Persius/hicric huggingface dataset:
SGOL1
Shugoshin-like 1 is a protein that in humans is encoded by the SGOL1 gene.

# Model organisms
Model organisms have been used in the study of SGOL1 function. A conditional knockout mouse line, called Sgol1tm1a(EUCOMM)Wtsi has been generated.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty six tests were carried out on mutant mice and three significant abnormalities were observed. No homozygous mutant embryos were identified during gestation, and thus none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice and a decreased regulatory T cell number was observed in male animals.

# Mechanisms
A physical mechanism that guarantees the accurate segregation of sister chromatids during mitosis arises from the ring shaped cohesin complex consisting of 4 subunits (SMC1A/B, SMC3, SCC1, and SA1/2 in humans).  This complex encircles the two sister chromatids and resists the pulling force of microtubules. The characteristic X-shape chromosomes are formed due to the centromeric cohesin protected by Shugoshin-PP2A complex.
Kinetochore localization of Sgo1-PP2A is dependent upon phosphorylation on histone H2A of nucleosome, which is the important substrate of spindle checkpoint kinase BUB1. Centromeric cohesin and H2A-pT120 specify two distinct pools of Sgo1-PP2A at inner centromeres and kinetochores respectively, while the CDK1/cyclin B phosphorylation on Sgo1 is essential for Sgo1-PP2A to protect centromeric cohesin, not only for bringing PP2A to cohesin, but also physically shield out the negative regulator WAPAL from cohesin.
SGOL2
Shugoshin-like 2 (S. pombe), also known as SGOL2, is a protein which in humans is encoded by the SGOL2 gene.

# Function
Shugoshin-like 2 (SGOL2) is one of the two mammalian orthologs of the Shugoshin/Mei-S322 family of proteins that regulate sister chromatid cohesion by protecting the integrity of a multiprotein complex named cohesin. This protective system is essential for faithful chromosome segregation during mitosis and meiosis, which is the physical basis of Mendelian inheritance.

## Model organisms
Model organisms have been used in the study of SGOL2 function. A conditional knockout mouse line, called Sgol2tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty two tests were carried out on mutant mice but no significant abnormalities were observed.
Using another genetically engineered mouse that lacks Sgol2 function, and siRNA experiments in oocytes, it has been shown that disruption of the mouse SGOL2 does not cause any alteration in sister chromatid cohesion in embryonic cultured fibroblasts and adult somatic tissues.  Moreover, although these mutant mice also develop normally and survive to adulthood without any apparent alteration, both male and female Sgol2-deficient mice from this line are infertile. By different approaches it was demonstrated that SGOL2 is necessary for protecting centromeric cohesion during mammalian meiosis I. In vivo, the loss of SGOL2 promotes a premature release of the meiosis-specific REC8 cohesin complexes from anaphase I centromeres. This molecular alteration is manifested cytologically by the complete loss of centromere cohesion at metaphase II leading to single chromatids and physiologically with the formation of aneuploid gametes that give rise to infertility.
SH2B2
SH2B adapter protein 2 is a protein that in humans is encoded by the SH2B2 gene.

# Function
The protein encoded by this gene is expressed in B lymphocytes and contains pleckstrin homology and src homology 2 (SH2) domains. In Burkitt lymphoma cell lines, it is tyrosine phosphorylated in response to B cell receptor stimulation. Because it binds Shc independent of stimulation and Grb2 after stimulation, it appears to play a role in signal transduction from the receptor to Shc/Grb2.

# Interactions
SH2B2 has been shown to interact with TrkA and Cbl gene.
SHOX2
Short stature homeobox 2, also known as homeobox protein Og12X or paired-related homeobox protein SHOT, is a protein that in humans is encoded by the SHOX2 gene.

# Function
SHOX2 is a member of the homeobox family of genes that encode proteins containing a 60-amino acid residue motif that represents a DNA-binding domain. Homeobox proteins have been characterized extensively as transcriptional regulators involved in pattern formation in both invertebrate and vertebrate species.

# Clinical significance
Several human genetic disorders are caused by aberrations in human homeobox genes. This locus represents a pseudoautosomal homeobox gene that is thought to be responsible for idiopathic short stature, and it is implicated in the short stature phenotype of Turner syndrome patients. This gene is considered to be a candidate gene for Cornelia de Lange Syndrome.
SHOX2 localises on chromosome 3, so it is an autosomal and not a pseudoautosomal homeobox (SHOX, which localises on the PAR1 region of chromosome X and Y, has a pseudoautosomal hereditability).
SIAH2
E3 ubiquitin-protein ligase SIAH2 is an enzyme that in humans is encoded by the SIAH2 gene.

# Function
This gene encodes a protein that is a member of the seven in absentia homolog (SIAH) family. The protein is an E3 ligase and is involved in ubiquitination and proteasome-mediated degradation of specific proteins. The activity of this ubiquitin ligase has been implicated in regulating cellular response to hypoxia.

# Interactions
SIAH2 has been shown to interact with PEG10, Synaptophysin, PEG3 and VAV1.
SIRT4
Sirtuin 4, also known as SIRT4, is a protein which in humans is encoded by the SIRT4 gene.

# Function
This gene encodes a member of the sirtuin family of proteins which are homologs of the Sir2 gene in budding yeast. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been fully determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP-ribosyltransferase activity. The protein encoded by this gene is included in class IV of the sirtuin family.
SIRT4 is a mitochondrial ADP-ribosyltransferase that inhibits mitochondrial glutamate dehydrogenase 1 activity, thereby downregulating insulin secretion in response to amino acids. It has been shown that SIRT4 regulates fatty acid oxidation and mitochondrial gene expression in liver and muscle cells.
SIRT5
Sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae), also known as SIRT5 is a protein which in humans in encoded by the SIRT5 gene and in other species by the orthologous Sirt5 gene.
This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and belong to the class III of the  superfamily, and are dependent on NAD+ as co-factor of enzymatic activities. SIRT5 is one of the three sirtuins localized primarily to the mitochondrion.

# Structure
Alternative splicing of this gene results in two transcript variants. The protein structure of SIRT5 has been resolved and shows high degrees of structural conservation with other sirtuins, such as the ancestral yeast protein and human SIRT2.

# Function
SIRT5 has been found to exhibit enzymatic activities as a deacetylase, desuccinylase, and demalonylase, capable of removing acetyl, succinyl, and malonyl groups from the lysine residues of proteins. SIRT5 deacetylases and regulates carbamoyl phosphate synthetase (CPS1), the rate-limiting and initiating step of the urea cycle in liver mitochondria. Deacetylation of CPS1 stimulates its enzymatic activity. Mice with deletion of SIRT5 show elevated ammonia levels after a prolonged fast, whereas in contrast, mice overexpressing SIRT5 show increased CPS1 activity, suggesting one of the functions of SIRT5 may be to regulate the urea cycle. SIRT5 also interacts with and deacetylates cytochrome c. Large-scale profiling studies of SIRT5 deacetylase activity have uncovered over 700 protein substrates, including proteins localized to the mitochondria, the cytosol and other sub cellular localization. The identities of SIRT5 desuccinylation substrates suggest that SIRT5-mediated desuccinylation may be involved in energy metabolism.
The physiological consequences of SIRT5 molecular functions in human is under investigation but may involved regulations of mitochondrial metabolism.

# Interactions
NAD+
Cytochrome c 
Carbamoyl phosphate synthetase (CPS1)
SIRT7
NAD-dependent deacetylase sirtuin-7 is an enzyme that in humans is encoded by the SIRT7 gene.

# Function
This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP-ribosyltransferase activity. The protein encoded by this gene is included in class IV of the sirtuin family.
In humans cells, SIRT7 has only been shown to interact with two other molecules: RNA polymerase I (RNA Pol I) and upstream binding factor (UBF). SIRT7 is localized to the nucleolus and interacts with RNA Pol I. Chromatin immunoprecipitation studies demonstrate that SIRT7 localizes to rDNA, and coimmunoprecipitation shows that SIRT7 binds RNA Pol I. In addition SIRT7 interacts with UBF, a major component of the RNA Pol I initiation complex. It is not known whether or not SIRT7 is modifying RNA Pol I and/or UBF, and if so, what those modifications are.
SIRT7 is expressed more in metabolically active tissues, such as liver and spleen, and less in non-proliferating tissues, such as heart and brain. Furthermore, it has been shown that SIRT7 is necessary for rDNA transcription. Knock down of SIRT7 in HEK293 cells resulted in decreased rRNA levels. This same study found that this SIRT3 knockdown decreased the amount of RNA Pol I associated with rDNA, suggesting that SIRT7 may be required for rDNA transcription. Knock down SIRT7 led to reduced RNA Pol I levels, but RNA Pol I mRNA levels did not change. This suggests that SIRT7 plays a crucial role in connecting the function of chromatin remodeling complexes to RNA Pol I machinery during transcription.
SIRT7 may help attenuate DNA damage and thereby promoting cellular survival under conditions of genomic stress.

## DNA repair
Depletion of SIRT7 results in impaired repair of DNA double-strand breaks (DSBs) by the process of non-homologous end joining (NHDJ).  DSBs are one of the most significant types of DNA damage leading to genome instability.  SIRT7 is recruited to DSBs where it specifically deacylates histone H3 at lysine 18.  This affects the focal accumulation of the DNA damage response factor 53BP1, a protein that promotes NHEJ by protecting DNA from end resection.

## Accelerated aging
Sirt7 mutant mice show phenotypic and molecular features of accelerated aging.  These features include premature curvature of the spine, reduced weight and fat content, compromised hematopoietic stem cell function and leukopenia, and multiple organ disfunction.

# Clinical relevance
This gene has been found to be involved in maintenance of oncogenic transformation.
SIVA1
Apoptosis regulatory protein Siva is a protein that in humans is encoded by the SIVA1 gene.
This gene encodes a protein with an important role in the apoptotic (programmed cell death) pathway induced by the CD27 antigen, a member of the tumor necrosis factor receptor (TFNR) superfamily. The CD27 antigen cytoplasmic tail binds to the N-terminus of this protein. Two alternatively spliced transcript variants encoding distinct proteins have been described.

# Interactions
SIVA1 has been shown to interact with CD27.

# Siva (protein)
Siva protein is a zinc-containing intracellular ligand of the CD4 receptor that promotes HIV-1 envelope-induced apoptosis in T-lymphoid cells. Recent research has demonstrated that Siva is  a direct transcriptional target for the tumor-suppressors p53 and E2F1.
SKAP1
Src kinase-associated phosphoprotein 1 is an adapter protein that in humans is encoded by the SKAP1 gene.
This gene encodes a T cell adapter protein, a class of intracellular molecules with modular domains capable of recruiting additional proteins but that exhibit no intrinsic enzymatic activity. The encoded protein contains a unique N-terminal region followed by a PH domain and C-terminal SH3 domain. Along with the adhesion and degranulation-promoting adapter protein, the encoded protein plays a critical role in inside-out signaling by coupling T-cell antigen receptor stimulation to the activation of integrins.
The demonstration that SKAP1 regulates LFA-1 adhesion was made by retroviral infection  and by the SKAP1 deficient mouse.   Additional work has implicated SKAP1 in binding to the exchange factor RasGRP1 and in regulating ERK activation in T-cells.

# Interactions
SKAP1 has been shown to interact with FYN, PTPRC and FYB.
SMC1A
Structural maintenance of chromosomes protein 1A is a protein that in humans is encoded by the SMC1A gene.

# Function
Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1L2 or the protein encoded by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in an area of the X-chromosome that escapes X inactivation.

# Interactions
SMC1A has been shown to interact with SMC3 and Ataxia telangiectasia mutated.
SMCO4
SMCO4 (Single-pass membrane protein with coiled-coil domains 4) is a human gene that encodes the FN5 protein.  The FN5 protein is a single-pass transmembrane protein, which means that one end of the protein will remain in the cytoplasm, while the other end of the protein is exposed to the interior of the cell.

# Gene Properties
The SMCO4 gene is located on chromosome 11, with specific chromosomal coordinates of 11q13.3-q23.3 in Homo sapiens. SMCO4 has two common aliases: C11orf75 (Chromosome 11 Open Reading Frame 75) and FN5.

# mRNA features
SMCO4 has 7 isoforms in Homo sapiens.  The SMCO4 isoform 1 has 9 exons, while the rest of the isoforms have varying amounts of rxons.    These isoforms are listed in the table below, with their accession numbers for reference.

# Protein
MRQLKGKPKKETSKDKKERKQAMQEARQQITTVVLPTLAVVVLLIVVFVYVATRPTITE
The protein that is encoded by SMCO4 is rich in phosphorylable amino acids and has a high pH. There are no predicted protein repeats.  There is evidence that the protein is present in the outer membrane of the mitochondria. The absence of an N-terminal signal peptide shows that the protein does not have the ability to leave the organelle it is in, which correlates with the knowledge that it is a transmembrane protein.

## Structure
The structure of the FN5 protein is not yet known, but the protein qualities are useful in predicting the protein's structure.   There is no evidence that the protein would take on any Beta-turns;  its secondary structure would be composed of only alpha-helixes.  There are two separate helixes: the transmembrane helix and the alpha helix.

# Expression

## Expression Analysis
SMCO4 expression in humans was predicted to be highest in the salivary glands.   Overall, there was RNA tissue expression shown in 37 human tissues and expression of the protein in 71 cell types.

## Regulation of Expression
SMCO4 is not ubiquitously expressed throughout humans.  There is evidence that the expression of SMCO4 is easily manipulated by many different factors, making constant expression unlikely.  One example of this expression regulation comes from an experiment that showed increased SMCO4 expression in the presence of Gamma-tocotrienol.

# Predicted Interactions
SMCO4 is predicted to interact with the following proteins:

# Conservation
Two microRNAs, miR-124-3p.1 and miR-183-5p.1, are thought to be highly conserved throughout variety of vertebrates.   TheseicroRio RNAs are both neuronal in nature.

## Orthologs
Orthologs of SMCO4 were found in a variety of species, including mammals, birds, reptiles, amphibians, insects and parasites.  The primates were consistently found to have the highest sequence identity with the human SMCO4 sequence, followed closely by an extinct fish species called Latimeria chalumnae.  There was no evidence of SMCO4 presence in yeast species.
SMOC2
SPARC-related modular calcium-binding protein 2 is a protein that in humans is encoded by the SMOC2 gene.

# Clinical relevance
This gene has been shown mutated in clinical cases of major dental developmental defects.
Brachycephalic dogs show a shortening of the snout along with a widening of the hard palate. This skull form is highly associated with disorders of breathing and of the eyes. Brachycephaly in dogs is correlated to a retrotransposon induced missplicing the SMOC2 gene.
SMYD3
SET and MYND domain-containing protein 3 is a protein that in humans is encoded by the SMYD3 gene.

# Function
SMYD3 is a histone methyltransferase that plays a role in transcriptional regulation as a member of an RNA polymerase complex.

# Model organisms
Model organisms have been used in the study of SMYD3 function. A conditional knockout mouse line, called Smyd3tm2a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty three tests were carried out on homozygous mutant adult mice, however no significant abnormalities were observed.

# Interactions
SMYD3 has been shown to interact with Heat shock protein 90kDa alpha (cytosolic), member A1 and POLR2A.
SMYD3 trimethylates a lysine residue on MAP3K2, which causes crosstalk into the MAP kinase signaling pathway in Ras-driven cancers.
SMYD4
SET and MYND domain-containing protein 4 is a protein that in humans is encoded by the SMYD4 gene.

# Model organisms
Model organisms have been used in the study of SMYD4 function. A conditional knockout mouse line, called Smyd4tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty six tests were carried out on homozygous mutant adult mice, however no significant abnormalities were observed.
SNAI2
Zinc finger protein SNAI2 is a protein that in humans is encoded by the SNAI2 gene.

# Function
This gene encodes a member of the Snail superfamily of C2H2-type zinc finger transcription factors. The encoded protein acts as a transcriptional repressor that binds to E-box motifs and is also likely to repress E-cadherin transcription in breast carcinoma. This protein is involved in epithelial-mesenchymal transitions and has antiapoptotic activity. It regulates differentiation and migration of neural crest cells along with other genes (e.g. FOXD3, SOX9 and SOX10, BMPs) in embryonic life. Mutations in this gene may be associated with sporadic cases of neural tube defects.

# Function
The human embryonic protein SNAI2, commonly known as SLUG, is a zinc finger transcriptional repressor which downregulates expression of E-cadherin in premigratory neural crest cells; thus, SNAI2 induces tightly bound epithelial cells to break into a loose mesenchymal phenotype, allowing gastrulation of mesoderm in the developing embryo. Structurally similar to anti-apoptotic Ces-1 in C. elegans, SLUG is a negative regulator of productive cell death in the developing embryo and adults.

# Clinical significance
Widely expressed in human tissues, SLUG is most notably absent in peripheral blood leukocytes, adult liver, and both fetal and adult brain tissues. SLUG plays a role in breast carcinoma as well as leukemia by downregulation of E-cadherin, which supports mesenchymal phenotype by shifting expression from a Type I to Type II cadherin profile. Maintenance of mesenchymal phenotype enables metastasis of tumor cells, though SLUG is expressed in carcinomas regardless to invasiveness. A knockout model using chick embryos has also showed inhibition of mesodermal and neural crest delamination; chick embryo Slug gain of function appears to increase neural crest production. Mutations in Slug are associated with loss of pregnancy during gastrulation in some animals.

# Interactions
BMPs precede expression of SLUG, and are suspected as the immediate upstream inducers of gene expression.
SNX17
Sorting nexin-17 is a protein that in humans is encoded by the SNX17 gene.

# Function
This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members, but contains a B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin.

# Interactions
SNX17 has been shown to interact with Low density lipoprotein receptor-related protein 8