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Coffea canephora: 10 kbp from chr1:1..10,000
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Coffea canephora
Coffea canephora (Scaffolds)
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Tracks
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A. Reference Gene Annotation (manually editable)
A. Reference Gene Annotation (manually editable)
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CDS
[?]
mRNA
[?]
Gene
[?]
Polypeptide
[?]
B. Reference Combiner prediction (Gaze automatic prediction) (Denoeud et al. 2014)
B. Reference Combiner prediction (Gaze automatic prediction) (Denoeud et al. 2014)
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CDS
[?]
mRNA
[?]
Polypeptide
[?]
Gene
[?]
Non coding miRNA
[?]
C. Ab-initio Gene predictions (automatic)
C. Ab-initio Gene predictions (automatic)
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FGenesH predictions
Snap predictions
D. Repetitive elements
D. Repetitive elements
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LTR retrotransposons (by LTR_STRUC)
Repbase BlastX
[?]
SSR
[?]
MITE (by Mite Hunter)
Repbase tBlastX
[?]
TEs predicted by REPET (2 iterations)
[?]
MITE (by MUST)
SINE (by SINE_Finder)
TEs predicted by REPET (3 iterations)
[?]
E. Similarity with cDNA or EST
E. Similarity with cDNA or EST
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56216 home-made unigenes
Canephora Solexa Contigs (stem, leaf, flower)
Coffea Gmorse models (using RNASeq)
Arabica 454 Contigs (Stephane)
Catura 454 Contigs
Public ESTs
F. Similarity with gene and protein sequences
F. Similarity with gene and protein sequences
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Other Uniprot matches
Selected proteins matches
G.1. RNA-Seq Coverage
G.1. RNA-Seq Coverage
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Old leaves 1
Stem and flower 1
Young leaves 1
Old leaves 2
Stem and flower 2
Young leaves 2
G.2. RNA-Seq Coverage
G.2. RNA-Seq Coverage
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Old leaves 1 (uniquely mapped)
Stem and flower 1 (uniquely mapped)
Young leaves 1 (uniquely mapped)
Old leaves 2 (uniquely mapped)
Stem and flower 2 (uniquely mapped)
Young leaves 2 (uniquely mapped)
G.3. RNA-Seq Coverage (Indian)
G.3. RNA-Seq Coverage (Indian)
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Leaf
Root
Pistil
Stamen
G.4. RNA-Seq RPKM (all tissues)
G.4. RNA-Seq RPKM (all tissues)
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RPKM
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I. Miscellaneous
I. Miscellaneous
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3-frame translation (forward)
[?]
BES BstYI
[?]
DNA/GC Content
3-frame translation (reverse)
[?]
BES HindIII
[?]
J. Initial predicted genes
J. Initial predicted genes
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Initial predicted genes
K. Manually annotated genes
K. Manually annotated genes
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Manually annotated genes
L. Genotyping
L. Genotyping
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Genotyped SNPs
[?]
Overview
Overview
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Scaffolds
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Analysis
Analysis
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Restriction Sites
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