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PR00218

Identifier
PERIPHERNRDS  [View Relations]  [View Alignment]  
Accession
PR00218
No. of Motifs
6
Creation Date
11-JUL-1994  (UPDATE 07-JUN-1999)
Title
Peripherin (RDS)/ROM-1 family signature
Database References

PROSITE; PS00930 RDS_ROM1
BLOCKS; BL00930
PFAM; PF00824 RDS_ROM1
INTERPRO; IPR000830
Literature References
1. CONNELL, G.J. AND MOLDAY, R.S.
Molecular cloning, primary structure, and orientation of the vertebrate
photoreceptor cell protein peripherin in the rod outer segment disk
membrane.
BIOCHEMISTRY 29 4691-4698 (1990).
 
2. BASCOM, R.A., SCHAPPERT, K. AND MCINNES, R.R.
Cloning of the human ROM1 genes: genomic organization and sequence
conservation.
HUM.MOL.GENET. 2 385-391 (1993).

Documentation
The outer segments of vertebrate rod photoreceptor cells are specialised 
organelles that function in the transduction of light into electrical
signals as part of the visual excitation process [1]. These organelles
contain thousands of closely-stacked disk membranes, which have distinctly
different protein compositions in their lamellar and rim regions [1]: the
lamellae are host to the visual receptors, while peripherin and a similar
protein, Rom1, which span the membrane 4 times, are localised in the rims
[1]. Although the function of these proteins is unknown, they may play a
part in disk biogenesis, possibly anchoring the disk to the cytoskeleton
of the rod cell [1,2]. Deletion mutations cause serious visual disorders,
including autosomal dominant retinitis pigmentosa, autosomal dominant
punctata albescens and butterfly macular degeneration [1].
 
PERIPHERNRDS is a 6-element fingerprint that provides a signature for the
RDS/ROM1 peripherin family. The fingerprint was derived from an initial 
alignment of 4 sequences: motifs 1-3 and 6 span the 4 transmembrane (TM)
regions; and motifs 4 and 5 correspond to highly-conserved regions in
the hydrophilic loop between TM domains 3 and 4 - motif 5 includes the
region encoded by PROSITE pattern RDS_ROM1 (PS00930), which contains 3
of 7 totally conserved cysteines. Two iterations on OWL23.2 were
required to reach convergence, at which point a true set comprising 7
sequences was identified.
 
An update on SPTR37_9f identified a true set of 11 sequences, and 3
partial matches.
Summary Information
  11 codes involving  6 elements
1 codes involving 5 elements
2 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6111111111111
5110111
4200222
3000000
2000000
123456
True Positives
RDS_BOVIN     RDS_CANFA     RDS_CHICK     RDS_FELCA     
RDS_HUMAN RDS_MOUSE RDS_RAT RDS_XENLA
ROM1_BOVIN ROM1_HUMAN ROM1_MOUSE
True Positive Partials
Codes involving 5 elements
RDS2_CHICK
Codes involving 4 elements
RDS1_XENLA RDS2_XENLA
Sequence Titles
RDS_BOVIN   PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) - BOS TAURUS (BOVINE). 
RDS_CANFA PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) - CANIS FAMILIARIS (DOG).
RDS_CHICK PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) (PHOTORECEPTOR OUTER SEGMENT MEMBRANE GLYCOPROTEIN 1) (CRDS1) - GALLUS GALLUS (CHICKEN).
RDS_FELCA PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) - FELIS SILVESTRIS CATUS (CAT).
RDS_HUMAN PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) - HOMO SAPIENS (HUMAN).
RDS_MOUSE PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) - MUS MUSCULUS (MOUSE).
RDS_RAT PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) - RATTUS NORVEGICUS (RAT).
RDS_XENLA PERIPHERIN (RETINAL DEGENERATION SLOW PROTEIN) (XRDS38) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
ROM1_BOVIN ROD OUTER SEGMENT MEMBRANE PROTEIN 1 (ROSP1) - BOS TAURUS (BOVINE).
ROM1_HUMAN ROD OUTER SEGMENT MEMBRANE PROTEIN 1 (ROSP1) - HOMO SAPIENS (HUMAN).
ROM1_MOUSE ROD OUTER SEGMENT MEMBRANE PROTEIN 1 (ROSP1) - MUS MUSCULUS (MOUSE).

RDS2_CHICK PHOTORECEPTOR OUTER SEGMENT MEMBRANE GLYCOPROTEIN 2 (CRDS2) - GALLUS GALLUS (CHICKEN).

RDS1_XENLA RDS/PERIPHERIN-LIKE PROTEIN XRDS35 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
RDS2_XENLA RDS/PERIPHERIN-LIKE PROTEIN XRDS36 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Scan History
OWL23_2    2  100  NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 2 15 NSINGLE
Initial Motifs
Motif 1  width=23
Element Seqn Id St Int Rpt
GLWLMNWFSVLAGIIIFSLGLFL RDS_HUMAN 19 19 -
GLWLMNWLSVLAGIVLFSLGLFL RDS_RAT 19 19 -
GLWLMNWFSVLAGIIIFGLGLFL RDS_BOVIN 18 18 -
GLWLLSWLLALAGGVILLCSGHL ROM1_HUMAN 20 20 -
GIWLLSWLLALVGGLTLLCSGHL ROM1_MOUSE 20 20 -
GLWLMNWLSVLAGIVIFSLGLFL CATPERIPH 17 17 -
GLWLMNWLSVLAGIVLFSLGLFL RDS_MOUSE 19 19 -

Motif 2 width=20
Element Seqn Id St Int Rpt
VPNSLIGMGVLSCVFNSLAG RDS_HUMAN 60 18 -
VPNSLIGVGVLSCVFNSLAG RDS_BOVIN 59 18 -
VPNSLIGMGVLSCVFNSLAG CATPERIPH 58 18 -
LPQTALAAGTVALGTGLGGA ROM1_MOUSE 62 19 -
LPQAALAAGAVALGTGLVGV ROM1_HUMAN 62 19 -
VPNSLIGVGVLSCVFNSLAG RDS_MOUSE 60 18 -
VPNSLIGVGVLSCVFNSLAG RDS_RAT 60 18 -

Motif 3 width=21
Element Seqn Id St Int Rpt
LAVCVLFNVVLFLVALCCFLL RDS_BOVIN 101 22 -
LVVCVLFNIVLFLVALCCFLM CATPERIPH 100 22 -
LAVCIFFNVILFLVALCCFLL RDS_MOUSE 102 22 -
LAICVLFNIILFLVALCCFLL RDS_HUMAN 102 22 -
LAVCVFFNVILFLVALCCFLL RDS_RAT 102 22 -
LVAGTAGGGGLLVVALGLALA ROM1_HUMAN 104 22 -
LAVGTAAGGGLLTLALGLALA ROM1_MOUSE 104 22 -

Motif 4 width=29
Element Seqn Id St Int Rpt
ELQLRYHCCGRHGYKDWFGVQWVSSRYLD ROM1_HUMAN 161 36 -
LLQIEFKCCGNNGFRDWFEIQWISNRYLD CATPERIPH 156 35 -
ELQLRYHCCGRHGYKDWFGVQWVSNRYLD ROM1_MOUSE 161 36 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_MOUSE 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_HUMAN 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_RAT 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_BOVIN 157 35 -

Motif 5 width=27
Element Seqn Id St Int Rpt
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_HUMAN 198 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_MOUSE 198 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_RAT 198 11 -
SNVDGRYLVDGVPFSCCNPNSPRPCIQ RDS_BOVIN 197 11 -
SNVEGLYLTDGVPFSCCNPHSPRPCLQ ROM1_HUMAN 201 11 -
SNVEGLYLIDGVPFSCCNPHSPRPCLQ ROM1_MOUSE 201 11 -
SNVDGRYLVDGVPFSCCNPNSPRPCIQ CATPERIPH 196 11 -

Motif 6 width=22
Element Seqn Id St Int Rpt
MGVVTLLIWLFEVSITAGLRFL RDS_RAT 265 40 -
LGSILAVTLLLQILVLLGLRYL ROM1_MOUSE 268 40 -
MGVVTLLVWLFEVSITAGLRYL RDS_MOUSE 265 40 -
LGSMLAVTFLLQALVLLGLRYL ROM1_HUMAN 268 40 -
MGAVTLLVWLFEVSITIGLRYL CATPERIPH 263 40 -
TGAVTLLVWLFEVTITVGLRYL RDS_BOVIN 264 40 -
MGVVTLLIWLFEVTITIGLRYL RDS_HUMAN 265 40 -
Final Motifs
Motif 1  width=23
Element Seqn Id St Int Rpt
GLWLMNWLSVLAGIVIFSLGLFL RDS_FELCA 19 19 -
GLWLMNWLSVLAGIVLFSLGLFL RDS_MOUSE 19 19 -
GLWLMNWFSVLAGIIIFSLGLFL RDS_HUMAN 19 19 -
GLWLMNWLSVLAGIVLFSLGLFL RDS_RAT 19 19 -
GLWLMNWLSVLAGIVIFSLGLFL RDS_CANFA 19 19 -
GLWLMNWFSVLAGIIIFGLGLFL RDS_BOVIN 18 18 -
GLWLMNWFSVFAGIIVFSMGLFL RDS_CHICK 19 19 -
GLWLMNWCCVLAGIALFSMGVFL RDS_XENLA 19 19 -
GLWLLSWLLALAGGVILLCSGHL ROM1_HUMAN 20 20 -
GLWLLSWLLVLVGGLTLLCSGHL ROM1_BOVIN 20 20 -
GIWLLSWLLALVGGLTLLCSGHL ROM1_MOUSE 20 20 -

Motif 2 width=20
Element Seqn Id St Int Rpt
VPNSLIGMGVLSCVFNSLAG RDS_FELCA 60 18 -
VPNSLIGVGVLSCVFNSLAG RDS_MOUSE 60 18 -
VPNSLIGMGVLSCVFNSLAG RDS_HUMAN 60 18 -
VPNSLIGVGVLSCVFNSLAG RDS_RAT 60 18 -
VPNSLIVMGVLSCVFNSLAG RDS_CANFA 60 18 -
VPNSLIGVGVLSCVFNSLAG RDS_BOVIN 59 18 -
VPNSLILMGILSCAFNGFAG RDS_CHICK 60 18 -
VPNSLILMGSLACALNAFPG RDS_XENLA 60 18 -
LPQAALAAGAVALGTGLVGV ROM1_HUMAN 62 19 -
LPQVALAASAVALGTGLVGS ROM1_BOVIN 62 19 -
LPQTALAAGTVALGTGLGGA ROM1_MOUSE 62 19 -

Motif 3 width=21
Element Seqn Id St Int Rpt
LVVCVLFNIVLFLVALCCFLM RDS_FELCA 102 22 -
LAVCIFFNVILFLVALCCFLL RDS_MOUSE 102 22 -
LAICVLFNIILFLVALCCFLL RDS_HUMAN 102 22 -
LAVCVFFNVILFLVALCCFLL RDS_RAT 102 22 -
LAVCVLFNIALFLVTLCCFLM RDS_CANFA 102 22 -
LAVCVLFNVVLFLVALCCFLL RDS_BOVIN 101 22 -
LALCFFFNILLFFVALICFLM RDS_CHICK 102 22 -
LIICLIFNIFIFFTGVVCFLT RDS_XENLA 102 22 -
LVAGTAGGGGLLVVALGLALA ROM1_HUMAN 104 22 -
LVAGTAGGGGLLVLALGLALA ROM1_BOVIN 104 22 -
LAVGTAAGGGLLTLALGLALA ROM1_MOUSE 104 22 -

Motif 4 width=29
Element Seqn Id St Int Rpt
LLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_FELCA 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_MOUSE 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_HUMAN 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_RAT 158 35 -
MLQIEFRCCGNNGFRDWFEIQWISNRYLD RDS_CANFA 158 35 -
MLQIEFKCCGNNGFRDWFEIQWISNRYLD RDS_BOVIN 157 35 -
MLQIEFKCCGNNGFKDWFEIQWISNRYLD RDS_CHICK 158 35 -
LLQIEFKCCGNNGFRDWFELQWVSNRYLG RDS_XENLA 158 35 -
ELQLRYHCCGRHGYKDWFGVQWVSSRYLD ROM1_HUMAN 161 36 -
ELQLRHHCCGRHGYKDWFGIQWVSNRYLD ROM1_BOVIN 161 36 -
ELQLRYHCCGRHGYKDWFGVQWVSNRYLD ROM1_MOUSE 161 36 -

Motif 5 width=27
Element Seqn Id St Int Rpt
SNVDGRYLVDGVPFSCCNPNSPRPCIQ RDS_FELCA 198 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_MOUSE 198 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_HUMAN 198 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_RAT 198 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_CANFA 198 11 -
SNVDGRYLVDGVPFSCCNPNSPRPCIQ RDS_BOVIN 197 11 -
SNVDGRYLVDGVPFSCCNPSSPRPCIQ RDS_CHICK 198 11 -
SNVDGKYLIDGVPFSCCNPSSPRPCIQ RDS_XENLA 198 11 -
SNVEGLYLTDGVPFSCCNPHSPRPCLQ ROM1_HUMAN 201 11 -
SNVEGLYLIDGVPFSCCNPHSPRPCLQ ROM1_BOVIN 201 11 -
SNVEGLYLIDGVPFSCCNPHSPRPCLQ ROM1_MOUSE 201 11 -

Motif 6 width=22
Element Seqn Id St Int Rpt
MGAVTLLVWLFEVSITIGLRYL RDS_FELCA 265 40 -
MGVVTLLVWLFEVSITAGLRYL RDS_MOUSE 265 40 -
MGVVTLLIWLFEVTITIGLRYL RDS_HUMAN 265 40 -
MGVVTLLIWLFEVSITAGLRFL RDS_RAT 265 40 -
MGAVTLLVWLFEVTITIGLRYL RDS_CANFA 265 40 -
TGAVTLLVWLFEVTITVGLRYL RDS_BOVIN 264 40 -
MGAVVLLVWLFEMSVMVGLRLL RDS_CHICK 265 40 -
MGGMVFLVWIMEMAVMIGLRFL RDS_XENLA 265 40 -
LGSMLAVTFLLQALVLLGLRYL ROM1_HUMAN 268 40 -
LGNMLAVTFLLQTLVLLGLRYL ROM1_BOVIN 268 40 -
LGSILAVTLLLQILVLLGLRYL ROM1_MOUSE 268 40 -