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PR00904

Identifier
FRATAXIN  [View Relations]  [View Alignment]  
Accession
PR00904
No. of Motifs
7
Creation Date
06-JUN-1998  (UPDATE 10-JUN-1999)
Title
Frataxin signature
Database References

INTERPRO; IPR001794
Literature References
1. CAMPUZANO, V., MONTERMINI, L., MOLTO, M.D., PIANESE, L., COSSEE, M.,
CAVALCANTI, F., MONROS, E., RODIUS, F., DUCLOS, F., MONTICELLI, A.,
CANIZARES, J., KOUTNIKOVA, H., BIDICHANDANI, S.I., GELLERA, C., BRICE, A.,
TROUILLAS, P., DEMICHELE, G., FILLA, A., DEFRUTOS, R., PALAU, F., 
DIDONATO, S., MANDEL, J.L., COCOZZA, S., KOENIG, M. AND PANDOLFO, M.
Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA
triplet repeat expansion.
SCIENCE 271 1423-1427 (1996).
 
2. DURR, A., COSSEE, M., AGID, Y., CAMPUZANO, V., MIGNARD, C., PENET, C.,
MANDEL, J.L., BRICE, A. AND KOENIG, M. 
Clinical and genetic abnormalities in patients with Friedreichs ataxia. 
NEW ENGLAND J.MED. 335(16) 1169-1175 (1996).
 
3. KOUTNIKOVA, H., CAMPUZANO, V., FOURY, F., DOLLE, P., CAZZALINI, O. 
AND KOENIG, M. 
Studies of human, mouse and yeast homologues indicate a mitochondrial
function for frataxin 
NAT.GENET. 16(4) 345-351 (1997). 

Documentation
Friedreich ataxia is a progressive neurodegenerative disorder caused by
loss of function mutations in the gene encoding frataxin (FRDA). Frataxin
mRNA is predominantly expressed in tissues with a high metabolic rate 
(including liver, kidney, brown fat and heart). Mouse and yeast frataxin
homologues contain a potential N-terminal mitochondrial targeting sequence,
and human frataxin has been observed to co-localise with a mitochondrial
protein. Furthermore, disruption of the yeast gene has been shown to result
in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a
mitochondrial disease caused by a mutation in the nuclear genome
(specifically, expansion of an intronic GAA triplet repeat).
 
FRATAXIN is a 7-element fingerprint that provides a signature for frataxin.
The fingerprint was derived from an initial alignment of 3 sequences: the
motifs were drawn from short conserved regions spanning the full alignment
length. A single iteration on OWL30.2 was required to reach convergence, no
further sequences being identified beyond the starting set. Two partial
matches were found: AF028240 is a human frataxin gene splice variant, and
CELF59G14 is a C.elegans sequence whose N-terminal domain shows high
similarity to motifs 6 and 7 (and lower similarity also to motifs 4 and 5) -
the C-terminal domain is a protein tyrosine phosphatase.
 
An update on SPTR37_9f identified a true set of 3 sequences, and 1
partial match.
Summary Information
   3 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
73333333
60000000
50000000
40000000
30000000
20000011
1234567
True Positives
O35943        Q15294        Q16595        
True Positive Partials
Codes involving 2 elements
Q21055
Sequence Titles
O35943      FRATAXIN PRECURSOR - MUS MUSCULUS (MOUSE).    
Q15294 FRATAXIN PRECURSOR (FRIEDREICH'S ATAXIA PROTEIN) - HOMO SAPIENS (HUMAN).
Q16595 FRATAXIN PRECURSOR (FRIEDREICH'S ATAXIA PROTEIN) - HOMO SAPIENS (HUMAN).

Q21055 PTP-2 PROTEIN (EC 3.1.3.48) - CAENORHABDITIS ELEGANS.
Scan History
OWL30_2    1  100  NSINGLE    
SPTR37_9f 2 5 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
WTLGRRAVAGLL HSFRDA5 2 2 -
WTLGRRAVAGLL HSFRDA6 2 2 -
WAFGGRAAVGLL MMU95736 2 2 -

Motif 2 width=16
Element Seqn Id St Int Rpt
PRPAELAPLCGRRGLR HSFRDA5 28 14 -
PRPAELAPLCGRRGLR HSFRDA6 28 14 -
PRWREPIVTCGRRGLH MMU95736 27 13 -

Motif 3 width=16
Element Seqn Id St Int Rpt
QIWNVKKQSVYLMNLR HSFRDA5 64 20 -
QIWNVKKQSVYLMNLR HSFRDA6 64 20 -
QILNIKKQSVCVVHLR MMU95736 61 18 -

Motif 4 width=19
Element Seqn Id St Int Rpt
LDETTYERLAEETLDSLAE HSFRDA5 90 10 -
LDETTYERLAEETLDSLAE HSFRDA6 90 10 -
LDETAYERLAEETLDSLAE MMU95736 87 10 -

Motif 5 width=20
Element Seqn Id St Int Rpt
EFFEDLADKPYTFEDYDVSF HSFRDA5 108 -1 -
EFFEDLADKPYTFEDYDVSF HSFRDA6 108 -1 -
EFFEDLADKPYTLEDYDVSF MMU95736 105 -1 -

Motif 6 width=16
Element Seqn Id St Int Rpt
GVLTVKLGGDLGTYVI HSFRDA5 130 2 -
GVLTVKLGGDLGTYVI HSFRDA6 130 2 -
GVLTIKLGGDLGTYVI MMU95736 127 2 -

Motif 7 width=16
Element Seqn Id St Int Rpt
INKQTPNKQIWLSSPS HSFRDA5 145 -1 -
INKQTPNKQIWLSSPS HSFRDA6 145 -1 -
INKQTPNKQIWLSSPS MMU95736 142 -1 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
WTLGRRAVAGLL Q15294 2 2 -
WTLGRRAVAGLL Q16595 2 2 -
WAFGGRAAVGLL O35943 2 2 -

Motif 2 width=16
Element Seqn Id St Int Rpt
PRPAELAPLCGRRGLR Q15294 28 14 -
PRPAELAPLCGRRGLR Q16595 28 14 -
PRWREPIVTCGRRGLH O35943 27 13 -

Motif 3 width=16
Element Seqn Id St Int Rpt
QIWNVKKQSVYLMNLR Q15294 64 20 -
QIWNVKKQSVYLMNLR Q16595 64 20 -
QILNIKKQSVCVVHLR O35943 61 18 -

Motif 4 width=19
Element Seqn Id St Int Rpt
LDETTYERLAEETLDSLAE Q15294 90 10 -
LDETTYERLAEETLDSLAE Q16595 90 10 -
LDETAYERLAEETLDSLAE O35943 87 10 -

Motif 5 width=20
Element Seqn Id St Int Rpt
EFFEDLADKPYTFEDYDVSF Q15294 108 -1 -
EFFEDLADKPYTFEDYDVSF Q16595 108 -1 -
EFFEDLADKPYTLEDYDVSF O35943 105 -1 -

Motif 6 width=16
Element Seqn Id St Int Rpt
GVLTVKLGGDLGTYVI Q15294 130 2 -
GVLTVKLGGDLGTYVI Q16595 130 2 -
GVLTIKLGGDLGTYVI O35943 127 2 -

Motif 7 width=16
Element Seqn Id St Int Rpt
INKQTPNKQIWLSSPS Q15294 145 -1 -
INKQTPNKQIWLSSPS Q16595 145 -1 -
INKQTPNKQIWLSSPS O35943 142 -1 -