The gene models and other genome annotation in XenMine are provided by a variety of source databases including: XenMine, JGI and other data sources. Read more

Query for sequence:

• Retrieve UTR Sequence for a gene(s).
• Retrieve Sequence in fasta for a particular feature type.

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ChIP-Seq experiment results. Read more

Query for chipseq:

• Retrieve binding sites that overlap a specific gene
• Retrieve ChIP targets for a given target at a given stage
• Retrieve binding sites that overlap a specific gene and their expression FPKM values.
• Retrieve all genes associated with ChIP-Seq peaks for a given transcription factor
• Retrieve genes that overlap a given peak coordinates i.e annotate your peak.
• Retrieve all genes located within the specified chromosome coordinate range and the binding sites that overlap the genes.

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RNA-Seq experiment results. Read more

Query for rnaseq:

• Retrieve RNA-Seq Expression FPKM scores for a given gene at a given time.
• Retrieve RNA-Seq Expression scores for a given gene.
• Retrieve binding sites that overlap a specific gene and their expression FPKM values.
• Retrieve RNA-Seq Expression FPKM scores for a given gene in specific tissue

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XenMine loads Interaction, Expression and Gene Ontology annotation from Xenbase. Read more

Query for xenbase:

• Retrieve Orthologs for a given gene(s).
• Retrieve all genes curated from a Publication.
• Retrieve genes co-cited in a paper for a specific gene
• Find all literature associated with a gene.

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Genes, Chromosomes, Scaffolds. Read more

Query for genomics:

• Retrieve all genes for given species of Xenopus.
• Retrieve all GO annotations for a specified gene(s).
• Retrieve all genes on given scaffold/chromosome.
• Retrieve gene models for a given gene.

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