SOGA2

SOGA2, also known as Suppressor of glucose autophagy associated 2 or CCDC165,is a is_associated_with::protein that in humans is encoded by the SOGA2 is_associated_with::gene. SOGA2 has 2 human paralogs, is_associated_with::SOGA1 and is_associated_with::SOGA3. In humans, the gene coding sequence is 151,349 base pairs long, with an mRNA of 6092 base pairs, and a protein sequence of 1586 amino acids. The SOGA2 gene is conserved in gorilla, baboon, galago, rat, mouse, cat, and more. There is distant conservation seen in organisms such as zebra finches and anoles. SOGA2 is ubiquitously expressed in humans, with especially high expression in brain (especially the cerebellum and hippocampus), colon, pituitary gland, small intestine, spinal chord, testis and fetal brain.

Locus
The SOGA2 gene is located from 8717369 - 8832775 on the short arm of chromosome 18 (18p11.22).

Paralogs
There are two main paralogs to SOGA2: human protein is_associated_with::SOGA1 and human protein is_associated_with::SOGA3. SOGA1 has been shown to be involved in suppression of glucose by autophagy. The rate at which orthologs diverge from SOGA2 human(measured by % identity) places the approximate duplication event of SOGA1 from SOGA2 at ~254.1 MYA and the duplication event of SOGA3 from SOGA2 ~329.1 MYA.

Orthologs
Many orthlogs have been identified in Eukaryotes.



Homologous Domains
SOGA2 is conserved farthest back in its N-terminal region, where it contains its three domains of unknown function.

Protein internal composition
SOGA2 is rich in is_associated_with::glycine (ratio r of SOGA2 composition to average human protein is 1.723), is_associated_with::glutamate (r = 1.647), and is_associated_with::arganine (r = 1.357). It also has a lower than usual composition of is_associated_with::tyrosine (r = 0.3406), is_associated_with::isoleucine (r = 0.4430), is_associated_with::phenylalanine (r = 0.5808), and is_associated_with::valine (r = 0.6161).

Primary structure and isoforms
SOGA2 has 4 isoforms: Q9Y4B5-1, Q9Y4B5-2, Q9Y4B5-3, Q9Y4B5-4. [[File:Isoforms.png|thumb|none|750px|A graphic depicting the 4 different isoforms of SOGA2. Isoform 1 is canonical. Modification Key:
 * E → ELRGPPVLPEQSVSIEELQGQLVQAARLHQEETETFTNKIHK
 * Q → QNCCGYPRINIEEETLGFTRLPAGSTVKTLKSLGLQRLE
 * NQTVLLTAPWGL → ELPCSALAPS...LHGLSQYNSL]]

Domains and motifs
SOGA2 contains Domain of Unknown Function 4201 (DUF4201) from aa 16-235. This domain is specific to the Coiled Coil Domain Containing family of proteins in eukaryotes. It also contains two copies of Domain of Unknown Function 3166 (DUF3166): one from aa 140-235 and one from aa 269-364.

Post-translational modifications
SOGA2 is expected to undergo a number of post-translational modifications. Modifications of human SOGA2 that are shared by orthologs include:


 * Sumoylation at amino acids 87, 152, 235, 392, and 1379.


 * Sulfination at tyrosines 14 and 1249.


 * Phosphorylation at a number of sites, highlighted in the following graphic:



Secondary structure
The consensus of the prediction software PELE, GOR4, and SOSUICoil is that the secondary structure of SOGA2 is dominated by alpha helices with interspersed regions of random coil. GOR4 indicated that SOGA2 is dominated by alpha-helices; it predicted a mere 5.61% of residues in an extended strand (parallel or antiparallel Beta-sheet) conformation, as opposed to 47.79% alpha helix and 46.6% random coils.



Tertiary structure
SOGA2 shares sequence features in its highly conserved N-terminal region. This homology allows prediction of its tertiary structure on the basis of homology to published 3d structures via Phyre2 and NCBI structure.

Promoter
The promoter for human SOGA2 is below.

Gene expression data
The EST profile shows that, in humans, SOGA2 is highly expressed in many sites throughout the body, including bone, brain, ear, eye, and many others. There are a large number of transcripts in liver cancer samples. Human microarray data shows that SOGA2 is moderately expressed, with especially high expression in brain (especially the cerebellum and hippocampus), colon, pituitary gland, small intestine, spinal chord, testis and fetal brain. Brain-tissue specific microarray data shows that SOGA2 has high expression throughout the posterior lobe of the cerebellar hemispheres and posterial lobe of the vermis in the mouse brain. There is low expression in most other areas of the brain.

Transcript variants
In humans, the SOGA2 gene produces 17 different transcripts, 8 of which form a protein product (one undergoes nonsense mediated decay). The main transcript in humans is transcript ID ENST00000359865, or SOGA2-001.

Possible transcription factors
Possible transcription factors for human SOGA2 include:


 * Modulator recognition factor 2
 * cAMP-responsive element binding protein 1
 * alternative splicing variant of FOXP1
 * MDS1/EVI1-like gene 1
 * Ikaros 2, possible regulator of lymphocyte differentiation

Interactions
Protein complex co-immunoprecipitation (is_associated_with::Co-IP) experiments revealed interacting proteins such as is_associated_with::cell death regulators, ATP-binding cassette (ABC) transporters and is_associated_with::protein kinase A binding proteins.

The 540 interacting proteins include is_associated_with::ABCF1, is_associated_with::ACTB, is_associated_with::ACTL6A, is_associated_with::BCLAF1, is_associated_with::BCLAF1, is_associated_with::CHEK1, and MAGEE2.

K-nearest neighbor analysis by wolf pSort indicates that in humans, SOGA2 is focused mainly in the nucleus, cytoplasm, and the cytonuclear space. There is a small chance that it is localizes to the golgi.

A number of protein interactants were also identified via the STRING database, including is_associated_with::MARK2, is_associated_with::MARK4, and is_associated_with::PPP2R2B.

Clinical significance
SOGA2 has no currently known disease associations or mutations.