SustainPineDB

Assembly Name: SustainPine v3.0

UniGene Name: sp_v3.0_unigene539

Length: 2117 nt

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

UniGene Fasta (sense)

>sp_v3.0_unigene539
GGACGCGATTAATACGAACCATGTCTACAAGGGGCTGTTGTTACTTCTTTTATATTTTCCCTCCCCGCTGGTTTGGTTGTTTAACCGTTGAGCTCCGGTTCGAATCATTGGATACGCAATTTATAGCGTGAGAGGATCTTGGAAACGTGCAAATTTTCATTATGGATTTCACTAACACTCGAGGTTTTGTAATCGGGGTTGTGCTAATGAGTCTCTCGTTTTCTTTGGCGTTTTCCTCTGTGGTGTTTTTTGAATCTTTTGATGGGCCATGGGAGGGTCATTGGATTCCATCTAATAAGGAAGATTACAAAGGAAAGTGGAAGCATGGAAAGAATGATGCTTATAATGATTATGGCTTGCTTGTCAGTGAGACGGCAAGGAAATATGGTATAGTGGTTGAGACACCAAAAGTGCATTTCAATAATGATCCAGTGGTTCTGCAATATGATCTGAAGACACAGAATGGACTGGAATGTGGGGGTGCATATTTGAAGTTTTTAATGCCCCAGAAGGTTGGATGGGACCCAAAACACTTTGATAACGAGTCTCCTTATTCTATCATGTTTGGTCCTGATAAATGTGGTTCCACCAACAAAGTCCACTTTATCTTTCGCCACAAACACCCTAAGACAGATAAGTATGTTGAGCACCATTTGAAATACCCTCCAGTTCCTACAGCTGATAGAGTCACTCACATATATACTGCAATCATCTATCCAAATAACACAGTCAGGATTCTTATAGATGGAGAAGAAAAGAAGACTGCTCATTTTCTTTCTGAGGATTTTGATCCTCCTGTTCTGCCTCCTAAGACAATACCTGACCCCGATGACAAGAAACCTGAAGATTGGGATGAGCGAGCTAAAATTCCAGATCTAGAAGCTAAGAAGCCTGATGACTGGGATGAGGATGCACCTATGAAAATTGAGGATCTCGAGGCAGAGGAGGCTGAAGGGTGGCTAGATGACGAACCGGTGGATATAGATGACGTGGAGGCTATGAAACCTGATGATTGGGATGATGAAGAAGACGGGGAATGGAAAGCTCCTAAGATTTCGAATCCTAAATGTGAATTGGTACCAGGTTGTAGCAAATGGAAAAGGCCATTTAAGAGGAACCCTAACTTTAAAGGAAAATGGTATCCACCTATAATTGACAATCCAAACTACAAGGGAATCTGGAAACCTCGTCAGATTCCTAATCCAGATTATTTTGAGTTGGATCGTCCAAACTTGGAAGCAATTGCTGCTATAGGAATTGAAATCTGGACTGTGCAGGATGGAATGTTATTTGACAATATTTTGATTTCTGATGATGATTCTGATGCCAAGGAATACCGGGACAAATATTGGAAACCAAAGTTTGAAGTTGAGAAAGATAAACAAAAGACAGAAGAAGAAGCTGGGGCTCACATATTGGGATTTCTTGCTGGTATCAAGGGTAAAATTATTCATTCACTATATAAGTTTGCAGATGTTCCATCACTGTCACCATACAAGAAAAATTTCAGCGATTTGATTCAGGAGGGTGAGAAGGCTCCTAATTTGACCATTGGTATTTTGGTATCCATTTTAGCGGTTCTTGTCACTTGCATATACAAGCTTATTTTCGAAAGAAAGAAAGCTCTACCATTGCAGGTCATTGCGAAGAATAACAAACAGGGTTCTCGCAGCTCTTCTTCAGATAAAAGCAGCACGTAAGAAGAGCCTAGTGGAAACGCAGAAGAGAAGGATGAAGAGCCTTTTGGAGAAATTGAGAAGGAAGAAGAAGAAACATCTAGTACATGCCATCGAAGTACAAGAAGGGAGACTCATGTGGAAGAATATACAAGTGCCTGTTGTTAGTTGCCAAAAATGAATTTACGTTAGCTTCATAGGTGCGAATGATAGATTTCTTGTCAAAGATTAGCGGTGGACATGTTCGCTTCTAGACCTGCACTTGCAAAATACTCAAGTCCAATGGTAACTATGCATTCCGAGGGAACATAAAAGTTTCACCCACTATAAACTCAGTGGAAACTTCTCTCTTTAGGCTGGTCCTTTTCCAGGACATGGGGGGTTTTCCCAGTAGGATTGCCAATCTGTCCTCACAGCTCAAATAATTAAAATGAGATTTGG

Ace file of the UniGene sp_v3.0_unigene539 (antisense)

Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	Calnexin homolog n=2 Tax=Glycine max RepID=CALX_SOYBN	-	-	0.0	59%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	0.0	64%
Sma3	Calreticulin	-	-	4.68e-17	-

Source	Gene names
Sma3	At5g07340; At5g61790; CAX1; CHLREDRAFT_108711; CNX; CNX1; CRH; CRH1; Crt1; EEF22; GSVIVT00006229001; GSVIVT00011650001; GSVIVT00028103001; Gm cnx-1; Gm crt-1; LOC_Os07g14270; LeCNX61.0; MAC9.11; MICPUCDRAFT_2468; MICPUN_67567; OJ1058_C08.34-1; OJ1058_C08.

Source	GOs	Term	Type	Identity
Sma3	mitochondrion	GO:0005739	Cellular Component	-
Sma3	vacuole	GO:0005773	Cellular Component	-
Sma3	endoplasmic reticulum	GO:0005783	Cellular Component	-
Sma3	endoplasmic reticulum lumen	GO:0005788	Cellular Component	-
Sma3	endoplasmic reticulum membrane	GO:0005789	Cellular Component	-
Sma3	plasma membrane	GO:0005886	Cellular Component	-
Sma3	plant-type cell wall	GO:0009505	Cellular Component	-
Sma3	chloroplast	GO:0009507	Cellular Component	-
Sma3	integral to membrane	GO:0016021	Cellular Component	-
Sma3	calcium ion binding	GO:0005509	Molecular Function	-
Sma3	sugar binding	GO:0005529	Molecular Function	-
Sma3	zinc ion binding	GO:0008270	Molecular Function	-
Sma3	unfolded protein binding	GO:0051082	Molecular Function	-
Sma3	protein folding	GO:0006457	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	Transcription regulator LuxR, C-terminal	IPR000792	-	-
Sma3	Calreticulin/calnexin	IPR001580	-	-
Sma3	Calreticulin/calnexin, P	IPR009033	-	-
Sma3	Calreticulin	IPR009169	-	-
Sma3	Concanavalin A-like lectin/glucanase, subgroup	IPR013320	-	-
Sma3	Calreticulin/calnexin, conserved site	IPR018124	-	-

Source	Species	ID	Description	Identity
ATG	Arabidoptis thaliana	AT5G07340.2	Calreticulin family protein chr5:2317300-2319458 FORWARD LENGTH=540	63%
RefSeq	Arabidopsis thaliana	NP_196351.1	calnexin2 [Arabidopsis thaliana]	63%
RefSeq	Populus trichocarpa	XP_002321768.1	predicted protein [Populus trichocarpa]	61%

Full-Lengther Next Prediction

Fln status: Putative Complete

Fln database: coniferopsida.fasta

Fln subject: C0PT78

Fln msg: query STOP codon too far from subject stop. Distance to subject end: 33 aas, putative chimeric sequence, your sequence is shorter than subject: 513 - 549

Fln protein: MDFTNTRGFVIGVVLMSLSFSLAFSSVVFFESFDGPWEGHWIPSNKEDYKGKWKHGKNDAYNDYGLLVSETARKYGIVVETPKVHFNNDPVVLQYDLKTQNGLECGGAYLKFLMPQKVGWDPKHFDNESPYSIMFGPDKCGSTNKVHFIFRHKHPKTDKYVEHHLKYPPVPTADRVTHIYTAIIYPNNTVRILIDGEEKKTAHFLSEDFDPPVLPPKTIPDPDDKKPEDWDERAKIPDLEAKKPDDWDEDAPMKIEDLEAEEAEGWLDDEPVDIDDVEAMKPDDWDDEEDGEWKAPKISNPKCELVPGCSKWKRPFKRNPNFKGKWYPPIIDNPNYKGIWKPRQIPNPDYFELDRPNLEAIAAIGIEIWTVQDGMLFDNILISDDDSDAKEYRDKYWKPKFEVEKDKQKTEEEAGAHILGFLAGIKGKIIHSLYKFADVPSLSPYKKNFSDLIQEGEKAPNLTIGILVSILAVLVTCIYKLIFERKKALPLQVIAKNNKQGSRSSSSDKSST*

Protein Length: 514

Fln nts: GGACGCGATTAATACGAACCATGTCTACAAGGGGCTGTTGTTACTTCTTTTATATTTTCCCTCCCCGCTGGTTTGGTTGTTTAACCGTTGAGCTCCGGTTCGAATCATTGGATACGCAATTTATAGCGTGAGAGGATCTTGGAAACGTGCAAATTTTCATT_-_ATGGATTTCACTAACACTCGAGGTTTTGTAATCGGGGTTGTGCTAATGAGTCTCTCGTTTTCTTTGGCGTTTTCCTCTGTGGTGTTTTTTGAATCTTTTGATGGGCCATGGGAGGGTCATTGGATTCCATCTAATAAGGAAGATTACAAAGGAAAGTGGAAGCATGGAAAGAATGATGCTTATAATGATTATGGCTTGCTTGTCAGTGAGACGGCAAGGAAATATGGTATAGTGGTTGAGACACCAAAAGTGCATTTCAATAATGATCCAGTGGTTCTGCAATATGATCTGAAGACACAGAATGGACTGGAATGTGGGGGTGCATATTTGAAGTTTTTAATGCCCCAGAAGGTTGGATGGGACCCAAAACACTTTGATAACGAGTCTCCTTATTCTATCATGTTTGGTCCTGATAAATGTGGTTCCACCAACAAAGTCCACTTTATCTTTCGCCACAAACACCCTAAGACAGATAAGTATGTTGAGCACCATTTGAAATACCCTCCAGTTCCTACAGCTGATAGAGTCACTCACATATATACTGCAATCATCTATCCAAATAACACAGTCAGGATTCTTATAGATGGAGAAGAAAAGAAGACTGCTCATTTTCTTTCTGAGGATTTTGATCCTCCTGTTCTGCCTCCTAAGACAATACCTGACCCCGATGACAAGAAACCTGAAGATTGGGATGAGCGAGCTAAAATTCCAGATCTAGAAGCTAAGAAGCCTGATGACTGGGATGAGGATGCACCTATGAAAATTGAGGATCTCGAGGCAGAGGAGGCTGAAGGGTGGCTAGATGACGAACCGGTGGATATAGATGACGTGGAGGCTATGAAACCTGATGATTGGGATGATGAAGAAGACGGGGAATGGAAAGCTCCTAAGATTTCGAATCCTAAATGTGAATTGGTACCAGGTTGTAGCAAATGGAAAAGGCCATTTAAGAGGAACCCTAACTTTAAAGGAAAATGGTATCCACCTATAATTGACAATCCAAACTACAAGGGAATCTGGAAACCTCGTCAGATTCCTAATCCAGATTATTTTGAGTTGGATCGTCCAAACTTGGAAGCAATTGCTGCTATAGGAATTGAAATCTGGACTGTGCAGGATGGAATGTTATTTGACAATATTTTGATTTCTGATGATGATTCTGATGCCAAGGAATACCGGGACAAATATTGGAAACCAAAGTTTGAAGTTGAGAAAGATAAACAAAAGACAGAAGAAGAAGCTGGGGCTCACATATTGGGATTTCTTGCTGGTATCAAGGGTAAAATTATTCATTCACTATATAAGTTTGCAGATGTTCCATCACTGTCACCATACAAGAAAAATTTCAGCGATTTGATTCAGGAGGGTGAGAAGGCTCCTAATTTGACCATTGGTATTTTGGTATCCATTTTAGCGGTTCTTGTCACTTGCATATACAAGCTTATTTTCGAAAGAAAGAAAGCTCTACCATTGCAGGTCATTGCGAAGAATAACAAACAGGGTTCTCGCAGCTCTTCTTCAGATAAAAGCAGCACGTAA___GAAGAGCCTAGTGGAAACGCAGAAGAGAAGGATGAAGAGCCTTTTGGAGAAATTGAGAAGGAAGAAGAAGAAACATCTAGTACATGCCATCGAAGTACAAGAAGGGAGACTCATGTGGAAGAATATACAAGTGCCTGTTGTTAGTTGCCAAAAATGAATTTACGTTAGCTTCATAGGTGCGAATGATAGATTTCTTGTCAAAGATTAGCGGTGGACATGTTCGCTTCTAGACCTGCACTTGCAAAATACTCAAGTCCAATGGTAACTATGCATTCCGAGGGAACATAAAAGTTTCACCCACTATAAACTCAGTGGAAACTTCTCTCTTTAGGCTGGTCCTTTTCCAGGACATGGGGGGTTTTCCCAGTAGGATTGCCAATCTGTCCTCACAGCTCAAATAATTAAAATGAGATTTGG

Fln Alignment:

Contig539___DGPWEGHWIPSNKEDYKGKWKHGKNDAYNDYGLLVSETARKYGIVVETPKVHFNNDP-VVLQYDLKTQNGLECGGAYLKFLMPQKVGWDPKHFDNESPYSIMFGPDKCGSTNKVHFIFRHKHPKTDKYVEHHLKYPPVPTADRVTHIYTAIIYPNNTVRILIDGEEKKTAHFLS-EDFDPPVLXXXXXXXXXXXXXXXXDERAKIPDLEAKKPDDWDEDAPMKIEDLEAEEAEGWLDDEPVDIDDVEAMKPXXXXXXXXXXWKAPKISNPKCELVPGCSKWKRPFKRNPNFKGKWYPPIIDNPNYKGIWKPRQIPNPDYFELDRPNLEAIAAIGIEIWTVQDGMLFDNILISDDDSDAKEYRDKYWKPKFEVEKDKQKTEEEAGAHILGFLAGIKGKIIHSLYKFADVPSLSPYKKNFSDLIQEGEKAPNLTIGILVSILAVLVTCIYKLIFERKKALPLQVIAKNNK
C0PT78_____________DESFDGRWIASQKEDYKGVWKHEKSEGHEDYGLLVSEVAKKYAIVRELPETIDPKDGLVVLQYEVRLQNGLECGGAYLKYLRPQEAGWKPAEFDNESPYSIMFGPDKCGATNKVHFIYKHKNPKSGEYVEHHLKYPPSTPSDKLTHVYTAILKPNNEVRILIDGEEKKKANLLSGDDFEPALIPPETIPDPEDKKPEDWDERAKIPDPDAKKPEDWDEDAPMEIEDLEAVKPEGWLDDEPEEIDDPESTKPDDWDDEEDGEWEAPKVSNPKCDEAPGCGEWTRPMKSNPDYKGKWYAPMIDNPNYKGIWKPQQIPNPDFFELEKPDLEPIAAIGIEIWTMQDGILFDNILITGDEKVAEEYRVKTWKEKFTIEKEREPS-EDVDVPLPGELSGLQKKIFDVLYRIANIPFLDAYKLKIIDLIEQGEKKPNLTIGILVAVLLVILTAVYRVLFGSKKQ-PVQVAELNTQ

SNPs (tot: 15)

Position	A %	C %	G %	T %	Probability
795	16	83			0.994512
835			14	85	0.993533
836	14	85			0.993533
837		85	14		0.993533
838	85			14	0.993533
839			14	85	0.993533
840	14	85			0.993533
842	14			85	0.993533
846	14	85			0.993533
847	85		14		0.993533
851	14	85			0.993533
852	85	14			0.993533
855		14		85	0.993533
856			14	85	0.993533
980	33	66			0.997452

SSRs (tot: 2)

Start position	End position	Sequence	Length
346	357	TTC TTC TTC TTC	12
495	507	CTTT CTTT CTTT C	13

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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