SustainPineDB

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Assembly info
Unigenes
SNPs
SSRs
Descriptions
GOs
ECs
KEGGs
InterPros
miRNAs

Assembly Name: SustainPine v2.0

UniGene Name: sp_v2.0_unigene83469

Length: 571 nt

Origin of reads: Biogeco1 v2

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

UniGene Fasta (sense)

>sp_v2.0_unigene83469
TCGTGGTGCCGTAGAAGCCAGTTAAGGAAGCCTTGTGGCTTCGTCAGATCCTTGTCAGAGTTTGGCTTTCAGCAGCAGCATCCGACTACACTTTGGTGTGATAATCAAAGTGCCATTCAACTATGCAAAGATCCAGTCCAACATCAGCGCAGCAAACACAGCGAAATACACATGCACTTCATCAGAAAGCTCATTCATGACCATGTTCTTGAAGTGCAATATTGTTCAACCGATGATCAAGTTGCAGACATCTTTACAAAGGCTCTCACAGAGGAGGAAGTTCACTAAACTTCGATTTATGGTTGGAGTTCAAGAAGTTGTCACTAAGGGGGATAGGCTCTAATGCCTCATTCATTTTCCTATTGCGTCATCTTTGTACATCCTTCAATCCCATCCCAAATTGTTCTTAAGGGGGGATGTTAAGATATTCTGACACATAGGAAATAATGAAATATAACTTGGTCTAGTGTATAGTTAGGAAAAGTGTGTTTCTTTAGTATGTACTTTTTGTATCTTGCAATATGATAGTCATGATATGTTTTGGACATGAGTGACAGCCAAGGTCACGACG

Ace file of the UniGene sp_v2.0_unigene83469 (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:

Go to the Tablet ACE viewer Web

Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	Putative polyprotein n=1 Tax=Oryza sativa Japonica Group RepID=Q7Y141_ORYSJ	-	-	1.0e-14	43%
FL-Next	sp=Retrovirus-related Pol polyprotein from transposon TNT 1-94; Nicotiana tabacum (Common tobacco).	-	-	0.0	39%
Blast2go	retrotransposon unclassified	-	-	1.29307e-16	69%

Source	InterPros	Term	Type	Identity
Sma3	Integrase, catalytic core	IPR001584	-	-
Sma3	Zinc finger, CCHC-type	IPR001878	-	-
Sma3	Reverse transcriptase, RNA-dependent DNA polymerase	IPR013103	-	-

Full-Lengther Next Prediction

Fln status: C-terminus

Fln database: sp_plants

Fln subject: P10978

Fln msg: your sequence is shorter than subject: 96 - 1328

Fln protein: SWCRRSQLRKPCGFVRSLSEFGFQQQHPTTLWCDNQSAIQLCKDPVQHQRSKHSEIHMHFIRKLIHDHVLEVQYCSTDDQVADIFTKALTEEEVH*

Protein Length: 97

Fln nts: TCGTGGTGCCGTAGAAGCCAGTTAAGGAAGCCTTGTGGCTTCGTCAGATCCTTGTCAGAGTTTGGCTTTCAGCAGCAGCATCCGACTACACTTTGGTGTGATAATCAAAGTGCCATTCAACTATGCAAAGATCCAGTCCAACATCAGCGCAGCAAACACAGCGAAATACACATGCACTTCATCAGAAAGCTCATTCATGACCATGTTCTTGAAGTGCAATATTGTTCAACCGATGATCAAGTTGCAGACATCTTTACAAAGGCTCTCACAGAGGAGGAAGTTCACTAA___ACTTCGATTTATGGTTGGAGTTCAAGAAGTTGTCACTAAGGGGGATAGGCTCTAATGCCTCATTCATTTTCCTATTGCGTCATCTTTGTACATCCTTCAATCCCATCCCAAATTGTTCTTAAGGGGGGATGTTAAGATATTCTGACACATAGGAAATAATGAAATATAACTTGGTCTAGTGTATAGTTAGGAAAAGTGTGTTTCTTTAGTATGTACTTTTTGTATCTTGCAATATGATAGTCATGATATGTTTTGGACATGAGTGACAGCCAAGGTCACGACG

Fln Alignment:

AllPineV4_rep_c144279___RSLSEFGFQQQHPTTLWCDNQSAIQLCKDPVQHQRSKHSEIHMHFIRKLIHDHVLEVQYCSTDDQVADIFTKAL
P10978_______________RFLQELGLHQKE-YVVYCDSQSAIDLSKNSMYHARTKHIDVRYHWIREMVDDESLKVLKISTNENPADMLTKVV

SNPs (tot: 10)

Position	A %	C %	G %	T %	Probability
237	33	66			0.997455
242		33		33	0.997753
261		33		66	0.997456
264	66			33	0.997452
272	33	66			0.997452
281	33		66		0.997452
291	33		66		0.997452
298	33	66			0.997453
303		66		33	0.997452
342		66		33	0.997453

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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