SMIM40 (small integral membrane protein 40) is a 79-amino-acid (about 9 kDa) protein encoded on chromosome 6p21.32, in the extended MHC region immediately upstream of DAXX. It has a single predicted helical transmembrane segment (residues 35-55), flanked by an acidic N-terminal segment and a short acidic C-terminal tail. It defines its own small protein family (Pfam SMIM40), with no recognised relationship to characterised proteins. Orthologues are found only in therian mammals, including marsupials and rodents. The protein has been detected by mass spectrometry in a large-scale liver proteome study, and its RNA is enriched in retina. Its membrane localisation is predicted from sequence; the specific membrane, topology, partners and biological role are unknown, and no functional study of SMIM40 has been published.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to membrane, based on the single predicted helical transmembrane segment (residues 35-55). Reason: Correct, though general. A 21-residue hydrophobic helix in a 79-residue protein makes SMIM40 a single-pass integral membrane protein. No experiment identifies the specific membrane, so a more precise location cannot be given. This is the only annotation the gene carries and the only one the evidence supports. Supporting Evidence: file:human/SMIM40/SMIM40-uniprot.txt FT TRANSMEM 35..55 file:human/SMIM40/SMIM40-uniprot.txt CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000255}; Single-pass membrane |
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Download this section (compressed HTML)Q: Is SMIM40 expressed as protein in the retina, and in which cell type and membrane?
Q: Is SMIM40 co-regulated with its immediate neighbour DAXX, or does it share regulatory elements with the surrounding MHC class II region genes?
Experiment: Localise the mouse orthologue in retina sections with cell-type and organelle markers (antibody or knock-in tag), determine topology by protease protection, and examine retinal structure and function in a knockout.
Hypothesis: SMIM40 is a retinal single-pass membrane protein of a defined compartment.
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