In silico-initiated cloning and molecular characterization of cortexin 3, a novel human gene specifically expressed in the kidney and brain, and well conserved in vertebrates

International Journal of Molecular Medicine

Volumn 20, Issue 4, 2007, Pages 501-510

  Wang, Hai Tao ^a   Chang, Ji Wu ^b   Guo, Zhi ^a   Li, Bao Guo ^a  

^a TIANJIN MEDICAL UNIVERSITY   (China)

^b SECOND HOSPITAL OF TIANJIN MEDICAL UNIVERSITY   (China)

Author keywords

Alternative splicing; Bioinformatics; Digital gene expression displayer; In silico cloning; Tissue specific gene; Transmembrane protein

Indexed keywords

CORTEXIN 3, HUMAN; ISOPROTEIN; MEMBRANE PROTEIN; MESSENGER RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANIMAL; ANTIBODY SPECIFICITY; ARTICLE; BIOLOGY; BRAIN; CHEMISTRY; CLUSTER ANALYSIS; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; HUMAN; KIDNEY; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BRAIN; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; KIDNEY; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; ORGAN SPECIFICITY; PROTEIN ISOFORMS; RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; VERTEBRATES;

EID: 38449122773     PISSN: 11073756     EISSN: 1791244X     Source Type: Journal    
DOI: 10.3892/ijmm.20.4.501     Document Type: Article

References (30)

1. Maniatis T, Goodbourn S and Fischer JA: Regulation of inducible and tissue-specific gene expression. Science 236: 1237-1245, 1987. (Pubitemid 17087887)
2. Hakalahti L, Vihko P, Henttu P, Autio-Harmainen H, Soini Y and Ihko R: Evaluation of PAP and PSA gene expression in prostatic hyperplasia and prostatic carcinoma using Northern blot analyses, in situ hybridization and immunohistochemical stainings with monoclonal and bispecific antibodies. Int J Cancer 55: 590-597, 1993.
3. Troyer JK, Beckett ML and Wright GL Jr: Detection and characterization of the prostate-specific membrane antigen (PSMA) in tissue extracts and body fluids. Int J Cancer 62: 552-558, 1995.
4. Zhang Y, Proenca R, Maffei M, Barone M, Leopold L and Friedman JM: Positional cloning of the mouse obese gene and its human homologue. Nature 372: 425-432, 1994. (Pubitemid 24365442)
5. Fickett JW: Coordinate positioning of MEF2 and myogenin binding sites. Gene 172: GC19-GC32, 1996.
6. Fickett JW: Quantitative discrimination of MEF2 sites. Mol Cell Biol 16: 437-441, 1996.
7. Maser RL and Calvet JP: Analysis of differential gene expression in the kidney by differential cDNA screening, subtractive cloning, and mRNA differential display. Semin Nephrol 15: 29-42, 1995.
8. Takenaka M, Imai E, Kaneko T, et al: Isolation of genes identified in mouse renal proximal tubule by comparing different gene expression profiles. Kidney Int 53: 562-572, 1998.
9. Hu E, Chen Z, Fredrickson TA, et al: Rapid isolation of tissue-specific genes from rat kidney. Exp Nephrol 9: 156-164, 2001.
10. Lisitsyn N and Wigler M: Cloning the differences between two complex genomes. Science 259: 946-951, 1993. (Pubitemid 23080660)
11. Liang P and Pardee AB: Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257: 967-971, 1992.
12. Diatchenko L, Lau Y-FC, Campbell AP, et al: Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93: 6025-6030, 1996.
13. Strausberg RL, Greenhut SF, Grouse LH, Schaefer CF and Buetow KH: In silico analysis of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol 11: S66-S71, 2001.
14. Shen D, He J and Chang HR: In silico identification of breast cancer genes by combined multiple high throughput analyses. Int J Mol Med 15: 205-212, 2005.
15. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 12: 656-664, 2002.
16. Nakai K and Horton P: PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24: 34-36, 1999.
17. Hofmann K and Stoffel W: TMbase - A database of membrane spanning protein segments. Biol Chem Hoppe-Seyler 374: 166, 1993.
18. Moller S, Croning MDR and Apweiler R: Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646-653, 2001.
19. McGuffin LJ, Bryson K and Jones DT: The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405, 2000.
20. Walker JM (ed): The Proteomics Protocols Handbook. Humana Press, pp571-607, 2005.
21. Higgins DG, Thompson JD, Gibson TJ, et al: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680, 1994.
22. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG: The clustal x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882, 1997. (Pubitemid 28022245)
23. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ: Basic local alignment search tool. J Mol Biol 5: 403-410, 1990. (Pubitemid 20364473)
24. Kozak M: An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15: 8125-8148, 1987.
25. Olesen C, Hansen C, Bendsen E, et al: Identification of human candidate genes for male infertility by digital differential display. Mol Hum Reprod 7: 11-20, 2001.
26. Scheurle D, DeYoung MP, Binninger DM, Page H, Jahanzeb M and Narayanan R: Cancer gene discovery using digital differential display. Cancer Res 60: 4037-4043, 2000.
27. Wistow G, Bernstein SL, Wyatt MK, et al: Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Mol Vis 8: 196-204, 2002.
28. van der Velden AW and Thomas AA: The role of the 5′ untranslated region of an mRNA in translation regulation during development. Int J Biochem Cell Biol 31: 87-106, 1999. (Pubitemid 29094792)
29. de Moor CH and Richter JD: Translational control in vertebrate development. Int Rev Cytol 203: 567-608, 2001.
30. Ureta-Vidal A, Ettwiller L and Birney E: Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet 4: 251-262, 2003.