Printable version Screen version +/- font size on/off fixed menus Accessions & refs Help Slide Show

Ortholog conservation Domain conservation Secondary structure 3D structure More Home

Analysis of p.(Leu1572Phe) variant, USH2A gene, usherin protein (5202 residues)

• Ortholog conservation:

  
  
  

  Number of sequences	AAPI*	AAPIR**	Number of divergencies	Number of mutant	Number of gaps	Conservation of L1572	Conservation - gap
  17	55.91%	71.68%	6 details	0 details	0 details	11 / 17 (64.71%)	11 / 17 (64.71%)

  
  
  

  Divergencies:

  Bos taurus - I	Gasterosteus aculeatus - I	Takifugu rubripes - I	Strongylocentrotus purpurat - V	Ciona intestinalis - I
  Ciona savignyi - I

  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 1572). 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.

  |

  |

  |

  1572

  |

  |

  Homo sapiens

  -

  -

  -

  G

  L

  I

  V

  F

  A

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  K

  G

  R

  L

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  P

  V

  E

  V

  T

  T

  T

  Pan troglodytes

  -

  -

  -

  G

  L

  I

  V

  F

  A

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  K

  G

  R

  L

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  P

  V

  E

  V

  T

  T

  T

  Equus caballus

  -

  -

  -

  G

  L

  I

  V

  F

  A

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  N

  G

  H

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  S

  V

  E

  V

  T

  T

  T

  Bos taurus

  -

  -

  -

  G

  L

  I

  V

  F

  A

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  I

  Q

  L

  K

  N

  G

  R

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  A

  V

  E

  V

  T

  T

  T

  Canis familiaris

  -

  -

  -

  G

  L

  I

  V

  F

  A

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  N

  G

  R

  P

  C

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  S

  M

  E

  V

  T

  T

  T

  Cavia porcellus

  -

  -

  -

  G

  L

  I

  L

  F

  A

  A

  S

  P

  G

  D

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  E

  G

  R

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  P

  V

  V

  V

  T

  T

  T

  Rattus norvegicus

  -

  -

  -

  G

  L

  I

  L

  L

  A

  L

  H

  P

  D

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  S

  G

  R

  P

  Y

  F

  L

  Y

  N

  P

  Q

  -

  -

  G

  S

  L

  V

  E

  V

  T

  T

  A

  Mus musculus

  -

  -

  -

  G

  L

  I

  L

  L

  A

  L

  S

  P

  G

  D

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  T

  L

  Q

  L

  K

  N

  G

  R

  P

  Y

  F

  L

  Y

  N

  S

  Q

  -

  -

  G

  T

  L

  V

  E

  V

  T

  P

  T

  Monodelphis domestica

  -

  -

  -

  G

  L

  I

  M

  L

  A

  V

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  F

  A

  L

  Q

  L

  K

  S

  G

  R

  P

  Y

  F

  L

  Y

  D

  P

  Q

  -

  -

  G

  S

  A

  V

  V

  V

  T

  T

  T

  Taeniopygia guttata

  -

  -

  -

  G

  L

  I

  F

  F

  S

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  I

  A

  L

  Q

  L

  K

  S

  G

  R

  P

  Y

  F

  L

  F

  D

  P

  Q

  K

  K

  G

  S

  A

  V

  A

  V

  T

  P

  T

  Gallus gallus

  -

  -

  -

  G

  L

  I

  F

  F

  S

  A

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  Y

  I

  A

  L

  Q

  L

  R

  S

  G

  R

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  A

  V

  A

  V

  T

  P

  T

  Danio rerio

  -

  -

  -

  G

  L

  L

  L

  F

  A

  V

  S

  P

  G

  E

  -

  -

  -

  -

  Q

  E

  E

  Y

  V

  A

  L

  Q

  I

  H

  N

  G

  R

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  A

  S

  A

  V

  A

  L

  S

  P

  R

  Gasterosteus aculeatus

  -

  -

  -

  G

  L

  L

  L

  C

  A

  F

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  F

  L

  A

  I

  Q

  L

  K

  N

  G

  Q

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  A

  V

  A

  V

  R

  A

  Q

  Takifugu rubripes

  -

  -

  -

  G

  L

  L

  L

  A

  A

  F

  S

  P

  G

  N

  -

  -

  -

  -

  Q

  E

  E

  F

  V

  A

  I

  Q

  I

  K

  D

  G

  R

  P

  Y

  F

  L

  F

  D

  P

  Q

  -

  -

  G

  S

  A

  V

  V

  V

  T

  V

  Q

  Strongylocentrotus purpurat

  P

  A

  S

  A

  L

  L

  M

  F

  A

  A

  S

  D

  G

  E

  -

  -

  -

  -

  Q

  E

  E

  M

  I

  V

  V

  Q

  L

  R

  E

  G

  R

  P

  W

  F

  I

  F

  D

  P

  Q

  -

  -

  -

  G

  G

  V

  A

  G

  A

  T

  P

  Ciona intestinalis

  -

  -

  -

  C

  L

  L

  F

  L

  A

  A

  S

  P

  L

  S

  S

  G

  G

  L

  R

  Q

  E

  Y

  L

  V

  I

  Q

  L

  K

  D

  G

  R

  P

  W

  F

  L

  F

  D

  A

  Q

  -

  -

  N

  N

  P

  T

  S

  V

  T

  T

  N

  Ciona savignyi

  -

  -

  -

  C

  L

  L

  F

  L

  A

  A

  S

  P

  L

  S

  S

  G

  G

  I

  R

  Q

  E

  Y

  L

  V

  I

  H

  L

  K

  D

  G

  R

  P

  W

  F

  L

  F

  D

  A

  Q

  -

  -

  N

  N

  P

  T

  S

  V

  T

  P

  T

  
  

  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 Laminin G-like 1.

  1517

  1709

  	~ 180 residue module, reported to interact with various ligands in various proteins. Its role in usherin is unknown.

  
  
  
  
  

  Laminin G-like 1 of usherin domain alignment including p.L1572 residue.

  
  
  

  Number of sequences	AAPID*** (from aa 1517 to aa 1709)	AAPIR!	Number of divergencies	Number of mutant	Number of gaps	Conservation of L1572	Conservation - gap
  337	20.28%	24.21%	137 details	3	2	198 / 337 (58.75%)	198 / 335 (59.10%)

  
  
  

  Divergencies

  Residues present in more than 10% of the sequences are highlighted in blue.

  A - 0.59%

  C - 0.89%

  F - 0.89%

  I - 14.54%

  M - 1.48%

  T - 0.30%

  V - 21.66%

  Y - 0.30%

  If we just consider Laminin G-like domain of usherin, we can add that:
  
  on 2 sequences, conservation is 1/2 (50.00%),
  or 1/2 (50.00%) if you do not take the gaps into account.

  ***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated).
  ^!AAPIR is here compared with AAPID.

  Show Venn diagram of alignment

  Display WebLogo for the region

  Click on the top-left corner to enlarge.

  

  Display complete alignment (Clustal format)

  Display region alignment (21 residues, Fasta format)

  Display methods

  Alignments have all been extracted from Prosite⁽⁴⁾, except alignment of vlgr1 calx-beta domains which comes from Pfam⁽⁵⁾. Pictures of proteins have been performed using MyDomains - Image Creator. WebLogos are drawn with WebLogo 3⁽¹⁴⁾

• Secondary structure analysis:

  Residu L1572 is predicted to belong to a β strand. Probability is 0.965.

  Direct environment is as follow:

  E	Y	F	A	L1572	Q	L	K	K

  
  
  

  Observed frequencies in β strands:
  L: 1.1
  F: 1.35

  Mutant residu is more 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 usherin

• 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 1572    
    
    
    
    
  • Graphical display of the region at NCBI (including SNPs)

See accession numbers of sequences used or references.

Execution time: 2 wallclock secs ( 0.12 usr 0.01 sys + 1.40 cusr 0.59 csys = 2.12 CPU)