Human Gene PDLIM7 (uc003mhc.1) Description and Page Index
  Description: Homo sapiens PDZ and LIM domain 7 (enigma) (PDLIM7), transcript variant 1, mRNA.
RefSeq Summary (NM_005451): The protein encoded by this gene is representative of a family of proteins composed of conserved PDZ and LIM domains. LIM domains are proposed to function in protein-protein recognition in a variety of contexts including gene transcription and development and in cytoskeletal interaction. The LIM domains of this protein bind to protein kinases, whereas the PDZ domain binds to actin filaments. The gene product is involved in the assembly of an actin filament-associated complex essential for transmission of ret/ptc2 mitogenic signaling. The biological function is likely to be that of an adapter, with the PDZ domain localizing the LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr5:176,910,395-176,924,602 Size: 14,208 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr5:176,910,645-176,923,513 Size: 12,869 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:176,910,395-176,924,602)mRNA (may differ from genome)Protein (457 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PDLI7_HUMAN
DESCRIPTION: RecName: Full=PDZ and LIM domain protein 7; AltName: Full=LIM mineralization protein; Short=LMP; AltName: Full=Protein enigma;
FUNCTION: 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 (By similarity).
SUBUNIT: Binds via its LIM zinc-binding 3 domain (LIM 3) 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 domain 2 (LIM 2). Probably part of a complex with SHC and the RET dimer. Interacts with TPM2. Interacts with TBX4 and TBX5 (By similarity).
INTERACTION: Q9NRR5:UBQLN4; NbExp=2; IntAct=EBI-350517, EBI-711226;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cytoplasm, cytoskeleton (By similarity). Note=Colocalizes with RET to the cell periphery and in some cytoskeletal components. Colocalizes with TPM2 near the Z line in muscle. Co-localizes with TBX4 and TBX5 to actin filaments (By similarity).
TISSUE SPECIFICITY: Isoform 1 and isoform 2 are expressed ubiquitously, however, isoform 2 predominates in skeletal muscle, isoform 1 is more abundant in lung, spleen, leukocytes and fetal liver.
DOMAIN: The LIM zinc-binding 2 (LIM 2) domain interacts with TBX4 (By similarity).
DOMAIN: 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).
DOMAIN: Anchored to cell periphery via its N-terminal PDZ domain.
SIMILARITY: Contains 3 LIM zinc-binding domains.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SEQUENCE CAUTION: Sequence=AAC37565.1; Type=Frameshift; Positions=103, 128, 161, 183, 195, 245;

-  MalaCards Disease Associations
  MalaCards Gene Search: PDLIM7
Diseases sorted by gene-association score: pleural empyema (8), dental pulp calcification (8), n syndrome (7), bare lymphocyte syndrome, type i (4), pharynx cancer (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 253.54 RPKM in Colon - Sigmoid
Total median expression: 2749.90 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.8085-0.386 Picture PostScript Text
3' UTR -95.40250-0.382 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001478 - PDZ
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain
PF00595 - PDZ domain (Also known as DHR or GLGF)

SCOP Domains:
50156 - PDZ domain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2Q3G
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NR12
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0001503 ossification
GO:0006898 receptor-mediated endocytosis
GO:0007275 multicellular organism development
GO:0007411 axon guidance
GO:0030036 actin cytoskeleton organization
GO:0030154 cell differentiation
GO:0045669 positive regulation of osteoblast differentiation

Cellular Component:
GO:0001725 stress fiber
GO:0001726 ruffle
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005913 cell-cell adherens junction
GO:0005925 focal adhesion
GO:0015629 actin cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AK131426 - Homo sapiens cDNA FLJ16550 fis, clone PROST2009320.
AF345904 - Homo sapiens LIM mineralization protein 1 mRNA, complete cds.
AF345905 - Homo sapiens LIM mineralization protein 2 mRNA, complete cds.
AF345906 - Homo sapiens LIM mineralization protein 3 mRNA, complete cds.
BC001093 - Homo sapiens PDZ and LIM domain 7 (enigma), mRNA (cDNA clone MGC:3269 IMAGE:3506748), complete cds.
BC007648 - Homo sapiens PDZ and LIM domain 7 (enigma), mRNA (cDNA clone IMAGE:3538103), with apparent retained intron.
AF265209 - Homo sapiens ENIGMA protein mRNA, complete cds.
AK096826 - Homo sapiens cDNA FLJ39507 fis, clone PROST2017617, highly similar to Homo sapiens ENIGMA protein mRNA.
BC067806 - Homo sapiens PDZ and LIM domain 7 (enigma), mRNA (cDNA clone IMAGE:5287820).
JD319195 - Sequence 300219 from Patent EP1572962.
JD053852 - Sequence 34876 from Patent EP1572962.
JD115411 - Sequence 96435 from Patent EP1572962.
JD369927 - Sequence 350951 from Patent EP1572962.
JD123250 - Sequence 104274 from Patent EP1572962.
JD194459 - Sequence 175483 from Patent EP1572962.
JD055847 - Sequence 36871 from Patent EP1572962.
JD401306 - Sequence 382330 from Patent EP1572962.
JD077333 - Sequence 58357 from Patent EP1572962.
JD121393 - Sequence 102417 from Patent EP1572962.
KJ892731 - Synthetic construct Homo sapiens clone ccsbBroadEn_02125 PDLIM7 gene, encodes complete protein.
DQ892135 - Synthetic construct clone IMAGE:100004765; FLH183328.01X; RZPDo839B01142D PDZ and LIM domain 7 (enigma) (PDLIM7) gene, encodes complete protein.
DQ895329 - Synthetic construct Homo sapiens clone IMAGE:100009789; FLH183325.01L; RZPDo839B01141D PDZ and LIM domain 7 (enigma) (PDLIM7) gene, encodes complete protein.
AB528311 - Synthetic construct DNA, clone: pF1KE0786, Homo sapiens PDLIM7 gene for PDZ and LIM domain 7, without stop codon, in Flexi system.
BC084575 - Homo sapiens PDZ and LIM domain 7 (enigma), mRNA (cDNA clone MGC:99612 IMAGE:6729368), complete cds.
DQ291143 - Homo sapiens enigma-like mRNA, partial sequence.
CU674544 - Synthetic construct Homo sapiens gateway clone IMAGE:100017313 5' read PDLIM7 mRNA.
BC014521 - Homo sapiens PDZ and LIM domain 7 (enigma), mRNA (cDNA clone IMAGE:3690154), complete cds.
KJ892732 - Synthetic construct Homo sapiens clone ccsbBroadEn_02126 PDLIM7 gene, encodes complete protein.
KJ901960 - Synthetic construct Homo sapiens clone ccsbBroadEn_11354 PDLIM7 gene, encodes complete protein.
CU688348 - Synthetic construct Homo sapiens gateway clone IMAGE:100022931 5' read PDLIM7 mRNA.
JD186288 - Sequence 167312 from Patent EP1572962.
JD127620 - Sequence 108644 from Patent EP1572962.
JD187408 - Sequence 168432 from Patent EP1572962.
JD391588 - Sequence 372612 from Patent EP1572962.
JD478880 - Sequence 459904 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NR12 (Reactome details) participates in the following event(s):

R-HSA-8855915 2x p-5Y-RET:GDNF:GFRA complexes bind RET interactors
R-HSA-8853659 RET signaling
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENIGMA, NM_005451, NP_005442, PDLI7_HUMAN, Q14250, Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9, Q9NR12
UCSC ID: uc003mhc.1
RefSeq Accession: NM_005451
Protein: Q9NR12 (aka PDLI7_HUMAN)
CCDS: CCDS4422.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005451.3
exon count: 13CDS single in 3' UTR: no RNA size: 1709
ORF size: 1374CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2505.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.