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PR00828

Identifier
FORMIN  [View Relations]  [View Alignment]  
Accession
PR00828
No. of Motifs
10
Creation Date
07-MAR-1998  (UPDATE 18-JUN-1999)
Title
Formin signature
Database References

INTERPRO; IPR001265
Literature References
1. WOYCHIK, R.P., MAAS, R.L., ZELLER, R., VOGT, T.F. AND LEDER, P.
limb deformity gene. 
NATURE 346 850-853 (1990).
 
2. JACKSON-GRUSBY, L., KUO, A. AND LEDER, P.
A variant limb deformity transcript expressed in the embryonic mouse limb
defines a novel formin. 
GENES DEV. 6 29-37 (1992). 
 
3. TRUMPP, A., BLUNDELL, P.A., DE LA POMPA, J.L. AND ZELLER, R.
The chicken limb deformity gene encodes nuclear proteins expressed in
specific cell types during morphogenesis. 
GENES DEV. 6 14-28 (1992). 

Documentation
Vertebrate limb formation is an evolutionarily conserved process programmed
by an array of morphogenetic genes [1]. The formins are a set of protein
isoforms encoded by the alternatively spliced transcripts arising from the
murine limb deformity (ld) locus [2]. Mutations in this locus disrupt
formation of the anteroposterior axis of the embryonic limb.
 
Formins are found in the adult kidney, testis, limb, ovary, brain, small
intestine, salivary and harderian glands, and throughout the embryo. In the 
developing limb bud, the protein is expressed in the apical ectodermal ridge
and mesenchymal compartment, predominantly in the posterior region [3].
During kidney morphogenesis, early expression is restricted to the
epithelial compartment of the pronephros and mesonephros [3].
 
FORMIN is a 10-element fingerprint that provides a signature for formin
limb deformity proteins. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning the C-terminal half of the alignment - motifs 1-3 precede a central
pro-rich region, and motifs 4-10 lie C-terminal to it. A single iteration
on OWL30.0 was required to reach convergence, no further sequences being
identified beyond the starting set. A single partial match was found, 
DMU34258, a sequence from a Drosophila maternal effect gene (cappuccino)
that is related to the vertebrate limb deformity locus.
 
An update on SPTR37_9f identified a true set of 3 sequences, and 1
partial match.
Summary Information
   3 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 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
103333333333
90000000000
80000000000
70000000000
60000000000
50000000000
40000000000
30000000000
20000100010
12345678910
True Positives
FOR4_MOUSE    FORM_CHICK    FORM_MOUSE    
True Positive Partials
Codes involving 2 elements
Q24120
Sequence Titles
FOR4_MOUSE  FORMIN 4 (LIMB DEFORMITY PROTEIN) - MUS MUSCULUS (MOUSE). 
FORM_CHICK FORMIN (LIMB DEFORMITY PROTEIN) - GALLUS GALLUS (CHICKEN).
FORM_MOUSE FORMIN (LIMB DEFORMITY PROTEIN) - MUS MUSCULUS (MOUSE).

Q24120 CAPPUCCINO - DROSOPHILA MELANOGASTER (FRUIT FLY).
Scan History
OWL30_0    1  50   NSINGLE    
SPTR37_9f 2 50 NSINGLE
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
PTEQDDRTPGRLQAVWPPPK FOR4_MOUSE 462 462 -
PTEQDDRTPGRLQAVWPPPK FORM_MOUSE 688 688 -
PSEQDDKTPGRLQTVWPPPK FORM_CHICK 468 468 -

Motif 2 width=23
Element Seqn Id St Int Rpt
KYTEAEYQAAILHLKREHKEEIE FOR4_MOUSE 492 10 -
KYTEAEYQAAILHLKREHKEEIE FORM_MOUSE 718 10 -
KYTEAEYQAAILHLKREHKEEIE FORM_CHICK 498 10 -

Motif 3 width=22
Element Seqn Id St Int Rpt
TDDDCSPKAFRNVCIQTDRETF FOR4_MOUSE 566 51 -
TDDDCSPKAFRNVCIQTDRETF FORM_MOUSE 792 51 -
TEDDNLPKTYRNVCIQTDRETF FORM_CHICK 573 52 -

Motif 4 width=24
Element Seqn Id St Int Rpt
AAPTLWDSLEEPHIRDTSEFEYLF FOR4_MOUSE 786 198 -
AAPTLWDSLEEPHIRDTSEFEYLF FORM_MOUSE 1012 198 -
AIPTLWESLEEPDILDTTEFEYLF FORM_CHICK 793 198 -

Motif 5 width=23
Element Seqn Id St Int Rpt
HLEMKDIQQAIFTVDDSVVDLET FOR4_MOUSE 854 44 -
HLEMKDIQQAIFTVDDSVVDLET FORM_MOUSE 1080 44 -
HLEMKDIQQAILCVDDSVVDLET FORM_CHICK 861 44 -

Motif 6 width=20
Element Seqn Id St Int Rpt
YYETSKEEDLKLLDKPEQFL FOR4_MOUSE 896 19 -
YYETSKEEDLKLLDKPEQFL FORM_MOUSE 1122 19 -
YYQTSKEEELKLLDKPEQFL FORM_CHICK 903 19 -

Motif 7 width=20
Element Seqn Id St Int Rpt
LLHMKSVKDILALILAFGNY FOR4_MOUSE 958 42 -
LLHMKSVKDILALILAFGNY FORM_MOUSE 1184 42 -
LLNMTSVKEILGLILAFGNY FORM_CHICK 965 42 -

Motif 8 width=22
Element Seqn Id St Int Rpt
DFFLASQVKFEDLLKDLRKLKR FOR4_MOUSE 1041 63 -
DFFLASQVKFEDLLKDLRKLKR FORM_MOUSE 1303 99 -
DFFQASQVKFEDLIKDLRKLKR FORM_CHICK 1048 63 -

Motif 9 width=20
Element Seqn Id St Int Rpt
YVFMVWFEFCSDFKTIWKRE FOR4_MOUSE 1137 74 -
YVFMVWFEFCSDFKTIWKRE FORM_MOUSE 1399 74 -
YVFTVWYEFCSDFKTIWKRE FORM_CHICK 1144 74 -

Motif 10 width=23
Element Seqn Id St Int Rpt
EKKVETKKINPTASLKERLRQKE FOR4_MOUSE 1178 21 -
EKKVETKKINPTASLKERLRQKE FORM_MOUSE 1440 21 -
EKKVETKKINPTASLKERLRQKE FORM_CHICK 1185 21 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
PTEQDDRTPGRLQAVWPPPK FOR4_MOUSE 462 462 -
PTEQDDRTPGRLQAVWPPPK FORM_MOUSE 688 688 -
PSEQDDKTPGRLQTVWPPPK FORM_CHICK 468 468 -

Motif 2 width=23
Element Seqn Id St Int Rpt
KYTEAEYQAAILHLKREHKEEIE FOR4_MOUSE 492 10 -
KYTEAEYQAAILHLKREHKEEIE FORM_MOUSE 718 10 -
KYTEAEYQAAILHLKREHKEEIE FORM_CHICK 498 10 -

Motif 3 width=22
Element Seqn Id St Int Rpt
TDDDCSPKAFRNVCIQTDRETF FOR4_MOUSE 566 51 -
TDDDCSPKAFRNVCIQTDRETF FORM_MOUSE 792 51 -
TEDDNLPKTYRNVCIQTDRETF FORM_CHICK 573 52 -

Motif 4 width=24
Element Seqn Id St Int Rpt
AAPTLWDSLEEPHIRDTSEFEYLF FOR4_MOUSE 786 198 -
AAPTLWDSLEEPHIRDTSEFEYLF FORM_MOUSE 1012 198 -
AIPTLWESLEEPDILDTTEFEYLF FORM_CHICK 793 198 -

Motif 5 width=23
Element Seqn Id St Int Rpt
HLEMKDIQQAIFTVDDSVVDLET FOR4_MOUSE 854 44 -
HLEMKDIQQAIFTVDDSVVDLET FORM_MOUSE 1080 44 -
HLEMKDIQQAILCVDDSVVDLET FORM_CHICK 861 44 -

Motif 6 width=20
Element Seqn Id St Int Rpt
YYETSKEEDLKLLDKPEQFL FOR4_MOUSE 896 19 -
YYETSKEEDLKLLDKPEQFL FORM_MOUSE 1122 19 -
YYQTSKEEELKLLDKPEQFL FORM_CHICK 903 19 -

Motif 7 width=20
Element Seqn Id St Int Rpt
LLHMKSVKDILALILAFGNY FOR4_MOUSE 958 42 -
LLHMKSVKDILALILAFGNY FORM_MOUSE 1184 42 -
LLNMTSVKEILGLILAFGNY FORM_CHICK 965 42 -

Motif 8 width=22
Element Seqn Id St Int Rpt
DFFLASQVKFEDLLKDLRKLKR FOR4_MOUSE 1041 63 -
DFFLASQVKFEDLLKDLRKLKR FORM_MOUSE 1303 99 -
DFFQASQVKFEDLIKDLRKLKR FORM_CHICK 1048 63 -

Motif 9 width=20
Element Seqn Id St Int Rpt
YVFMVWFEFCSDFKTIWKRE FOR4_MOUSE 1137 74 -
YVFMVWFEFCSDFKTIWKRE FORM_MOUSE 1399 74 -
YVFTVWYEFCSDFKTIWKRE FORM_CHICK 1144 74 -

Motif 10 width=23
Element Seqn Id St Int Rpt
EKKVETKKINPTASLKERLRQKE FOR4_MOUSE 1178 21 -
EKKVETKKINPTASLKERLRQKE FORM_MOUSE 1440 21 -
EKKVETKKINPTASLKERLRQKE FORM_CHICK 1185 21 -