Doryteuthis pealeii gene pages Help

Annotation: Dpe Pita v0.3, release December 22, 2023
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Gene pages v0.2

Find gene

Find genes based on gene symbols, JGI IDs (Dpe v2.1), or matches to human or fly (Drosophila melanogaster) proteins (gene symbols). Pita has combined JGI gene symbols if multiple transcripts were merged into a single gene model.

Search is case-sensitive. Human gene symbols are in upper case, Doryteuthis JGI and Pita gene symbols are based on human gene symbols. Fly gene symbols can be capitalized, but often are not (cf. Wikipedia).

Partial search strings may result in more matches; regex special characters (regular expressions) can be used for more elaborate searches (but slashes and white space are not allowed). For example, ^CDH will match CDH genes but not the many PCDH genes, while ^HOX[A,B] and ^HOX.1 will find matches to HOXA and HOXB genes, and HOXB1, HOXA10 and HOXC11 respectively. Note that other gene symbols may still show up in the results if the search string matches the gene symbols in best matches or orthologs.

See release notes (below) for more information on Pita gene annotation.

Search results include the following fields:

1. Pita v0.3 "combined_symbols" (see release notes)
2. JGI v2.1 Dopeav ID
3. JGI v2.1 gene symbol
4. Best hit in the human proteome (of all open reading frames tested)
5. Best hit in the fly (D. melanogaster) proteome
6. Best hit in the bobtails squid (E. scolopes) proteome
7. Genes in the Doryteuthis paralogs group of human ortholigs
8. Orthologous human genes

For the BLASTP results on the gene pages, only reading frames where the best match has an E-value smaller than 1e-04 are included. The frame is a number [1-3]. If followed by "M", the sequence with the best hit starts with a start codon (usually a substring of the sequence). The best match is not always the "M"-frame, potentially due to imperfect genome assembly or gene models (missing upstream exons or fragmented gene annotations).

Release notes Dpe Pita v0.3

• Annotation: pita_genes_v0.3.bed, pita_genes_v0.3.bed_12to.gtf
• Number gene models: 24967
• Release date: December 22, 2023
• Associated genome: Dpe_v2.1
• Download: doi 10.5281/zenodo.15222685
• Comments, questions: gertjan.veenstra.{at}.ru.nl

Usage

• Annotation available in two commonly used formats (bed, gtf).
• Additional information on gene IDs: pita_all_ids.txt. This file links different types of IDs associated with genes in other annotations. Note that more than one id / gene from previous annotations can be associated with a gene in the current gene annotation. The file pita_all_ids.txt contains the following columns: uniqid, pita_id, JGI_mRNA_id, JGI_Dopeav_id, JGI_gene_symbol, combined_symbols.
• Use with genome assembly Dpe_v2.1. It has named chromosomes, contrary to UCB_Dpea_1

More information

• This annotation used Pita ("Pita Improves Transcript Annotation"; https://github.com/simonvh/pita), with the following input data: short read RNA-seq data (different tissues and stages of development) and H3K4me3 ChIP-seq data for improving the 5' ends of genes (branchial and systemic heart and two developmental stages).
• pita_genes_v0.3 associates gene IDs and gene symbols of JGI annotation with the pita gene models and complements pita annotation with non-overlapping JGI models (non-overlapping at exon level). This improves mappability (1.38 compared to 1.31, see numbers below).
• For this release the gene IDs in previous gene annotations are documented in a separate file (pita_all_ids.txt), allowing for a complete and easy comparison with previous (JGI) gene annotation or analyses. The information on IDs and gene symbols is also available on the Dory gene pages: https://veenstralab.nl/dpe.
• Gene names in v0.3 correspond to the "combined_symbols" column in pita_all_ids.txt. JGI gene symbols are combined (joined with underscores) if more than one gene symbol is associated with (parts of) the gene in the new gene annotation. For example, two (partial) ISL genes in previous annotations have been combined to ISL2_ISL1.These have been made unique by adding a suffix _[number] if more than one instance exists. For example, there are almost 5900 genes without a proper gene symbol (named NA, numbered from NA through NA_5888 in the current annotation).
• The mapping efficiency of RNA-seq data has improved compared to previous releases, including the JGI gff3 and original pita annotation. Relative mapping efficiencies of 1, 1.31, and 1.38 were observed for respectively JGI gff3, pita (Chana, 2021), and pita_genes_v0.3.
• Non-chromosomal scaffolds (scDpe) have been left out, except for two scaffolds that may correspond to mitochondrial DNA (blast match with mitochondrial DNA of a related species, Doryteuthis opalescens). This means the gene models on these scaffolds (from original JGI annotation) can be used for calculating QC metrics in single cell data. None of the mitochondrial genes have been named with a proper gene symbol in the JGI annotation ('NA'), and have therefore been renamed to MT-NA through MT-NA_22 in the current annotation.
• Contributors: Chana van der Heijden, Simon van Heeringen, Saskia Heffener, Caroline Albertin, Gert Jan Veenstra

Known issues

• Gene symbols are combined with underscore by pita based on JGI v2.1 gene symbols, but in JGI v2.1 some gene symbols were already combined with a hyphen in between. This leads to different combinations (for example ZNF112_ZNF559-ZNF177, ZNF559-ZNF177, ZNF559_ZNF177) which are all different genes.
• Underscores are not accepted in gene names in Seurat. This can be solved by substituting the underscore with a period.
• Genes / transcripts newly identified by Pita (with unique IDs such as Dpe30:64556374-64557498_), do not have an NA_[number] name or gene symbol. Some of these are non-coding transcripts.
• This gene annotation is far from perfect: There are still incomplete or fragmented gene models, and some gene models have frame shifts. It is a work in progess ... for which we will need resources ...