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PR01214

Identifier
GSYNUCLEIN  [View Relations]  [View Alignment]  
Accession
PR01214
No. of Motifs
4
Creation Date
02-OCT-1999
Title
Gamma-synuclein signature
Database References
PRINTS; PR01211 SYNUCLEIN
INTERPRO; IPR002462
Literature References
1. LAVEDAN, C.
The synuclein family.
GENOME RES. 8 871-880 (1998).
 
2. TOBE, T., NAKAJO, S., TANAKA, A., MITOYA, A., OMATA, K., NAKAYA, K.,
TOMITA, M. AND NAKAMURA, Y.
Cloning and characterization of the cDNA encoding a novel brain-specific
14kDa protein.
J.NEUROCHEM. 59 1624-1629 (1992).
 
3. GEORGE, J.M., JIN, H., WOODS, W.S. AND CLAYTON, D.F.
Characterization of a novel protein regulated during the critical period
for song learning in the zebra finch.
NEURON 15 361-372 (1995).
 
4. NINKINA, N.N., ALIMOVA-KOST, M.V., PATERSON, J.W.E., DELANEY, L.,
COHEN, B.B., IMREH, S., GNUCHEV, N.V., DAVIES, A.M. AND BUCHMAN, V.L.
Organization, expression and polymorphism of the human persyn gene.
HUM.MOL.GENET. 7 1417-1424 (1998). 

Documentation
Human synuclein has been shown to belong to a gene family [1]. To date, 
three different proteins, termed alpha, beta and gamma, have been 
characterised. The amino acid sequences of synucleins share a similar
overall structure: hydropathy analysis reveals a central hydrophobic domain
of ~30 amino acids, flanked by highly hydrophilic stretches; the N-terminal
flanking region contains four repeating motifs (EKTKEGV); and the C-terminal
domain is rich in glutamic acid and proline [2]
 
Synelfin, a homologue of synuclein, is a soluble presynaptic protein that 
is predicted to form an amphipathic alpha-helical structure typical of the
lipid-binding domain in apolipoproteins [3]. This protein is believed to
serve a novel function critical to the regulation of vertebrate neural
plasticity [3]. 
 
As with other synucleins, gamma-synuclein, or persyn, is believed to be
involved in the pathogenesis of human neurodegenerative diseases [4]. By
contrast with other synucleins, however, high levels of gamma-synuclein
mRNA expression have also been found in advanced breast carcinomas,
suggesting an involvement of the protein in breast tumour progression [4]. 
The protein may also be over-expressed in ovarian cancer [1].
 
GSYNUCLEIN is a 4-element fingerprint that provides a signature for
gamma-synucleins. The fingerprint was derived from an initial alignment of
3 sequences: the motifs were drawn from short conserved regions spanning
virtually the full alignment length, focusing on those sections that
characterise the gamma-synucleins but distinguish them from the rest of the
synuclein family - motif 1 spans the region between the third and final EKT
repeats; motif 2 lies in the hydrophobic domain; and motifs 3 and 4 span
the Glu-Pro-rich C-terminal domain. A single iteration on SPTR37_10f was 
required to reach convergence, no further sequences being identified beyond
the starting set. Three partial matches were also found, all of which are 
alpha-synucleins that match motifs 1 and 2.
Summary Information
   3 codes involving  4 elements
0 codes involving 3 elements
3 codes involving 2 elements
Composite Feature Index
43333
30000
23300
1234
True Positives
Q9Z0F7        SYUG_HUMAN    SYUG_RAT      
True Positive Partials
Codes involving 2 elements
SYU1_RAT SYU2_RAT SYUA_MOUSE
Sequence Titles
Q9Z0F7      PERSYN - MUS MUSCULUS (MOUSE).                
SYUG_HUMAN GAMMA-SYNUCLEIN (PERSYN) (BREAST CANCER-SPECIFIC GENE 1 PROTEIN) - HOMO SAPIENS
SYUG_RAT GAMMA-SYNUCLEIN (SENSORY NEURON SYNUCLEIN) - RATTUS NORVEGICUS (RAT).

SYU1_RAT ALPHA-SYNUCLEIN, FORMS 1 AND 3 - RATTUS NORVEGICUS (RAT).
SYU2_RAT ALPHA-SYNUCLEIN, FORM 2 - RATTUS NORVEGICUS (RAT).
SYUA_MOUSE ALPHA-SYNUCLEIN (NON-A BETA COMPONENT OF AD AMYLOID) (NACP) - MUS MUSCULUS (MOUS
Scan History
SPTR37_10f 1  10   NSINGLE    
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
KENVVQSVTSVA Q9Z0F7 45 45 -
KGERGTSVTSVA SYUG_RAT 45 45 -
KENVVQSVTSVA SYUG_HUMAN 45 45 -

Motif 2 width=24
Element Seqn Id St Int Rpt
ANAVSEAVVSSVNTVANKTVEEAE Q9Z0F7 63 6 -
ANAVSEAVVSSVNTVATETVEEAE SYUG_RAT 63 6 -
ANAVSEAVVSSVNTVATKTVEEAE SYUG_HUMAN 63 6 -

Motif 3 width=19
Element Seqn Id St Int Rpt
VTTGVVRKEDLEPPAQDQE Q9Z0F7 90 3 -
VTTGVVRKEDLEPPAQDQE SYUG_RAT 90 3 -
VTSGVVRKEDLRPSAPQQE SYUG_HUMAN 90 3 -

Motif 4 width=14
Element Seqn Id St Int Rpt
KEQEENEEAKSGED Q9Z0F7 110 1 -
KEQEEGEEAKSGGD SYUG_RAT 110 1 -
EKEEVAEEAQSGGD SYUG_HUMAN 114 5 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
KENVVQSVTSVA Q9Z0F7 45 45 -
KGERGTSVTSVA SYUG_RAT 45 45 -
KENVVQSVTSVA SYUG_HUMAN 45 45 -

Motif 2 width=24
Element Seqn Id St Int Rpt
ANAVSEAVVSSVNTVANKTVEEAE Q9Z0F7 63 6 -
ANAVSEAVVSSVNTVATETVEEAE SYUG_RAT 63 6 -
ANAVSEAVVSSVNTVATKTVEEAE SYUG_HUMAN 63 6 -

Motif 3 width=19
Element Seqn Id St Int Rpt
VTTGVVRKEDLEPPAQDQE Q9Z0F7 90 3 -
VTTGVVRKEDLEPPAQDQE SYUG_RAT 90 3 -
VTSGVVRKEDLRPSAPQQE SYUG_HUMAN 90 3 -

Motif 4 width=14
Element Seqn Id St Int Rpt
KEQEENEEAKSGED Q9Z0F7 110 1 -
KEQEEGEEAKSGGD SYUG_RAT 110 1 -
EKEEVAEEAQSGGD SYUG_HUMAN 114 5 -