SustainPineDB

Assembly Name: SustainPine v2.0

UniGene Name: sp_v2.0_unigene9935

Length: 2245 nt

Origin of reads: Inia v1 Biogeco1 v2 Biogeco2 v2 Biogeco3 v1 Uagpf v2 Uma v2

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

UniGene Fasta (sense)

>sp_v2.0_unigene9935
ACTCATGAGTGGGTAGATTCTGGGGTATCCATTGTATCAGATGGGTGGACAAATATTAAAAAACCAACATTTGATAAATGTTCTTGGTGTTTCTTCTAGTGGTGCAGTATTTATTGCATGTCATGACTCCTCCTCCGTCGCTGCAACCGCACCAAACATTGCAGATCTCCTATTGAAATCAATCAAAGATGTTGGTCCGAATAATGTGGTTCAAGTGATCACAGAACATTGCAGCAAATTGTAAGGCAGCAGGAAGAATTATTGAGCGTACTTATCCACACATCTTTTGGTCTGGGTGCCTGGTTCACACATTGAACCTTTTGATGCATGATATTGTGAAGCACAAAGAATGTGGGTGGATTATTGAGCTTTACAGGAGAGGGAAGTAGCTCATTAAATTCATCACAGGGCATACAAGGGTAAACTACTTCTATGGCACTTACTCCAAGTTGCAATTGCTTAAAATTGCAAAGACAAGATTTGCTAGTTATTACCTCACCTTTAGGCGGCTAGTAAAGGTGAGACAAGCTTTAACTAATATGGTGTGTGCTGAAACATGGGATGAAATTAACACTGACATAGATGGTGCTAATGCAGTCAAGGACACTGTTCTTGACAGTTACTTTTGGTCACAGGTTAAATATGTTTTGCAATTCACCAAACCAATTTATTACATGATCAAGTTTGCAGATTCAGATCGACCAGTAATTGGGGAGGTGTATGAGCAAATGGATAGCATGTTGGGGCAGATTAAAGACATTGTTGAGCCTAGAGATACCACCTTGTACAATTATATTCGTGTAGAGGTGGAAAACCGATGGGAAATGCTAAATGTTCCATTGCATGCATTAGCATATGTTTTGACACCTAAATACTATCATCCATCATGGCTTTCAACACCAGCACCTAGGGGGGGAAGCAGGAGAAAACCACACCAAGATCAAGAGGTTCACAAAAATATATGGCTGCATTGAGTAAATTAATCCCTGATGAGGAGGAGGCTGCATTGGTACGGAGACAGGTGAGCAACTATACGCTCAACACTGGTCCATTTGGGAGCATGCATGCAATTAAAGATCGAGAGACTTTTTCTGCTCTTGAGTGGTGGAACATGCATGGAGGGGGTACTCCACTTCTACAGAGTTTGGCATTGCGGGTGCTATCACAGGTGGTAAACACTTCTTCTGCAGAGAGGTGTTGGAGCTCTTATTCTTTCATCCACAGTGTTAAAAGGAACAGGTTGAGTTTAGACCGGGCAGAGAGCTTGGTTTATGTTCATTACAACTTGCGATTGTTGTCCCATTACTGTGAAGATGCAAAGTCTAATAAAGACTTGTTGATTTGGGACAAGAATCCAGAGGAGCCCAATTTGGAGGATGGAGTGTTGCGATTAGAGCAATTAGAGGATGCTCTTATCCAGGATGATGATGATCGTGTTGAGATGCCACCCCCATCTGGTCCCTTGGTTCCTAGGTTCCATGGTTCAACACCAATAGCAGGGGGTTCGTCTTCATCAGTTTTAGTGCCACAACTTCCACAGCTGAGATTCGTGAAAGAGACTGGTGCAATGTTGTCACCTGCCATTTGGATGATCCTTGTGCATACACATGGCGTCTTCAGAACTTTGTAATTGGTGAACATATTTTGAAGCCATGTTTGGAGGATCCAACACCAGTGAAGTGCTTGGAACAGAAGGAGGGTGGCTTGAGCGGTTTAATCTTCAATCGGGGATTAGTCGAGGGACATATATTGATATAGGGGAAAAACGACAATGTGCACACAATGGAGCAGTGGTTGGTCTGGCATGTGATGCTACAAATGCCCTTTTAATAAGTGGAGGCTATAACGGAGACATTAAGGTTTGGGATTTCAAGGGGCGTGAGCTAAAGTTCCGATGGGAAATTGAGGTCCCATTAATTAAGATCGTATATCACCCAGGAAATGGTATTCTAGCAACTGCAGCAGATGATATGATTCTTCGTTTATTCGATGTCACTGCCATGCGACTTGTGCGCATATTTGTTGGGCACATGGACCGTGTCACTGATTTGTGTTTTAGTGGAGATGGGAAGTGGTTGTTGTCATCTAGTATGGATGGGACCATAAGAGTTTGGGATGTAATTTCGTCTAGGCAACTCAATGCAATGCGCATGGATTCAGCTGTAACAGCTTTGTCATTGTCACCGGGTATGGATATGCTGGCAACTACCCATGTTGGTCACAATGGCATCTATCTCTGGACATT

Ace file of the UniGene sp_v2.0_unigene9935 (antisense)

Annotations

Source	Descriptions	Term	Type	Identity
AutoFact	similar to beta-transducins (Pfam: PF00400, Score=71.7, E=1.5e-17, N=6) [Arabidopsis thaliana] emb\|CAB81036.1\| putative WD-repeat membrane protein [Arabidopsis thaliana]	-	-	62%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	42%
Blast2go	wd-repeat membrane protein	-	-	75%

Source	GOs	Term	Type	Identity
Blast2go	rRNA processing	GO:0006364	Biological Process	75%
Blast2go	nucleotide binding	GO:0000166	Molecular Function	75%
Blast2go	small-subunit processome	GO:0032040	Cellular Component	75%
Blast2go	CUL4 RING ubiquitin ligase complex	GO:0080008	Cellular Component	75%

Source	InterPros	Term	Type	Identity
Sma3	WD40 repeat	IPR001680	-	-
Sma3	Small-subunit processome, Utp21	IPR007319	-	-
Sma3	WD40/YVTN repeat-like-containing domain	IPR015943	-	-
Sma3	Homeobox, conserved site	IPR017970	-	-
Sma3	WD40-repeat-containing domain	IPR017986	-	-
Sma3	WD40 repeat, conserved site	IPR019775	-	-
Sma3		IPR019782	-	-

Full-Lengther Next Prediction

Fln status: Putative Complete

Fln database: coniferopsida.fasta

Fln subject: D5A8W4

Fln msg: query STOP codon too far from subject stop. Distance to subject end: 38 aas, putative chimeric sequence, Unexpected STOP codon in 5 prime region, your sequence is shorter than subject: 223 - 478

Fln protein: MAALSKLIPDEEEAALVRRQVSNYTLNTGPFGSMHAIKDRETFSALEWWNMHGGGTPLLQSLALRVLSQVVNTSSAERCWSSYSFIHSVKRNRLSLDRAESLVYVHYNLRLLSHYCEDAKSNKDLLIWDKNPEEPNLEDGVLRLEQLEDALIQDDDDRVEMPPPSGPLVPRFHGSTPIAGGSSSSVLVPQLPQLRFVKETGAMLSPAIWMILVHTHGVFRTL*

Protein Length: 224

Fln nts: ACTCATGAGTGGGTAGATTCTGGGGTATCCATTGTATCAGATGGGTGGACAAATATTAAAAAACCAACATTTGATAAATGTTCTTGGTGTTTCTTCTAGTGGTGCAGTATTTATTGCATGTCATGACTCCTCCTCCGTCGCTGCAACCGCACCAAACATTGCAGATCTCCTATTGAAATCAATCAAAGATGTTGGTCCGAATAATGTGGTTCAAGTGATCACAGAACATTGCAGCAAATTGTAAGGCAGCAGGAAGAATTATTGAGCGTACTTATCCACACATCTTTTGGTCTGGGTGCCTGGTTCACACATTGAACCTTTTGATGCATGATATTGTGAAGCACAAAGAATGTGGGTGGATTATTGAGCTTTACAGGAGAGGGAAGTAGCTCATTAAATTCATCACAGGGCATACAAGGGTAAACTACTTCTATGGCACTTACTCCAAGTTGCAATTGCTTAAAATTGCAAAGACAAGATTTGCTAGTTATTACCTCACCTTTAGGCGGCTAGTAAAGGTGAGACAAGCTTTAACTAATATGGTGTGTGCTGAAACATGGGATGAAATTAACACTGACATAGATGGTGCTAATGCAGTCAAGGACACTGTTCTTGACAGTTACTTTTGGTCACAGGTTAAATATGTTTTGCAATTCACCAAACCAATTTATTACATGATCAAGTTTGCAGATTCAGATCGACCAGTAATTGGGGAGGTGTATGAGCAAATGGATAGCATGTTGGGGCAGATTAAAGACATTGTTGAGCCTAGAGATACCACCTTGTACAATTATATTCGTGTAGAGGTGGAAAACCGATGGGAAATGCTAAATGTTCCATTGCATGCATTAGCATATGTTTTGACACCTAAATACTATCATCCATCATGGCTTTCAACACCAGCACCTAGGGGGGGAAGCAGGAGAAAACCACACCAAGATCAAGAGGTTCACAAAAATAT_-_ATGGCTGCATTGAGTAAATTAATCCCTGATGAGGAGGAGGCTGCATTGGTACGGAGACAGGTGAGCAACTATACGCTCAACACTGGTCCATTTGGGAGCATGCATGCAATTAAAGATCGAGAGACTTTTTCTGCTCTTGAGTGGTGGAACATGCATGGAGGGGGTACTCCACTTCTACAGAGTTTGGCATTGCGGGTGCTATCACAGGTGGTAAACACTTCTTCTGCAGAGAGGTGTTGGAGCTCTTATTCTTTCATCCACAGTGTTAAAAGGAACAGGTTGAGTTTAGACCGGGCAGAGAGCTTGGTTTATGTTCATTACAACTTGCGATTGTTGTCCCATTACTGTGAAGATGCAAAGTCTAATAAAGACTTGTTGATTTGGGACAAGAATCCAGAGGAGCCCAATTTGGAGGATGGAGTGTTGCGATTAGAGCAATTAGAGGATGCTCTTATCCAGGATGATGATGATCGTGTTGAGATGCCACCCCCATCTGGTCCCTTGGTTCCTAGGTTCCATGGTTCAACACCAATAGCAGGGGGTTCGTCTTCATCAGTTTTAGTGCCACAACTTCCACAGCTGAGATTCGTGAAAGAGACTGGTGCAATGTTGTCACCTGCCATTTGGATGATCCTTGTGCATACACATGGCGTCTTCAGAACTTTGTAATTGGTGAACATATTTTGAAGCCATGTTTGGAGGATCCAACACCAGTGAAGTGCTTGGAACAGAAGGAGGGTGGCTTGAGCGGTTTAATCTTCAATCGGGGATTAGTCGAGGGACATATATTGATATAGGGGAAAAACGACAATGTGCACACAATGGAGCAGTGGTTGGTCTGGCATGTGATGCTACAAATGCCCTTTTAATAAGTGGAGGCTATAACGGAGACATTAAGGTTTGGGATTTCAAGGGGCGTGAGCTAAAGTTCCGATGGGAAATTGAGGTCCCATTAATTAAGATCGTATATCACCCAGGAAATGGTATTCTAGCAACTGCAGCAGATGATATGATTCTTCGTTTATTCGATGTCACTGCCATGCGACTTGTGCGCATATTTGTTGGGCACATGGACCGTGTCACTGATTTGTGTTTTAGTGGAGATGGGAAGTGGTTGTTGTCATCTAGTATGGATGGGACCATAAGAGTTTGGGATGTAATTTCGTCTAGGCAACTCAATGCAATGCGCATGGATTCAGCTGTAACAGCTTTGTCATTGTCACCGGGTATGGATATGCTGGCAACTACCCATGTTGGTCACAATGGCATCTATCTCTGGACATT

Fln Alignment:

Contig9935___WWNMHGGGTPLLQSLALRVLSQVVNTSSAERCWSSYSFIHSVKRNRLSLDRAESLVYVHYNLRLLSHYCE---DAKSNK-----DLLIWDKNPEEPNLEDGVLRLEQLEDA
D5A8W4______________WWENYGATTPILQKMAIRVLSQTCSSSGCERNWSVFEKIHTKKRNRLDTSCLNDLVYVHYNLRLWVKQLEIKIDARAISLDEIDTTAAWRVEVEEPVAENA---LDWLEDS

SNPs (tot: 98)

Position	A %	C %	G %	T %	Probability
343	83	16			0.994512
344	83	16			0.994512
345		16		83	0.994512
346	16			83	0.994512
421	80		20		0.995493
426		80		20	0.995493
427	80		20		0.995493
436	80			20	0.995493
442			20	80	0.995493
456		80		20	0.995493
825	33	66			0.997452
836			90	10	0.90298
837	90			10	0.90298
839		90	10		0.90298
840	90		10		0.90298
843		90		10	0.90298
859	10	90			0.90298
860	10		90		0.90298
863	80		20		0.999996
870	90		10		0.90298
872	30	70			1.0
879	90		10		0.90298
882	20		80		0.999996
886		10		90	0.90298
890		90		10	0.90298
892	30		70		1.0
894	90	10			0.90298
910	71			28	1.0
911	57		28	14	1.0
920	14			85	0.993533
926	85			14	0.993533
936	14			85	0.993533
942	42		57		1.0
956	85		14		0.993533
958		85		14	0.993533
977	85		14		0.993533
989		85		14	0.993533
993		71		28	1.0
994		85		14	0.993533
1009	42	57			1.0
1021	85		14		0.993533
1024		42	14	42	1.0
1107	18	72		9	0.999994
1124		90	10		0.90298
1145	90			10	0.90298
1149	90		10		0.90298
1153	10		90		0.90298
1154	20	80			0.999996
1156	11		88		0.923564
1164		87		12	0.992554
1174		28		71	1.0
1176	85	14			0.993533
1178		14		85	0.993533
1180	28		71		1.0
1185	12	87			0.992554
1192		87	12		0.992554
1209	25		75		1.0
1211	11		88		0.923564
1213	18		81		0.999994
1226	36	54		9	1.0
1227	18	72		9	0.999994
1228			18	81	0.999994
1235	36		63		1.0
1241	81			18	0.999994
1242			18	81	0.999994
1251		90		10	0.90298
1254		90		10	0.90298
1259		90		10	0.90298
1263	12		87		0.992554
1265		12		87	0.992554
1282	42		42	14	1.0
1283		85		14	0.993533
1295		20		40	1.0
1310	80		20		0.995493
1327	20			80	0.995493
1329		80		20	0.995493
1332	25	75			0.996473
1334			25	75	0.996473
1340		66		33	0.997452
1358	66		33		0.997452
1399	33	66			0.997452
1417		66		33	0.997452
1435			66	33	0.997452
1543	75		25		0.996473
1547		75		25	0.996473
1553	25		75		0.996473
1558	25		75		0.996473
1564	25		75		0.996473
1569		75	25		0.996473
1593		25	75		0.996473
1598	66			33	0.997452
2024	28			71	1.0
2026	28		71		1.0
2055	16		83		0.994512
2069	16		83		0.994512
2087	50	50			1.0
2100			60	40	1.0
2133		66	33		0.997452

SSRs (tot: 1)

Start position	End position	Sequence	Length
814	825	ATC ATC ATC ATC	12

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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