PaperBLAST

Full List of Papers Linked to NP_061349.3

NP_061349 neutral amino acid transporter A from Mus musculus
O35874 Neutral amino acid transporter A from Mus musculus

• Protein Expression of Amino Acid Transporters Is Altered in Isolated Cerebral Microvessels of 5xFAD Mouse Model of Alzheimer's Disease.
  Puris, Molecular neurobiology 2023
  • GeneRIF: Protein Expression of Amino Acid Transporters Is Altered in Isolated Cerebral Microvessels of 5xFAD Mouse Model of Alzheimer's Disease.
• Air pollution exposure increases ABCB1 and ASCT1 transporter levels in mouse cortex.
  Puris, Environmental toxicology and pharmacology 2022 (PubMed)
  • GeneRIF: Air pollution exposure increases ABCB1 and ASCT1 transporter levels in mouse cortex.
• Inhibitors of the Neutral Amino Acid Transporters ASCT1 and ASCT2 Are Effective in In Vivo Models of Schizophrenia and Visual Dysfunction.
  Li, The Journal of pharmacology and experimental therapeutics 2018 (PubMed)
  • GeneRIF: The ability of L-4FPG to penetrate the brain makes this compound a useful tool to further evaluate the function of ASCT1 and ASCT2 transporters in the CNS.
• ASCT1 (Slc1a4) transporter is a physiologic regulator of brain d-serine and neurodevelopment.
  Kaplan, Proceedings of the National Academy of Sciences of the United States of America 2018
  • GeneRIF: ASCT1, rather than ASCT2, is a component of the brain serine shuttle. ASCT1-KO mice display motor and neurodevelopmental deficits reminiscent of ASCT1 missense mutations in humans.
• Expression of L-serine biosynthetic enzyme 3-phosphoglycerate dehydrogenase (Phgdh) and neutral amino acid transporter ASCT1 following an excitotoxic lesion in the mouse hippocampus.
  Jeon, Neurochemical research 2009 (PubMed)
  • GeneRIF: Results demonstrate injury-induced changes in Phgdh and ASCT1 expression.
• Segmental and complementary expression of L-serine biosynthetic enzyme 3-phosphoglycerate dehydrogenase and neutral amino acid transporter ASCT1 in the mouse kidney.
  Takasaki, Biomedical research (Tokyo, Japan) 2007 (PubMed)
  • GeneRIF: either Phgdh or ASCT1 is provided to each segment of renal tubules, suggesting that metabolic interplay mediated by L-serine biosynthesis and supply may exist in the kidney
• Neutral amino acid transporter ASCT1 is preferentially expressed in L-Ser-synthetic/storing glial cells in the mouse brain with transient expression in developing capillaries.
  Sakai, The Journal of neuroscience : the official journal of the Society for Neuroscience 2003
  • GeneRIF: ASCT1 expression was gradually downregulated in neuronal populations during late embryonic and neonatal periods, whereas its high expression was transmitted to radial glial cells and then to astrocytes; ASCT1 appears regulated to meet metabolic demands
• N-linked glycosylation and sequence changes in a critical negative control region of the ASCT1 and ASCT2 neutral amino acid transporters determine their retroviral receptor functions.
  Marin, Journal of virology 2003
  • GeneRIF: results strongly suggest that combinations of amino acid sequence changes and N-linked oligosaccharides in a critical carboxyl-terminal region of extracellular loop 2 (ECL2) control retroviral utilization of both the ASCT1 and ASCT2 receptors
• The envelope glycoprotein of human endogenous retrovirus type W uses a divergent family of amino acid transporters/cell surface receptors.
  Lavillette, Journal of virology 2002
  • GeneRIF: used as receptor by HERV-W Env glycoprotein when their sites for N-glycosylation are eliminated by mutagenesis
• Proteomic Analysis of Protective Effects of Dl-3-n-Butylphthalide against mpp + -Induced Toxicity via downregulating P53 pathway in N2A Cells
  Zhao, Proteome science 2023
  • “...mobility group protein B3 6.00E-05 O54724 Cavin1 Caveolae-associated protein 1 0.007188 O35887 Calu Calumenin 0.000147 O35874 Slc1a4 Neutral amino acid transporter A 0.029691 O35690 Phox2b Paired mesoderm homeobox protein 2B 0.000918 O35639 Anxa3 Annexin A3 5.15E-05 O35601 Fyb1 FYN-binding protein 1 0.000189 O35075 Dscr3 Down syndrome...”
• Protein expression alteration in hippocampus upon genetic repression of AMPKα isoforms.
  Yang, Hippocampus 2021
  • “...in hippocampus of AMPK1 cKO mice. Description Accession Fold change Neutral amino acid transporter A O35874 3.333 Kininogen-1 O08677 3 NEDD8-activating enzyme E1 regulatory subunit Q8VBW6 3 Protein kinase C and casein kinase substrate in neurons protein 2 + Q9WVE8 2.5 Polyadenylate-binding protein 1 P29341 2.333...”
• Proteomic and transcriptomic study of brain microvessels in neonatal and adult mice.
  Porte, PloS one 2017
  • “...- - - Q9JHL1 Slc9a3r2 5.220.82 10.591.22 24.531.31 4.43 - 22.90 - 4 - Transport O35874 Slc1a4 7.550.55 4.171.14 1.480.28 1.09 17.60 - - - - P31648 Slc6a1 6.630.42 3.210.21 2.930.33 6.75 - - - 4 - Q9Z2Z6 Slc25a20 0.260.06 0.660.08 0.410.03 - 6.04 1.85 -...”
• Label-Free Neuroproteomics of the Hippocampal-Accumbal Circuit Reveals Deficits in Neurotransmitter and Neuropeptide Signaling in Mice Lacking Ethanol-Sensitive Adenosine Transporter.
  Oliveros, Journal of proteome research 2017
  • “...4 Q05BD6 GRM8 Glu-R, metabotropic 8 GluR and CREB signaling, Syn-LTP 2.36 1.1 10 4 O35874 SLC1A4 solute carrier family 1 member 4 GluR signaling, Syn-LTP 2.12 1.6 10 2 Q68ED2 GRM7 Glu-R, metabotropic 7 GluR and CREB signaling, Syn-LTP 1.63 4.7 10 4 Q543V3 IRS1...”
• Proteomics analysis of amyloid and nonamyloid prion disease phenotypes reveals both common and divergent mechanisms of neuropathogenesis.
  Moore, Journal of proteome research 2014
  • “...APOD Apolipoprotein D 56.2 55 --- --- Q91 72 HPX Hemopexin 23.1 2 --- --- O35874 SLC1A4 Neutral amino acid transporter A 9.2 3 --- --- P08226 APOE Apolipoprotein E 7.6 5 --- --- P61148 FGF1 Heparin-binding growth factor 1 7.4 47 --- --- Q00493 CPE...”
• Structural features of the glutamate transporter family
  Slotboom, Microbiology and molecular biology reviews : MMBR 1999
  • “...407 400 412 425 O19105 O15758 P51912 P43007 O35874 AF003006 P51906 P51907 O95135 P31597 P43005 P43003 P46411 P24942 737473 AF018256 O35544 O35921 P48664 O00341...”

New Search

Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.