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UniProt release 2015_12

Published December 9, 2015

Headline

Host proteins SERINC3 and SERINC5 decrease HIV-1 infectivity

It has long been known that the HIV-1 nef (“negative regulatory factor”) protein increases the infectivity of the HIV-1 virion (PMID:7981973). This mysterious protein is only found in primate lentiviruses. Its function is to manipulate the host’s cellular machinery and thus to allow infection, survival or replication of the virus. The abundant research performed on this topic has unraveled many phenotypes associated with nef, mainly in restricting host protein expression to cellular membrane. However, all these various functions have not allowed a clear understanding of the virion infectivity phenotype, although they have revealed the way HIV-1 avoids the host’s immune response.

Two recent papers in Nature have shown that nef actually prevents the incorporation of host SERINC3 and SERINC5 proteins into the HIV-1 virion. These proteins dramatically decrease virion infectivity when they are part of its membrane. This study improves the understanding of nef function in virion infectivity. The means used by nef to achieve this function are still unknown, but are related to its capacity to prevent specific host proteins from reaching the plasma membrane. Human SERINC3 and SERINC5 functions are still not well understood, but further study on these proteins will reveal their antiviral action.

As of this release, HIV-1 nef and human proteins SERINC3 and SERINC5 have been updated and are publicly available.

UniProtKB news

Displaying human UniProtKB sequence annotations in genome browser tracks

Genome browser tracks allow users to align sequence annotations to the reference genome data and genome annotations. Both UCSC and Ensembl genome browsers have custom tracks for displaying external annotations in their browsers. UniProt would like to announce the beta release of new genome tracks which allow the alignment of protein sequence annotations in our resource to a reference genome. These UniProt genome tracks include genomic locations of protein sequences and annotations such as active sites, metal binding sites, post-translational modifications, variants and domains with supporting literature evidence where available. Each species represented by the genome annotation tracks resource will have protein sequences and annotations defined by the BED and bigBed formats.
The beta release is available in the new dedicated ‘genome_annotation_tracks’ directory on the UniProt FTP site and provides tracks for human with the release of additional species in the future. UniProt would welcome your feedback on this new resource.

Cross-references to SwissLipids

Cross-references have been added to SwissLipids, a comprehensive reference database that links mass spectrometry-based lipid identifications to curated knowledge of lipid structures, metabolic reactions, enzymes and interacting proteins.

SwissLipids is available at http://www.swisslipids.org.

The format of the explicit links is:

Resource abbreviation SwissLipids
Resource identifier SwissLipids identifier

Cross-references to SwissLipids may be isoform-specific (e.g. Q08477). The general format of isoform-specific cross-references was described in release 2014_03.

Example: P52824

Show all entries having a cross-reference to SwissLipids.

Text format

Example: P52824

DR   SwissLipids; SLP:000000740; -.

XML format

Example: P52824

<dbReference type="SwissLipids" id="SLP:000000740"/>

RDF format

Example: P52824

uniprot:P52824
  rdfs:seeAlso <http://purl.uniprot.org/swisslipids/SLP:000000740> .
<http://purl.uniprot.org/swisslipids/SLP:000000740>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/SwissLipids> . 

Cross-references to MalaCards

Cross-references have been added to MalaCards, an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes.

The MalaCards disease and disorders database is organized into “disease cards”, each integrating prioritized information, and listing numerous known aliases for each disease, along with a variety of annotations, as well as inter-disease connections.

MalaCards is available at http://www.malacards.org.

The format of the explicit links is:

Resource abbreviation MalaCards
Resource identifier Gene symbol

Example: P26439

Show all entries having a cross-reference to MalaCards.

Text format

Example: P26439

DR   MalaCards; HSD3B2; -.

XML format

Example: P26439

<dbReference type="MalaCards" id="HSD3B2"/>

RDF format

Example: P26439

uniprot:P26439
  rdfs:seeAlso <http://purl.uniprot.org/malacards/HSD3B2> .
<http://purl.uniprot.org/malacards/HSD3B2> 
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/MalaCards> .

Change of UniProtKB annotation cardinality constraints

Each UniProtKB entry may contain a variable number of different annotation topics. Most topics can be present more than once in a given entry (e.g. when a precursor protein is cleaved into chains/peptides with different functions, each one is described in a separate Function annotation). But some topics had been limited to occur no more than once per entry. We have lifted this restriction to allow for more flexibility and granularity in our annotations.

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

Deleted diseases:

  • Fanconi anemia complementation group M
  • Paget disease of bone
  • Spinocerebellar ataxia, autosomal recessive, 5

Changes to the controlled vocabulary for PTMs

New term for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):

  • PolyADP-ribosyl aspartic acid

New terms for the feature key ‘Cross-link’ (‘CROSSLNK’ in the flat file):

  • 2-(S-cysteinyl)-methionine (Cys-Met)
  • Cyclopeptide (Cys-Ile)

UniProt service news

Retirement of UniProt BioMart

Based on user surveys and service evaluations, we decided to retire our UniProt BioMart service. For those who relied on the UniProt BioMart for tasks such as ID mapping, bulk retrieval of entries, or programmatic access to entry annotations, we have alternative services that will satisfy your needs. Please visit our YouTube channel and help pages for tutorials and more information about these services:

Please contact us if you have questions about this change.

Retirement of UniProt Distributed Annotation System (DAS)

The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It was first released in 2001 and UniProt had started to provide its data following the DAS protocol in July 2004. DAS has fulfilled a valuable role in integrating distributed and varied data, particularly for display in genome browsers and other applications that feature data visualisation, but unfortunately the level of usage of DAS in 2015 can no longer justify support and maintenance and we have therefore retired the UniProt DAS server.

Documentation on programmatic access to UniProt data can be found on the UniProt website.

Please contact us if you have questions about this change.