{ "bcoid": "GLY_000134", "title": "Mouse Refseq Protein Function", "description": "The Mouse RefSeq Protein Function contains biological function annotaion of mouse [taxid:10090] genes ...", "filename": "mouse_protein_function_refseq.csv", "filetype": "csv", "categories": { "species": "Mus Musculus", "molecule": "Protein", "tags": "Protein Function", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q61718-1...", "RefSeq..." ], [ "Q61718-1...", "RefSeq..." ] ], "headers": [ "uniprotkb_ca...", "database_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_name" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "annotation" } ], [ "Q61718-1", "RefSeq", "NP_996753.1", "21172865", "A distinct subset of plasmacytoid dendritic cells (pDC) is responsible for nearly all IFN-alpha production, while in bone marrow and spleen, cells that ultimately differentiate into pDC produce little or no IFN-alpha and instead promote immune tolerance." ], [ "Q61718-1", "RefSeq", "NP_996753.1", "16611902", "Results suggest that activation of the Ras/Raf/MEK pathway downregulates IFN-induced antiviral response" ], [ "Q8K5B8-1", "RefSeq", "NP_034593.1", "27977683", "We find a subtle impact of deleting the Hotair locus upon the expression of the neighboring Hoxc11 and Hoxc12 genes in cis. Our results do not support any substantial role for Hotair during mammalian development in vivo Publication Status: Online-Only" ], [ "Q8BVG4-1", "RefSeq", "NP_766212.2", "29693275", "The effect of CD26-deficiency on dipeptidyl peptidase 8 and 9 expression profiles in a mouse model of Crohn's disease." ], [ "Q8BVG4-1", "RefSeq", "NP_766212.2", "29709545", "Dipeptidyl peptidase 9 (DPP9) knock-in mice (DPP9(ki/ki) mice)express a catalytically inactive S729A mutant of DPP9 enzyme. DPP9(ki/ki) mice show reduced number of lymphoid and myeloid cells in fetal liver and postnatal blood but their hematopoietic cells are fully functional and able to reconstitute lymphoid and myeloid lineages even in competitive mixed chimeras." ], [ "Q8BVG4-1", "RefSeq", "NP_766212.2", "28887018", "Lack of DPP9 activity in mice leads to impaired tongue development, suckling defect and subsequent neonatal lethality." ], [ "Q8BVG4-1", "RefSeq", "NP_766212.2", "28256001", "Changes induced by DPP9 gene silencing in macrophages suggest possible role of DPP9 in regulation of proliferation and activation status, as well as in peptide processing within endosomal/vesicular compartment." ], [ "Q8BVG4-1", "RefSeq", "NP_766212.2", "23704821", "Suggest roles for DPP8 and DPP9 in lymphocyte activation and apoptosis and in hepatocytes during liver disease pathogenesis." ], [ "Q8BVG4-1", "RefSeq", "NP_766212.2", "19581630", "DP8 and DP9 tissue and cellular expression" ], [ "A0A0B4J1F4-1", "RefSeq", "NP_001036057.1", "19605364", "Txnip regulates cellular metabolism independent of its binding to thioredoxin and the arrestin domains are crucial structural elements in metabolic functions of alpha-arrestin proteins" ], [ "Q9JMG3-1", "RefSeq", "NP_071863.1", "24240191", "HOPS has distinct, isoform-specific functions in the nucleolus, nucleus, and cytoplasm." ], [ "Q9JMG3-1", "RefSeq", "NP_071863.1", "22890319", "HOPS acts as a functional bridge in the interaction between NPM and p19(Arf)" ], [ "Q9JMG3-1", "RefSeq", "NP_071863.1", "20582322", "Results implicate Tmub1 in the regulation of locomotor activity and wakefulness and suggest that Tmub1 binds to and functions together with CAMLG Publication Status: Online-Only" ], [ "Q9JMG3-1", "RefSeq", "NP_071863.1", "18665261", "Transmission; it contributes to maintain the synaptic surface number of the GluR2-containing AMPARs by facilitating the recycling of GluR2 to the plasma membrane Publication Status: Online-Only" ], [ "Q9JMG3-1", "RefSeq", "NP_071863.1", "18418082", "HOPS is involved in centrosome assembly and maintenance." ], [ "Q9DAX9-1", "RefSeq", "NP_080101.1", "18780968", "Amyloid beta precursor protein gene is associated with Alzheimer's disease" ], [ "Q8K4Z0-1", "RefSeq", "NP_659194.1", "19833108", "LGI2 distribution in the vertical limb of the diagonal band and in putative hippocampal interneurons suggests that the function of these genes might be related to the generation of hippocampal theta rhythm." ], [ "O88845-1", "RefSeq", "NP_064305.2", "17485678", "These studies suggest a role for AKAP10 in heart rhythm control." ], [ "O88845-1", "RefSeq", "NP_064305.2", "14531807", "D-AKAP2 may play an important role in the parathyroid hormone (PTH)-mediated regulation of NaPi-IIa by compartmentalization of PKA." ], [ "O88845-1", "RefSeq", "NP_064305.2", "12206784", "Deuterium exchange-mass spectrometry (DXMS) and limited proteolysis to probe the folded regions of D-AKAP2, providing for the first time insight into the intra-domain dynamics of a scaffold protein" ], [ "Q8BSN9-1", "RefSeq", "NP_001317352.1", "20869947", "These results introduce FASTKD3 as an essential component of mitochondrial respiration that may modulate energy balance in cells exposed to adverse conditions by functionally coupling mitochondrial protein synthesis to respiration." ], [ "Q9CQA3-1", "RefSeq", "NP_075863.2", "30159755", "The present study identified a potential role for the tumor microenvironment in influencing phenotypic features of SDHB-mutated Pheochromocytomas and paragangliomas." ], [ "Q08890-1", "RefSeq", "NP_034628.2", "29648648", "We also show that mucopolysaccharidosis type II patient fibroblasts harboring different mutations spanning the IDS gene exhibit perturbed FGF signaling-related markers expression. Our work opens a new venue to discover possible druggable novel key targets in mucopolysaccharidosis type II Erratum:[Hum Mol Genet. 2018 Jul 1;27(13):2407. PMID: 29917101]" ], [ "Q3UFT3-1", "RefSeq", "NP_001028617.2", "24003223", "Data indicate that a subtype of GAREM, GAREM2, is specifically expressed in the mouse, rat, and human brain." ], [ "P58269-1", "RefSeq", "NP_001254554.1", "18765789", "DPF3 adds a further layer of complexity to the BAF complex by representing a tissue-specific anchor between histone acetylations as well as methylations and chromatin remodeling." ], [ "Q8BFT9-1", "RefSeq", "NP_081081.1", "19013223", "These results indicate that msvop is a central nervous system-specific gene and could be utilized for elucidating gene regulation in neuronal cells." ], [ "P60710-1", "RefSeq", "NP_031419.1", "30012594", "Essential nucleotide- and protein-dependent functions of Actb/beta-actin." ], [ "Q571F8-1", "RefSeq", "NP_001028436.2", "29274472", "Data (including data from studies in knockout/transgenic mice) suggest Ppp2ca supports cortical neuronal growth and cognitive function via regulating p73/Gls2 signal transduction in neurons of hippocampus. Ppp2ca gene knock-out results in embryonic cortical atrophy with learning/memory deficits. (Ppp2ca = protein phosphatase 2a catalytic subunit alpha isoform; p73 = transformation related protein 73; Gls2 = glutaminase-2)" ], [ "Q571F8-1", "RefSeq", "NP_001028436.2", "27466601", "Gls2 expression is regulated by the dietary protein/carbohydrate ratio. This effect was not observed in Ppara-null mice." ], [ "Q571F8-1", "RefSeq", "NP_001028436.2", "22679499", "Study demonstrated expression of alternative transcripts of the mammalian Gls2 gene. Transcriptional mechanisms giving rise to GLS2 variants and isolation of novel GLS2 transcripts in human, rat and mouse are presented." ], [ "Q571F8-1", "RefSeq", "NP_001028436.2", "20351271", "Phosphate-activated glutaminase (GLS2) is a p53-inducible regulator of glutamine metabolism and reactive oxygen species" ], [ "O35089-1", "RefSeq", "NP_034050.1", "23522044", "Cornichon-2 and cornichon-3 dictate subunit-specific AMPA receptor trafficking and synaptic transmission." ], [ "O35089-1", "RefSeq", "NP_034050.1", "21343286", "Transmembrane AMPA receptor regulatory proteins and cornichon-2 allosterically regulate AMPA receptor antagonists and potentiators." ], [ "O35089-1", "RefSeq", "NP_034050.1", "21172611", "Cornichon homolog 2 (CNIH-2) associates with TARP gamma-8 in hippocampus postsynaptic densities; CNIH-2 protein levels are diminished in transmembrane AMPA receptor regulatory protein (TARP) gamma-8 knockout mice." ], [ "Q9DCD6-1", "RefSeq", "NP_062723.1", "28604719", "Cells that lacked GABARAPs and mice that lacked Gate-16 alone were defective in the IFN-gamma-induced clearance of vacuolar pathogens such as Toxoplasma. GABARAPs are uniquely required for antimicrobial host defense through cytosolic distribution of interferon-inducible GTPases." ], [ "Q9DCD6-1", "RefSeq", "NP_062723.1", "28497576", "GABAergic synapse is proposed as a focus of aging. (Review) Review article" ], [ "Q9DCD6-1", "RefSeq", "NP_062723.1", "28320742", "Development of LC3/GABARAP sensors containing a LIR and a hydrophobic domain to monitor autophagy." ], [ "Q9DCD6-1", "RefSeq", "NP_062723.1", "27124579", "Ablation of GABARAP inhibits tumor initiation and progression through enhancement of both antitumor immunity and cell death signaling. Publication Status: Online-Only" ], [ "Q8C9X1-1", "RefSeq", "NP_808292.1", "18829862", "Data suggest that sentan is the first molecular component of the ciliary tip to bridge the cell membrane and peripheral singlet microtubules, making the distal portion of the cilia narrow and stiff to allow for better airway clearance or ovum transport." ], [ "Q9D4J7-1", "RefSeq", "NP_081918.1", "28607179", "Active maintenance of a precise chromatin landscape is essential for sustaining proper leukemia cell identity and that loss of a single factor (PHF6) can cause focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition" ], [ "Q9D4J7-1", "RefSeq", "NP_081918.1", "25556700", "These results place miR-128 upstream of PHF6 in a pathway vital for cortical lamination as well as for the development of neuronal morphology and intrinsic excitability. Publication Status: Online-Only" ], [ "Q9D4J7-1", "RefSeq", "NP_081918.1", "23791194", "As part of a cell-intrinsic transcriptional pathway, PHF6 regulates neuronal migration in the brain." ], [ "Q9D4J7-1", "RefSeq", "NP_081918.1", "17698420", "Strongest Phf6 gene expression and nuclear localisation of Phf6 protein were observed in the developing central nervous system, the anterior pituitary gland, the primordia of facial structures and the limb buds." ], [ "A2ACT7-1", "RefSeq", "NP_034066.2", "26429145", "Results show that absence of Col IX induces early developmental, structural and biomechanical alterations in both vertebral body and intervertebral disc which eventually cause severe degenerative changes in the aging spine." ], [ "Q9WU01-1", "RefSeq", "NP_573498.1", "25505328", "Deletion of SLM2 modifies alternative splicing of its paralog Slm1 and stabilizes its mRNA in hippocampus." ], [ "Q9WU01-1", "RefSeq", "NP_573498.1", "15471878", "Expression of active BRK/Sik results in increased SLM-1 and SLM-2 phosphorylation which has functional relevance and leads to inhibition of their RNA-binding" ], [ "Q9WU01-1", "RefSeq", "NP_573498.1", "12397030", "SLIM1 localizes in an integrin-dependent manner to the nucleus and focal adhesions where it functions downstream of integrin activation to promote cell spreading and migration." ], [ "Q8VBX4-1", "RefSeq", "NP_659192.2", "30254197", "Data show that the development of langerhans cells (LC) from embryonic and bone marrow-derived progenitors and langerin(+ )conventional dendritic cells (DC) is regulated by the retinoic acid receptor alpha (RARalpha)-retinoic acid (RA) axis. Publication Status: Online-Only" ], [ "Q8VBX4-1", "RefSeq", "NP_659192.2", "29631057", "Binding analysis between purified long and short forms of langerin and a series of keratin sulfate disaccharide components shows that the binding critically requires the 6-sulfation of Gal and that the long form of langerin displays higher affinity than the short form." ], [ "Q8VBX4-1", "RefSeq", "NP_659192.2", "15191546", "Developmentally regulated expression of Langerin isoforms provides a mechanism by which Langerin involvement in antigen uptake and processing could be regulated." ], [ "Q8VBX4-1", "RefSeq", "NP_659192.2", "11978773", "Molecular cloning and expression of Langerin transcripts in dendritic cells Erratum:[Int Immunol. 2002 Jul;14(7):831. Clusen, Bjoern [corrected to Clausen, Bjorn E]]" ], [ "Q149C2-1", "RefSeq", "NP_082994.1", "21945076", "Homozygous Traf3ip1 mutants are not viable and have both neural developmental defects and polydactyly, phenotypes typical of mutants with ciliary assembly defects." ], [ "Q149C2-1", "RefSeq", "NP_082994.1", "19253336", "Data show that overexpression of IFT54/Traf3ip1 displaces IFT20 from the Golgi apparatus. IFT54s effect on IFT20 is a dominant negative phenotype caused by its overexpression." ], [ "Q6NZM9-1", "RefSeq", "NP_997108.1", "30134825", "These findings are the first to define activated HDAC4 as a crucial regulator for myocardial ischemia and reperfusion injury. Publication Status: Online-Only" ], [ "Q6NZM9-1", "RefSeq", "NP_997108.1", "29632070", "Results identify HDAC4 as an epigenetic regulator of neuronal morphology that controls dendritic arborization via the expression of VEGFD" ], [ "Q8K120-1", "RefSeq", "NP_076188.3", "29467254", "BDNF regulates the timing of neurodevelopment via a novel mechanism of extranuclear sequestration of NFATc4 in Golgi. This leads to accelerated derepression of an NFI temporal occupancy gene program in cerebellar granule cells that includes Bdnf itself, revealing an autoregulatory loop within the program driven by BDNF and NFATc4." ], [ "Q8K120-1", "RefSeq", "NP_076188.3", "27307045", "Ca(2+)/calcineurin (CaN)/nuclear factor of activated T-cells (NFAT) c4 axis is required for neuritin-induced Kv4.2 transcriptional expression and potentiation of IA densities in cerebellum granule neurons." ], [ "Q8K120-1", "RefSeq", "NP_076188.3", "12370307", "NFATc4 is not regulated by calcineurin and is not essential for hypertrophic growth" ], [ "Q8K120-1", "RefSeq", "NP_076188.3", "11997522", "Phosphorylation of NFATc4 by p38 mitogen-activated protein kinases." ], [ "P68033-1", "RefSeq", "NP_033738.1", "28847732", "This study provides novel insights into the complex genetic regulation of Actc1 expression in early adult skeletal muscles." ], [ "P98086-1", "RefSeq", "NP_031598.2", "30126455", "C1qa(-/-) mice did not show any differences in photoreceptor loss or inflammation at 7 days compared to wild-type Publication Status: Online-Only" ], [ "Q9R087-1", "RefSeq", "NP_035951.1", "28869591", "Adult female Gpc6-/- mice were compared with wild-type control mice of identical C57BL/6 background. Consistent with the phenotype of omodysplasia 1, Gpc6-/-mice had femurs and vertebrae that were shorter than those of wild-type mice. They also had increased femoral bone mineral content and increased cortical thickness." ], [ "Q9R087-1", "RefSeq", "NP_035951.1", "28696225", "GPC6 stimulates Hh signaling by binding to Hh and Ptc1 at the cilium and increasing the interaction of the receptor and ligand to promote the growth of developing long bones." ], [ "J3QNX5-1", "RefSeq", "NP_001193950.1", "26623514", "This study indicates that AMPAR function is very precisely controlled by the cell-type specific expression of the CKAMP family members 39, 52 and 59. Erratum:[Elife. 2018 Oct 11;7:. PMID: 30306889] Publication Status: Online-Only" ], [ "Q0VBL6-1", "RefSeq", "NP_058564.2", "29054108", "Phosphorylation of inhibitory PAS domain protein (IPAS) at Ser184 by MAPK-activated protein kinase 2 (MK2 or MAPKAPK2) enhances the proapoptotic function of IPAS." ], [ "Q0VBL6-1", "RefSeq", "NP_058564.2", "25847716", "Report suggests that BV-2 microglial cells express HIF-3a under inflammatory conditions and that its activation differed from that of HIF-1a" ], [ "Q0VBL6-1", "RefSeq", "NP_058564.2", "25626335", "MRNA of HIF-2alpha and Ets-1 were significantly increased by HIF-3alpha ablation. Both factors activate the VE-cadherin gene, the transcriptional repression of these factors by HIF-3alpha is important for silencing the irrelevant expression of the VE-cadherin gene." ], [ "Q0VBL6-1", "RefSeq", "NP_058564.2", "17125738", "These data suggest an involvement of the HIF system in metabolic derangements as for instance caused by diabetes." ], [ "Q0VBL6-1", "RefSeq", "NP_058564.2", "12119283", "Alternative splicing and expression of IPAS is induced by hypoxia." ], [ "Q0VBL6-1", "RefSeq", "NP_058564.2", "9840812", "Identity of third HIF alpha class member, HIF-3alpha. mRNA expression information by mouse MTN. Experimental proof of dimerization with ARNT/HIF-1beta." ], [ "Q61830-1", "RefSeq", "NP_032651.2", "29467756", "These results show that MR protects against a pathogenic inflammatory macrophage response induced by mannan and is associated with induction of ROS. Publication Status: Online-Only" ], [ "Q61830-1", "RefSeq", "NP_032651.2", "28317806", "Findings show that TLR6 and mannose receptor participate as macrophage receptors for Mycobacterium lepraemurium" ], [ "Q6P9Q4-1", "RefSeq", "NP_808367.2", "28708292", "FHOD1 is regulated by ROCK for cytoplasm actin assembly and spindle migration during mouse oocyte meiosis." ], [ "Q6P9Q4-1", "RefSeq", "NP_808367.2", "25125170", "Report FODH1 expression in cardiomyocytes." ], [ "Q6P9Q4-1", "RefSeq", "NP_808367.2", "24331927", "We report here that a major formin in mouse fibroblasts, FHOD1, is recruited to integrin clusters, resulting in actin assembly." ], [ "Q6P9Q4-1", "RefSeq", "NP_808367.2", "21605332", "Letter: G-protein coupled and ITAM receptor regulation of the formin FHOD1 through Rho kinase in platelets." ], [ "P20490-1", "RefSeq", "NP_038544.1", "26940508", "Analysis of the conformation and thermal stability of the high-affinity IgE Fc receptor beta chain polymorphic proteins has been presented." ], [ "P20490-1", "RefSeq", "NP_038544.1", "23443658", "Chemotaxis toward antigen is controlled in mast cells by a cross-talk among FcepsilonRI, tetraspanin CD9, transmembrane adaptor proteins NTAL and LAT, and cytoskeleton-regulatory proteins of the ERM family" ], [ "P20490-1", "RefSeq", "NP_038544.1", "22875843", "Findings indicate that SLP-76 is an essential signaling component for basophil activation downstream of both FcepsilonRI and the IL-3 receptor." ], [ "Q32M07-1", "RefSeq", "NP_001029046.2", "24740601", "In addition to AK1 and AK2, which we previously demonstrated are present in outer dense fibers and mitochondrial sheath of the mouse sperm tail, we show that another AK, AK8, is present in a third flagellar compartment, the axoneme." ], [ "Q32M07-1", "RefSeq", "NP_001029046.2", "21746835", "Congenital hydrocephalus and rhinosinusitis in Ak8 null mice" ], [ "Q8K3W0-2", "RefSeq", "NP_653124.1", "28436570", "Bre enhances osteoblastic differentiation by promoting the Mdm2-mediated degradation of p53." ], [ "Q8K3W0-2", "RefSeq", "NP_653124.1", "27001068", "Results demonstrate a role for BRE in both replicative senescence and DNA damage-induced premature senescence. This can be attributed to BRE being required for BRCA1-A complex-driven HR DNA repair Publication Status: Online-Only" ], [ "Q8K3W0-2", "RefSeq", "NP_653124.1", "24395041", "Depletion of BRE also increased tumor cell apoptosis, and decreased both local and metastatic tumor growth." ] ] }, "readme": "Name\n - Mouse Refseq Protein Function\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-03-16T15:38:06.344586\n\nModified on\n - 2019-09-12T17:33:58.575554\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse RefSeq Protein Function contains biological function annotaion of mouse [taxid:10090] genes from GeneRIF section in the NCBI RefSeq database The data is downloaded from NCBI RefSeq and is processed into a dataset by GlyGen. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen\n\nDescription Domain\n Keywords\n - protein function\n - NCBI RefSeq\n - geneRIF\n - PMID\n\n Pipeline Steps\n - Step-1: The script extract-from-gp.py extracts protein function information from NCBI RefSeq gpff format files and maps it to the UniProtKb canonical accessions for a final dataset output in a csv format\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/pipeline/extractor/extract-from-endpoint.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: mouse_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/mouse_protein_xref_refseq.csv\n Name: efseq_protein_all_10090.gpff\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/source/refseq_protein_all_10090.gpff\n Output Subdomain\n Name: mouse_protein_function_refseq.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/mouse_protein_function_refseq.csv\n Name: mouse_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/mouse_protein_function_refseq.stat.csv\n\nFields\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"8071\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"8071\"\n Name: \"database_name\"\n Description: \"The name of the source database\"\n Unique Values: \"1\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"20384\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"19986\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/mouse_protein_function_refseq.csv" }