This track is composed of genes/mRNAs predicted by Mark Yandell's Maker that are supported by high quality evidence, such as est and protein homology.
Predicted Genes/mRNAs:
Any maker predictions that do not have high quality evidence as support are located in this track.
Human Curated Genes/mRNAs:
Any human curated genes/mRNAs. Currently, only genes investigated by Alejandro Sanchez Alvarado with Apollo are presented in this track, and are identified by the three letter designation ASA, followed by a gene number and transcript number (ASA.00084.01).
Phenotype/Expression
cDNA microarray:
All ESTs were aligned to the genome using blat (see ESTs aligned with Blat). The microarray result associated with a particular EST is mapped to every alignment of that EST to the genome. A arrow centered on an EST indicates up- or down-regulation in comparison to the control (green for up, red for down, gray for no change) of that EST in the experiment listed in the arrow's label (above the arrow). The logbase 2 change is displayed below the arrow. (AY066135.Irradiation.TimeCourse.24hr)
RNAi Phenotype:
A bar that spans the length of the EST that was used to disrupt gene function by RNA intereference is employed in this track. The description of the resulting phenotype is located under the bar. (RNAi:AY967490)
In Situ:
A track that links to in situ images of the EST that is aligned to this particular region of the genome. (AY967481:insitu)
Sequence Similarity
454 contigs aligned with BLAT:
Contigs prepared from 454 sequencing reads were aligned to the genome using the Blat algorithm and standard psl output. BLAT is designed to quickly find sequences of 90% and greater a score of 30.
BLASTX Hits:
These are WUBLASTX (nucleotide to protein, via six-frame translation) similarity hits of genomic sequence, run against reference protein datasets from the genomes of E. coli, Saccharomyces cerevisiae, Drosophila melanogaster, C. elegans, platyhelminthes, Ciona intestinalis, mouse and human. Cutoffs of 40% identity and 1e-5 were used.
BLASTX Exonerate:
These are the outputs from BLASTX Hits alignments of the S. mediterranea genome to reference protein databases and polished with the splice-site aware algorithm Exonerate (protein2genome) to align protein to genomic sequences (Comput Appl Biosci 1997 Aug; 13(4) 477-8. pmid:9283765).
EST BLASTN:
These are contigs of S. mediterranea expressed sequence tags (ESTs) aligned to the S. mediterranea genome. Cutoffs of 85% identity and 1e-10 were used.
EST BLASTN Exonerate:
These are contigs of S. mediterranea expressed sequence tags (ESTs) aligned to the S. mediterranea genome and polished with Exonerate (EST2genome) to align spliced DNA sequences to unspliced genomic DNA (Comput Appl Biosci 1997 Aug; 13(4) 477-8. pmid:9283765).
ESTs aligned with BLAT:
These are all available individual S. mediterranea expressed sequence tags (ESTs) aligned to the S. mediterranea genome using James Kent's BLAT program [ http://genome.cse.ucsc.edu/cgi-bin/hgBlat]. This track shows the best unique location for each EST (1e-95 with at least 45% alignment). Output is in the WUBLAST format.
Maker predictions BLASTP to Swissprot:
These are alignments of predicted proteins from Maker gene models against Swissprot. A cutoff of 1e-3 and 40% alignment with the protein hit was used.
Maker predictions RPS-BLAST to PFAM domains:
These are alignments of predicted proteins from Maker gene models against PFAM using NCBI RPS-Blast. A cutoff of 1e-3 and 40% alignment with the protein hit was used.
Maker predictions RPS-BLAST to SMART domains:
These are alignments of predicted proteins from Maker gene models against SMART using NCBI RPS-Blast. A cutoff of 1e-3 and 40% alignment with the protein hit was used.
Repeat Regions:
This tracks shows areas of the genome containing interspersed repeats and low complexity DNA sequences as identified by RepeatMasker using a S. mediterranea specific repeat library.
Species TBLASTN
C.elegans proteome TBLASTN against Genome:
The C.elegans proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3 and 30% alignment with the protein query were used.
D.mel proteome TBLASTN against Genome:
The D.melanogaster proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3 and 30% alignment with the protein query were used.
Human proteome TBLASTN against Genome:
The H.sapien proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3 and 30% alignment with the protein query were used.
M.mus proteome TBLASTN against Genome:
The M.musculus proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3 and 30% alignment with the protein query were used.
Tools
6-frame translation:
Indicates the translation of sequence in all possible reading frames of the genomic sequence.
Coding Segments:
This track shows the reading frames of coding segments (also known as "CDS" features).
DNA/GC Content:
Shows the percentage of GC content along genomic DNA. The S. mediterranea genome is AT rich. If the zoom is set to 100bp, the actual sequence of the genomic contig can be viewed.
Non-Coding RNA:
mapping of mature miRNA sequences (RNA. 2006 Sep;12(9):1640-9. Epub 2006 Jul 18) to the genome with the use of BLAST (Marc Friedlaender). (sme-miR-2b)
