SustainPineDB

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Assembly info
Unigenes
SNPs
SSRs
Descriptions
GOs
ECs
KEGGs
InterPros
miRNAs

Assembly Name: SustainPine v3.0

UniGene Name: sp_v3.0_unigene108714

Length: 312 nt

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

UniGene Fasta (sense)

>sp_v3.0_unigene108714
AGATCATTCACAGGGCTGGAGGAGCTATATACCTTTTCCGTGGACGAAATTACAATTACAAAACACGACCTATGAATCCCTTGATGCTTTGGAAGCCTGCAGCAGCTGTTTATCCAAGACTGATTGAACGGGCTCCAGGAGGGTTAACCTTCGAAGAAGCAAAAGAATTACGTAAAAGGGGACGGTCACTGCTTCCAATCTGCAAACTCTCAAAAAATGGTGTGTATTTGAATCTTGCAAAGGATGTTAGAGATGCCTTTGAAGTAAGTGATCTGGTTCGGGTAAATTGTCAAGGCTTAAATCCAAGTGATT

Ace file of the UniGene sp_v3.0_unigene108714 (antisense)

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Annotations

Source	Descriptions	Term	Type	e value	Identity
AutoFact	CRS2-associated factor 2, chloroplastic n=2 Tax=Arabidopsis RepID=CAF2P_ARATH	-	-	1.0e-38	72%
FL-Next	sp=CRS2-associated factor 2, chloroplastic; Arabidopsis thaliana (Mouse-ear cress).	-	-	0.0	72%
Sma3	Chloroplastic group IIA intron splicing facilitator CRS2-associated factor 2	-	-	1.134e-12	-

Source	Gene names
Sma3	At1g23400; At2g20020; At4g31010; CAF1; CAF2; F26F24.27; F28C11.4; F6I18.80; GSVIVT00002735001; GSVIVT00016688001; GSVIVT00026315001; GSVIVT00027343001; LOC_Os01g21990; LOC_Os01g31110; LOC_Os08g07790; OJ1126_G08.1; OJ1134_B10.1; OSJNBa0011P19.4; OSJNBa0029

Source	GOs	Term	Type	Identity
Sma3	mitochondrion	GO:0005739	Cellular Component	-
Sma3	chloroplast	GO:0009507	Cellular Component	-
Sma3	ribonucleoprotein complex	GO:0030529	Cellular Component	-
Sma3	RNA binding	GO:0003723	Molecular Function	-
Sma3		GO:0031202	Molecular Function	-
Sma3	Group II intron splicing	GO:0000373	Biological Process	-
Sma3	mRNA processing	GO:0006397	Biological Process	-
Sma3	RNA splicing	GO:0008380	Biological Process	-

Source	InterPros	Term	Type	e value	Identity
Sma3	RNA-binding, CRM domain	IPR001890	-	0.0	-
Sma3	Chaperonin TCP-1, conserved site	IPR002194	-	0.0	-

Source	Species	ID	Description	e value	Identity
ATG	Arabidoptis thaliana	AT1G23400.1	CAF2, ATCAF2 RNA-binding CRS1 / YhbY (CRM) domain-containing protein chr1:8312199-8314740 REVERSE LENGTH=564	0.0	72%
RefSeq	Arabidopsis thaliana	NP_173754.2	CRS2-associated factor 2 [Arabidopsis thaliana]	0.0	72%
RefSeq	Populus trichocarpa	XP_002315689.1	predicted protein, partial [Populus trichocarpa]	5.60519e-45	66%

Full-Lengther Next Prediction

Fln status: Internal

Fln database: sp_plants

Fln subject: Q9LDA9

Fln msg: Distance to subject end: 188 aas, your sequence is shorter than subject: 103 - 564

Fln protein: IIHRAGGAIYLFRGRNYNYKTRPMNPLMLWKPAAAVYPRLIERAPGGLTFEEAKELRKRGRSLLPICKLSKNGVYLNLAKDVRDAFEVSDLVRVNCQGLNPSD

Protein Length: 104

Fln nts: AGATCATTCACAGGGCTGGAGGAGCTATATACCTTTTCCGTGGACGAAATTACAATTACAAAACACGACCTATGAATCCCTTGATGCTTTGGAAGCCTGCAGCAGCTGTTTATCCAAGACTGATTGAACGGGCTCCAGGAGGGTTAACCTTCGAAGAAGCAAAAGAATTACGTAAAAGGGGACGGTCACTGCTTCCAATCTGCAAACTCTCAAAAAATGGTGTGTATTTGAATCTTGCAAAGGATGTTAGAGATGCCTTTGAAGTAAGTGATCTGGTTCGGGTAAATTGTCAAGGCTTAAATCCAAGTGATT

Fln Alignment:

AllPine_a_c41788___IIHRAGGAIYLFRGRNYNYKTRPMNPLMLWKPAAAVYPRLIERAPGGLTFEEAKELRKRGRSLLPICKLSKNGVYLNLAKDVRDAFEVSDLVRVNCQGLNPSD
Q9LDA9________________IIHRVGGVVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSD

SNPs (tot: 4)

Position	A %	C %	G %	T %	Probability
117	33		66		0.997452
118		33	66		0.997452
120	66			33	0.997452
121			66	33	0.997452

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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