SustainPineDB

Assembly Name: SustainPine v3.0

UniGene Name: sp_v3.0_unigene3828

Length: 2917 nt

UniGene Fasta

>sp_v3.0_unigene3828
TGAGTATAGTGCTGGATGTCAATGTCGAACCTGCCACTACACCATGGGATCCTGCAAAAGCATATCTATTTGCTCCTATAGTAGCTGAAAATGTTTCAGATCCAATGAAGGAGATAGATTGGTCACTGATTGAAAAGGTCTTGAGCACTGATGCTTGGAATAATCCGCTTCAGCGGGCTCGTCCAGATGTTTATCTTGGTACAGATGAACGTACACTTGGTGGTGATCGAAGAGAATATGGCTTTGGAAAATTGCGTTATGGTATGGCATTTGGGCAAAAGTCACATCCAACGTATGGAATCAGAGGGGCAGTAGCACAGTTTGATGTTGTGAAAGCATCAGGATTAGTTCCTTCTCTTAGATGTCATTGACAACTTGCAGGATGAAGCTCCACCTGGGAAGTTGTGGATGGCTGATGGATACATTGAAATAGAGGAACTTGTGGGGAAAATCATAACTGCAGCTCACTCTGGAAAGCGGTTTTATGTTGATTCAGTTCGTTTTGAGATGAATGCAGACAGTTCATTTCCAAGGAAAGAGGGTTACTTAGGTCCAGTAGAATACAGTTCATATGCTGACTACTACAGACAAAAGTATGGAGTGCAATTGGCTTGCAAGAAGCAACCTCTAATAAGAGGACGTGGTGTCTCATACTGCAAGAATTTGCTTTCTCCAAGATTTGAATCTACCGAGAGCAATGCAGAGGAAACATTAGACAAGACCTATTACGTCATGCTTCCACCAGAACTGTGCTTGGTGCATCCATTGCCAGGACACCTTGTTAGAGGTGCACAGCGATTGCCATCAGTGATGAGGAGAGTTGAGAGCATGCTTCTTGCAGTTCAGCTTAAGCATGAAATCAACTATCCAATTTCAGCTTCCAAGATTTTGGAAGCTTTGACTGCTGCATCTTGTCAGGAGACGTTCTGCTATGAAAGGGCAGAACTTCTAGGAGATGCATATCTGAAGTGGGTTGTTAGTAGATGCTTGTTTCTGAAATATCCTCAGAAACATGAGGGACAACTTACACGCATGAGGCAACAGACTGTGAGTAATGTTGTGCTGTATCAATATGCTCTGGACAAAGGTCTACAGGCCTATATTCAGGCAGATCGCTTTGCTCCATCTAGATGGGCTGCTCCAGGTGTGCTTCCAGTCTTTGATGAAGATACCAATGAAGCAGACAATACAGAGATCATGGATGATGTGGAGCACAGCCCCCAGAGTGAAACAGGTACGCACAAAAATGCTCATCTTGAAGAGTTTGAGGATGAACCTATGGAGGATGGAGAGATTGAGGGTGATTCCAGCTGTTACAGGGTTCTGTCAAGCAAGACATTAGCAGATGTCGTTGAAGCTTTGATTGGAGTTTATTATGTTGAAGGGGGAAAGAAAGCAGCTGTCCATCTTATGAATTGGATAGGAATTCCAACAGAATTTGACCCTAAAGAAGGTGAACTAGCTAGGCGTGGATGCAAGGTTCCTGAATCTGTTATGAGGAGTATTGATTTTGATAAGTTAGAAGGTGCCTTAAATTATAAATTCAATGAGAAAAGTTTGTTGGTTGAGGCTATAACACACGCCTCGCGGCCCTCATCAGGAGTGTCTTGCTATCAGCGATTGGAATTTGTTGGAGATGCAGTTTTAGATCATCTCATAACAAGACATCTCTTCTTTACATATACGGACCTTCCACCTGGGCGCCTTACTGATTTGCGCGCTGCAGCAGTGAACAATGAGAACTTTGCACGTGTTGCAGTGAAAAACAAACTTCATTTACATTTGCGACATGGATCAACTGCATTAGAAGCACAGATCCGTGACTTTGTAAAGGACATTGAAGTGGAACTTGATAAACCAGGAGTGAATTCCTTTGGTCTTGGAGACTTCAAGGCTCCAAAAGTCCTTGGTGATATAGTGGAATCGATAGCTGGAGCAATATTTCTTGATAAAGTTCTTGACACAGCCAAAGTGTGGGAGGTATTCCAACCTTTACTACAGCCTATGGTGACTCCAGAGACACTTCCCATGCACCCAGTTCGTGAACTTCAAGAGCGCTGTCAACAGCAGGCTGAGGGTTTAGAGTACAAGGCCTCACGAACAGGAAATATGGCTACAGTTGAAGTTTTTGTTGATGGAGTCCAGATTGGTTTCGCTCAAAACCCACAGAAGAAAATGGCACAGAAATTAGCAGCTCGAAATGCTCTTGTCATATTGAAGGAAAAGGAAGCAGAGGAGACAAAGGCTGATGGTATGAATAATGGAGATGGAACAGCTGGGAAGAAGAATGGAAATCAAACTTTCACACGGCAAACTCTGAATGACATTTGTCTCAGGAGACAGTGGCCAATGCCTCAATATAGGTGTATAAGTGAAGGCGGGCCAGCTCATGCAAAGAGATTTACTTACTCTGTGCGCGTACATACAACAGAGAGAGGATGGACAGATGACTGCGTGGGCGAACCAATGCCTAGTGTGAAGAAGGCAAAGGATTCTGCGGCAATGCTGTTGCTAGAACTTCTCAAGCGCTGGCCTGATCATTGAAGACAGTTCCACCTAATCTACATATTCTCAAAGGAATGTAATTCTTAGTGGACCATTTTATGAGTCATCTAATTTTCTTGGTATAGTTGTCCAATGTCTCCATTGCCTAAACATATTCACTTATATGTGGGGCTATAAGTCAGAGATTGGATATTACCGTTTAGAGCTCCAAATTATTTTCATAAATACATGTTGAGTCTACAGGTTGGCATTGGACACATAAGAATGTAGACTGATTAATTTCAGTTTTATTCAAATCAACAGCTAAAAGTCGTTTTCGCACCGATTTTTTGTGGGGCTTCCGTAAGGAATGATATTATCGCAATGAAATTGAACGCAAACATTATTTTGGGAAATTGAACGCCAAATGTCG

Ace file of the UniGene sp_v3.0_unigene3828

Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	DsRNA-specific nuclease dicer and related ribonuclease n=2 Tax=Physcomitrella patens RepID=A9RV91_PHYPA	-	-	0.0	74%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	0.0	40%
Sma3	DsRNA-specific nuclease dicer and related ribonuclease	-	-	1.06e-11	-

Source	ECs	Term	Type	e value	Identity
Sma3	Ribonuclease III.	EC:3.1.26.3	-	5.38e-07	-

Source	Gene names
Sma3	At1g01040; CAF; DCL1504; DCL1a; DCL1b; DCL902; GSVIVT00025923001; GSVIVT00026189001; LOC_Os03g02970; LOC_Os10g34430; MtrDRAFT_AC150443g32v2; OJ1705B08.11; OSJNBa0029C15.23; OSJNBb0027A16.25; Os03g0121800; Os06g0358800; OsI_09779; OsI_22916; OsJ_09217; OsJ

Source	GOs	Term	Type	Identity
Sma3	intracellular	GO:0005622	Cellular Component	-
Sma3	nuclear dicing body	GO:0010445	Cellular Component	-
Sma3	DNA binding	GO:0003677	Molecular Function	-
Sma3	RNA binding	GO:0003723	Molecular Function	-
Sma3	double-stranded RNA binding	GO:0003725	Molecular Function	-
Sma3	helicase activity	GO:0004386	Molecular Function	-
Sma3	ribonuclease III activity	GO:0004525	Molecular Function	-
Sma3	protein binding	GO:0005515	Molecular Function	-
Sma3	ATP binding	GO:0005524	Molecular Function	-
Sma3	ATP-dependent helicase activity	GO:0008026	Molecular Function	-
Sma3	cytokinesis	GO:0000910	Biological Process	-
Sma3	RNA processing	GO:0006396	Biological Process	-
Sma3	virus induced gene silencing	GO:0009616	Biological Process	-
Sma3	embryonic pattern specification	GO:0009880	Biological Process	-
Sma3	flower development	GO:0009908	Biological Process	-
Sma3	vegetative to reproductive phase transition of meristem	GO:0010228	Biological Process	-
Sma3	production of ta-siRNAs involved in RNA interference	GO:0010267	Biological Process	-
Sma3	production of lsiRNA involved in RNA interference	GO:0010599	Biological Process	-
Sma3	primary miRNA processing	GO:0031053	Biological Process	-
Sma3	mRNA cleavage involved in gene silencing by miRNA	GO:0035279	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	Ribonuclease III domain	IPR000999	-	-
Sma3	Double-stranded RNA-binding	IPR001159	-	-
Sma3	Helicase, C-terminal	IPR001650	-	-
Sma3	Argonaute/Dicer protein, PAZ	IPR003100	-	-
Sma3	Dicer double-stranded RNA-binding fold	IPR005034	-	-
Sma3	Helicase/UvrB domain	IPR006935	-	-
Sma3	DNA/RNA helicase, DEAD/DEAH box type, N-terminal	IPR011545	-	-
Sma3	Helicase, superfamily 1/2, ATP-binding domain	IPR014001	-	-
Sma3		IPR014021	-	-
Sma3	Double-stranded RNA-binding-like	IPR014720	-	-
Sma3	Aldo/keto reductase, conserved site	IPR018170	-	-

Source	Species	ID	Description	Identity
ATG	Arabidoptis thaliana	AT1G01040.2	DCL1 dicer-like 1 chr1:23519-31079 FORWARD LENGTH=1910	75%
RefSeq	Arabidopsis thaliana	NP_001184881.1	endoribonuclease Dicer [Arabidopsis thaliana]	75%
RefSeq	Populus trichocarpa	XP_002302679.1	dicer-like protein [Populus trichocarpa]	76%

Full-Lengther Next Prediction

Fln status: Putative Complete

Fln database: coniferopsida.fasta

Fln subject: B8LN71

Fln msg: query STOP codon too far from subject stop. Distance to subject end: 113 aas, putative chimeric sequence,

Fln protein: MADGYIEIEELVGKIITAAHSGKRFYVDSVRFEMNADSSFPRKEGYLGPVEYSSYADYYRQKYGVQLACKKQPLIRGRGVSYCKNLLSPRFESTESNAEETLDKTYYVMLPPELCLVHPLPGHLVRGAQRLPSVMRRVESMLLAVQLKHEINYPISASKILEALTAASCQETFCYERAELLGDAYLKWVVSRCLFLKYPQKHEGQLTRMRQQTVSNVVLYQYALDKGLQAYIQADRFAPSRWAAPGVLPVFDEDTNEADNTEIMDDVEHSPQSETGTHKNAHLEEFEDEPMEDGEIEGDSSCYRVLSSKTLADVVEALIGVYYVEGGKKAAVHLMNWIGIPTEFDPKEGELARRGCKVPESVMRSIDFDKLEGALNYKFNEKSLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITRHLFFTYTDLPPGRLTDLRAAAVNNENFARVAVKNKLHLHLRHGSTALEAQIRDFVKDIEVELDKPGVNSFGLGDFKAPKVLGDIVESIAGAIFLDKVLDTAKVWEVFQPLLQPMVTPETLPMHPVRELQERCQQQAEGLEYKASRTGNMATVEVFVDGVQIGFAQNPQKKMAQKLAARNALVILKEKEAEETKADGMNNGDGTAGKKNGNQTFTRQTLNDICLRRQWPMPQYRCISEGGPAHAKRFTYSVRVHTTERGWTDDCVGEPMPSVKKAKDSAAMLLLELLKRWPDH*

Protein Length: 713

Fln nts: TGAGTATAGTGCTGGATGTCAATGTCGAACCTGCCACTACACCATGGGATCCTGCAAAAGCATATCTATTTGCTCCTATAGTAGCTGAAAATGTTTCAGATCCAATGAAGGAGATAGATTGGTCACTGATTGAAAAGGTCTTGAGCACTGATGCTTGGAATAATCCGCTTCAGCGGGCTCGTCCAGATGTTTATCTTGGTACAGATGAACGTACACTTGGTGGTGATCGAAGAGAATATGGCTTTGGAAAATTGCGTTATGGTATGGCATTTGGGCAAAAGTCACATCCAACGTATGGAATCAGAGGGGCAGTAGCACAGTTTGATGTTGTGAAAGCATCAGGATTAGTTCCTTCTCTTAGATGTCATTGACAACTTGCAGGATGAAGCTCCACCTGGGAAGTTGTGG_-_ATGGCTGATGGATACATTGAAATAGAGGAACTTGTGGGGAAAATCATAACTGCAGCTCACTCTGGAAAGCGGTTTTATGTTGATTCAGTTCGTTTTGAGATGAATGCAGACAGTTCATTTCCAAGGAAAGAGGGTTACTTAGGTCCAGTAGAATACAGTTCATATGCTGACTACTACAGACAAAAGTATGGAGTGCAATTGGCTTGCAAGAAGCAACCTCTAATAAGAGGACGTGGTGTCTCATACTGCAAGAATTTGCTTTCTCCAAGATTTGAATCTACCGAGAGCAATGCAGAGGAAACATTAGACAAGACCTATTACGTCATGCTTCCACCAGAACTGTGCTTGGTGCATCCATTGCCAGGACACCTTGTTAGAGGTGCACAGCGATTGCCATCAGTGATGAGGAGAGTTGAGAGCATGCTTCTTGCAGTTCAGCTTAAGCATGAAATCAACTATCCAATTTCAGCTTCCAAGATTTTGGAAGCTTTGACTGCTGCATCTTGTCAGGAGACGTTCTGCTATGAAAGGGCAGAACTTCTAGGAGATGCATATCTGAAGTGGGTTGTTAGTAGATGCTTGTTTCTGAAATATCCTCAGAAACATGAGGGACAACTTACACGCATGAGGCAACAGACTGTGAGTAATGTTGTGCTGTATCAATATGCTCTGGACAAAGGTCTACAGGCCTATATTCAGGCAGATCGCTTTGCTCCATCTAGATGGGCTGCTCCAGGTGTGCTTCCAGTCTTTGATGAAGATACCAATGAAGCAGACAATACAGAGATCATGGATGATGTGGAGCACAGCCCCCAGAGTGAAACAGGTACGCACAAAAATGCTCATCTTGAAGAGTTTGAGGATGAACCTATGGAGGATGGAGAGATTGAGGGTGATTCCAGCTGTTACAGGGTTCTGTCAAGCAAGACATTAGCAGATGTCGTTGAAGCTTTGATTGGAGTTTATTATGTTGAAGGGGGAAAGAAAGCAGCTGTCCATCTTATGAATTGGATAGGAATTCCAACAGAATTTGACCCTAAAGAAGGTGAACTAGCTAGGCGTGGATGCAAGGTTCCTGAATCTGTTATGAGGAGTATTGATTTTGATAAGTTAGAAGGTGCCTTAAATTATAAATTCAATGAGAAAAGTTTGTTGGTTGAGGCTATAACACACGCCTCGCGGCCCTCATCAGGAGTGTCTTGCTATCAGCGATTGGAATTTGTTGGAGATGCAGTTTTAGATCATCTCATAACAAGACATCTCTTCTTTACATATACGGACCTTCCACCTGGGCGCCTTACTGATTTGCGCGCTGCAGCAGTGAACAATGAGAACTTTGCACGTGTTGCAGTGAAAAACAAACTTCATTTACATTTGCGACATGGATCAACTGCATTAGAAGCACAGATCCGTGACTTTGTAAAGGACATTGAAGTGGAACTTGATAAACCAGGAGTGAATTCCTTTGGTCTTGGAGACTTCAAGGCTCCAAAAGTCCTTGGTGATATAGTGGAATCGATAGCTGGAGCAATATTTCTTGATAAAGTTCTTGACACAGCCAAAGTGTGGGAGGTATTCCAACCTTTACTACAGCCTATGGTGACTCCAGAGACACTTCCCATGCACCCAGTTCGTGAACTTCAAGAGCGCTGTCAACAGCAGGCTGAGGGTTTAGAGTACAAGGCCTCACGAACAGGAAATATGGCTACAGTTGAAGTTTTTGTTGATGGAGTCCAGATTGGTTTCGCTCAAAACCCACAGAAGAAAATGGCACAGAAATTAGCAGCTCGAAATGCTCTTGTCATATTGAAGGAAAAGGAAGCAGAGGAGACAAAGGCTGATGGTATGAATAATGGAGATGGAACAGCTGGGAAGAAGAATGGAAATCAAACTTTCACACGGCAAACTCTGAATGACATTTGTCTCAGGAGACAGTGGCCAATGCCTCAATATAGGTGTATAAGTGAAGGCGGGCCAGCTCATGCAAAGAGATTTACTTACTCTGTGCGCGTACATACAACAGAGAGAGGATGGACAGATGACTGCGTGGGCGAACCAATGCCTAGTGTGAAGAAGGCAAAGGATTCTGCGGCAATGCTGTTGCTAGAACTTCTCAAGCGCTGGCCTGATCATTGA___AGACAGTTCCACCTAATCTACATATTCTCAAAGGAATGTAATTCTTAGTGGACCATTTTATGAGTCATCTAATTTTCTTGGTATAGTTGTCCAATGTCTCCATTGCCTAAACATATTCACTTATATGTGGGGCTATAAGTCAGAGATTGGATATTACCGTTTAGAGCTCCAAATTATTTTCATAAATACATGTTGAGTCTACAGGTTGGCATTGGACACATAAGAATGTAGACTGATTAATTTCAGTTTTATTCAAATCAACAGCTAAAAGTCGTTTTCGCACCGATTTTTTGTGGGGCTTCCGTAAGGAATGATATTATCGCAATGAAATTGAACGCAAACATTATTTTGGGAAATTGAACGCCAAATGTCG

Fln Alignment:

Contig3828___VMRRVESMLLAVQLKHEI--NYP----ISASKILEALTAASCQETFCYERAELLGDAYLKWVVSRCLFLKYPQKHEGQLTRMRQQTVSNVVLYQYALDKGLQAYIQADRFAPSRWAAPGVLPVFDEDTNE---------ADNTEIMDDVEHSPQSETGTHKNAHLXXXXXXXXXXXXXXXXSSCYRVLSSKTLADVVEALIGVYYVEGGKKAAVHLMNWIGIPTEFDPK-EGELARRGCKVPESVMRSIDFDKLEGALNYKFNEKSLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITRHLFFTYTDLPPGRLTDLRAAAVNNENFARVAVKNKLHLHLRHGSTALEAQIRDFVKDIEVELDKPGVNSFGLGDFKAPKVLGDIVESIAGAIFLDKVLDTAKVWEVFQPLLQPMVTPETLPMHPVRELQERCQQQAEGLEY-KASR-TGNMATVEVFVDGVQI-----GFAQNPQKKMAQKLAARNALVILK
B8LN71______________MMHRLENLLVAIELKELLTASFPEGSLVTASRVLEAITTERCMEGFSLERLEVLGDAFLKYAVSRRLFLVYDKLDEGQLTKKRSNAIKNSNLYKRAKGKGFPAYIRDEYFDPKQYFALG-RPCKNVCTPELVHMIHYFEGDNT--MTDTDFTSVKCTKRHHWLHM-------------------------KTIADVVEALIGAYLVDSGFGAALAFLKWIGIEIDFDTSLVGEVCIRS-RNNLSLIKCIDIDELERLLGYNFSYKGLLLEAFAHPSFNEHNGGCYQRLEFLGDAVLDYIITSYLYSVYPDMKPGYLTDMRSMTVNNESFACVAVRHGLYMYLIQKSDSLSSAVTKYV-DFMKALFTADRDSCDEPEPKCPKVLGDIVESFAGALVIDTGFDLDCVWKLMLNILQPIVTPETLCLQPVRELSEVCQHHNLTLDYVKASKGNGNGYLVEAKVSGKKVSGSVGGTGTRTSIKDAKKVASKDALLKLK

SNPs (tot: 31)

Position	A %	C %	G %	T %	Probability
629		16		83	0.994512
643	20		80		0.995493
645			80	20	0.995493
802			14	85	0.993533
804		85	14		0.993533
817	12		87		0.992554
818			87	12	0.992554
819	87		12		0.992554
820			87	12	0.992554
917	11			88	0.923564
918		88		11	0.923564
919	88		11		0.923564
965		14		85	0.993533
1117			88	11	0.923564
1220		50		50	1.0
1313		85	14		0.993533
1314			14	85	0.993533
1352		85		14	0.993533
1455	11		88		0.923564
1461		88		11	0.923564
1677	20	80			0.995493
1679			20	80	0.995493
1680			20	80	0.995493
1685	80		20		0.995493
1793	81		18		0.999994
1888		16	83		0.994512
2104	66		33		0.997452
2105		66	33		0.997452
2106	66		33		0.997452
2264	88		11		0.923564
2594	86			13	1.0

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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