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UniProtKB - Q9Z1Z9 (PDLI7_RAT)

Entry version 141 (07 Apr 2021)
Sequence version 1 (01 May 1999)
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Protein

PDZ and LIM domain protein 7

Gene

Pdlim7

Organism
Rattus norvegicus (Rat)
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

May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway.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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionDevelopmental protein
Biological processDifferentiation, Osteogenesis
LigandMetal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-RNO-8853659, RET signaling

<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%5Fand%5Ftaxonomy%5Fsection">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:
PDZ and LIM domain protein 7
Alternative name(s):
LIM mineralization protein
Short name:
LMP
Protein enigma
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:Pdlim7
Synonyms:Enigma, Lim1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiRattus norvegicus (Rat)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri10116 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 17

Organism-specific databases

Rat genome database

More...RGDi		628769, Pdlim7

<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, Cytoskeleton

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000758831 – 457PDZ and LIM domain protein 7Add BLAST457

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei78PhosphoserineBy similarity1
Modified residuei96PhosphothreonineCombined sources1
Modified residuei103Asymmetric dimethylarginineBy similarity1
Modified residuei111PhosphoserineBy similarity1
Modified residuei247PhosphoserineBy similarity1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		Q9Z1Z9

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

More...PaxDbi		Q9Z1Z9

PRoteomics IDEntifications database

More...PRIDEi		Q9Z1Z9

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		Q9Z1Z9

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

More...PhosphoSitePlusi		Q9Z1Z9

<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

Expressed in kidney, heart, brain, lung, and skeletal muscle. Overexpression results in the synthesis of an unidentified soluble factor which acts on cells in the osteoblast lineage causing them to differentiate and secrete BMP-2.1 Publication

<p>This subsection of the 'Expression' section provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified 'at the protein level'.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

At E14 expressed in mesenchymal tissue surrounding the cartilaginous anlage of immature bones, and in the future joint spaces. As endochondral ossification progresses, and the hypertrophic cartilage zone is replaced by mineralized bone, expression appears in the mineralizing portion of the bone. Expressed in mesoderm derived bones of the skull base and neural crest-derived endochondral bones such as the proximal mandible.1 Publication

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Induced by glucocorticoid or BMP6.

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSRNOG00000013653, Expressed in quadriceps femoris and 21 other tissues

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		Q9Z1Z9, RN

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Binds via its LIM zinc-binding 3 domain (LIM 3) domain to endocytic codes of INSR, but not with those of IGF1R, LDLR, TFRC, or EGFR.

Interacts with various PKC isoforms through the LIM zinc-binding domains. Binds to RET in a phosphorylation-independent manner via its LIM zinc-binding 2 domain (LIM 2). Probably part of a complex with SHC and the RET dimer.

Interacts with TPM2, TBX4 and TBX5 (By similarity).

Interacts (via LIM domains) with SIPA1L1.

By similarity1 Publication

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

Protein interaction database and analysis system

More...IntActi		Q9Z1Z9, 1 interactor

STRING: functional protein association networks

More...STRINGi		10116.ENSRNOP00000018899

<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		Q9Z1Z9

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%5Fand%5Fdomains%5Fsection">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>Domaini1 – 85PDZPROSITE-ProRule annotationAdd BLAST85
Domaini280 – 338LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST59
Domaini339 – 398LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST60
Domaini399 – 457LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST59

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The LIM zinc-binding 2 (LIM 2) interacts with TBX4.By similarity
The LIM zinc-binding 3 (LIM 3) domain provides the structural basis for recognition of tyrosine-containing tight turn structures. This domain is necessary and sufficient for interaction with TBX5 (By similarity).By similarity
Anchored to cell periphery via its N-terminal PDZ domain.By similarity

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG1703, Eukaryota

Ensembl GeneTree

More...GeneTreei		ENSGT00940000159626

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_001357_8_1_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q9Z1Z9

Identification of Orthologs from Complete Genome Data

More...OMAi		HQCHKII

Database of Orthologous Groups

More...OrthoDBi		1013114at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q9Z1Z9

TreeFam database of animal gene trees

More...TreeFami		TF106408

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		2.30.42.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001478, PDZ
IPR036034, PDZ_sf
IPR001781, Znf_LIM

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00412, LIM, 3 hits
PF00595, PDZ, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00132, LIM, 3 hits
SM00228, PDZ, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF50156, SSF50156, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00478, LIM_DOMAIN_1, 2 hits
PS50023, LIM_DOMAIN_2, 3 hits
PS50106, PDZ, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q9Z1Z9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDSFKVVLEG PAPWGFRLQG GKDFNVPLSI SRLTPGGKAA QAGVAVGDWV 
        60         70         80         90        100
LSIDGENAGS LTHIEAQNKI RACGERLSLG LSRAQPAQSK PQKALTPPAD 
       110        120        130        140        150
PPRYTFAPSA SLNKTARPFG APPPTDSALS QNGQLLRQLV PDASKQRLME 
       160        170        180        190        200
NTEDWRPRPG TGQSRSFRIL AHLTGTEFMQ DPDEEFMKKS SQVPRTEAPA 
       210        220        230        240        250
PASTIPQESW PGPTTPSPTS RPPWAVDPAF AERYAPDKTS TVLTRHSQPA 
       260        270        280        290        300
TPTPLQNRTS IVQAAAGGGT GGGSNNGKTP VCHQCHKIIR GRYLVALGHA 
       310        320        330        340        350
YHPEEFVCSQ CGKVLEEGGF FEEKGAIFCP SCYDVRYAPS CAKCKKKITG 
       360        370        380        390        400
EIMHALKMTW HVPCFTCAAC KTPIRNRAFY MEEGAPYCER DYEKMFGTKC 
       410        420        430        440        450
RGCDFKIDAG DRFLEALGFS WHDTCFVCAI CQINLEGKTF YSKKDKPLCK 

SHAFSHV
Length:457
Mass (Da):49,913
Last modified:May 1, 1999 - 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:iB4EE3142D5A90D72
GO

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
AF095585 mRNA Translation: AAD13197.1
BC078693 mRNA Translation: AAH78693.1

NCBI Reference Sequences

More...RefSeqi		NP_775148.1, NM_173125.1
XP_017455959.1, XM_017600470.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSRNOT00000018899; ENSRNOP00000018899; ENSRNOG00000013653

Database of genes from NCBI RefSeq genomes

More...GeneIDi		286908

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		rno:286908

UCSC genome browser

More...UCSCi		RGD:628769, rat

<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
AF095585 mRNA Translation: AAD13197.1
BC078693 mRNA Translation: AAH78693.1
RefSeqiNP_775148.1, NM_173125.1
XP_017455959.1, XM_017600470.1

3D structure databases

SMRiQ9Z1Z9
ModBaseiSearch...

Protein-protein interaction databases

IntActiQ9Z1Z9, 1 interactor
STRINGi10116.ENSRNOP00000018899

PTM databases

iPTMnetiQ9Z1Z9
PhosphoSitePlusiQ9Z1Z9

Proteomic databases

jPOSTiQ9Z1Z9
PaxDbiQ9Z1Z9
PRIDEiQ9Z1Z9

Genome annotation databases

EnsembliENSRNOT00000018899; ENSRNOP00000018899; ENSRNOG00000013653
GeneIDi286908
KEGGirno:286908
UCSCiRGD:628769, rat

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		9260
RGDi628769, Pdlim7

Phylogenomic databases

eggNOGiKOG1703, Eukaryota
GeneTreeiENSGT00940000159626
HOGENOMiCLU_001357_8_1_1
InParanoidiQ9Z1Z9
OMAiHQCHKII
OrthoDBi1013114at2759
PhylomeDBiQ9Z1Z9
TreeFamiTF106408

Enzyme and pathway databases

ReactomeiR-RNO-8853659, RET signaling

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q9Z1Z9

Gene expression databases

BgeeiENSRNOG00000013653, Expressed in quadriceps femoris and 21 other tissues
GenevisibleiQ9Z1Z9, RN

Family and domain databases

Gene3Di2.30.42.10, 1 hit
InterProiView protein in InterPro
IPR001478, PDZ
IPR036034, PDZ_sf
IPR001781, Znf_LIM
PfamiView protein in Pfam
PF00412, LIM, 3 hits
PF00595, PDZ, 1 hit
SMARTiView protein in SMART
SM00132, LIM, 3 hits
SM00228, PDZ, 1 hit
SUPFAMiSSF50156, SSF50156, 1 hit
PROSITEiView protein in PROSITE
PS00478, LIM_DOMAIN_1, 2 hits
PS50023, LIM_DOMAIN_2, 3 hits
PS50106, PDZ, 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 nameiPDLI7_RAT
<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: Q9Z1Z9
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: May 1, 1999
Last modified: April 7, 2021
This is version 141 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

<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

Reference proteome
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