Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SCYL3 Gene

Aliases for SCYL3 Gene

  • SCY1 Like Pseudokinase 3 2 3 5
  • Ezrin-Binding Protein PACE-1 3 4
  • SCY1-Like, Kinase-Like 3 2 3
  • SCY1-Like Protein 3 3 4
  • PACE1 3 4
  • Protein-Associating With The Carboxyl-Terminal Domain Of Ezrin 3
  • Ezrin-Binding Partner PACE-1 (PACE-1) 3
  • Ezrin-Binding Partner PACE-1 2
  • SCY1-Like 3 (S. Cerevisiae) 2
  • SCY1-Like 3 3
  • PACE-1 3

External Ids for SCYL3 Gene

Previous GeneCards Identifiers for SCYL3 Gene

  • GC01M166554
  • GC01M168088
  • GC01M141044

Summaries for SCYL3 Gene

Entrez Gene Summary for SCYL3 Gene

  • This gene encodes a protein with a kinase domain and four HEAT repeats. The encoded protein interacts with the C-terminal domain of ezrin, an ERM protein, and may play a role in cell adhesion and migration. Alternative splicing results in multiple transcript variants encoding multiple isoforms. [provided by RefSeq, Jun 2012]

GeneCards Summary for SCYL3 Gene

SCYL3 (SCY1 Like Pseudokinase 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and binding. An important paralog of this gene is SCYL1.

UniProtKB/Swiss-Prot for SCYL3 Gene

  • May play a role in regulating cell adhesion/migration complexes in migrating cells.

Gene Wiki entry for SCYL3 Gene

Additional gene information for SCYL3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCYL3 Gene

Genomics for SCYL3 Gene

GeneHancer (GH) Regulatory Elements for SCYL3 Gene

Promoters and enhancers for SCYL3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J169889 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 682.9 +2.0 2031 5.5 ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC SCYL3 METTL18 C1orf112 RN7SL333P KIFAP3 MRPS10P1 ENSG00000230704 HAUS4P1 RPL29P7 BLZF1
GH01J169793 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 57.3 +99.2 99204 2.3 SMAD1 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 METTL18 C1orf112 SCYL3 RN7SL333P GORAB KIFAP3
GH01J169707 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 35.4 +183.9 183929 4.9 HDGF PKNOX1 YBX1 GLI4 ZNF2 ZBTB7B IRF4 ZNF280A ZNF207 ZNF143 SELL METTL18 RN7SL333P SCYL3 GORAB C1orf112 SELP GC01M169692
GH01J169482 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 24.1 +408.7 408696 5.7 CLOCK MLX FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC MEF2D ENSG00000213062 GC01P169486 SLC19A2 SCYL3 METTL18 RN7SL333P NME7 C1orf112 CCDC181 PIR61656
GH01J169308 Enhancer 1.1 Ensembl ENCODE 31.5 +584.9 584916 1.9 PKNOX1 ATF1 ARNT TCF12 ZNF766 ATF7 KDM4B NCOA1 REST ZNF592 ENSG00000235575 METTL18 NME7 SCYL3 C1orf112 RN7SL333P ATP1B1 ENSG00000237707 GC01P169294 GC01P169296
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCYL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCYL3 gene promoter:
  • deltaCREB
  • CREB
  • GATA-1
  • Evi-1
  • c-Ets-1
  • STAT1
  • Elk-1
  • MEF-2A

Genomic Locations for SCYL3 Gene

Genomic Locations for SCYL3 Gene
44,637 bases
Minus strand
44,637 bases
Minus strand

Genomic View for SCYL3 Gene

Genes around SCYL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCYL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCYL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCYL3 Gene

Proteins for SCYL3 Gene

  • Protein details for SCYL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein-associating with the carboxyl-terminal domain of ezrin
    Protein Accession:
    Secondary Accessions:
    • A8K8Z2
    • Q5THA6
    • Q5THA8
    • Q8IZN9
    • Q96C56
    • Q9UBK6

    Protein attributes for SCYL3 Gene

    742 amino acids
    Molecular mass:
    82857 Da
    Quaternary structure:
    • Interacts with EZR/VIL2 C-terminal domain.

    Alternative splice isoforms for SCYL3 Gene


neXtProt entry for SCYL3 Gene

Post-translational modifications for SCYL3 Gene

No data available for DME Specific Peptides for SCYL3 Gene

Domains & Families for SCYL3 Gene

Gene Families for SCYL3 Gene

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

Protein Domains for SCYL3 Gene

Suggested Antigen Peptide Sequences for SCYL3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The protein kinase domain is predicted to be catalytically inactive.
  • Belongs to the protein kinase superfamily.
  • The protein kinase domain is predicted to be catalytically inactive.
  • Belongs to the protein kinase superfamily.
genes like me logo Genes that share domains with SCYL3: view

Function for SCYL3 Gene

Molecular function for SCYL3 Gene

UniProtKB/Swiss-Prot Function:
May play a role in regulating cell adhesion/migration complexes in migrating cells.

Phenotypes From GWAS Catalog for SCYL3 Gene

Gene Ontology (GO) - Molecular Function for SCYL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005488 binding IEA --
GO:0005515 protein binding IPI 12651155
GO:0005524 ATP binding IEA --
GO:0016301 NOT kinase activity IDA 12651155
genes like me logo Genes that share ontologies with SCYL3: view
genes like me logo Genes that share phenotypes with SCYL3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SCYL3

Clone Products

  • Addgene plasmids for SCYL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCYL3 Gene

Localization for SCYL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCYL3 Gene

Cytoplasm. Golgi apparatus. Cell projection, lamellipodium. Note=Colocalized with EZR/VIL2, actin and CD44 in lamellipodia.

Subcellular locations from

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 SCYL3 gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
cytosol 3
extracellular 2
cytoskeleton 2
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubules (1)
  • Nuclear bodies (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCYL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA,IEA 12651155
GO:0005794 Golgi apparatus IDA,IEA 12651155
GO:0030027 lamellipodium IEA,IDA 12651155
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with SCYL3: view

Pathways & Interactions for SCYL3 Gene

SuperPathways for SCYL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCYL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA --
GO:0016477 cell migration NAS 12651155
genes like me logo Genes that share ontologies with SCYL3: view

No data available for Pathways by source and SIGNOR curated interactions for SCYL3 Gene

Drugs & Compounds for SCYL3 Gene

No Compound Related Data Available

Transcripts for SCYL3 Gene

Unigene Clusters for SCYL3 Gene

SCY1-like 3 (S. cerevisiae):
Representative Sequences:

Clone Products

  • Addgene plasmids for SCYL3

Alternative Splicing Database (ASD) splice patterns (SP) for SCYL3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16
SP1: - - -
SP2: - - - -
SP3: - - - -
SP5: - - - - -
SP6: -
SP7: - -
SP8: - -
SP9: -

Relevant External Links for SCYL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCYL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCYL3 Gene

Protein differential expression in normal tissues from HIPED for SCYL3 Gene

This gene is overexpressed in Salivary gland (23.2), Stomach (12.2), Breast (9.5), and Heart (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SCYL3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCYL3 Gene:


SOURCE GeneReport for Unigene cluster for SCYL3 Gene:


mRNA Expression by UniProt/SwissProt for SCYL3 Gene:

Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for SCYL3 Gene

  • Kidney(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with SCYL3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCYL3 Gene

Orthologs for SCYL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCYL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCYL3 34 33
  • 99.46 (n)
(Canis familiaris)
Mammalia SCYL3 34 33
  • 87.72 (n)
(Bos Taurus)
Mammalia SCYL3 34 33
  • 86.31 (n)
(Rattus norvegicus)
Mammalia Scyl3 33
  • 82.33 (n)
(Mus musculus)
Mammalia Scyl3 16 34 33
  • 81.97 (n)
(Monodelphis domestica)
Mammalia SCYL3 34
  • 71 (a)
(Ornithorhynchus anatinus)
Mammalia SCYL3 34
  • 69 (a)
(Gallus gallus)
Aves SCYL3 34 33
  • 69.47 (n)
(Anolis carolinensis)
Reptilia SCYL3 34
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia scyl3 33
  • 61.13 (n)
(Danio rerio)
Actinopterygii scyl3 34 33
  • 57.41 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta CG1344 34
  • 26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
Species where no ortholog for SCYL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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 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 SCYL3 Gene

Gene Tree for SCYL3 (if available)
Gene Tree for SCYL3 (if available)
Evolutionary constrained regions (ECRs) for SCYL3: view image

Paralogs for SCYL3 Gene

Paralogs for SCYL3 Gene

genes like me logo Genes that share paralogs with SCYL3: view

Variants for SCYL3 Gene

Sequence variations from dbSNP and Humsavar for SCYL3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000003424 -- 169,887,288(-) G/C intron_variant
rs1000035839 -- 169,867,959(-) T/C intron_variant
rs1000054230 -- 169,892,581(-) G/A intron_variant
rs1000062604 -- 169,881,596(-) C/G intron_variant
rs1000225022 -- 169,856,679(-) T/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCYL3 Gene

Variant ID Type Subtype PubMed ID
esv2662442 CNV deletion 23128226
esv2719428 CNV deletion 23290073
esv2758976 CNV gain+loss 17122850
esv3542422 CNV deletion 23714750
esv8223 CNV gain 19470904
nsv1078878 OTHER inversion 25765185
nsv428268 CNV gain+loss 18775914
nsv954764 CNV deletion 24416366

Variation tolerance for SCYL3 Gene

Residual Variation Intolerance Score: 51.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.89; 67.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCYL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCYL3 Gene

Disorders for SCYL3 Gene

Additional Disease Information for SCYL3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SCYL3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCYL3 Gene

Publications for SCYL3 Gene

  1. PACE-1, a novel protein that interacts with the C-terminal domain of ezrin. (PMID: 12651155) Sullivan A … Thorne RF (Experimental cell research 2003) 2 3 4 22 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. (PMID: 19064610) Cheung CL … Kung AW (Human molecular genetics 2009) 3 44 58
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  5. 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 58

Products for SCYL3 Gene

Sources for SCYL3 Gene

Loading form....