-	-	63%

Source	InterPros	Term	Type	Identity
Sma3	Reverse transcriptase	IPR000477	-	-
Sma3	Chromo domain/shadow	IPR000953	-	-
Sma3	Integrase, catalytic core	IPR001584	-	-
Sma3	Carbonic anhydrase	IPR001765	-	-
Sma3	Zinc finger, CCHC-type	IPR001878	-	-
Sma3	Protein translocase complex, SecE/Sec61-gamma subunit	IPR001901	-	-
Sma3	Peptidase aspartic, active site	IPR001969	-	-
Sma3	NB-ARC	IPR002182	-	-
Sma3	DNA-binding WRKY	IPR003657	-	-
Sma3	Retrotransposon gag protein	IPR005162	-	-
Sma3	General substrate transporter	IPR005828	-	-
Sma3	Protein of unknown function DUF594	IPR007658	-	-
Sma3	Domain of unknown function DUF834	IPR008552	-	-
Sma3	Reverse transcriptase, RNA-dependent DNA polymerase	IPR013103	-	-
Sma3	Retroviral aspartyl protease	IPR013242	-	-
Sma3	Zinc finger, H2C2-type, histone UAS binding	IPR015416	-	-
Sma3	Carbonic anhydrase, prokaryotic-like, conserved site	IPR015892	-	-
Sma3	Protein kinase, ATP binding site	IPR017441	-	-

Full-Lengther Next Prediction

Fln status: Internal

Fln database: tr_plants

Fln subject: Q8SA93

Fln msg: Unexpected stop codon in the beginning of your sequence, Unexpected STOP codon at 3' end. Distance to subject end: 1406 aas, your sequence is shorter than subject: 82 - 2749

Fln protein: VVTLAVTHFF*CR*LGIFMIHLKQAIYEKEMLAILHALKKWRPYPMGRHFKVKMDHDSLKYILEQILSLEENKMGHKDVGL*

Protein Length: 83

Fln nts: CGTCGTGACCTTGGCTGTCACTCATTTTTTTTGATGTAGGTGATTGGGTATTTTTATGATACATCTCAAGCAAGCTATTTATGAGAAGGAAATGTTGGCAATACTACATGCACTTAAGAAATGGCGACCTTACCCAATGGGAAGACACTTCAAGGTAAAAATGGATCATGATAGTCTTAAATACATTTTAGAACAAATATTATCATTAGAAGAAAACAAAATGGGTCACAAAGATGTTGGGTTATGACTTCGAAATCATCTACAAAAAAGGGAAGCTGAGTGACAGCCAAGGTCACGACG

Fln Alignment:

uagpf_mira_rep_c93345___HLKQAIYEKEMLAILHALKKWRPYPMGRHFKVKMDHDSLKYILEQILS
Q8SA93________________HLKLAAYERELIGLVQAVRHWRPYLWGRHFAVRTDHYSLKYLLDQRLS

SNPs (tot: 26)

Position	A %	C %	G %	T %	Probability
95	33			66	0.997476
96	66		33		0.997476
98	33		33	33	0.997749
118	33			66	0.997456
121	66		33		0.997454
128	66		33		0.997452
129		75		25	0.996475
139		66		33	0.997452
141	66		33		0.997452
147	75		25		0.996478
149		66		33	0.997452
158		33		66	0.997452
168	25	25	50		0.995533
169		20	80		0.995505
173	80		20		0.995493
176		20		80	0.995493
179		80		20	0.995505
187			20	80	0.995493
191		20		80	0.995493
192	20		80		0.995493
197			25	75	0.996474
199	33	33	33		0.997753
201	75		25		0.996473
204			75	25	0.996473
218	25	75			0.996473
233			75	25	0.996473

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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