Aliases for LIMD2 Gene

Aliases for LIMD2 Gene

  • LIM Domain Containing 2 2 3 5
  • LIM Domain-Containing Protein 2 3 4
  • Testicular Tissue Protein Li 106 3
  • MGC10986 2
  • LIMD2 5

External Ids for LIMD2 Gene

Previous GeneCards Identifiers for LIMD2 Gene

  • GC17M059127
  • GC17M061773
  • GC17M057141

Summaries for LIMD2 Gene

GeneCards Summary for LIMD2 Gene

LIMD2 (LIM Domain Containing 2) is a Protein Coding gene. Diseases associated with LIMD2 include Fraser Syndrome 1. An important paralog of this gene is TES.

UniProtKB/Swiss-Prot Summary for LIMD2 Gene

  • Acts as an activator of the protein-kinase ILK, thereby regulating cell motility (PubMed:24590809).

Additional gene information for LIMD2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LIMD2 Gene

Genomics for LIMD2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIMD2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIMD2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIMD2

Top Transcription factor binding sites by QIAGEN in the LIMD2 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Elk-1
  • Ik-2
  • NRF-2
  • RFX1

Genomic Locations for LIMD2 Gene

Genomic Locations for LIMD2 Gene
chr17:63,695,888-63,701,227
(GRCh38/hg38)
Size:
5,340 bases
Orientation:
Minus strand
chr17:61,773,249-61,778,532
(GRCh37/hg19)
Size:
5,284 bases
Orientation:
Minus strand

Genomic View for LIMD2 Gene

Genes around LIMD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMD2 Gene

Proteins for LIMD2 Gene

  • Protein details for LIMD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BT23-LIMD2_HUMAN
    Recommended name:
    LIM domain-containing protein 2
    Protein Accession:
    Q9BT23
    Secondary Accessions:
    • D3DU16
    • Q96S91

    Protein attributes for LIMD2 Gene

    Size:
    127 amino acids
    Molecular mass:
    14070 Da
    Quaternary structure:
    • Interacts with ILK (PubMed:24590809).
    Miscellaneous:
    • May play a role in tumor progression via its ability to activate the ILK protein-kinase activity.

    Three dimensional structures from OCA and Proteopedia for LIMD2 Gene

neXtProt entry for LIMD2 Gene

Post-translational modifications for LIMD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LIMD2 Gene

Domains & Families for LIMD2 Gene

Gene Families for LIMD2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LIMD2 Gene

InterPro:
Blocks:
  • Zn-binding protein, LIM
ProtoNet:

Suggested Antigen Peptide Sequences for LIMD2 Gene

GenScript: Design optimal peptide antigens:
  • LIM domain-containing protein 2 (LIMD2_HUMAN)
genes like me logo Genes that share domains with LIMD2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LIMD2 Gene

Function for LIMD2 Gene

Molecular function for LIMD2 Gene

UniProtKB/Swiss-Prot Function:
Acts as an activator of the protein-kinase ILK, thereby regulating cell motility (PubMed:24590809).
UniProtKB/Swiss-Prot Induction:
Over-expressed in breast, bladder, melanoma and thyroid cancer cell lines and tumors (at protein level).

Phenotypes From GWAS Catalog for LIMD2 Gene

Gene Ontology (GO) - Molecular Function for LIMD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMD2: view
genes like me logo Genes that share phenotypes with LIMD2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIMD2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LIMD2 Gene

Localization for LIMD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIMD2 Gene

Cytoplasm. Nucleus. Note=Mainly found in cytoplasm, concentrated in membrane ruffles and in streaks reminiscent of focal adhesion plaques (PubMed:24590809). Also found in nucleus (PubMed:24590809). {ECO:0000269 PubMed:24590809}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LIMD2 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIMD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with LIMD2: view

Pathways & Interactions for LIMD2 Gene

PathCards logo

SuperPathways for LIMD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LIMD2 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LIMD2 Gene

Drugs & Compounds for LIMD2 Gene

No Compound Related Data Available

Transcripts for LIMD2 Gene

mRNA/cDNA for LIMD2 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIMD2

Alternative Splicing Database (ASD) splice patterns (SP) for LIMD2 Gene

No ASD Table

Relevant External Links for LIMD2 Gene

GeneLoc Exon Structure for
LIMD2

Expression for LIMD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LIMD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LIMD2 Gene

This gene is overexpressed in Whole Blood (x22.5) and Spleen (x5.2).

Protein differential expression in normal tissues from HIPED for LIMD2 Gene

This gene is overexpressed in CD8 Tcells (15.8), NK cells (14.2), Peripheral blood mononuclear cells (9.5), CD4 Tcells (9.2), Blymphocyte (8.0), and Monocytes (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LIMD2 Gene



Protein tissue co-expression partners for LIMD2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIMD2

SOURCE GeneReport for Unigene cluster for LIMD2 Gene:

Hs.591166

Evidence on tissue expression from TISSUES for LIMD2 Gene

  • Nervous system(4.5)
  • Liver(2.9)
  • Muscle(2.7)
  • Lymph node(2.6)
  • Intestine(2.5)
  • Heart(2.4)
  • Spleen(2)
genes like me logo Genes that share expression patterns with LIMD2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIMD2 Gene

Orthologs for LIMD2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LIMD2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LIMD2 30 31
  • 99.74 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LIMD2 30 31
  • 94.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LIMD2 30 31
  • 93.96 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Limd2 30
  • 90.55 (n)
Oppossum
(Monodelphis domestica)
Mammalia LIMD2 31
  • 90 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Limd2 30 17 31
  • 89.76 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LIMD2 31
  • 86 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LIMD2 30 31
  • 84.55 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LIMD2 31
  • 82 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia limd2 30
  • 70.25 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC560139 30
  • 79.61 (n)
limd2 31
  • 71 (a)
OneToOne
Species where no ortholog for LIMD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LIMD2 Gene

ENSEMBL:
Gene Tree for LIMD2 (if available)
TreeFam:
Gene Tree for LIMD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIMD2: view image

Paralogs for LIMD2 Gene

Paralogs for LIMD2 Gene

(5) SIMAP similar genes for LIMD2 Gene using alignment to 4 proteins:

  • LIMD2_HUMAN
  • J3KRR0_HUMAN
  • J3QL69_HUMAN
  • J3QQM5_HUMAN
genes like me logo Genes that share paralogs with LIMD2: view

Variants for LIMD2 Gene

Additional dbSNP identifiers (rs#s) for LIMD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for LIMD2 Gene

Variant ID Type Subtype PubMed ID
nsv819101 CNV gain 19587683
nsv952356 CNV deletion 24416366

Variation tolerance for LIMD2 Gene

Residual Variation Intolerance Score: 52.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.42; 9.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIMD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIMD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIMD2 Gene

Disorders for LIMD2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LIMD2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
fraser syndrome 1
  • frasrs1
- elite association - COSMIC cancer census association via MalaCards
Search LIMD2 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with LIMD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIMD2 Gene

Publications for LIMD2 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  4. ATG5 is required for B cell polarization and presentation of particulate antigens. (PMID: 30196744) Arbogast F … Gros F (Autophagy 2019) 3
  5. LIMD2 targeted by miR‑34a promotes the proliferation and invasion of non‑small cell lung cancer cells. (PMID: 30221696) Wang F … Liu D (Molecular medicine reports 2018) 3

Products for LIMD2 Gene

  • Signalway Proteins for LIMD2

Sources for LIMD2 Gene