This gene encodes a transcriptional regulator belonging to the SCY1-like family of kinase-like proteins. The protein has a divergent N-terminal kinase domain that is thought to be catalytically inactive, and can bind specific DNA sequences through its C-terminal domain. It activates transcription of the telomerase reverse transcriptase and DNA polymerase beta genes. The protein... See more...

Aliases for SCYL1 Gene

Aliases for SCYL1 Gene

  • SCY1 Like Pseudokinase 1 2 3 5
  • Telomerase Regulation-Associated Protein 2 3 4
  • Teratoma-Associated Tyrosine Kinase 2 3 4
  • GKLP 2 3 4
  • TAPK 2 3 4
  • TEIF 2 3 4
  • TRAP 2 3 4
  • Telomerase Transcriptional Elements-Interacting Factor 2 3
  • Coated Vesicle-Associated Kinase Of 90 KDa 3 4
  • N-Terminal Kinase-Like Protein 3 4
  • SCY1-Like, Kinase-Like 1 2 3
  • SCY1-Like Protein 1 3 4
  • HT019 2 3
  • NKTL 2 3
  • NTKL 3 4
  • P105 2 3
  • Likely Ortholog Of Mouse N-Terminal Kinase-Like Protein 3
  • Telomerase Transcriptional Element-Interacting Factor 4
  • SCY1-Like 1 (S. Cerevisiae) 2
  • N-Terminal Kinase-Like 2
  • MGC78454 2
  • SCAR21 3
  • CVAK90 4
  • SCYL1 5

External Ids for SCYL1 Gene

Previous HGNC Symbols for SCYL1 Gene

  • NTKL

Previous GeneCards Identifiers for SCYL1 Gene

  • GC11P066974
  • GC11P065542
  • GC11P065068
  • GC11P065069
  • GC11P065049
  • GC11P065292
  • GC11P061619

Summaries for SCYL1 Gene

Entrez Gene Summary for SCYL1 Gene

  • This gene encodes a transcriptional regulator belonging to the SCY1-like family of kinase-like proteins. The protein has a divergent N-terminal kinase domain that is thought to be catalytically inactive, and can bind specific DNA sequences through its C-terminal domain. It activates transcription of the telomerase reverse transcriptase and DNA polymerase beta genes. The protein has been localized to the nucleus, and also to the cytoplasm and centrosomes during mitosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SCYL1 Gene

SCYL1 (SCY1 Like Pseudokinase 1) is a Protein Coding gene. Diseases associated with SCYL1 include Spinocerebellar Ataxia, Autosomal Recessive 21 and Spinocerebellar Ataxia 21. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is SCYL2.

UniProtKB/Swiss-Prot Summary for SCYL1 Gene

  • Regulates COPI-mediated retrograde protein traffic at the interface between the Golgi apparatus and the endoplasmic reticulum (PubMed:18556652). Involved in the maintenance of the Golgi apparatus morphology (PubMed:26581903). Has no detectable kinase activity in vitro (PubMed:18556652).
  • Isoform 6 acts as transcriptional activator. It binds to three different types of GC-rich DNA binding sites (box-A, -B and -C) in the beta-polymerase promoter region. It also binds to the TERT promoter region.

Gene Wiki entry for SCYL1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCYL1 Gene

Genomics for SCYL1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCYL1 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 SCYL1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCYL1

Top Transcription factor binding sites by QIAGEN in the SCYL1 gene promoter:
  • Arnt
  • c-Ets-1
  • c-Myb
  • E47
  • ER-alpha
  • Meis-1b
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • Pax-5

Genomic Locations for SCYL1 Gene

Genomic Locations for SCYL1 Gene
chr11:65,525,077-65,538,710
(GRCh38/hg38)
Size:
13,634 bases
Orientation:
Plus strand
chr11:65,292,548-65,306,182
(GRCh37/hg19)
Size:
13,635 bases
Orientation:
Plus strand

Genomic View for SCYL1 Gene

Genes around SCYL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCYL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCYL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCYL1 Gene

Proteins for SCYL1 Gene

  • Protein details for SCYL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96KG9-SCYL1_HUMAN
    Recommended name:
    N-terminal kinase-like protein
    Protein Accession:
    Q96KG9
    Secondary Accessions:
    • A6NJF1
    • Q96G50
    • Q96KG8
    • Q96KH1
    • Q9HAW5
    • Q9HBL3
    • Q9NR53

    Protein attributes for SCYL1 Gene

    Size:
    808 amino acids
    Molecular mass:
    89631 Da
    Quaternary structure:
    • Interacts with GORAB. Interacts with COPA, COPB1 and COPB2 (By similarity). Homooligomer. Interacts with AP2B1.
    SequenceCaution:
    • Sequence=AAG09726.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAG17902.1; Type=Frameshift; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 3]: Non-canonical splice junctions.

    Alternative splice isoforms for SCYL1 Gene

neXtProt entry for SCYL1 Gene

Post-translational modifications for SCYL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SCYL1 Gene

Domains & Families for SCYL1 Gene

Gene Families for SCYL1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for SCYL1 Gene

InterPro:
Blocks:
  • HEAT repeat
ProtoNet:

Suggested Antigen Peptide Sequences for SCYL1 Gene

GenScript: Design optimal peptide antigens:
  • Teratoma-associated tyrosine kinase (NTKL_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96KG9

UniProtKB/Swiss-Prot:

SCYL1_HUMAN :
  • The protein kinase domain is predicted to be catalytically inactive.
  • Belongs to the protein kinase superfamily.
Domain:
  • The protein kinase domain is predicted to be catalytically inactive.
Family:
  • Belongs to the protein kinase superfamily.
genes like me logo Genes that share domains with SCYL1: view

Function for SCYL1 Gene

Molecular function for SCYL1 Gene

UniProtKB/Swiss-Prot Function:
Regulates COPI-mediated retrograde protein traffic at the interface between the Golgi apparatus and the endoplasmic reticulum (PubMed:18556652). Involved in the maintenance of the Golgi apparatus morphology (PubMed:26581903). Has no detectable kinase activity in vitro (PubMed:18556652).
UniProtKB/Swiss-Prot Function:
Isoform 6 acts as transcriptional activator. It binds to three different types of GC-rich DNA binding sites (box-A, -B and -C) in the beta-polymerase promoter region. It also binds to the TERT promoter region.

Phenotypes From GWAS Catalog for SCYL1 Gene

Gene Ontology (GO) - Molecular Function for SCYL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0004672 protein kinase activity IEA --
GO:0004713 protein tyrosine kinase activity NAS 10843802
GO:0005524 ATP binding IEA --
GO:0045296 cadherin binding HDA 25468996
genes like me logo Genes that share ontologies with SCYL1: view
genes like me logo Genes that share phenotypes with SCYL1: view

Human Phenotype Ontology for SCYL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCYL1 Gene

MGI Knock Outs for SCYL1:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCYL1

CRISPR Products

miRNA for SCYL1 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCYL1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCYL1 Gene

Localization for SCYL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCYL1 Gene

Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Endoplasmic reticulum-Golgi intermediate compartment. Golgi apparatus, cis-Golgi network. Note=Localized to the Endoplasmic reticulum-Golgi intermediate and cis-Golgi in an ARF1-independent manner.
[Isoform 1]: Cytoplasm. Note=Cytoplasmic throughout the cell cycle.
[Isoform 2]: Cytoplasm. Note=Cytoplasmic throughout the cell cycle.
[Isoform 3]: Cytoplasm. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Cytoplasmic during interphase and centrosomal during mitosis, it localizes to the centrosomes in a microtubule-independent manner.
[Isoform 6]: Nucleus.

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 SCYL1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
golgi apparatus 5
nucleus 4
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SCYL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm ISS 12783284
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment IEA,IDA 18556652
GO:0005794 Golgi apparatus IEA,IDA 18556652
GO:0005801 cis-Golgi network IDA 18556652
genes like me logo Genes that share ontologies with SCYL1: view

Pathways & Interactions for SCYL1 Gene

PathCards logo

SuperPathways for SCYL1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCYL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER IDA 18556652
GO:0006954 inflammatory response IEA --
GO:0016192 vesicle-mediated transport IEA --
GO:0018108 peptidyl-tyrosine phosphorylation IEA --
genes like me logo Genes that share ontologies with SCYL1: view

No data available for Pathways by source and SIGNOR curated interactions for SCYL1 Gene

Drugs & Compounds for SCYL1 Gene

(2) Drugs for SCYL1 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Grn163l Investigational Pharma Target 0

(1) Additional Compounds for SCYL1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SCYL1: view

Transcripts for SCYL1 Gene

mRNA/cDNA for SCYL1 Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
15 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 SCYL1

Alternative Splicing Database (ASD) splice patterns (SP) for SCYL1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b ^ 15a ·
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13:

ExUns: 15b · 15c ^ 16a · 16b ^ 17a · 17b · 17c ^ 18 ^ 19
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for SCYL1 Gene

GeneLoc Exon Structure for
SCYL1

Expression for SCYL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCYL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SCYL1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.9) and Bone marrow mesenchymal stem cell (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SCYL1 Gene



Protein tissue co-expression partners for SCYL1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCYL1

SOURCE GeneReport for Unigene cluster for SCYL1 Gene:

Hs.238839

mRNA Expression by UniProt/SwissProt for SCYL1 Gene:

Q96KG9-SCYL1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for SCYL1 Gene

  • Nervous system(4.7)
  • Liver(4.5)
  • Eye(4.4)
  • Skin(3.4)
  • Muscle(2.8)
  • Lung(2.6)
  • Blood(2.4)
  • Intestine(2.2)
  • Bone marrow(2.2)
  • Heart(2)
  • Kidney(2)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with SCYL1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCYL1 Gene

Orthologs for SCYL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SCYL1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SCYL1 30 31
  • 99.41 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SCYL1 30 31
  • 90.24 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SCYL1 30 31
  • 89.17 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Scyl1 30 17 31
  • 87.63 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Scyl1 30
  • 87.39 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SCYL1 31
  • 59 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SCYL1 31
  • 56 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SCYL1 31
  • 53 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia scyl1 30
  • 67.91 (n)
Str.394 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.2240 30
Zebrafish
(Danio rerio)
Actinopterygii wu:fk36e11 30
  • 66.33 (n)
SCYL1 (1 of 2) 31
  • 64 (a)
OneToMany
SCYL1 (2 of 2) 31
  • 64 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2322 30
Fruit Fly
(Drosophila melanogaster)
Insecta yata 30 31
  • 56.78 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001091 30
  • 52.35 (n)
Worm
(Caenorhabditis elegans)
Secernentea W07G4.3 30 31
  • 46.71 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CEX1 31 33
  • 20 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G40730 30
  • 48.31 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0819900 30
  • 50.22 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU04279 30
  • 49.35 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 47 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.5507 30
Species where no ortholog for SCYL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chicken (Gallus gallus)
  • 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)
  • 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)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SCYL1 Gene

ENSEMBL:
Gene Tree for SCYL1 (if available)
TreeFam:
Gene Tree for SCYL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCYL1: view image

Paralogs for SCYL1 Gene

Paralogs for SCYL1 Gene

genes like me logo Genes that share paralogs with SCYL1: view

Variants for SCYL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCYL1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
691875 Pathogenic: Spinocerebellar ataxia type 21 65,536,099(+) C/CT FRAMESHIFT_VARIANT
692036 Pathogenic: Spinocerebellar ataxia, autosomal recessive 21 65,526,274(+) A/T NONSENSE
708799 Benign/Likely Benign: not provided 65,537,838(+) G/T MISSENSE_VARIANT
709287 Benign: not provided 65,537,979(+) G/A MISSENSE_VARIANT
721009 Benign: not provided 65,531,677(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SCYL1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCYL1 Gene

Variant ID Type Subtype PubMed ID
esv2671903 CNV deletion 23128226
nsv361 CNV insertion 18451855
nsv555212 CNV loss 21841781
nsv951018 CNV deletion 24416366

Variation tolerance for SCYL1 Gene

Residual Variation Intolerance Score: 50.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.00; 49.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCYL1 Gene

Human Gene Mutation Database (HGMD)
SCYL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCYL1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCYL1 Gene

Disorders for SCYL1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for SCYL1 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SCYL1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCYL1_HUMAN
  • Spinocerebellar ataxia, autosomal recessive, 21 (SCAR21) [MIM:616719]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR21 is characterized by cerebellar atrophy and ataxia with onset in early childhood. Patients also manifest recurrent episodes of liver failure, hepatic fibrosis and a peripheral neuropathy. {ECO:0000269 PubMed:26581903}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with SCYL1: view

No data available for Genatlas for SCYL1 Gene

Publications for SCYL1 Gene