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0  structures 83  species 0  interactions 606  sequences 4  architectures

Family: Otopetrin (PF03189)

Summary: Otopetrin

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This is the Wikipedia entry entitled "Otopetrin family". More...

Otopetrin family Edit Wikipedia article

Otopetrin
Identifiers
Symbol Otopetrin
Pfam PF03189
InterPro IPR004878

In molecular biology, the otopetrin family is a group of proteins that is restricted to the metazoa. The structure of otopetrin-1 shows it to have 12 transmembrane domains, with three conserved sub-domains (OD-1 to OD-III).[1] Otopetrins modulate calcium homeostasis and influx of calcium in response to extracellular ATP.[2]

The otopetrins are required for normal formation of otoconia/otoliths in the inner ear. Otoconia are minute biomineral particles embedded in a gelatinous membrane that overlies the sensory epithelium in the inner ear. Gravity and acceleration cause the octoconia to deflect the stereocilia of sensory hair cells. Otoconia are required for normal processing of information regarding spatial orientation and acceleration.[3][4][2]


[edit] References

  1. ^ Hughes I, Binkley J, Hurle B, Green ED, Sidow A, Ornitz DM (2008). "Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members". BMC Evol. Biol. 8: 41. doi:10.1186/1471-2148-8-41. PMC 2268672. PMID 18254951. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2268672. 
  2. ^ a b Hughes, I.; Saito, M.; Schlesinger, P. H.; Ornitz, D. M. (2007). "Otopetrin 1 activation by purinergic nucleotides regulates intracellular calcium". Proceedings of the National Academy of Sciences 104 (29): 12023–12028. doi:10.1073/pnas.0705182104. PMC 1924595. PMID 17606897. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1924595.  edit
  3. ^ s�Llner, C.; Schwarz, H.; Geisler, R.; Nicolson, T. (2004). "Mutated otopetrin 1 affects the genesis of otoliths and the localization of Starmaker in zebrafish". Development Genes and Evolution 214 (12): 582–590. doi:10.1007/s00427-004-0440-2. PMID 15480759.  edit
  4. ^ Hughes, I.; Blasiole, B.; Huss, D.; Warchol, M. E.; Rath, N. P.; Hurle, B.; Ignatova, E.; David Dickman, J. et al (2004). "Otopetrin 1 is required for otolith formation in the zebrafish Danio rerio". Developmental Biology 276 (2): 391–402. doi:10.1016/j.ydbio.2004.09.001. PMC 2522322. PMID 15581873. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2522322.  edit

[edit] Further reading

This article incorporates text from the public domain Pfam and InterPro IPR004878

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004878

The otopetrins are a group of proteins that are restricted to the metazoa. The structure of otopetrin-1 (SWISSPROT) shows it to have 12 transmembrane domains, with three conserved sub-domains (OD-1 to OD-III) [PUBMED:18254951]. Otopetrins modulate calcium homeostasis and influx of calcium in response to extracellular ATP.

The otopetrins are required for normal formation of otoconia/otoliths in the inner ear. Otoconia are minute biomineral particles embedded in a gelatinous membrane that overlies the sensory epithelium in the inner ear. Gravity and acceleration cause the octoconia to deflect the stereocilia of sensory hair cells. Otoconia are required for normal processing of information regarding spatial orientation and acceleration.

Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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  Seed
(12)
Full
(606)
Representative proteomes NCBI
(578)
Meta
(1)
RP15
(124)
RP35
(164)
RP55
(306)
RP75
(443)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(12)
Full
(606)
Representative proteomes NCBI
(578)
Meta
(1)
RP15
(124)
RP35
(164)
RP55
(306)
RP75
(443)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_2323 (release 6.5)
Previous IDs: DUF270;
Type: Family
Author: Mifsud W
Number in seed: 12
Number in full: 606
Average length of the domain: 212.80 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 64.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.9 22.9
Noise cut-off 22.7 22.4
Model length: 441
Family (HMM) version: 8
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Species distribution

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