This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patie... See more...

Aliases for ABLIM3 Gene

Aliases for ABLIM3 Gene

  • Actin Binding LIM Protein Family Member 3 2 3 5
  • Actin-Binding LIM Protein 3 3 4
  • KIAA0843 2 4
  • AbLIM-3 3 4
  • Actin Binding LIM Protein Family, Member 3 2
  • Actin-Binding LIM Protein Family Member 3 4
  • HMFN1661 3
  • ABLIM3 5

External Ids for ABLIM3 Gene

Previous GeneCards Identifiers for ABLIM3 Gene

  • GC05P148549
  • GC05P148501
  • GC05P143667

Summaries for ABLIM3 Gene

Entrez Gene Summary for ABLIM3 Gene

  • This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patients. [provided by RefSeq, Sep 2016]

GeneCards Summary for ABLIM3 Gene

ABLIM3 (Actin Binding LIM Protein Family Member 3) is a Protein Coding gene. Diseases associated with ABLIM3 include Aromatic L-Amino Acid Decarboxylase Deficiency and Fetal Erythroblastosis. Among its related pathways are Netrin-1 signaling and Axon guidance. Gene Ontology (GO) annotations related to this gene include actin binding. An important paralog of this gene is ABLIM1.

UniProtKB/Swiss-Prot Summary for ABLIM3 Gene

  • May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Gene Wiki entry for ABLIM3 Gene

Additional gene information for ABLIM3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ABLIM3 Gene

Genomics for ABLIM3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ABLIM3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J149140 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 625.3 +1.3 1281 4.9 GATAD2A CTCF HNRNPL TEAD4 REST RFX1 ZNF692 RCOR2 FOXA1 ZNF143 ABLIM3 HMGXB3 FBXO38 ENSG00000251330 SH3TC2 ADRB2 AFAP1L1
GH05J149243 Promoter 0.3 EPDnew 600.1 +102.5 102537 0.1 ABLIM3 AFAP1L1 ENSG00000248647 ENSG00000253406
GH05J149161 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 16.7 +20.4 20354 3.2 HNRNPL GATAD2A REST TFE3 SOX13 RBFOX2 RXRB IKZF2 SP1 GABPA ABLIM3 AFAP1L1 ENSG00000248647 ENSG00000253406 CARMN IL17B SH3TC2
GH05J149060 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 12.4 -79.1 -79100 4.6 TEAD4 SOX13 IKZF1 PKNOX1 REST CEBPA TCF7 HMBOX1 NFE2 CEBPB SH3TC2 SH3TC2-DT MIR584 RF01016-011 lnc-IL17B-7 ABLIM3 lnc-ABLIM3-3 ADRB2
GH05J149170 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 9.3 +32.1 32070 7 GATAD2A TFE3 SOX13 RBFOX2 PKNOX1 RXRB IRF2 BRD4 GABPA CEBPA AFAP1L1 ENSG00000248647 ENSG00000253406 ABLIM3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ABLIM3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ABLIM3

Top Transcription factor binding sites by QIAGEN in the ABLIM3 gene promoter:
  • AML1a
  • E47
  • Hand1
  • LCR-F1
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • RFX1
  • Sox5

Genomic Locations for ABLIM3 Gene

Genomic Locations for ABLIM3 Gene
chr5:149,141,447-149,260,542
(GRCh38/hg38)
Size:
119,096 bases
Orientation:
Plus strand
chr5:148,521,046-148,640,105
(GRCh37/hg19)
Size:
119,060 bases
Orientation:
Plus strand

Genomic View for ABLIM3 Gene

Genes around ABLIM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ABLIM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ABLIM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ABLIM3 Gene

Proteins for ABLIM3 Gene

  • Protein details for ABLIM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94929-ABLM3_HUMAN
    Recommended name:
    Actin-binding LIM protein 3
    Protein Accession:
    O94929
    Secondary Accessions:
    • A8K121
    • Q19VH3
    • Q658S1
    • Q68CI5
    • Q9BV32

    Protein attributes for ABLIM3 Gene

    Size:
    683 amino acids
    Molecular mass:
    77802 Da
    Quaternary structure:
    • Directly interacts with F-actin and ABRA.
    SequenceCaution:
    • Sequence=BAA74866.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ABLIM3 Gene

    Alternative splice isoforms for ABLIM3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ABLIM3 Gene

Post-translational modifications for ABLIM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ABLIM3 Gene

Domains & Families for ABLIM3 Gene

Gene Families for ABLIM3 Gene

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

Protein Domains for ABLIM3 Gene

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

Suggested Antigen Peptide Sequences for ABLIM3 Gene

GenScript: Design optimal peptide antigens:
  • Actin-binding LIM protein family member 3 (ABLM3_HUMAN)
genes like me logo Genes that share domains with ABLIM3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ABLIM3 Gene

Function for ABLIM3 Gene

Molecular function for ABLIM3 Gene

UniProtKB/Swiss-Prot Function:
May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Phenotypes From GWAS Catalog for ABLIM3 Gene

Gene Ontology (GO) - Molecular Function for ABLIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
GO:0051015 actin filament binding IBA 21873635
genes like me logo Genes that share ontologies with ABLIM3: view
genes like me logo Genes that share phenotypes with ABLIM3: view

Animal Model Products

CRISPR Products

miRNA for ABLIM3 Gene

miRTarBase miRNAs that target ABLIM3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ABLIM3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ABLIM3 Gene

Localization for ABLIM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ABLIM3 Gene

Cytoplasm.

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 ABLIM3 gene
Compartment Confidence
cytoskeleton 5
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ABLIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IDA 22684256
GO:0005737 cytoplasm IEA --
GO:0015629 actin cytoskeleton IBA 21873635
GO:0030027 lamellipodium IDA 22684256
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with ABLIM3: view

Pathways & Interactions for ABLIM3 Gene

PathCards logo

SuperPathways for ABLIM3 Gene

genes like me logo Genes that share pathways with ABLIM3: view

Pathways by source for ABLIM3 Gene

1 KEGG pathway for ABLIM3 Gene
1 Qiagen pathway for ABLIM3 Gene
  • Netrin Signaling

Gene Ontology (GO) - Biological Process for ABLIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0007010 cytoskeleton organization IEA --
GO:0030032 lamellipodium assembly IMP 22684256
GO:0030036 actin cytoskeleton organization IEA --
GO:0045944 positive regulation of transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with ABLIM3: view

No data available for SIGNOR curated interactions for ABLIM3 Gene

Drugs & Compounds for ABLIM3 Gene

No Compound Related Data Available

Transcripts for ABLIM3 Gene

mRNA/cDNA for ABLIM3 Gene

11 REFSEQ mRNAs :
11 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 ABLIM3

Alternative Splicing Database (ASD) splice patterns (SP) for ABLIM3 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b ^ 17 ^
SP1: - - - - -
SP2: - - - - - - - -
SP3: - - - - -
SP4:
SP5: - - -
SP6:
SP7:

ExUns: 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24
SP1:
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for ABLIM3 Gene

GeneLoc Exon Structure for
ABLIM3

Expression for ABLIM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ABLIM3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ABLIM3 Gene

This gene is overexpressed in Liver (x4.9).

Protein differential expression in normal tissues from HIPED for ABLIM3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (27.8), Liver (10.3), and Heart (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ABLIM3 Gene



Protein tissue co-expression partners for ABLIM3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ABLIM3

SOURCE GeneReport for Unigene cluster for ABLIM3 Gene:

Hs.49688

mRNA Expression by UniProt/SwissProt for ABLIM3 Gene:

O94929-ABLM3_HUMAN
Tissue specificity: Expressed predominantly in heart and brain.

Evidence on tissue expression from TISSUES for ABLIM3 Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Heart(4.4)
  • Blood(4.3)
  • Stomach(4.2)
  • Intestine(4.2)
  • Muscle(2.3)
genes like me logo Genes that share expression patterns with ABLIM3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ABLIM3 Gene

Orthologs for ABLIM3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ABLIM3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ABLIM3 30 31
  • 99.76 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ABLIM3 30 31
  • 94.19 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ABLIM3 30 31
  • 93.41 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ablim3 30
  • 92 (n)
Oppossum
(Monodelphis domestica)
Mammalia ABLIM3 31
  • 92 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Ablim3 30 17 31
  • 91.84 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ABLIM3 31
  • 81 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ABLIM3 30 31
  • 82 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ABLIM3 31
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ablim3 30
  • 76.1 (n)
Zebrafish
(Danio rerio)
Actinopterygii ablim3 31 31
  • 74 (a)
OneToMany
ABLIM3 (2 of 3) 31
  • 74 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005425 30
  • 52.46 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Unc-115a 30
  • 49.17 (n)
Species where no ortholog for ABLIM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 ABLIM3 Gene

ENSEMBL:
Gene Tree for ABLIM3 (if available)
TreeFam:
Gene Tree for ABLIM3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ABLIM3: view image

Paralogs for ABLIM3 Gene

Paralogs for ABLIM3 Gene

(6) SIMAP similar genes for ABLIM3 Gene using alignment to 2 proteins:

  • ABLM3_HUMAN
  • D6RHE7_HUMAN
genes like me logo Genes that share paralogs with ABLIM3: view

Variants for ABLIM3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ABLIM3 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
768041 Benign: not provided 149,200,412(+) G/A SYNONYMOUS_VARIANT
770916 Benign: not provided 149,242,519(+) C/A SYNONYMOUS_VARIANT,INTRON_VARIANT
770917 Benign: not provided 149,242,522(+) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT
rs386352274 Uncertain Significance: not provided 149,247,895(+) G/A SYNONYMOUS_VARIANT
rs386352275 Uncertain Significance: not provided 149,247,814(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for ABLIM3 Gene

Structural Variations from Database of Genomic Variants (DGV) for ABLIM3 Gene

Variant ID Type Subtype PubMed ID
dgv3190n106 CNV deletion 24896259
dgv3404e59 CNV duplication 20981092
esv1009293 CNV deletion 20482838
esv1067040 CNV insertion 17803354
esv1591742 CNV deletion 17803354
esv1941617 CNV deletion 18987734
esv2159994 CNV deletion 18987734
esv2319677 CNV deletion 18987734
esv2479942 CNV deletion 19546169
esv2599932 CNV deletion 19546169
esv2730903 CNV deletion 23290073
esv2730904 CNV deletion 23290073
esv2742645 CNV deletion 23290073
esv3566798 CNV deletion 23714750
esv3566799 CNV deletion 23714750
esv3570490 CNV loss 25503493
esv3575887 CNV gain 25503493
esv3607137 CNV gain 21293372
esv3607138 CNV gain 21293372
nsv328915 CNV deletion 16902084
nsv329799 CNV deletion 16902084
nsv517567 CNV gain 19592680
nsv830517 CNV gain 17160897

Variation tolerance for ABLIM3 Gene

Residual Variation Intolerance Score: 70.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.84; 48.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ABLIM3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ABLIM3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ABLIM3 Gene

Disorders for ABLIM3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ABLIM3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
aromatic l-amino acid decarboxylase deficiency
  • aadc deficiency
fetal erythroblastosis
  • ef - erythroblastosis foetalis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ABLIM3

genes like me logo Genes that share disorders with ABLIM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ABLIM3 Gene

Publications for ABLIM3 Gene

  1. Actin binding LIM protein 3 (abLIM3). (PMID: 16328021) Krupp M … Teufel A (International journal of molecular medicine 2006) 2 3 23
  2. abLIM3 is a novel component of adherens junctions with actin-binding activity. (PMID: 20709423) Matsuda M … Furuse M (European journal of cell biology 2010) 2 3
  3. Two novel members of the ABLIM protein family, ABLIM-2 and -3, associate with STARS and directly bind F-actin. (PMID: 17194709) Barrientos T … Frey N (The Journal of biological chemistry 2007) 3 4
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  5. Expression profiling and differential screening between hepatoblastomas and the corresponding normal livers: identification of high expression of the PLK1 oncogene as a poor-prognostic indicator of hepatoblastomas. (PMID: 15221005) Yamada S … Nakagawara A (Oncogene 2004) 3 4

Products for ABLIM3 Gene

  • Signalway Proteins for ABLIM3

Sources for ABLIM3 Gene