OpenProt release 2_2 - February 19 2025
OpenProt enables improved mapping of the proteome. In addition to currently annotated CDSs and proteins, OpenProt displays the sequence, functional annotation and expression evidence of previously hidden alternative ORFs (AltORFs) and their corresponding alternative proteins (AltProts).
| Column | Description |
|---|---|
| protein accession | Protein accession numbers. Proteins annotated in OpenProt have an accession number starting either with IP (for Inferred Protein, i.e. predicted AltProt) or with II (Inferred Isoform, i.e. novel predicted isoform of RefProt). Protein accession numbers for RefProts originate from Ensembl, NCBI RefSeq or UniProtKB annotations. |
| protein accession (others) | Protein accession numbers (others). |
| protein type | Protein type: Protein type (AltProt, RefProt or Isoform). AltProts are predicted proteins from translation of AltORFs (mRNA or ncRNA). RefProts are proteins from translation of reported CDSs (mRNA). Isoforms are novel predicted proteins from translation of AltORFs (mRNA or ncRNA) that share a clear sequence homology with a RefProt from the same gene. |
| protein length (a.a.) | Protein length (amino acids). |
| molecular weight (kDa) | Protein molecular weight (kDa). |
| isoelectric point | Isoelectric point predicted using BioPerl v1.006924. |
| frame | Reading frame (+1, +2 or +3). The reading frame for the three-nucleotide codons is determined with respect to the first nucleotide of each transcript (+1 reading frame). AltORFs completely nested within CDSs must be in a different reading frame than the CDSs. AltORFs present in UTRs or in ncRNAs may be in any of the 3 reading frames. |
| gene symbol | Gene symbol. |
| chr | Chromosome. |
| start genomic coordinates | ATG genomic coordinates (1-start, fully-closed). Genomic coordinates of the predicted AltORF or the annotated CDS from the first nucleotide of the start codon to the last nucleotide of the stop codon. |
| stop genomic coordinates | Stop genomic coordinates (1-start, fully-closed). Genomic coordinates of the predicted AltORF or the annotated CDS from the first nucleotide of the start codon to the last nucleotide of the stop codon. |
| strand | Strand (+ or -). |
| transcript accession | Transcript accession numbers from Ensembl or NCBI RefSeq annotations. |
| type | Type of transcript (mRNA or ncRNA). |
| localization | AltORF localization in a specific transcript. Within mRNAs, the localization of AltORFs is defined according to the localization of the predicted TIS with respect to the annotated CDS TIS, and there are three possible localizations: "5'UTR", "CDS" and "3'UTR". For AltORFs within ncRNAs, the localization is indicated "-". |
| start transcript coordinates | AUG transcript coordinates (1-start, fully-closed). Transcript coordinates of the predicted AltORF or the annotated CDS from the first nucleotide of the start codon to the last nucleotide of the stop codon (1 = first nucleotide of the transcript). |
| stop transcript coordinates | Stop transcript coordinates (1-start, fully-closed). Transcript coordinates of the predicted AltORF or the annotated CDS from the first nucleotide of the start codon to the last nucleotide of the stop codon (1 = first nucleotide of the transcript). |
| MS score | Mass spectrometry score: Sum of unique peptide per study. |
| TE Translation Event score | Number of studies with at least one significant detection of translation. |
| Orthology Across 10 Species #:Species Names | Conservation score (0-10): Number and name of species with at least one ortholog. Names are abbreviated using the first letters of the species and subspecies names (e.g. Rattus norvegicus = RN). |
| Kozak motif | If the simplified Kozak sequence, RNNATGG (where R = A or G) derived from Kozak M, 1981 and 2002 (PMID: 7301588,12459250), is present (+) or not (-). |
| High-efficiency TIS motif | If the high-efficiency TIS motif (RYMRMVAUGGC, where Y = U or C, M = A or C, R = A or G, and V = A, C, or G) derived from Noderer WL et al., 2014 (PMID: 25170020) is present (+) or not (-). |
| Domains | Number of predicted domains (InterProScan 5.14-53.0). |
This file can be downloaded here
A selection of files that are available for download is available here
RefProts are proteins translated from annotated CDSs found in transcripts classified as mRNAs.
AltProts are predicted proteins translated from alternative ORFs (AltORFs) found in transcripts classified as mRNAs or from unannotated AltORFs found in transcripts classified as non-coding RNAs (ncRNAs). Within mRNAs, an altORF may be present in the UTRs or overlapping the annotated CDS in a frameshifted reading frame.
Isoforms are novel predicted proteins translated from alternative ORFs (AltORFs) found in transcripts classified as mRNAs or from unannotated AltORFs found in transcripts classified as non-coding RNAs (ncRNAs) that share a clear sequence homology with a RefProt from the same gene.
The files are consistently named following this pattern:
<species>-openprot-<version>-<refprots AND/OR altprots and isoforms>-<supporting evidence (MS) (IF ALL -> "all")>-<annotation>-<uniprot YES/NO (IF NO -> EMPTY)>.fasta.zip
<species>-openprot-<version>-<refprots AND/OR altprots and isoforms>-<supporting evidence (MS) (IF ALL -> "all")>-<annotation>-<uniprot YES/NO (IF NO -> EMPTY)>.tsv.zip
<species>: The systematic name of the species.
<version> : OpenProt release version
<refprot AND/OR altprot and isoforms> : Reference and/or alternative proteins
<supporting evidence (MS)>: Mass spectrometry detection evidence of alternative proteins and isoforms newly annotated in OpenProt
<annotations>: Genome annotations
fasta (protein) : All files in these directories are FASTA database files with protein sequences
fasta (dna) : All files in these directories are FASTA database files with DNA sequences
tsv: All files in these directories are tsv database files
Entries in file: 6
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