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Entry version 66 (16 Oct 2019)
Sequence version 1 (31 May 2011)
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Protein

LIM and senescent cell antigen-like-containing domain protein 3

Gene

LIMS3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score:

Annotation score:2 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 transcript 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

<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

<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

LigandMetal-binding, Zinc

<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:
LIM and senescent cell antigen-like-containing domain protein 3
Alternative name(s):
Particularly interesting new Cys-His protein 3
Short name:
PINCH-3
<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:LIMS3
Synonyms:PINCH3
<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>OrganismiHomo sapiens (Human)
<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 identifieri9606 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<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
  • UP000005640 <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 2

Organism-specific databases

Human Gene Nomenclature Database

More...
HGNCi
HGNC:30047 LIMS3

neXtProt; the human protein knowledge platform

More...
neXtProti
NX_P0CW19

<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

Keywords - Cellular componenti

Cytoplasm

<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

Organism-specific databases

DisGeNET

More...
DisGeNETi
100288695
96626

Open Targets

More...
OpenTargetsi
ENSG00000257207

The Pharmacogenetics and Pharmacogenomics Knowledge Base

More...
PharmGKBi
PA134917873

Miscellaneous databases

Pharos NIH Druggable Genome Knowledgebase

More...
Pharosi
P0CW19

Polymorphism and mutation databases

BioMuta curated single-nucleotide variation and disease association database

More...
BioMutai
LIMS3

Domain mapping of disease mutations (DMDM)

More...
DMDMi
334350997

<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_00002660131 – 117LIM and senescent cell antigen-like-containing domain protein 3Add BLAST117

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P0CW19

MassIVE - Mass Spectrometry Interactive Virtual Environment

More...
MassIVEi
P0CW19

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

More...
PaxDbi
P0CW19

PeptideAtlas

More...
PeptideAtlasi
P0CW19

PRoteomics IDEntifications database

More...
PRIDEi
P0CW19

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
4785
52518 [P0CW19-1]

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P0CW19

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...
PhosphoSitePlusi
P0CW19

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Detected in testis.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSG00000256977 Expressed in 86 organ(s), highest expression level in thoracic aorta

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
P0CW19 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
P0CW19 HS

Organism-specific databases

Human Protein Atlas

More...
HPAi
HPA058455

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
125178, 2 interactors

Protein interaction database and analysis system

More...
IntActi
P0CW19, 10 interactors

STRING: functional protein association networks

More...
STRINGi
9606.ENSP00000405165

<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

3D structure databases

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

More...
SMRi
P0CW19

Database of comparative protein structure models

More...
ModBasei
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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini70 – 117LIM zinc-bindingPROSITE-ProRule annotationAdd BLAST48

Keywords - Domaini

LIM domain

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG410JC6F Eukaryota
KOG2272 Eukaryota
ENOG410XP46 LUCA
ENOG41119KQ LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000153518

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000015300

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0CW19

Database of Orthologous Groups

More...
OrthoDBi
292981at2759

TreeFam database of animal gene trees

More...
TreeFami
TF314113

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR017351 PINCH
IPR001781 Znf_LIM

The PANTHER Classification System

More...
PANTHERi
PTHR24210 PTHR24210, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00412 LIM, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00132 LIM, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00478 LIM_DOMAIN_1, 1 hit
PS50023 LIM_DOMAIN_2, 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>Sequences (2+)i

<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.

This entry describes 2 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: P0CW19-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MAFSGRARPC IIPENEEIPR AALNTVHEAN GTEDERAVSK LQRRHSDVKV
60 70 80 90 100
YKEFCDFYAK FNMANALASA TCERCKGGFA PAETIVNSNG ELYHEQCFVC
110
AQCFQQFPEG LFYEERT
Length:117
Mass (Da):13,251
Last modified:May 31, 2011 - 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:iF260926C06DA51CE
GO
Isoform 2 (identifier: P0CW19-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     115-117: ERT → FEGRKYCEHD...ERGAILPAMP

Note: No experimental confirmation available.
Show »
Length:248
Mass (Da):28,092
Checksum:i22A55D36599CFCFF
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A0J9YXC7A0A0J9YXC7_HUMAN
LIM and senescent cell antigen-like...
LIMS4 LIMS3
398Annotation score:

Annotation score:2 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>
A0A0J9YYC1A0A0J9YYC1_HUMAN
LIM and senescent cell antigen-like...
LIMS3
55Annotation score:

Annotation score:1 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>

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_054392115 – 117ERT → FEGRKYCEHDFQMLFAPCCH QCGEFIIGRVIKAMNNSWHP ECFRCDLCQEVLADIGFVKN AGRHLCRPCHNREKARGLGK YICQKCHAIIDEQPLIFKND PYHPDHFNCANCGQEGSDCR CTGAERGAILPAMP in isoform 2. 1 Publication3

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AF288404 mRNA Translation: AAF99328.1
AK298340 mRNA Translation: BAG60588.1
AK316210 mRNA Translation: BAH14581.1
AC013271 Genomic DNA Translation: AAY14903.1
AC108938 Genomic DNA No translation available.
AC112229 Genomic DNA No translation available.
BC093812 mRNA Translation: AAH93812.1
BC112233 mRNA Translation: AAI12234.1

The Consensus CDS (CCDS) project

More...
CCDSi
CCDS2084.1 [P0CW19-1]

NCBI Reference Sequences

More...
RefSeqi
NP_001192217.1, NM_001205288.1 [P0CW19-1]
NP_277049.1, NM_033514.4 [P0CW19-1]

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENST00000437679; ENSP00000405165; ENSG00000256977 [P0CW19-1]
ENST00000631420; ENSP00000488227; ENSG00000256977 [P0CW19-2]

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
100288695
96626

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
hsa:100288695
hsa:96626

Keywords - Coding sequence diversityi

Alternative splicing

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<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
AF288404 mRNA Translation: AAF99328.1
AK298340 mRNA Translation: BAG60588.1
AK316210 mRNA Translation: BAH14581.1
AC013271 Genomic DNA Translation: AAY14903.1
AC108938 Genomic DNA No translation available.
AC112229 Genomic DNA No translation available.
BC093812 mRNA Translation: AAH93812.1
BC112233 mRNA Translation: AAI12234.1
CCDSiCCDS2084.1 [P0CW19-1]
RefSeqiNP_001192217.1, NM_001205288.1 [P0CW19-1]
NP_277049.1, NM_033514.4 [P0CW19-1]

3D structure databases

SMRiP0CW19
ModBaseiSearch...

Protein-protein interaction databases

BioGridi125178, 2 interactors
IntActiP0CW19, 10 interactors
STRINGi9606.ENSP00000405165

PTM databases

iPTMnetiP0CW19
PhosphoSitePlusiP0CW19

Polymorphism and mutation databases

BioMutaiLIMS3
DMDMi334350997

Proteomic databases

jPOSTiP0CW19
MassIVEiP0CW19
PaxDbiP0CW19
PeptideAtlasiP0CW19
PRIDEiP0CW19
ProteomicsDBi4785
52518 [P0CW19-1]

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
96626

Genome annotation databases

EnsembliENST00000437679; ENSP00000405165; ENSG00000256977 [P0CW19-1]
ENST00000631420; ENSP00000488227; ENSG00000256977 [P0CW19-2]
GeneIDi100288695
96626
KEGGihsa:100288695
hsa:96626

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
100288695
96626
DisGeNETi100288695
96626

GeneCards: human genes, protein and diseases

More...
GeneCardsi
LIMS3
HGNCiHGNC:30047 LIMS3
HPAiHPA058455
neXtProtiNX_P0CW19
OpenTargetsiENSG00000257207
PharmGKBiPA134917873

GenAtlas: human gene database

More...
GenAtlasi
Search...

Phylogenomic databases

eggNOGiENOG410JC6F Eukaryota
KOG2272 Eukaryota
ENOG410XP46 LUCA
ENOG41119KQ LUCA
GeneTreeiENSGT00940000153518
HOGENOMiHOG000015300
InParanoidiP0CW19
OrthoDBi292981at2759
TreeFamiTF314113

Miscellaneous databases

PharosiP0CW19

Protein Ontology

More...
PROi
PR:P0CW19

Gene expression databases

BgeeiENSG00000256977 Expressed in 86 organ(s), highest expression level in thoracic aorta
ExpressionAtlasiP0CW19 baseline and differential
GenevisibleiP0CW19 HS

Family and domain databases

InterProiView protein in InterPro
IPR017351 PINCH
IPR001781 Znf_LIM
PANTHERiPTHR24210 PTHR24210, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 1 hit
PS50023 LIM_DOMAIN_2, 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 nameiLIMS3_HUMAN
<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: P0CW19
Secondary accession number(s): A0A0A6YYD2, B4DPH6, Q9HB10
<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: May 31, 2011
Last sequence update: May 31, 2011
Last modified: October 16, 2019
This is version 66 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 programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

<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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
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