Persius/hicric huggingface dataset:
C4orf29
Chromosome 4 open reading frame 29 (C4orf29) is a protein that in Homo sapiens is encoded by the C4orf29 gene.

# Gene
C4orf29 is found on the positive strand of the human genome at 4q28.2. It is 74.4 kbp. The gene contains 17 exons. The longest mRNA transcript is composed of 13 exons and is 2200 base pairs.

# Homology

## Orthologs
Many orthologs to human C4orf29 have been discovered, with the most distant ortholog with high (over 90%) coverage is found in rice Oryza sativa. The protein is not found in fungi. Bacteria of the order Myxobacteria and genus Chitinimonas contain orthologous regions to the C4orf29 protein. The few bacterial homologs indicate a horizontal gene transfer event. The domain of unknown function, DUF2048, is conserved throughout orthologs.

# Protein
C4orf29 codes a 414 amino acid sequence of 46.9 kDa in humans. The predicted isoelectric point is 9.37. The domain of unknown function, DUF2048, is found from amino acid residues 25 to 414 in the precursor C4orf29 protein. This domain is part of the alpha/beta hydrolase superfamily, which comprises enzymes that catalyze fat metabolism. Predicted post-translational modifications include glycosylation at residues Ser287 and Ser319  and sumoylation at the motifs Phe240 to Gly243, Ala377 to Asp340, and Phe408 to Gly411.

# Expression
The protein product of C4orf29 in humans is predicted to be a secreted product. It is ubiquitously expressed at low to moderate levels. In humans, the protein is found at high levels the digestive tract and parathyroid gland. The homologous mouse protein 3110057O12Rik is expressed at high levels in the granule layer of the cerebellum.

# Clinical significance
C4orf29 contains highly variable numbers of Alu repeats. A low number of Alu repeats in the human C4orf29 protein is associated with increase prevalence of hepatocellular carcinoma (HCC) in Asian populations. This information is used as a genetic marker to determine genetic risk of HCC. 
Swine muscle transcriptome analysis indicates high expression of C4orf29 in swine with extreme low levels of fatty acid composition.
C57BL/6
C57BL/6, often referred to as "C57 black 6" or just "black 6" is a common inbred strain of lab mouse. It is probably the most widely used "genetic background" for genetically modifed mice for use as models of human disease. They are the most widely used lab mouse strain, due to the availability of congenic strains, easy breeding, robustness, and their relationship to GM models, making them ideal controls.

# Appearance and behavior
Dark brown, nearly black, coat. Easily irritable temperament. They have a tendency to bite, and cannot be handled like a typical pet mouse or even more docile laboratory strains such as BALB-C. They also have a tendency (shared with other mouse strains) to "overgroom" their cage-mates, resulting in large bald patches on their backs.

# C57BL/6 as a "Th1 responder"
C57BL/6 has certain immunophenotypes that distinguish it from other inbred strains like BALB/c. For example the immunological response to the same pathogen in C57BL/6 mice is often of an opposite spectrum compared to BALBb/c mice, namely C57BL/6 shows Th1 and BALB/c shows Th2 response in response to intracellular pathogen Leishmania major, where a Th1 response results in a resistant ie healer phenotype (since the pathogen is intracellular), whereas a Th2 response results in a susceptible (nonhealer) phenotype.
Though this trait had been observed in these two strains since 1988, in an article published in 2000 by Mills et al. these observations were systematized and generalized to other strains of mice. Even without biasing towards Th1 or Th2 by priming through infection, the strains differ in their macrophages' ability to be activated, as measured from their arginine metabolic programs when stimulated by Interferon gamma or LPS or both:
- M-1 macrophages from typical Th1 responders:C57BL/6 or B10.D2 mice, preferentially produce NO by action of iNOS
- M-2 macrophages from typical Th2 responders: DBA or BALB/c mice), preferentially produce ornithine and urea by action of argininase

# Response to diseases
Plasmodium (malaria)
- P. yoelii YM = lethal
- P. yoelii 17XL = lethal
- P. yoelii 17XNL = "non-lethal" (though up to 50% mortality is not unusual)
- P. berghii = lethal (with cerebral malaria)
- P. vinkii = lethal
- P. chabaudi AS = non-lethal
C6orf35
UPF0463 transmembrane protein C6orf35 is a protein that in humans is encoded by the C6orf35 (chromosome 6 open reading frame 35) gene.
This protein contains a DUF1358 domain (Domain of Unknown Function 1358).

# Domain
The C6orf35 protein has a conserved domain of unknown function pfam 07096, DUF 1358., which covers the first 121 aa of the protein. This domain is conserved in eukaryotes.

# Associated Proteins
Several predicted interacting proteins and functional sites on the protein have been identified.  One of the predicted interacting protein is MAP2K1IP1, which is a scaffold protein. This protein is known to be involved in the MAP Kinase pathway. The MAP Kinase pathway is associated with the Alzheimer's pathway through a protein called Tau or  MAPT. Excessive phosphorylation of this protein leads to aggregation of neurons which can cause Alzheimer's disease.
C6orf58
C6orf58 is a humangene located at locus 6q22.33 of chromosome 6 and encodes for UPF0762, a protein which is subsequently secreted after cleavage of a signal peptide. DUF781, which is the singular identifiable domain in UPF0762, is tied to liver development in an orthologous protein in zebrafish. The function of the human UPF0762 is not yet well characterized.

# Gene and mRNA

## Expression
While there are 3 splice variants of C6orf58, only one encodes a good protein. In humans, C6orf58 expressed sequence tags were primarily detected in the larynx and trachea. Transcripts were only detected during the adult stage of development. Experimental microarray data, however, reveals additional regions of C6orf58 expression, namely in the salivary gland, thyroid, and small intestine. Arsenic may also regulate expression as it increases methylation of the C6orf58 promoter.

## Gene Neighborhood
Genes within 500 Kilobases of C6orf58 include RSPO3, C6orf174, KIAA0408, RPL17P23, ECHDC1, RPL5P18, YWHAZP4, LOC100420743, LOC100421513, MRPS17P5, and THEMIS.

## Homology
A selected set of homologous sequences are listed below, with sequence identity being calculated in comparison to the human reference sequence.

# Protein

## Properties
Mass spectrometry has shown that the observed molecular weight of UPF0762 is 32kDa. It remains unclear why the observed molecular weight is less than predicted, even after accounting for cleavage of the signal peptide. Attachment of a sugar at the site of N-linked glycosylation would also increase the molecular weight.

## Homology
UPF0762 shows high homology in primates and orthologous proteins can be traced back as far as trichoplax adhaerens. The list of proteins below is not a comprehensive listing of UPF0762 orthologs. Sequence identity and similarity were determined using BLAST  with the reference human sequence as the query.

## Conserved domains
DUF781 is the singular domain of the protein and spans 318 of the protein's 330 amino acids. DUF781 has been linked to liver development in zebrafish.

## Post-translational modifications
Observed post-translational modifications include N-linked glycosylation at amino acid 69. A signal peptide, which is predicted to direct the protein to the endoplasmic reticulum for secretion, is cleaved from the first 20 amino acids of the peptide sequence. The missense mutation S18F detected in hepatocellular carcinoma significantly reduces the predicted cleavage score of the signal peptide.

## Interactions
Human C6orf58 has been reported to interact with the enzyme ribonucleotide reductase as encoded by the vaccinia virus through a yeast two-hybrid screen.

# Pathology
Statistical analysis has shown C6orf58 to be associated with pancreatic cancer survival time. In addition, a missense mutation at amino acid 18 has been observed in liver cancer cells where serine becomes phenylalanine. Analysis of the mutated protein sequence for a signal peptide shows cleavability at the regular amino acid 20 is lost.  DUF781's association with liver development and the missense mutation's association with liver cancer is a correlation that remains to be investigated.
C6orf62
Chromosome 6 open reading frame 62 (C6orf62), also known as X-trans-activated protein 12 (XTP12), is a gene that encodes a protein of the same name. The encoded protein is predicted to have a subcellular location within the cytosol.

# Gene and Transcript
In the DNA, C6orf62 is 12,529 base pairs long and is located at 6q22.3. It is located on chromosome 6 on position 22.3 (6q22.3). The mature mRNA sequence is 2498 base-pairs long with 5 exons and 4 intronic regions that translates a protein that is 229 amino acids long and two predicted isoforms of 160 amino acids and 200 amino acids.

# Protein
The main transcript is 229 amino acids long and is encoded from 5 exonic regions. There exists two transcript variants that are 200 amino acids and 160 amino acids long. There is a domain of unknown function (DUF4566) present in all three variants and spans positions 1-226 on the main transcript. The molecular weight of C6orf62 is 27.1 kDa and its isoelectric point is at a pH of 9.24. It is located subcellularly localized throughout the cytosol.

## Protein Interactions

# Expression
C6orf62 is broadly expressed within the human body, however, its protein abundance is not high. It is more heavily expressed in the gallbladder and testis, but it is not predicted to be expressed in the smooth muscle, lymph nodes, the spleen, ovaries, adipose tissue, and soft tissue.

# Homology
C6orf62 is highly conserved among vertebrates and has orthologs found in invertebrates.

## Orthologs in Select Mammals

## Orthologs in Select Ray-Finned Fish

## Orthologs in Select Amphibians

## Orthologs in Select Reptiles

## Orthologs in Select Birds
Orthologs in Select Invertebrates
C7orf25
C7orf25 protein UPF0415 (UPF0415) is a protein encoded on chromosome 7, in open reading frame 25 (C7orf25) and are located at domain of unknown function 1308. C7orf25 is located at the minus strand and encodes 12 proteins, one of them being UPF0415. This protein is believed to be active in the proteosome pathway. C7orf25 protein UPF0415 is not a transmembrane protein and has no signal peptide. UPF0415 has two isoforms, Q9BPX7-1 and Q9BPX7-2. Both consists of two exons that are both highly conserved among vertebrates.

# Background information

# Gene neighborhood
C7orf25 is an open reading frame that encodes 12 proteins. Most of these are of unknown function. One of these proteins is UPF0415 and another is PSMA2 which is also functional in the proteosome pathway. Other genes located near C7orf25 protein UPF0415 are TCP1P1, HECW1, MIR3943 and MRPL32.

# Predicted mRNA features

## Promoter
The promoter for the C7orf25 protein UPF0415 gene spans 600 base pairs from 42,951,804 to 42,952,404 with a predicted transcriptional start site that encodes a sequence of 1844 base pairs. The sequence spans from 42,908,726 to 42,912,090.  The promoter region and beginning of the C7orf25 gene (20,008,263 to 20,009,250) is not conserved past primates.  This region was used to determine transcription factor interactions.

### Transcription factors
Some of the main transcription factors that bind to the promoter are listed below.

# Function and expression
C7orf25 protein UPF0415 is believed to be active in ATP dependent protein breakdown in the proteosome pathway. It is expressed ubiquitously in humans.

# Homology
UPF0415 protein C7orf25  has one paralog which is FLJ18411. UPF0415 is also highly conserved in vertebrates. The following table shows a small selection of orthologs found using BLAST and BLAT  and their identity to C7orf25 protein UPF0415.

# Predicted protein features

## Post Translational Modifications
UPF0415 protein C7orf25 is not a transmembrane protein as it has no transmembrane domains. C7orf25 protein UPF0415 has multiple phosphorylation which are believed to be responsible in protein activation.
Multiple stem loops have been predicted in both 3` and 5`UTR and these are believed to be functional in gene transcription.
3`UTR and 5`UTR stem loops

# = Interactions
Other proteins that are known to interact with UPF0415 protein C7orf25 are FRA10AC1, FLJ23825 and TUBB (tubulin, beta class I) and only TUBB is associated with proteosome activity.

## Conceptual presentation
All post transnational modifications, genetic or proteomic factors that are relevant for UPF0415 protein C7orf25 transcription and regulation, mentioned above, are annotated in the conceptual translation.

# C7orf25
C7orf25 encodes 12 different transcripts. Two of these transcripts are (PSMA2 and UPF0415). No specific phenotypes or polymorphisms are yet to be related to mutations in C7orf25. This suggests that this reading frame is important for  survival in vertebrates. The picture below shows all predicted transcripts encoded in C7orf25.
C7orf30
C7ORF30 (chromosome 7 open reading frame 30) is a gene on chromosome 7 in humans that encodes the protein LOC_115416.  This protein localizes to mitochondria and is probably involved in mitochondrial translation or the biogenesis of the large subunit of the mitochondrial ribosome.

# Protein
LOC_115416 is a member of the DUF143 family (= domain of unknown function 143, Pfam PF02410) which is highly conserved in both prokaryotes and eukaryotes but not archaea.  Examples of mammalian conservation are given below using the ALIGN tool from the San Diego Supercomputer Center Biology Workbench.  Percentages indicate the identity shared by the human protein and the respective mammalian protein.  Accession numbers are from the NCBI database.
There are no known or predicted paralogs in Homo sapiens. That is, C7Orf30 is a single-copy gene.
The domain is from position 93 to 194 on the human protein and comprises 43.2% of the sequence.  This conserved domain is also present in the plant gene iojap, a pattern-striping gene in maize. However, since its function has been solved at least in bacteria, it is no longer a "domain of unknown function".

## Protein function
While the function of the protein in mitochondria is not conclusive its bacterial homolog has been shown to silence prokaryotic translation by blocking the two ribosomal subunits from joining, hence it was called RsfS (= ribosomal silencing factor in starvation or stationary phase, a synonym of RsfA).
Protein-protein interactions. RsfS has been shown via a yeast two-hybrid screen to interact with ribosomal protein L14 in four bacterial species as well as in mitochondria. C7Orf30 was shown to interact with CHMP protein which is part of the ESCRT-III complex (Endosomal Sorting Complex Required for Transport). DUF143 has also been shown to interact with UFD1, tRNA synthetases class II, and Cytidylyltransferase in various architectures.

## Properties
Bioinformatics predicted the following properties for LOC_115416:
- Molecular Weight:  26.2 KDal
- Isoelectric Point:  5.155

# Gene
C7ORF30 is located on chromosome 7 in humans and runs from 23,305,465 to 23,315,705.  There are four predicted exons in the human gene with conservation occurring across most mammalian species.  There is no conclusive data regarding whether the gene is ubiquitously expressed in human tissues, but expressed sequence tag databases show that it is expressed in many tissues.

## Neighboring Genes
C7ORF30 is neighbored by GPNMB upstream and IGF2BP3 downstream, however the latter gene is transcribed on the opposite strand running from the 3' to the 5' end.  There is some slight overlap of the untranslated regions of C7ORF30 and IGF2BP3 whereas the distance between C7ORF30 and GPNMB is 24,211 base pairs.
C7orf31
Chromosome Seven Open Reading Frame 31 (C7orf31) is a protein that in humans is encoded by the C7orf31 gene on chromosome seven.

# Gene/Locus
In humans, the C7orf31 gene is located at the locus 7p15.3   and stretches between position 25174316 and 25219817 (span 45502 bp).  It codes for at least 4 unique human isoforms: the primary isoform (590 aa; also denoted X1, X2, and CRA_c), isoform X4 (346 aa), isoform CRA_a (580 aa), and isoform CRA_b (380 aa).

# Transcript
In humans, C7orf31 codes for an mRNA strand that is 3609 base pairs long.  The human mRNA is composed of a 5' untranslated region that is 561 bases and a 3' untranslated region that is 1275 bases long.

# Protein
The primary protein encoded by C7orf31 in humans is 590 amino acids long with molecular weight 38334 Da.  The protein is part of a functionally uncharacterized family of proteins (pfam15093) with a domain of unknown function (DUF4555).

# Protein Orthology
The C7orf31 protein is well-conserved in mammals and birds, but is less conserved in more distant organisms.
C7orf31 does not have any paralogs in humans.

# Expression
In humans, C7orf31 is predicted to be localized in the cytosol, nucleus, mitochondrion, and peroxisome, and it is expressed in almost all tissues.  It is highly expressed especially in the testes.

# Interaction
Two-hybrid studies have found interactions between the proteins encoded by A8K5H9 and C7orf31,
A study in 2014 found C7orf31 to be a candidate as a centrosome-associated protein, using mass spectrometry on mammalian sperm cells centrioles.  The protein appears in the study alongside seven other centrosome-associated protein candidates.  Along with 2241 other proteins, C7orf31 also exhibited significant binding in a microarray experiment to -amyloids, a group of proteins associated with Alzheimer's disease.  Finally, in a protein-protein interaction network study, C7orf31 was found to associate with KLHL40, whose exact function is also not known.
C7orf61
Uncharacterized protein chromosome 7 open reading frame 61 is an asparagine-poor protein in humans encoded by the c7orf61 gene. The protein function is relatively unknown and is highly conserved in mammals.

# Gene

## Locus
C7orf61 is located on the reverse (or negative) DNA strand and is situated in chromosome 7 (7q22.1) from base pairs 100,456,615-100,464,271 - roughly 7,656 bp.  It has a total of 3 exons and lacks isoforms.

## mRNA
The mRNA is approximately 1019 bp and belongs to domain of unknown function 4703 (PFAM15775).

## Protein
In humans, the protein contains a total of 206 amino acids. The protein's molecular weight is 23.71 kDa and it's isoelectric point is 10.41. DUF4703 is positioned 22-206aa of the protein. Neither the gene or its protein has another known alias, but can be found with high affinity in several primate species.

## Composition
The amino acid composition of C7orf61 consists of high frequencies in leucine, serine, and charged valine. The protein has an unusual low frequency in asparagine, making it an asparagine-deficient protein , and contains higher frequencies of salt-bridge formations between glutamic acid, aspartic acid, lysine, and arginine.

## Characteristics and structure
The consent within secondary structure prediction tools CFSSP, SSPRED, and GOR4  is that the protein's secondary structure consist mainly of -helices (51.2%), with significant amounts of coiling (38.2%) and smaller fragments of beta strands (10.3%).

## Post-translational modifications
C7orf61 has several post-translation modification sites, most of which involve serine/threonine kinases - protein kinase C,  Casein kinase II,  DNA-dependent protein kinase, and Cyclin-dependent kinase 1. It is predicted to contain a Biparte nuclear localization signal (NLS_BP), a leucine-rich variant domain (LRV), and bacterial Ig-like domain (BIG-1).

## Subcellular localization
C7orf61 does not contain any trans-membrane domains or signal peptides. The protein is predicted to be localized in the Mitochondria, with little indication of extracellular activity.  Expanded analysis of amino acid sequence KFFRWVRRAWQRIISWVF near the N-terminal suggests the presence of a mitochondrial targeting signal. 

# Gene regulation
C7orf61 has high levels of expression in the testis and lower levels in the brain and connective tissues. Through the assessment of microarray experiments available on NCBI Geo, it's inferred that c7orf61 is under negative regulation. 

# Homology
C7orf61 does not have any paralogs. Analysis via NCBI tool BLASTt found the gene to be highly conserved in mammals and could not be traced farther back than 160 MYA. The following table contains a list of orthologs found in several mammalian sub-classes - this is not a comprehensive list for the proteins orthology.
C8orf58
Chromosome 8 open reading frame 58 is an uncharacterised protein that in humans is encoded by the C8orf58 gene. The protein is predicted to be localized in the nucleus.

# Gene
The C8orf58 gene is located on chromosome 8 at position 8p21.3. It spans a total of 4,550 base pairs and has seven exons. C8orf58 is flanked by the genes PDLIM2 and CCAR2. There are no aliases. It is defined as a protein coding gene.

# mRNA
C8orf58 produces three transcript splice variants. The transcript of variant 1 represents the longest transcript and encodes the largest protein. It is 2,062 base pairs and contains seven exons. There are two other splice variants, produced by alternative splice sites.
C8orf58 has a relatively short 5 region and a moderate 3 region. Both the 5 and 3 regions contain stem loops. There is one predicted miRNA binding site that found in the 3UTR of C8orf58.

# Protein
C8orf58 protein Isoform 1 is 365 amino acids long. Isoform 2 and Isoform 3 are 357 and 300 amino acids respectively. There is a kozak consensus sequence present, which confirms it is a protein coding sequence.
C8orf58 Isoform 1 has a molecular weight of 39.7 kDa and an isoelectric point of 8.29. It is proline and arginine rich and isoleucine, asparagine, phenylalanine, and tyrosine poor.
The predicted secondary structure of the C8orf58 protein include multiple alpha helices and one beta strands.

# Evolutionary history
It is part of the DUF4657 family, a family of proteins found in eukaryotes. Proteins in this family are typically between 305 and 370 amino acids in length. The Domain of Unknown Function (DUF) of C8orf58 is located between amino acids 73 to 364.

# Expression
According to the NCBI GEO profiles, C8orf58 is a narrowly expressed protein found in spleen, lung, thymus, prostate, and spinal cord tissue. It is constitutively expressed in these tissues.

# Post-translational modification
The bioinformatic tools on Expasy were used to determine potential post translational modification sites for the C8orf58 protein. There are two predicted phosphorylation sites and one predicted sumoylation site.

# Subcellular localization
According to PSORT II, C8orf58 is located in the nucleus. This is supported by the presence of a sumoylation site, which is involved in nucleic cytoplasmic transport.

# Interacting proteins
Two proteins have been found to interact with protein C8orf58, CENPH and metG1, which were found using two hybrid assay and the two hybrid pooling approach respectively. CENPH (Centromere Protein H) plays a critical role in centromere structure, kinetochore formation, and sister chromatid separation. MetG1 (MethioninetRNA ligase) is required for elongation of protein synthesis and the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

# Homology
An important paralog of this gene is ENSG00000248235. Orthologs of the human gene C8orf58 are limited to vertebrates of the animal kingdom.