Human Gene PDLIM2 (ENST00000308354.11) from GENCODE V49

Description: PDZ and LIM domain 2, transcript variant 2 (from RefSeq NM_021630.6)
Gencode Transcript: ENST00000308354.11
Gencode Gene: ENSG00000120913.25
Transcript (Including UTRs)
Position: hg38 chr8:22,578,741-22,594,298 Size: 15,558 Total Exon Count: 10 Strand: +
Coding Region
Position: hg38 chr8:22,578,780-22,593,910 Size: 15,131 Coding Exon Count: 10

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Methods

Data last updated at UCSC: 2025-09-17 13:57:07

Sequence and Links to Tools and Databases

Genomic Sequence (chr8:22,578,741-22,594,298)			mRNA (may differ from genome)		Protein (602 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	Gencode	GeneCards
HGNC	Lynx	MGI	OMIM	PubMed	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PDLI2_HUMAN DESCRIPTION: RecName: Full=PDZ and LIM domain protein 2; AltName: Full=PDZ-LIM protein mystique; FUNCTION: Probable adapter protein located at the actin cytoskeleton that promotes cell attachment. Necessary for the migratory capacity of epithelial cells. Overexpression enhances cell adhesion to collagen and fibronectin and suppresses anchorage independent growth. May contribute to tumor cell migratory capacity. SUBUNIT: Interacts with alpha-actinins ACTN1 and ACTN4, FLNA and MYH9 (By similarity). SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=May be partially nuclear. SUBCELLULAR LOCATION: Isoform 1: Cytoplasm, cytoskeleton. Note=Colocalizes with beta-1 integrin (ITGB1) and alpha-actinin but not with paxillin (PXN). SUBCELLULAR LOCATION: Isoform 2: Cytoplasm, cytoskeleton. SUBCELLULAR LOCATION: Isoform 3: Nucleus. SIMILARITY: Contains 1 LIM zinc-binding domain. SIMILARITY: Contains 1 PDZ (DHR) domain. SEQUENCE CAUTION: Sequence=AAG16633.1; Type=Frameshift; Positions=131; Sequence=AAL55747.1; Type=Frameshift; Positions=42, 207; Sequence=AAL65265.1; Type=Frameshift; Positions=237; Sequence=BAB15788.1; Type=Erroneous initiation;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: PDLIM2 Diseases sorted by gene-association score: cogan-reese syndrome (4)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin D001564 Benzo(a)pyrene C006780 bisphenol A C016403 2,4-dinitrotoluene C023035 3,4,5,3',4'-pentachlorobiphenyl D015127 9,10-Dimethyl-1,2-benzanthracene C068073 Am 580 D000638 Amiodarone D002117 Calcitriol D002251 Carbon Tetrachloride more ... click here to view the complete list

RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 19.63 RPKM in Spleen Total median expression: 109.54 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-11.40	39	-0.292	Picture	PostScript	Text
3' UTR	-147.10	388	-0.379	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)

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

2PA1 - X-ray MuPIT

3PDV - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q96JY6


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
Genome Browser	Genome Browser	No ortholog	Genome Browser	No ortholog	No ortholog
Gene Details
Gene Sorter
MGI	RGD		Ensembl
Protein Sequence	Protein Sequence		Protein Sequence
Alignment	Alignment		Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005515 protein binding GO:0046872 metal ion binding Cellular Component: GO:0005634 nucleus GO:0005737 cytoplasm GO:0005856 cytoskeleton

Descriptions from all associated GenBank mRNAs


	AK092968 - Homo sapiens cDNA FLJ35649 fis, clone SPLEN2013503, highly similar to Homo sapiens PDZ-LIM protein mystique mRNA. AX747829 - Sequence 1354 from Patent EP1308459. BC071774 - Homo sapiens PDZ and LIM domain 2 (mystique), mRNA (cDNA clone MGC:88416 IMAGE:4593207), complete cds. AK027800 - Homo sapiens cDNA FLJ14894 fis, clone PLACE1004506, weakly similar to Homo sapiens carboxyl terminal LIM domain protein (CLIM1) mRNA. AF289563 - Homo sapiens clone pp6345 unknown mRNA. BC021556 - Homo sapiens PDZ and LIM domain 2 (mystique), mRNA (cDNA clone MGC:31819 IMAGE:3959372), complete cds. JD406981 - Sequence 388005 from Patent EP1572962. JD254061 - Sequence 235085 from Patent EP1572962. JD459063 - Sequence 440087 from Patent EP1572962. JD389928 - Sequence 370952 from Patent EP1572962. AY007729 - Homo sapiens PDZ-LIM protein mystique mRNA, complete cds. AY070438 - Homo sapiens PDZ-LIM protein mystique variant mRNA, complete cds. AY217349 - Homo sapiens PDZ-LIM protein mRNA, complete cds. AK024498 - Homo sapiens FLJ00106 mRNA for FLJ00106 protein. DQ893664 - Synthetic construct clone IMAGE:100006294; FLH187455.01X; RZPDo839H0672D PDZ and LIM domain 2 (mystique) (PDLIM2) gene, encodes complete protein. EU176702 - Synthetic construct Homo sapiens clone IMAGE:100011499; FLH187454.01L; RZPDo839B06255D PDZ and LIM domain 2 (mystique) (PDLIM2) gene, encodes complete protein. AB384416 - Synthetic construct DNA, clone: pF1KSDF0106, Homo sapiens PDLIM2 gene for PDZ and LIM domain protein 2, complete cds, without stop codon, in Flexi system. AK055782 - Homo sapiens cDNA FLJ31220 fis, clone KIDNE2004262. AK090432 - Homo sapiens mRNA for FLJ00349 protein. AK056748 - Homo sapiens cDNA FLJ32186 fis, clone PLACE6002011, highly similar to PDZ and LIM domain protein 2. AK074031 - Homo sapiens mRNA for FLJ00072 protein. AK055582 - Homo sapiens cDNA FLJ31020 fis, clone HLUNG2000363. JD152476 - Sequence 133500 from Patent EP1572962. JD378136 - Sequence 359160 from Patent EP1572962. JD192302 - Sequence 173326 from Patent EP1572962. JD187934 - Sequence 168958 from Patent EP1572962. JD342886 - Sequence 323910 from Patent EP1572962. JD215208 - Sequence 196232 from Patent EP1572962. JD365902 - Sequence 346926 from Patent EP1572962. JD431583 - Sequence 412607 from Patent EP1572962. JD118966 - Sequence 99990 from Patent EP1572962. JD477129 - Sequence 458153 from Patent EP1572962. JD534706 - Sequence 515730 from Patent EP1572962. JD497207 - Sequence 478231 from Patent EP1572962. JD237496 - Sequence 218520 from Patent EP1572962. JD404365 - Sequence 385389 from Patent EP1572962. JD097987 - Sequence 79011 from Patent EP1572962. JD209578 - Sequence 190602 from Patent EP1572962. JD508691 - Sequence 489715 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: D3DSR5, ENST00000308354.1, ENST00000308354.10, ENST00000308354.2, ENST00000308354.3, ENST00000308354.4, ENST00000308354.5, ENST00000308354.6, ENST00000308354.7, ENST00000308354.8, ENST00000308354.9, J3KNH4, NM_021630, PDLI2_HUMAN, PP6345, Q7Z584, Q86WM8, Q8WZ29, Q96JY6, Q9H4L9, Q9H7I2, uc064laq.1 UCSC ID: ENST00000308354.11 RefSeq Accession: NM_021630.6 Protein: Q96JY6 (aka PDLI2_HUMAN) CCDS: CCDS6032.2

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.

GNF Expression Atlas 2 Data from U133A and GNF1H Chips