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Entry version 171 (11 Dec 2019)
Sequence version 1 (01 Oct 1994)
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Protein

U6 snRNA-associated Sm-like protein LSm2

Gene

LSM2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved in degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.8 Publications

Miscellaneous

Present with 2210 molecules/cell in log phase SD medium.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing, rRNA processing, tRNA processing

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-28929-MONOMER

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-430039 mRNA decay by 5' to 3' exoribonuclease

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm2
Alternative name(s):
Small nuclear ribonucleoprotein D homolog SNP3
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:LSM2
Synonyms:SMX5, SNP3
Ordered Locus Names:YBL026W
ORF Names:YBL0425
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome II

Organism-specific databases

Eukaryotic Pathogen Database Resources

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EuPathDBi
FungiDB:YBL026W

Saccharomyces Genome Database

More...
SGDi
S000000122 LSM2

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi35F → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication1
Mutagenesisi37N → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication1
Mutagenesisi63R → A: Strongly reduces affinity for poly-U RNA ends. 2 Publications1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001255591 – 95U6 snRNA-associated Sm-like protein LSm2Add BLAST95

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P38203

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P38203

PRoteomics IDEntifications database

More...
PRIDEi
P38203

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3.

Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. Likewise, LSM2 and LSM3 can assemble into a doughnut structure that binds PAT1 (in vitro).

Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.

7 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Show more details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
32672, 320 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-112 Lsm1-7-Pat1 complex
CPX-24 U6 snRNP complex
CPX-25 U4/U6.U5 tri-snRNP complex
CPX-32 U4/U6 snRNP
CPX-44 LSM2-8 complex
CPX-45 LSM1-7 complex
CPX-46 LSM2-7 complex

Database of interacting proteins

More...
DIPi
DIP-794N

Protein interaction database and analysis system

More...
IntActi
P38203, 83 interactors

Molecular INTeraction database

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MINTi
P38203

STRING: functional protein association networks

More...
STRINGi
4932.YBL026W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P38203 protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

195
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P38203

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000166937

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P38203

KEGG Orthology (KO)

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KOi
K12621

Identification of Orthologs from Complete Genome Data

More...
OMAi
EARYPHM

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01725 LSm2, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
IPR016654 U6_snRNA_Lsm2

The PANTHER Classification System

More...
PANTHERi
PTHR13829 PTHR13829, 1 hit

Pfam protein domain database

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Pfami
View protein in Pfam
PF01423 LSM, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF016394 U6_snRNA_Lsm2, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00651 Sm, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50182 SSF50182, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P38203-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLFFSFFKTL VDQEVVVELK NDIEIKGTLQ SVDQFLNLKL DNISCTDEKK
60 70 80 90
YPHLGSVRNI FIRGSTVRYV YLNKNMVDTN LLQDATRREV MTERK
Length:95
Mass (Da):11,163
Last modified:October 1, 1994 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC23856268CEE92E2
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
X77291 Genomic DNA Translation: CAA54505.1
Z35787 Genomic DNA Translation: CAA84845.1
BK006936 Genomic DNA Translation: DAA07094.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S45760

NCBI Reference Sequences

More...
RefSeqi
NP_009527.1, NM_001178266.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YBL026W_mRNA; YBL026W; YBL026W

Database of genes from NCBI RefSeq genomes

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GeneIDi
852255

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YBL026W

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77291 Genomic DNA Translation: CAA54505.1
Z35787 Genomic DNA Translation: CAA84845.1
BK006936 Genomic DNA Translation: DAA07094.1
PIRiS45760
RefSeqiNP_009527.1, NM_001178266.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80c1-95[»]
4C8QX-ray3.70B2-95[»]
4C92X-ray2.30B2-95[»]
4M75X-ray2.95B/I1-95[»]
4M77X-ray3.11B/I1-95[»]
4M78X-ray2.79B/I1-95[»]
4M7AX-ray2.78B/I1-95[»]
4M7DX-ray2.60B/I1-95[»]
4N0AX-ray3.15C/D/G1-95[»]
5GANelectron microscopy3.6021-95[»]
5NRLelectron microscopy7.20a1-95[»]
5VSUX-ray3.10B1-95[»]
5ZWMelectron microscopy3.40q1-95[»]
5ZWOelectron microscopy3.90q1-95[»]
6ASOX-ray2.71B1-95[»]
SMRiP38203
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi32672, 320 interactors
ComplexPortaliCPX-112 Lsm1-7-Pat1 complex
CPX-24 U6 snRNP complex
CPX-25 U4/U6.U5 tri-snRNP complex
CPX-32 U4/U6 snRNP
CPX-44 LSM2-8 complex
CPX-45 LSM1-7 complex
CPX-46 LSM2-7 complex
DIPiDIP-794N
IntActiP38203, 83 interactors
MINTiP38203
STRINGi4932.YBL026W

Proteomic databases

MaxQBiP38203
PaxDbiP38203
PRIDEiP38203

Genome annotation databases

EnsemblFungiiYBL026W_mRNA; YBL026W; YBL026W
GeneIDi852255
KEGGisce:YBL026W

Organism-specific databases

EuPathDBiFungiDB:YBL026W
SGDiS000000122 LSM2

Phylogenomic databases

HOGENOMiHOG000166937
InParanoidiP38203
KOiK12621
OMAiEARYPHM

Enzyme and pathway databases

BioCyciYEAST:G3O-28929-MONOMER
ReactomeiR-SCE-430039 mRNA decay by 5' to 3' exoribonuclease

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P38203
RNActiP38203 protein

Family and domain databases

CDDicd01725 LSm2, 1 hit
InterProiView protein in InterPro
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
IPR016654 U6_snRNA_Lsm2
PANTHERiPTHR13829 PTHR13829, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
PIRSFiPIRSF016394 U6_snRNA_Lsm2, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiLSM2_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P38203
Secondary accession number(s): D6VPX4
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: December 11, 2019
This is version 171 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names
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