C3orf14: Difference between revisions

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The human gene [[Chromosome 3]] [[open reading frame]] 14 is a gene of uncertain function located at 3p14.2 near [[fragile site]] FRBA3—which falls between this gene and the [[centromere]]<ref>{{cite journal|last=Thierry-Mieg|first=D|coauthors=Thierry-Mieg, J.|title=AceView: a comprehensive cDNA-supported gene and transcripts annotation|journal=Genome Biology|year=2006|volume=7|issue=Suppl 1|pages=S12}}</ref>. Its protein is expected to localize to the nucleus and bind DNA<ref>{{cite journal|last=Gasteiger|first=Elisabeth|coauthors=Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D. Appel, and Amos Bairoch|title=ExPASy: the proteomics server for in-depth protein knowledge and analysis.|journal=Nucleic Acids Research|date=July 1|year=2003|month=July|volume=31|issue=13|pages=3784 -3788|doi=10.1093/nar/gkg563|url=http://genomebiology.com/2006/7/s1/S12|accessdate=9 May 2011}}</ref> <ref>{{cite journal|last=Manish Kumar, Michael M. Gromiha and Gajendra PS Raghava|title=Identification of DNA-binding proteins using support vector machines and evolutionary profiles.|journal=BMC Bioinformatics|year=2007|volume=8:463}}</ref> . [[Homologs]] have been identified in all of the major animal groups, minus amphibians and insects<ref>{{cite journal|last=Pruitt, K. D., T. Tatusova, and D. R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35, no. Database (1): D61-D65. doi:10.1093/nar/gkl842.}}</ref>, tracing as far back as the sea anemone; indicating an origin of over 1000 mya, highlighting its importance in the animal [[genome]].
The human gene [[Chromosome 3]] [[open reading frame]] 14 is a gene of uncertain function located at 3p14.2 near [[fragile site]] FRBA3—which falls between this gene and the [[centromere]]<ref>{{cite journal|last=Thierry-Mieg|first=D|coauthors=Thierry-Mieg, J.|title=AceView: a comprehensive cDNA-supported gene and transcripts annotation|journal=Genome Biology|year=2006|volume=7|issue=Suppl 1|pages=S12}}</ref>. Its protein is expected to localize to the nucleus and bind DNA<ref>{{cite journal|last=Gasteiger|first=Elisabeth|coauthors=Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D. Appel, and Amos Bairoch|title=ExPASy: the proteomics server for in-depth protein knowledge and analysis.|journal=Nucleic Acids Research|date=July 1|year=2003|month=July|volume=31|issue=13|pages=3784 -3788|doi=10.1093/nar/gkg563|url=http://genomebiology.com/2006/7/s1/S12|accessdate=9 May 2011}}</ref> <ref>{{cite journal|last=Manish Kumar, Michael M. Gromiha and Gajendra PS Raghava|title=Identification of DNA-binding proteins using support vector machines and evolutionary profiles.|journal=BMC Bioinformatics|year=2007|volume=8:463|doi=10.1186/1471-2105-8-463}}</ref> . [[Homologs]] have been identified in all of the major animal groups, minus amphibians and insects<ref>{{cite journal|last=Pruitt, K. D., T. Tatusova, and D. R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35, no. Database (1): D61-D65. doi:10.1093/nar/gkl842.}}</ref>, tracing as far back as the sea anemone; indicating an origin of over 1000 mya, highlighting its importance in the animal [[genome]].


== Gene Aliases ==
== Gene Aliases ==
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[[Image:GCN4 coiled coil dimer 1zik rainbow.png|thumb|200px|right|Figure 1: A classic example of a [[coiled coil]]. This is an image of the characterized protein GCN4 [[leucine zipper]] (PDB accession code 1zik).]]
[[Image:GCN4 coiled coil dimer 1zik rainbow.png|thumb|200px|right|Figure 1: A classic example of a [[coiled coil]]. This is an image of the characterized protein GCN4 [[leucine zipper]] (PDB accession code 1zik).]]


The mRNA is composed of 6 [[exons]], and encodes a 15007.84 kD protein known as HT021<ref>{{cite journal|last=Thierry-Mieg, D., and J. Thierry-Mieg. 2006. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biology 7, no. Suppl 1: S12.}}</ref><ref>{{cite journal|last=Sauro|first=Herbert|coauthors=Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano|title=Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration OMICS|journal=A Journal of Integrative Biology|year=2003|volume=4|issue=12|pages=355-372|doi=10.1089/153623103322637670.}}</ref>. This protein has a pre-modification [[isoelectric point]] of 5.57 and [[alpha helices]] span most of its length <ref>{{cite journal|last=Sauro, Herbert M., Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano. 2003. Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration. OMICS: A Journal of Integrative Biology 7, no. 4 (12): 355-372. |doi=10.1089/153623103322637670.}}</ref>. Four sites of possible [[phosphorylation]] have been identified, and at least two sites of phosphorylation are conserved in all orthologs, as are two alpha helices. This protein is also predicted as a [[DNA binding protein]]<ref>{{cite journal|last=Manish Kumar, Michael M. Gromiha and Gajendra PS Raghava|title=Identification of DNA-binding proteins using support vector machines and evolutionary profiles.|journal=BMC Bioinformatics|year=2007|volume=8:463}}</ref>. The protein may assume a [[tertiary structure]] of a [[coiled coil]]<ref>{{cite journal|last=Combet C|coauthors=Blanchet C., Geourjon C. and Deléage G.|title=NPS@: Network Protein Sequence Analysis|journal=TIBS|year=2000|month=March|volume=No 3|issue=[291]:147-150|accessdate=9 May 2011}}</ref>.
The mRNA is composed of 6 [[exons]], and encodes a 15007.84 kD protein known as HT021<ref>{{cite journal|last=Thierry-Mieg, D., and J. Thierry-Mieg. 2006. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biology 7, no. Suppl 1: S12.}}</ref><ref>{{cite journal|last=Sauro|first=Herbert|coauthors=Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano|title=Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration OMICS|journal=A Journal of Integrative Biology|year=2003|volume=4|issue=12|pages=355-372|doi=10.1089/153623103322637670.}}</ref>. This protein has a pre-modification [[isoelectric point]] of 5.57 and [[alpha helices]] span most of its length <ref>{{cite journal|last=Sauro, Herbert M., Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano. 2003. Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration. OMICS: A Journal of Integrative Biology 7, no. 4 (12): 355-372. |doi=10.1089/153623103322637670.}}</ref>. Four sites of possible [[phosphorylation]] have been identified, and at least two sites of phosphorylation are conserved in all orthologs, as are two alpha helices. This protein is also predicted as a [[DNA binding protein]]<ref>{{cite journal|last=Manish Kumar, Michael M. Gromiha and Gajendra PS Raghava|title=Identification of DNA-binding proteins using support vector machines and evolutionary profiles.|journal=BMC Bioinformatics|year=2007|volume=8:463|doi=10.1186/1471-2105-8-463}}</ref>. The protein may assume a [[tertiary structure]] of a [[coiled coil]]<ref>{{cite journal|last=Combet C|coauthors=Blanchet C., Geourjon C. and Deléage G.|title=NPS@: Network Protein Sequence Analysis|journal=TIBS|year=2000|month=March|volume=No 3|issue=[291]:147-150|accessdate=9 May 2011}}</ref>.


== Expression ==
== Expression ==

Revision as of 03:59, 15 May 2011


The human gene Chromosome 3 open reading frame 14 is a gene of uncertain function located at 3p14.2 near fragile site FRBA3—which falls between this gene and the centromere[1]. Its protein is expected to localize to the nucleus and bind DNA[2] [3] . Homologs have been identified in all of the major animal groups, minus amphibians and insects[4], tracing as far back as the sea anemone; indicating an origin of over 1000 mya, highlighting its importance in the animal genome.

Gene Aliases

C3orf14
Identifiers
SymbolC3orf14
Alt. symbolsLOC57415, FLJ94553 and FLJ17473
HGNC25024
RefSeqNM_020685.3
UniProtQ9HBI5
Other data
LocusChr. 3 p14.2
Search for
StructuresSwiss-model
DomainsInterPro

C3orf14 is also known by the aliases LOC57415, FLJ94553 and FLJ17473.[5] Gene homologs found in other organisms are usually know by the name c3orf14-like, though some are known as LOC57415-like or HT021-like (protein name).

Protein Properties

Figure 1: A classic example of a coiled coil. This is an image of the characterized protein GCN4 leucine zipper (PDB accession code 1zik).

The mRNA is composed of 6 exons, and encodes a 15007.84 kD protein known as HT021[6][7]. This protein has a pre-modification isoelectric point of 5.57 and alpha helices span most of its length [8]. Four sites of possible phosphorylation have been identified, and at least two sites of phosphorylation are conserved in all orthologs, as are two alpha helices. This protein is also predicted as a DNA binding protein[9]. The protein may assume a tertiary structure of a coiled coil[10].

Expression

This gene was first identified in the hypothalamic-pituitary-adrenal axis (HPA axis)[11] . The GEO and EST profiles in NCBI, indicate that its expression level varies from tissue to tissue; however its reported expression is 1.2 times that of the average gene [12][13]. It has highest expression in the pancreas and nervous tissue (in humans). It is underexpressed in many cancer cell line, however this may be due to its close proximity to the tumor suppressor gene FHIT, and the chromosomal fragile site FRBA3. Breakage at this site inactivates FHIT and can lead to the loss of c3orf14.

Function

Since c3orf14 is not ubiquitously expressed, it is most likely not a housekeeping gene. Instead, it more likely plays an important role in the function of tissues with highest expression. It seems likely that this gene is a transcription factor, which regulates the expression of other genes important for the function of tissues where HT021 is expressed highest.

References

  1. ^ Thierry-Mieg, D (2006). "AceView: a comprehensive cDNA-supported gene and transcripts annotation". Genome Biology. 7 (Suppl 1): S12. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  2. ^ Gasteiger, Elisabeth (July 1). "ExPASy: the proteomics server for in-depth protein knowledge and analysis". Nucleic Acids Research. 31 (13): 3784–3788. doi:10.1093/nar/gkg563. Retrieved 9 May 2011. {{cite journal}}: Check date values in: |date= and |year= / |date= mismatch (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)
  3. ^ Manish Kumar, Michael M. Gromiha and Gajendra PS Raghava (2007). "Identification of DNA-binding proteins using support vector machines and evolutionary profiles". BMC Bioinformatics. 8:463. doi:10.1186/1471-2105-8-463.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  4. ^ Pruitt, K. D., T. Tatusova, and D. R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35, no. Database (1): D61-D65. doi:10.1093/nar/gkl842. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  5. ^ Bilofsky, Howard (11). "The GenBank® genetic sequence data bank". Nucleic Acids Research. 16 (5): 1861–1863. doi:10.1093/nar/16.5.1861. {{cite journal}}: Check |doi= value (help); Check date values in: |date= and |year= / |date= mismatch (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)
  6. ^ Thierry-Mieg, D., and J. Thierry-Mieg. 2006. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biology 7, no. Suppl 1: S12. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  7. ^ Sauro, Herbert (2003). "Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration OMICS". A Journal of Integrative Biology. 4 (12): 355–372. doi:10.1089/153623103322637670. {{cite journal}}: Check |doi= value (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  8. ^ Sauro, Herbert M., Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano. 2003. Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration. OMICS: A Journal of Integrative Biology 7, no. 4 (12): 355-372. doi:10.1089/153623103322637670. {{cite journal}}: Check |doi= value (help); Cite journal requires |journal= (help); Missing or empty |title= (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  9. ^ Manish Kumar, Michael M. Gromiha and Gajendra PS Raghava (2007). "Identification of DNA-binding proteins using support vector machines and evolutionary profiles". BMC Bioinformatics. 8:463. doi:10.1186/1471-2105-8-463.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  10. ^ Combet C (2000). "NPS@: Network Protein Sequence Analysis". TIBS. No 3 ([291]:147-150). {{cite journal}}: |access-date= requires |url= (help); |volume= has extra text (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)
  11. ^ Hu, RM (15). "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning". Proceedings of the National Academy of Sciences of the United States of America. 97 (17). doi:10.1073/pnas.160270997. {{cite journal}}: Check |doi= value (help); Check date values in: |date= and |year= / |date= mismatch (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)
  12. ^ Barrett, T. 2004. NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Research 33, no. Database issue (12): D562-D566. doi:10.1093/nar/gki022. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  13. ^ Thierry-Mieg, D., and J. Thierry-Mieg. 2006. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biology 7, no. Suppl 1: S12. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)

External links


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