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Discriminating Facts from Database Errors in Secreted Ly-6 Proteins
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Chris Southan
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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
1.
2.
3.
4.
Rat Urine
HPLC Intact MALDI N-Terminal Sequence High-speed microbore column
5.
6.
EST AA893514 vs.
dbEST: 30 Rat Hits at 95% to 100% Identity
7.
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
10.
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
13.
RUP1 Gene Structure
14.
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
16.
17.
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
23.
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
27.
28.
Mouse Ly-6-like Caltrin:
Sequence Errors, Unverified Reported Function, New Name and New Function?
29.
30.
31.
32.
33.
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
35.
VertebrateShort Ly6 Proteins
36.
Searches Against Rat
ESTs Confirmed the Three mRNAs as Chimeras J03621 L07806 L15618
37.
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;
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