PaperBLAST

Full List of Papers Linked to Q14157

UBP2L_HUMAN / Q14157 Ubiquitin-associated protein 2-like; Protein NICE-4; RNA polymerase II degradation factor UBAP2L from Homo sapiens (Human) (see 6 papers)

• function: Recruits the ubiquitination machinery to RNA polymerase II for polyubiquitination, removal and degradation, when the transcription-coupled nucleotide excision repair (TC-NER) machinery fails to resolve DNA damage (PubMed:35633597). Plays an important role in the activity of long-term repopulating hematopoietic stem cells (LT- HSCs) (By similarity). Is a regulator of stress granule assembly, required for their efficient formation (PubMed:29395067, PubMed:35977029). Required for proper brain development and neocortex lamination (By similarity).
  subunit: Interacts with BMI1 (PubMed:25185265). Part of a complex consisting of UBAP2L, BMI1 and RNF2 (PubMed:25185265). Interacts with G3BP1 (via NTF2 domain); promoting stress granule formation (PubMed:32302570).
• A systematic review and meta-analysis of proteomic and metabolomic alterations in anaphylaxis reactions
  Gallizzi, Frontiers in immunology 2024
  • “...A0AVT1 UBA6 UBA6 Ubiquitin-like modifier-activating enzyme 6 NA Q5T6F2 UBAP2 UBAP2 Ubiquitin-associated protein 2 NA Q14157 UBP2L UBAP2L Ubiquitin-associated protein 2-like NA Q9C0C9 UBE2O UBE2O (E3-independent) E2 ubiquitin-conjugating enzyme NA Q5T4S7 UBR4 UBR4 E3 ubiquitin-protein ligase UBR4 NA Q9Y5K5 UCHL5 UCHL5 Ubiquitin carboxyl-terminal hydrolase isozyme L5...”
• Coarse-Grained Simulation Study of the Association of Selected Dipeptides.
  Leśniewski, The journal of physical chemistry. B 2024
  • “...dipeptides extracted from the sequences of proteins that are known to phase-separate, namely, UBAP2L (Uniprot: Q14157), WTAP (Uniprot: Q15007), DDX4 (Uniprot: Q9NQI0), and elastin (Uniprot: P15502). The dipeptides studied are also the building blocks of larger peptides, which are now under investigation in our laboratory. The...”
• Blocking SLC7A11 attenuates the proliferation of esophageal squamous cell carcinoma cells.
  Li, Animal cells and systems 2024
  • “...Q13247 Serine/arginine-rich splicing factor 6 (SRSF6) 39586.34 11.42 1 1 0.0262 1 1 0.0262 37 Q14157 Ubiquitin-associated protein 2-like (UBAP2L) 114533.12 6.61 10 9 0.1058 5 5 0.0589 38 Q14694 Ubiquitin carboxyl-terminal hydrolase 10 (USP10) 87132.74 5.19 3 3 0.0426 1 1 0.0113 39 Q15058 Kinesin-like...”
• SRCAP is involved in porcine reproductive and respiratory syndrome virus activated Notch signaling pathway.
  Ding, Journal of virology 2024
  • “...0.5 343.55 20.81 0.007 Snf2-related CREBBP activator protein which transcriptionally regulate genes by chromatin remodeling Q14157 UBAP2L 20 28.9 114.53 19.59 0.028 Ubiquitin-associated protein 2-like P35580 MYH10 72 45.3 229.00 13.67 0.012 Myosin, heavy chain 10, non-muscle P61224 RAP1B 9 44 20.83 12.76 0.044 RAP1B, member...”
• Epstein-Barr Virus BGLF2 commandeers RISC to interfere with cellular miRNA function.
  Campbell, PLoS pathogens 2022
  • “...95|51 10.1 0.02521 SG [ 47 , 49 ] Q8N6T3 ARFGAP1 0 74|86 6.4 0.19704 Q14157 UBAP2L 0 71|81 10.4 0.06992 SG [ 47 , 49 ] O60573 EIF4E2 0 71|59 8.6 0.26531 SG and PB [ 47 ] Q14674 ESPL1 0 60|44 1 0.02453 Q9Y697...”
• Understanding the activating mechanism of the immune system against COVID-19 by Traditional Indian Medicine: Network pharmacology approach.
  Thirumal, Advances in protein chemistry and structural biology 2022
  • “...NA Q5T6F2 TYSND1 TYSND1 ENSG00000156521 28531 219743 611017 Q2T9J0 UBAP2L UBAP2L ENSG00000143569 29877 9898 616472 Q14157 UPF1 UPF1 ENSG00000005007 9962 5976 601430 Q92900 ITGB1 ITGB1 ENSG00000150093 6153 3688 135630 P05556 PUSL1 PUSL1 ENSG00000169972 26914 126789 NA Q8N0Z8 PVR PVR ENSG00000073008 9705 5817 173850 P15151 RAB2A RAB2A...”
• Protein and Signaling Pathway Responses to rhIL-6 Intervention Before Lobaplatin Treatment in Osteosarcoma Cells
  Wang, Frontiers in oncology 2021
  • “...fosB FOSB P01100 Proto-oncogene c-Fos FOS Fragile X mental retardation syndrome-related protein 1 (two connected) Q14157 Ubiquitin-associated protein 2-like UBAP2L P51114 Fragile X mental retardation syndroame-related protein 1 FXR1 STRING Ras GTPase-activating protein-binding protein 1 (five connected) P51114 Fragile X mental retardation syndrome-related protein 1 FXR1...”
  • “...retardation syndrome-related protein 1 FXR1 Q13283 Ras GTPase-activating protein-binding protein 1 G3BP1 Q14444 Caprin-1 CAPRIN1 Q14157 Ubiquitin-associated protein 2-like UBAP2L Fragile X mental retardation syndromerelated protein 1 (three connected) Q13283 Ras GTPase-activating protein-binding protein 1 G3BP1 Q9UN86 Ras GTPase-activating protein-binding protein 2 G3BP2 Q14444 Caprin-1 CAPRIN1...”
• Quantitative phosphoproteomic analysis reveals chemoresistance-related proteins and signaling pathways induced by rhIL-6 in human osteosarcoma cells
  Zhang, Cancer cell international 2021
  • “...kinase 13 MAPK13 Q15759 Mitogen-activated protein kinase 11 MAPK11 P53778 Mitogen-activated protein kinase 12 MAPK12 Q14157 Mitogen-activated protein kinase 14 MAPK14 P78527 DNA-dependent protein kinase catalytic subunit PRKDC P68400 Casein kinase II subunit alpha CSNK2A1 P49840 Glycogen synthase kinase-3 alpha GSK3A P49841 Glycogen synthase kinase-3 beta...”
• Quantification of FAM20A in human milk and identification of calcium metabolism proteins
  Patel, Physiological reports 2021
  • “...protein 4 [T22D4_HUMAN] MFGM CID TTC1 Q99614 Tetratricopeptide repeat protein 1 [TTC1_HUMAN] MFGM CID UBAP2L Q14157 Ubiquitinassociated protein 2like [UBP2L_HUMAN] MFGM CID UBTD2 Q8WUN7 Ubiquitin domaincontaining protein 2 [UBTD2_HUMAN] MFGM CID UQCRB P14927 Cytochrome bc1 complex subunit 7 [QCR7_HUMAN] MFGM CID UQCRFS1 P47985 Cytochrome bc1 complex...”
• Aging-related tau astrogliopathy (ARTAG): not only tau phosphorylation in astrocytes.
  Ferrer, Brain pathology (Zurich, Switzerland) 2018
• The human olfactory cleft mucus proteome and its age-related changes.
  Yoshikawa, Scientific reports 2018
  • “...1 P13693 19697 Translationally-controlled tumor protein 0.54 0.0061 4.9 0.3 2.8 0.1 3.8 0.1 2 Q14157 114579 Ubiquitin-associated protein 2-like 0.53 0.0082 0.2 0.0 0.0 0.0 0.1 0.0 3 Q8TD33 10578 Secretoglobin family 1C member 1 0.52 0.0085 5.0 0.2 0.0 0.0 2.5 0.1 4 P08185...”
• Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions.
  Veredas, Scientific reports 2017
  • “...than 3 phosphosites was only 10%. Nevertheless, there exist proteins such as ubiquitin-associated protein 2-like (Q14157) and kinesin light chain 2 (Q9H0B6) which possess sulfoxidable methionines (M466 and M612, respectively) that are surrounded by up to 8 different phosphosites. To further strengthen the conclusion that the...”
• Generation of metastatic melanoma specific antibodies by affinity purification.
  Schütz, Scientific reports 2016
  • “...1.22% P11388 DNA topoisomerase 2-alpha TOP2A 2.42% P20930 Filaggrin FLG 1.60% Q8WZ42 Titin TTN 0.24% Q14157 Ubiquitin-associated protein 2-like UBAP2L 6.26% Q9UPU9 Protein Smaug homolog 1 SAMD4A 8.91% Q7Z333 Probable helicase senataxin SETX 2.05% Q5SYE7 NHS-like protein 1 NHSL1 3.54% Q9P212 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 PLCE1...”
• The role of O-GlcNAc signaling in the pathogenesis of diabetic retinopathy.
  Semba, Proteomics. Clinical applications 2014
  • “...nuclear mitotic apparatus protein 1 P12270 nucleoprotein TPR Q9P2N6 KAT8 regulatory NSL complex subunit 3 Q14157 ubiquitin-associated protein 2-like Q09666 neuroblast differentation-associated protein AHNAK Q96HC4 PDZ and LIM domain protein 5 P49792 E3 SUMO-protein ligase RanBP2 Q9Y520 protein PRRC2C P02545 prelamin-A/C Q8WWI1 LIM domain only protein...”
• Abacavir induces loading of novel self-peptides into HLA-B*57: 01: an autoimmune model for HLA-associated drug hypersensitivity.
  Norcross, AIDS (London, England) 2012
  • “...1097.547 2.2 P55209 Nucleosome assembly protein 1-like 1 ISQPASGNTF 50 13.24 511.2522 (2) 1021.495 2.2 Q14157 Ubiquitin-associated protein2-like ITAGAHRLW 60 21.68 342.1937 (3) 1024.569 2.1 O00767 Acyl-CoA desaturase VAKVGQYTF 60 18.65 506.7774 (2) 1012.546 1.3 Q86Y39 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 VTYKNVPNW 60...”
• Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles.
  Naganuma, The EMBO journal 2012
• SH3 domain-based phototrapping in living cells reveals Rho family GAP signaling complexes
  Okada, Science signaling 2011
  • “...WNK1 Q9H4A3 NATALELPGLPLSLPQPS 52 Controls junctional ion transport by inhibiting WNK4 Ubiquitin-associated protein 2like UBAP2L Q14157 YSIPFPTPTTPLTGRDGS 45 Phosphoribosylformylglycinamidine synthase PFAS O15067 FPKASVPREPGGPSPRVA 24 ARHGAP4 Diaphanous homolog 1 DIAPH1 O60610 LPGGTAIPPPPPLPGSAR 100 Formin. Actin nucleation and elongation Splicing factor 3B subunit 2 SF3B2 Q13435 LQPPPPPPPPPPGLGLGF 68...”
• Global analysis of TDP-43 interacting proteins reveals strong association with RNA splicing and translation machinery
  Freibaum, Journal of proteome research 2010
  • “...SNRPD2 14 P62316 3 2 16 2 1 8 1.5 Ubiquitin-associated protein 2-like UBAP2L 115 Q14157 3 2 2 2 1 1 1.5 26S proteasome non-ATPase regulatory subunit 2 PSMD2 100 Q13200 3 3 4 2 2 3 1.5 40S ribosomal protein S13 RPS13 17 P62277...”
• Differential protein expression profiles in estrogen receptor-positive and -negative breast cancer tissues using label-free quantitative proteomics
  Rezaul, Genes & cancer 2010
  • “...3.34 0.84 0.25 0.881 Q16401 Q14157 PSMD5 UBAP2L Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial...”
• Nucleolin associates with the human cytomegalovirus DNA polymerase accessory subunit UL44 and is necessary for efficient viral replication.
  Strang, Journal of virology 2010
• A targeted proteomic analysis of the ubiquitin-like modifier nedd8 and associated proteins
  Jones, Journal of proteome research 2008
  • “...ubiquitin-protein ligase EDD1 (O95071), ubiquitinassociated protein 2-like (Q14157) (contains one UBA domain), E3 ubiquitin protein ligase HUWE1 (Q9NSL6), and...”
• PRAS40 and PRR5-like protein are new mTOR interactors that regulate apoptosis.
  Thedieck, PloS one 2007
  • “...PRAS40 and PRR5L. Our 2D LC-MS/MS approach also identified Transferrin Receptor 1 (P02786 Swiss-Prot), NICE-4 (Q14157 Swiss-Prot), Plectin 1 (Q6S383 Swiss-Prot), and Thymopoietin (P42166 Swiss-Prot) as potential mTOR binding proteins, but direct co-IP experiments indicated that these were non-specific binding proteins (data not shown). PRAS40 binds...”

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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.