Discriminating Facts from Database Errors in Secreted Ly-6 Proteins
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Presented at the University of Nottingham, 2005
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Discriminating Facts from Database Errors in Secreted Ly-6 Proteins
- 4. Rat Urine HPLC Intact MALDI N-Terminal Sequence High-speed microbore column
- 6. EST AA893514 vs. dbEST: 30 Rat Hits at 95% to 100% Identity
- 8. RUP3: Independent MS-based Identification by Wait et al. “Proteins of rat serum, urine and CSF:VI” Electrophoresis 22, 3043-3052 (2001) RUP1 MGKPILLLPLGLSLLMSSLLALQCFR CESLDSTGLCRVGR RICQTYPDEICAWVVVTTRD RUP2 MGKHILLLPLGLSLLMSSLLALQCFR CTSFDSTGFCHVGR QKCQTYPDEICAWVVVTTRD RUP3 MGKHILLLPLGLSLLMSSLLALQCFR CISFDSTGFCYVGR HICQTYPDEICAWVVVTTRD *** *********************** * **** * ***. ****************** RUP1 GKFVYGNQSCAECIGTTVEHGSLIISTNCCSATPFCNMVHP EST AA800439 RUP2 GKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR EST AA893514 RUP3 GKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR EST AA893518 ************* *********.***************
- 9. RUP Paralogues Define a New Family of Secreted Ly-6 Proteins
- 11. Three RUP-like Chimeras and a Pre-mRNA L07806 F1-ATPase inhibitor AF368860 UTR F1-ATPase inhib L15618 casein kinase II alpha J03621 mito succinyl-CoA synthase alpha
- 12. Translation Matches for the Chimeras Reveal a Cryptic Protein RUP-2 28 TSFDSTGFCHVGRQKCQTYPDEICAWVVVTTRDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR 101 TSFDSTGFCHVGRQKCQTYPDEICAWVVVTTRDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR 417 TSFDSTGFCHVGRQKCQTYPDEICAWVVVTTRDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR 196 L07806 Rattus rattus mitochondrial IF1 protein mRNA RUP-2: 59 RDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR 101 RDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR 708 RDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMVHR 580 L15618 Rat casein kinase II alpha subunit (CK2) mRNA RUP-2 24 CFRCTSFDSTGFCHVGRQKCQTYPDEICAWVVVTTRDGKFVYGNQSCAECNATTVEHGSLIVSTNCCSATPFCNMV 99 CF C + +S G C+ C +P E+CA V+T +DGKFVYGNQSCAEC+ TVEHGSLIVSTNCCSAT FCN+V 50 CFECGNLNSMGICNFRTAVCYAHPGEVCA-SVLTYKDGKFVYGNQSCAECSGRTVEHGSLIVSTNCCSATSFCNIV 274 J03621 Rat mitochondrial succinyl-CoA synthetase alpha subunit
- 15. Multiple Loci on Rat Chromosome 8: Erroneous Mapping of the Chimeras L15618 casein kinase II alpha L07806 F1-ATPase inhibitor AF198441 Rat RUP2 AF198442 Rat spleen protein 1
- 18. The L07806 Chimera Caused Errors in U niGene
- 19. RUP Gene Family on Rat 8q21
- 20. Rat and Mouse RUP Homologues are Highly Diverged
- 21. Sequences Conserved in Rat but Divergent in Mouse
- 22. Homologues in Five Mammals but True Orthology Unclear
- 24. Threading Reveals Homology between RUP1, Lynx1 and Snake Toxin Structures Lynx1, an Endogenous Toxin-like modulator of AChRs in the CNS,
- 25. Why so Few Apparent Orthologues?
- 26. P55000 : Antineoplastic Urinary Protein/S ecreted Mammalian Ly-6/uPAR Related Protein – Equivocal Annotation
- 28. Mouse Ly-6-like Caltrin: Sequence Errors, Unverified Reported Function, New Name and New Function?
- 34. Human Short Ly6 Proteins None - - 18 + - 11q24.2 113 LVLF31 Genset (sec), USDOH CyC PA2 - 21 + + 11q24.2 126 PATE HGS, ARS, Biovision (partial) Ly6 - 22 + + 8q24.3 103 SLURP1 Genentech, HGS, Incyte Ly6 103 22 + - 8q24.3 125 RGTR43 Genentch (sec/tm) ZymoGenetics Ly6 - 22 + + 8q24.3 97 SLURP2 Curagen, Hyseq, HGS (sec), Incyte (sec) Genset (partial) Ly6 91 19 + + 8q24.3 115 LYNX1 Patents InterPro GPI Sigpep ESTs Ens Chrom Size Name
- 36. Searches Against Rat ESTs Confirmed the Three mRNAs as Chimeras J03621 L07806 L15618
- 38. RUP Homologues Expand a New Sub-family of Secreted Ly-6 Proteins
- 39. 3D PSSM Fold Recognition Server
Notas del editor
- AA_DERWENT 1,226,302 sequences;