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Ortholog conservation Domain conservation Secondary structure 3D structure More Home

Analysis of p.(Leu154Trp) variant, USH3A gene, clarin 1 protein (232 residues)

• Ortholog conservation:

  
  
  

  Number of sequences	AAPI*	AAPIR**	Number of divergencies	Number of mutant	Number of gaps	Conservation of L154	Conservation - gap
  30	75.50%	80.69%	1 details	0 details	0 details	29 / 30 (96.67%)	29 / 30 (96.67%)

  
  
  

  Divergencies:

  Danio rerio - C

  The mutant residue cannot be found in the alignment.

  There is no gap in the alignment.

  *AAPI: Alignment Average Percentage Identity
  **AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 154). AAPIR appears in green if it is more than 10% compared to AAPI, in red if less than 10%.

  You can check the AAPIRs compared with AAPI of the whole alignment by clicking here. The help page will tell you more.

  Display alignment

  Click on the alignment to zoom in and out.

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  154

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  Homo sapiens

  T

  L

  H

  G

  P

  L

  G

  L

  Y

  L

  L

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  G

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  V

  Y

  K

  Pan troglodytes

  T

  L

  H

  G

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  L

  G

  L

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  L

  L

  S

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  E

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  I

  A

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  K

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  G

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  Y

  K

  Pongo pygmaeus

  T

  L

  H

  G

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  L

  G

  L

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  L

  L

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  F

  I

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  Gorilla gorilla

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  L

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  Macaca mulatta

  T

  L

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  L

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  L

  L

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  A

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  Otolemur garnettii

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  G

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  L

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  L

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  Y

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  Microcebus murinus

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  L

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  G

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  L

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  -

  Y

  L

  L

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  Rattus norvegicus

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  Mus musculus

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  Canis familiaris

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  Felis catus

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  Equus caballus

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  Pteropus vampyrus

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  Cavia porcellus

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  Bos taurus

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  Erinaceus europaeus

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  Tursiops truncatus

  T

  L

  H

  G

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  L

  G

  L

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  L

  L

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  E

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  Vicugna pacos

  T

  L

  H

  G

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  L

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  L

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  L

  L

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  Oryctolagus cuniculus

  T

  L

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  G

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  L

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  L

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  L

  L

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  F

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  Dipodomys ordii

  T

  L

  H

  G

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  L

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  L

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  Monodelphis domestica

  T

  L

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  Ornithorhynchus anatinus

  T

  L

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  Anolis carolinensis

  T

  L

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  Gallus gallus

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  K

  I

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  N

  F

  K

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  K

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  F

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  Taeniopygia guttata

  T

  L

  H

  G

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  L

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  L

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  I

  A

  N

  F

  K

  E

  G

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  F

  T

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  Xenopus tropicalis

  T

  L

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  G

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  L

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  L

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  C

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  Danio rerio

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  F

  G

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  N

  F

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  E

  H

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  N

  Y

  S

  E

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  L

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  Gasterosteus aculeatus

  T

  L

  Q

  G

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  L

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  L

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  L

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  I

  A

  N

  F

  N

  E

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  Q

  Takifugu rubripes

  M

  L

  Q

  G

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  D

  R

  I

  A

  N

  F

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  E

  V

  N

  F

  T

  F

  E

  Tetraodon nigroviridis

  T

  L

  Q

  G

  P

  V

  G

  L

  Y

  L

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  T

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  L

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  H

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  D

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  N

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  E

  L

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  F

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  F

  Q

  
  

  Species color legend (basic classification):

  Great apes | Other monkeys | Prosimians | Other mammals | Lizards | Birds | Amphibians | Fishes | Insects | Nematods | Tunicates | Echinoderms

  Show Venn diagram of alignment

  Display WebLogo for the region

  Click on the top-left corner to enlarge.

  

  Display alignment phylogenetic tree

  Click on the top-left corner to enlarge.

  
  

  Download tree in Newick format (right-click on the link, and choose 'Save target as').

  Display region alignment (21 residues, Fasta format)

  Display methods

  Ortholog sequences have been selected from the Ensembl⁽¹⁾ and NCBI websites. Alignment has been performed with ClustalW⁽²⁾, version 1.83 or 2.0.7. Trees have been built using Phylogeny.fr ⁽³⁾, based on the alignments. Software used is PhyML 3.0 aLRT with default parameters. Pictures of trees have been made using Phylip at Mobyle. AAPI and AAPIR have been calculated thanks to Bioperl. WebLogos are drawn with WebLogo 3⁽¹⁴⁾

  Accession numbers

• Domain conservation:

  The residue belongs to the domain Transmembrane 3.

  135

  155

  	Transmembrane domain, localized inside the plasmic membrane for Usher proteins, are often alpha helices.

  
  
  
  
  

  There are no alignments available concerning the domain Transmembrane of the protein clarin 1 or the residue is not present in the alignment.

• Secondary structure analysis:

  Residu L154 is predicted to belong to an α helice. Probability is 0.989.

  Direct environment is as follow:

  L	V	M	I	L154	F	A	S	E

  
  
  

  Observed frequencies in α helices:
  L: 1.16
  W: 0.98

  Mutant residu is less observed in this type of structure.

  Display methods

  Predictions of secondary structures have been made with PsiPred⁽⁹⁾ , version 2.5, using Protein Multiple Sequences Alignments as input, in order to increase the accuracy of the prediction. Amino acid frequencies have been calculated from a non redondant set defined by the RCSB. Details are provided here.

• 3D analysis:

  No 3D model available at this position.

  Check 3D coverage of clarin 1

• Additional ressources:

  
  
  
  • UNIPROT annotations
    

    The variation is not reported in Uniprot.

  • Click on the LOVD picture to check if a variant is described at position 154    
    
    
    
    
  • Graphical display of the region at NCBI (including SNPs)

See accession numbers of sequences used or references.

Execution time: 1 wallclock secs ( 0.01 usr 0.00 sys + 0.74 cusr 0.29 csys = 1.04 CPU)