UniProt release 2015_12
Published December 9, 2015
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.
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 identifier||SwissLipids identifier|
DR SwissLipids; SLP:000000740; -.
<dbReference type="SwissLipids" id="SLP:000000740"/>
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 identifier||Gene symbol|
DR MalaCards; HSD3B2; -.
<dbReference type="MalaCards" id="HSD3B2"/>
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
- Ablepharon-macrostomia syndrome
- Adams-Oliver syndrome 6
- Amyotrophic lateral sclerosis 5, juvenile
- Arthrogryposis, distal, 8
- Au-Kline syndrome
- Autism, X-linked 4
- Barber-Say syndrome
- Beukes familial hip dysplasia
- Cavitary optic disc anomalies
- Cerebro-oculo-facio-skeletal syndrome 3
- Combined oxidative phosphorylation deficiency 26
- Congenital anomalies of kidney and urinary tract 2
- Corneal dystrophy, Fuchs endothelial, 3
- Craniosynostosis 6
- Cutis laxa, autosomal dominant, 3
- Deafness, autosomal recessive, 66
- Distal spinal muscular atrophy, autosomal recessive, 2
- Dyskeratosis congenita, autosomal dominant, 6
- Dyskeratosis congenita, autosomal recessive, 7
- Epilepsy, hearing loss, and mental retardation syndrome
- Epithelial recurrent erosion dystrophy
- Glioma 9
- Heimler syndrome 1
- Heimler syndrome 2
- Herpes simplex encephalitis 7
- Immunodeficiency 41 with lymphoproliferation and autoimmunity
- Immunodeficiency 42
- Immunodeficiency, common variable, 12
- Infantile liver failure syndrome 2
- Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism
- Kosaki overgrowth syndrome
- Lateral meningocele syndrome
- MEND syndrome
- Mental retardation, X-linked 12
- Mental retardation, X-linked 102
- Mental retardation, autosomal dominant 40
- Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A9
- Neuropathy, hereditary motor and sensory, 6B
- Noonan syndrome 9
- Noonan syndrome 10
- Paget disease of bone 3
- Palmoplantar keratoderma and congenital alopecia 1
- Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
- Premature aging syndrome, Penttinen type
- Retinitis pigmentosa 73
- Retinitis pigmentosa 74
- Short-rib thoracic dysplasia 14 with polydactyly
- Short stature, microcephaly, and endocrine dysfunction
- Spastic paraplegia 9A, autosomal dominant
- Spastic paraplegia 9B, autosomal recessive
- Spondylocostal dysostosis 6, autosomal recessive
- Spondyloepiphyseal dysplasia, Stanescu type
- Spondyloocular syndrome
- Thyroid cancer, non-medullary, 4
- Thyroid cancer, non-medullary, 5
- Thyroid cancer, non-medullary, 2
- Amyotrophic lateral sclerosis 6 -> Amyotrophic lateral sclerosis 6, with or without frontotemporal dementia
- Charcot-Marie-Tooth disease 6 -> Neuropathy, hereditary motor and sensory, 6A
- Complete pure gonadal dysgenesis 46,XY type -> 46,XY sex reversal 7
- Congenital anomalies of the kidney and urinary tract -> Congenital anomalies of the kidney and urinary tract 1
- Congenital disorder of glycosylation 1V -> Congenital disorder of deglycosylation
- Distal spinal muscular atrophy, congenital non-progressive -> Neuronopathy, distal hereditary motor, 8
- Fanconi anemia -> Fanconi anemia, complementation group A
- Hereditary motor and sensory neuropathy, proximal type -> Neuropathy, hereditary motor and sensory, Okinawa type
- Hereditary motor and sensory neuropathy, Russe type -> Neuropathy, hereditary motor and sensory, Russe type
- HMG-CoA synthase deficiency -> 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency
- Ichthyosis, exfoliative, autosomal recessive, ichthyosis bullosa of Siemens-like -> Peeling skin syndrome 4
- Infantile liver failure syndrome 2 -> Interstitial lung and liver disease
- Juvenile Paget disease -> Paget disease of bone 5, juvenile-onset
- Keratoderma, palmoplantar, non-epidermolytic, focal -> Keratoderma, palmoplantar, non-epidermolytic, focal 1
- Macular dystrophy, corneal, 1 -> Macular dystrophy, corneal
- Myopathy, myosin storage -> Myopathy, myosin storage, autosomal dominant
- Paget disease of bone 2 -> Paget disease of bone 2, early-onset
- Primary avascular necrosis of femoral head -> Avascular necrosis of the femoral head, primary
- Progressive external ophthalmoplegia with mitochondrial DNA deletions autosomal recessive -> Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive, 1
- Rienhoff syndrome -> Loeys-Dietz syndrome 5
- Thyroid papillary carcinoma -> Thyroid cancer, non-medullary, 1
- Tooth agenesis selective 6 -> Dental anomalies and short stature
- 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.