SustainPineDB

Assembly Name: SustainPine v3.0

UniGene Name: sp_v3.0_unigene13030

Length: 2005 nt

UniGene Fasta

>sp_v3.0_unigene13030
AATTCACGAAAATGAGGAAACTTATTATTTAGGAAATGCTGAATCTCTAGTATTAAAACTGTGCTATAAACCCTTATGGTATTGCCTTTGCACTTTACGGGGATCGATCGCTGCATCTCTTATCAAAACACCTTGCGTTTGACTTTTGTAATCAGAGCGAGGGAAACACAAGACGAGTATTGATATTGATCTCTTCTGTTGATTTGTTGGCGATCGATTGGCTTTTGCCGGTGGTGGTGCTGGTTGAAGGGTTAGGGTTTTTTCTGTTCTGTTATTTTCGTAGGTGTGTCTGTTTTAGAATCAATGGCTGCCGCAGGCGGCAGTAGGAACCGTAACAACAACAATGGAGGGCGGAACCCTAATGCAGTTAACGATGAAACCTGATATTCGAAACTAGTGCGGGAGTGGAAGCAGTCTCCAGTTTGATCAGATGGGCATCCGTGACGACCTCCTTCGAGGTATTTACCAATATGGATTCGAGAAGCCTTCGGCCATTCAGCAGAGAGCAGTGATGCCTATCATCAATGGCAGAGATGTTATTGCGCAGGCCCAGTCTGGTACTGGAAAGACCTCCATGATTGCCCTCACCGTCTGTCAGATAATCGACACTTCCATACGAGAGGTTCAAGCTTTAATTGTGTCGCCTACACGAGAACTTGCGGCTCAAACAGAGAAAGTGATACTTGCCATAGGAGATTTCATAAACGTTCAAGCTCATGCATGTATCGGTGGTAAGAGTATTGGTGAGGATATCAGAAAACTGGAATATGGGGTTCATGTGGTATCAGGAACACCAGGAAGAGTGTGTGATATGATCAAACGCAGGACCCTAAGGACCAGAGCTATTAAACTACTTGTTCTCGATGAATCTGATGAAATGTTGAGCAGGGGTATTCAAAGACCAGATATATGATGTTTATCGATACCTTCCACCAGAGCTTCAGGTTGTGCTGATATCAGCAACTTTGCCACATGAGATTTTGGAGATTACAAACAAATTCATGACTGATCCTGTAAGAATCCTTGTCAAACGTGATGAATTGACACTGGAGGGCATCAAACAATTTTTTGTGGCTGTTGAAAGAGAGGAGTGGAAGTTTGACACCCTATGTGATCTATATGATACACTTACTATTACTCAGGCTGTCATATTTTGCAATACCAAAAGAAAGGTTGATTGGTTGACAGAAAAGATGCGAAGCAATAATTTCACTGTGTCTTCTATGCATGGAGACATGCCACAAAAAGAACGTGATGCAATTATGGCAGAATTTCGTGCAGGCACAACCCGTGTTTTAATCACAACAGATGTTTGGGCTCGTGGTCTTGATGTTCAGCAGGTTTCCTTGGTGATAAACTATGATCTTCCCAACAATCGTGAACTTTACATTCATAGAATTGGTCGCTCAGGTCGTTTCGGTCGAAAGGGTGTTGCAATAAATTTTGTTCGAAATGATGATATTAGGATACTAAGAGATATTGAGCAGTATTACAGTACTCAGATAGATGAAATGCCCATGAATGTGGCAGATCTGATCTAAATAATGCAATTATTCCAGCATGTAATATTAGCTACAACAAGTGTCCTGATGCCTGCTTAATTAGGACATGTTAAACATCCCCTGTATTTTCAGTAGCTGTGCTACATTTGCTTCAAAGAATGTTTTGTAGTGGCAAGCAGAGTGTCTCTCGGTGTTGTGCCTGCCAGATGTTGTATACTTCAAATTTCATGTCCAACGTGCTTATAGATTTTATAGTCTGTCCTGTAAGCTTCTGAGTGGAGCAGTTTAATGTTGACAGCACGAAAATGAATTTGCTTGTATTCTTTTATAATATTGACAGTCTGCAAAGTTTGACATCATCGTTAATCAGTTTAAAGGTTTGTGCTTTATTCGTATGATGTGATACATCGACCACATCTTTCCTGAATCCCAGAATAGAGCCTGGTTGTACAAGGGTTATATTAGTATTTATGGTAGCATAGAGGACTTGTTTTAACTAGAAC

Ace file of the UniGene sp_v3.0_unigene13030

Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	DEAD-box ATP-dependent RNA helicase 2 n=6 Tax=BEP clade RepID=RH2_ORYSJ	-	-	0.0	94%
FL-Next	tr=Putative uncharacterized protein; Picea sitchensis (Sitka spruce) (Pinus sitchensis).	-	-	0.0	80%
Sma3	Dead box ATP-dependent RNA helicase, putative	-	-	3.219e-09	-

Source	ECs	Term	Type	e value	Identity
Sma3	Hydrolases, Acting on acid anhydrides, In phosphorous-containing anhydrides.	EC:3.6.1.-	-	3.084e-11	-

Source	KEGGs	Term	e value	Identity
Sma3	Purine metabolism	00230	3.084e-11	%
Sma3	Lipopolysaccharide biosynthesis	00540	3.084e-11	%
Sma3	Folate biosynthesis	00790	3.084e-11	%
Sma3	Metabolic pathways	01100	3.084e-11	%

Source	Gene names
Sma3	AT1G54270; AT3G13920; At1g51380; At1g54270; At1g72730; At3g13920; At3g19760; B1131G07.20; CHLREDRAFT_188942; CHLREDRAFT_608; DH1; EIF4A; EIF4A3; F11M15.24; F20D21.9; F20D21_52; F28P22.8; F5D21.11; GSVIVT00016530001; GSVIVT00032180001; GSVIVT00034135001; G

Source	GOs	Term	Type	Identity
Sma3	cell wall	GO:0005618	Cellular Component	-
Sma3	nucleus	GO:0005634	Cellular Component	-
Sma3	nucleolus	GO:0005730	Cellular Component	-
Sma3	cytoplasm	GO:0005737	Cellular Component	-
Sma3	plasma membrane	GO:0005886	Cellular Component	-
Sma3	plant-type cell wall	GO:0009505	Cellular Component	-
Sma3	membrane	GO:0016020	Cellular Component	-
Sma3	nucleic acid binding	GO:0003676	Molecular Function	-
Sma3	RNA binding	GO:0003723	Molecular Function	-
Sma3	translation initiation factor activity	GO:0003743	Molecular Function	-
Sma3	helicase activity	GO:0004386	Molecular Function	-
Sma3	ATP binding	GO:0005524	Molecular Function	-
Sma3	ATP-dependent helicase activity	GO:0008026	Molecular Function	-
Sma3	rRNA processing	GO:0006364	Biological Process	-
Sma3	translation	GO:0006412	Biological Process	-

Source	InterPros	Term	Type	Identity
Sma3	RNA helicase, ATP-dependent, DEAD-box, conserved site	IPR000629	-	-
Sma3	Helicase, C-terminal	IPR001650	-	-
Sma3	WD40 repeat	IPR001680	-	-
Sma3	DNA/RNA helicase, DEAD/DEAH box type, N-terminal	IPR011545	-	-
Sma3	Helicase, superfamily 1/2, ATP-binding domain	IPR014001	-	-
Sma3	RNA helicase, DEAD-box type, Q motif	IPR014014	-	-
Sma3		IPR014021	-	-
Sma3	WD40/YVTN repeat-like-containing domain	IPR015943	-	-
Sma3	WD40-repeat-containing domain	IPR017986	-	-
Sma3	WD40 repeat, conserved site	IPR019775	-	-
Sma3		IPR019782	-	-

Source	Species	ID	Description	Identity
ATG	Arabidoptis thaliana	AT3G19760.1	EIF4A-III eukaryotic initiation factor 4A-III chr3:6863790-6866242 FORWARD LENGTH=408	91%
RefSeq	Arabidopsis thaliana	NP_188610.1	DEAD-box ATP-dependent RNA helicase 2 [Arabidopsis thaliana]	91%
RefSeq	Populus trichocarpa	XP_002310663.1	predicted protein [Populus trichocarpa]	90%

Full-Lengther Next Prediction

Fln status: Putative Complete

Fln database: coniferopsida.fasta

Fln subject: A9NUU4

Fln msg: Overlapping hits, possible frame ERROR between 422 and 422, Unexpected STOP codon in 5 prime region, your sequence is shorter than subject: 360 - 408

Fln protein: MGIRDDLLRGIYQYGFEKPSAIQQRAVMPIINGRDVIAQAQSGTGKTSMIALTVCQIIDTSIREVQALIVSPTRELAAQTEKVILAIGDFINVQAHACIGGKSIGEDIRKLEYGVHVVSGTPGRVCDMIKRRTLRTRAIKLLVLDESDEMLSRGIQRPDI*CLSIPSTRASGCADISNFAT*DFGDYKQIHD*SCKNPCQT**IDTGGHQTIFCGC*KRGVEV*HPM*SI*YTYYYSGCHILQYQKKG*LVDRKDAKQ*FHCVFYAWRHATKRT*CNYGRISCRHNPCFNHNRCLGSWS*CSAGFLGDKL*SSQQS*TLHS*NWSLRSFRSKGCCNKFCSK**Y*DTKRY*AVLQYSDR*

Protein Length: 361

Fln nts: AATTCACGAAAATGAGGAAACTTATTATTTAGGAAATGCTGAATCTCTAGTATTAAAACTGTGCTATAAACCCTTATGGTATTGCCTTTGCACTTTACGGGGATCGATCGCTGCATCTCTTATCAAAACACCTTGCGTTTGACTTTTGTAATCAGAGCGAGGGAAACACAAGACGAGTATTGATATTGATCTCTTCTGTTGATTTGTTGGCGATCGATTGGCTTTTGCCGGTGGTGGTGCTGGTTGAAGGGTTAGGGTTTTTTCTGTTCTGTTATTTTCGTAGGTGTGTCTGTTTTAGAATCAATGGCTGCCGCAGGCGGCAGTAGGAACCGTAACAACAACAATGGAGGGCGGAACCCTAATGCAGTTAACGATGAAACCTGATATTCGAAACTAGTGCGGGAGTGGAAGCAGTCTCCxxxxxxGATCAGATGGGCATCCGTGACGACCTCCTTCGAGGTATTTACCAATATGGATTCGAGAAGCCTTCGGCCATTCAGCAGAGAGCAGTGATGCCTATCATCAATGGCAGAGATGTTATTGCGCAGGCCCAGTCTGGTACTGGAAAGACCTCCATGATTGCCCTCACCGTCTGTCAGATAATCGACACTTCCATACGAGAGGTTCAAGCTTTAATTGTGTCGCCTACACGAGAACTTGCGGCTCAAACAGAGAAAGTGATACTTGCCATAGGAGATTTCATAAACGTTCAAGCTCATGCATGTATCGGTGGTAAGAGTATTGGTGAGGATATCAGAAAACTGGAATATGGGGTTCATGTGGTATCAGGAACACCAGGAAGAGTGTGTGATATGATCAAACGCAGGACCCTAAGGACCAGAGCTATTAAACTACTTGTTCTCGATGAATCTGATGAAATGTTGAGCAGGGGTATTCAAAGACCAGATATATGATGTTTATCGATACCTTCCACCAGAGCTTCAGGTTGTGCTGATATCAGCAACTTTGCCACATGAGATTTTGGAGATTACAAACAAATTCATGACTGATCCTGTAAGAATCCTTGTCAAACGTGATGAATTGACACTGGAGGGCATCAAACAATTTTTTGTGGCTGTTGAAAGAGAGGAGTGGAAGTTTGACACCCTATGTGATCTATATGATACACTTACTATTACTCAGGCTGTCATATTTTGCAATACCAAAAGAAAGGTTGATTGGTTGACAGAAAAGATGCGAAGCAATAATTTCACTGTGTCTTCTATGCATGGAGACATGCCACAAAAAGAACGTGATGCAATTATGGCAGAATTTCGTGCAGGCACAACCCGTGTTTTAATCACAACAGATGTTTGGGCTCGTGGTCTTGATGTTCAGCAGGTTTCCTTGGTGATAAACTATGATCTTCCCAACAATCGTGAACTTTACATTCATAGAATTGGTCGCTCAGGTCGTTTCGGTCGAAAGGGTGTTGCAATAAATTTTGTTCGAAATGATGATATTAGGATACTAAGAGATATTGAGCAGTATTACAGTACTCAGATAGATGA___AATGCCCATGAATGTGGCAGATCTGATCTAAATAATGCAATTATTCCAGCATGTAATATTAGCTACAACAAGTGTCCTGATGCCTGCTTAATTAGGACATGTTAAACATCCCCTGTATTTTCAGTAGCTGTGCTACATTTGCTTCAAAGAATGTTTTGTAGTGGCAAGCAGAGTGTCTCTCGGTGTTGTGCCTGCCAGATGTTGTATACTTCAAATTTCATGTCCAACGTGCTTATAGATTTTATAGTCTGTCCTGTAAGCTTCTGAGTGGAGCAGTTTAATGTTGACAGCACGAAAATGAATTTGCTTGTATTCTTTTATAATATTGACAGTCTGCAAAGTTTGACATCATCGTTAATCAGTTTAAAGGTTTGTGCTTTATTCGTATGATGTGATACATCGACCACATCTTTCCTGAATCCCAGAATAGAGCCTGGTTGTACAAGGGTTATATTAGTATTTATGGTAGCATAGAGGACTTGTTTTAACTAGAAC

Fln Alignment:

Contig13030___NLIFETSAGVEAVSSFDQMGIRDDLLRGIYQYGFEKPSAIQQRAVMPIINGRDVIAQAQSGTGKTSMIALTVCQIIDTSIREVQALIVSPTRELAAQTEKVILAIGDFINVQAHACIGGKSIGEDIRKLEYGVHVVSGTPGRVCDMIKRRTLRTRAIKLLVLDESDEMLSRGIQ
A9NUU4_______________NLIFETSPGVEVISSFDQMGIRDDLLRGIYQYGFEKPSAIQQRAVMPIINGRDVIAQAQSGTGKTSMIALAVCQIIDTSIREVQALIVSPTRELAAQTEKVILAIGDFINVQAHACIGGKSIGEDIRKLEYGVHVVSGTPGRVCDMIKRRTLRTRAVKLLVLDESDEMLSRGFK

SNPs (tot: 26)

Position	A %	C %	G %	T %	Probability
74		60	40		1.0
76		40		60	1.0
77	60		40		1.0
80	40		60		1.0
81		40		60	1.0
82	60	40			1.0
86		60	40		1.0
89			40	60	1.0
96		40		60	1.0
97	40			60	1.0
117			20	80	0.995493
188		25		75	0.996473
505		83	16		0.994512
506	83		16		0.994512
805	66		33		0.997452
1018	83		16		0.994512
1019			16	83	0.994512
1599	97		2		0.969538
1711		96		3	0.988113
1713	3		96		0.988113
1782	3			96	0.986325
1785			96	3	0.986325
1838	3			90	0.996531
1871	8			91	0.999766
1876	60		20	20	0.99255
1877	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