Selenocysteine lyase (SCLY; EC 4.4.1.16) catalyzes the pyridoxal 5-prime phosphate-dependent conversion of L-selenocysteine to L-alanine and elemental selenium (Mihara et al., 2000 [PubMed 10692412]).[supplied by OMIM, Mar 2008] See more...

Aliases for SCLY Gene

Aliases for SCLY Gene

  • Selenocysteine Lyase 2 3 4 5
  • SCL 2 3 4
  • EC 4.4.1.16 4 51
  • HSCL 3 4
  • Putative Selenocysteine Lyase 2
  • SCLY 5

External Ids for SCLY Gene

Previous GeneCards Identifiers for SCLY Gene

  • GC02P236925
  • GC02P237558
  • GC02P238985
  • GC02P239256
  • GC02P238751
  • GC02P238634
  • GC02P230761

Summaries for SCLY Gene

Entrez Gene Summary for SCLY Gene

  • Selenocysteine lyase (SCLY; EC 4.4.1.16) catalyzes the pyridoxal 5-prime phosphate-dependent conversion of L-selenocysteine to L-alanine and elemental selenium (Mihara et al., 2000 [PubMed 10692412]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SCLY Gene

SCLY (Selenocysteine Lyase) is a Protein Coding gene. Diseases associated with SCLY include Somatization Disorder and Dependent Personality Disorder. Among its related pathways are Viral mRNA Translation and Selenocompound metabolism. Gene Ontology (GO) annotations related to this gene include transferase activity and lyase activity. An important paralog of this gene is NFS1.

UniProtKB/Swiss-Prot Summary for SCLY Gene

  • Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium.

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

Genomics for SCLY Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCLY 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
GH02J238059 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 600.7 -0.1 -123 3.6 ZNF221 SP1 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 TFE3 IKZF1 NFKBIZ SCLY lnc-ILKAP-6 ESPNL ILKAP UBE2F HES6 KLHL30 UBE2F-SCLY
GH02J238096 Promoter/Enhancer 1 EPDnew Ensembl ENCODE 609.8 +35.7 35677 1.2 TEAD4 ZIC2 USF1 POLR2A SIN3A USF2 NR3C1 SCLY ESPNL HES6 lnc-ILKAP-4 UBE2F-SCLY
GH02J238083 Promoter 0.3 EPDnew 600.4 +22.4 22413 0.1 SCLY lnc-ILKAP-4 ESPNL UBE2F-SCLY
GH02J238094 Promoter 0.3 EPDnew 600.3 +33.4 33448 0.1 SCLY lnc-ILKAP-4 ESPNL UBE2F-SCLY
GH02J237963 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 21.6 -94.1 -94149 6.2 CEBPG SP1 CREB1 GATAD2A ZNF629 TFE3 LEF1 IKZF1 NFKBIZ ZNF692 UBE2F UBE2F-SCLY lnc-ILKAP-5 ILKAP SCLY ENSG00000227252 RAMP1 TRAF3IP1 ENSG00000225057 ESPNL
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the SCLY gene promoter:
  • AP-1
  • AREB6
  • ATF-2
  • c-Jun
  • FOXD1
  • GATA-1
  • Lmo2
  • LyF-1
  • MZF-1
  • Zic3

Genomic Locations for SCLY Gene

Genomic Locations for SCLY Gene
chr2:238,060,924-238,099,413
(GRCh38/hg38)
Size:
38,490 bases
Orientation:
Plus strand
chr2:238,969,530-239,008,054
(GRCh37/hg19)
Size:
38,525 bases
Orientation:
Plus strand

Genomic View for SCLY Gene

Genes around SCLY on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SCLY Gene

Proteins for SCLY Gene

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

    Protein Symbol:
    Q96I15-SCLY_HUMAN
    Recommended name:
    Selenocysteine lyase
    Protein Accession:
    Q96I15
    Secondary Accessions:
    • B9A068
    • J3KN06
    • Q53SN1
    • Q53SN8
    • Q7L670
    • Q9NVT7
    • Q9NZR7

    Protein attributes for SCLY Gene

    Size:
    445 amino acids
    Molecular mass:
    48149 Da
    Cofactor:
    Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=BAA91659.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SCLY Gene

    Alternative splice isoforms for SCLY Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCLY Gene

Selected DME Specific Peptides for SCLY Gene

Q96I15:
  • DYNATTP
  • NFRPGTENTPMIAGLG
  • VTFVPVSKV
  • RDYLEERL
  • IFTSGGTESNNLVI
  • EAWGNPSS

Post-translational modifications for SCLY Gene

  • Ubiquitination at Lys307 and Lys341
  • Modification sites at PhosphoSitePlus

Protein Products

  • Signalway Proteins for SCLY
  • Abcam proteins for SCLY

Domains & Families for SCLY Gene

Gene Families for SCLY Gene

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

Protein Domains for SCLY Gene

Suggested Antigen Peptide Sequences for SCLY Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55776, highly similar to Homo sapiens selenocysteine lyase (SCLY), mRNA (B4DDP9_HUMAN)
  • Selenocysteine lyase (SCLY_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96I15

UniProtKB/Swiss-Prot:

SCLY_HUMAN :
  • Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.
Family:
  • Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.
genes like me logo Genes that share domains with SCLY: view

Function for SCLY Gene

Molecular function for SCLY Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=AH2 + L-selenocysteine = A + H(+) + hydrogenselenide + L-alanine; Xref=Rhea:RHEA:11632, ChEBI:CHEBI:13193, ChEBI:CHEBI:15378, ChEBI:CHEBI:17499, ChEBI:CHEBI:29317, ChEBI:CHEBI:57843, ChEBI:CHEBI:57972; EC=4.4.1.16;.
UniProtKB/Swiss-Prot Induction:
Up-regulated in acute glomerulonephritis. Regulated by JUN/AP-1.

Enzyme Numbers (IUBMB) for SCLY Gene

Phenotypes From GWAS Catalog for SCLY Gene

Gene Ontology (GO) - Molecular Function for SCLY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 21044950
GO:0009000 selenocysteine lyase activity IEA --
GO:0016597 amino acid binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SCLY: view
genes like me logo Genes that share phenotypes with SCLY: view

Animal Models for SCLY Gene

MGI Knock Outs for SCLY:
  • Scly Scly<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for SCLY Gene

miRTarBase miRNAs that target SCLY

Inhibitory RNA Products

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

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCLY Gene

Localization for SCLY Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCLY Gene

Cytoplasm, cytosol.

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 SCLY gene
Compartment Confidence
cytosol 5
mitochondrion 3
nucleus 2
golgi apparatus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCLY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:1902494 catalytic complex IEA --
genes like me logo Genes that share ontologies with SCLY: view

Pathways & Interactions for SCLY Gene

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

Gene Ontology (GO) - Biological Process for SCLY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001887 selenium compound metabolic process TAS --
GO:0006520 cellular amino acid metabolic process TAS 10692412
GO:0016261 selenocysteine catabolic process IEA --
genes like me logo Genes that share ontologies with SCLY: view

No data available for SIGNOR curated interactions for SCLY Gene

Drugs & Compounds for SCLY Gene

(8) Drugs for SCLY Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 16
Selenium Approved, Investigational, Vet_approved Pharma Enzyme, substrate 227
Ammonia Approved Pharma 0
Water Approved Pharma 0
Pyruvic acid Approved, Investigational Nutra 0

(2) Additional Compounds for SCLY Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Hydrogen selenide
  • [SeH2]
  • H2Se
  • Hydroselenic acid
  • Hydroselenate
  • Dihydrogen monoselenide
Methaneselenol
  • Methaneselenol
genes like me logo Genes that share compounds with SCLY: view

Transcripts for SCLY Gene

mRNA/cDNA for SCLY Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
21 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 SCLY

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

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

ExUns: 14a · 14b ^ 15a · 15b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SCLY Gene

GeneLoc Exon Structure for
SCLY

Expression for SCLY Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SCLY Gene

This gene is overexpressed in Heart (15.2), Peripheral blood mononuclear cells (7.3), and Lymph node (7.0).

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



Protein tissue co-expression partners for SCLY Gene

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

SOURCE GeneReport for Unigene cluster for SCLY Gene:

Hs.731909

Evidence on tissue expression from TISSUES for SCLY Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Skin(3)
  • Blood(2.2)
genes like me logo Genes that share expression patterns with SCLY: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCLY Gene

Orthologs for SCLY Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SCLY Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SCLY 30 31
  • 98.49 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SCLY 30 31
  • 83.46 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SCLY 30 31
  • 83.18 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Scly 30 17 31
  • 82.05 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Scly 30
  • 81.16 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SCLY 31
  • 74 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SCLY 31
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SCLY 30 31
  • 70.59 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SCLY 31
  • 62 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia scly 30
  • 62.51 (n)
Zebrafish
(Danio rerio)
Actinopterygii scly 30 31
  • 63.21 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Qtzl 31
  • 22 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea F13H8.9 30 31 32
  • 48.64 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NFS1 31
  • 29 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 49 (a)
OneToOne
Species where no ortholog for SCLY 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)
  • 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 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)

Evolution for SCLY Gene

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

Paralogs for SCLY Gene

Paralogs for SCLY Gene

(1) SIMAP similar genes for SCLY Gene using alignment to 17 proteins:

  • SCLY_HUMAN
  • B4DDP9_HUMAN
  • C9JNL5_HUMAN
  • E7ESG3_HUMAN
  • E7ESH3_HUMAN
  • F8WBU3_HUMAN
  • F8WCL3_HUMAN
  • H0Y396_HUMAN
  • H7C1N7_HUMAN
  • H7C1S7_HUMAN
  • H7C277_HUMAN
  • H7C280_HUMAN
  • H7C2H3_HUMAN
  • H7C2M1_HUMAN
  • H7C3V9_HUMAN
  • H7C4A1_HUMAN
  • L8E8S1_HUMAN
genes like me logo Genes that share paralogs with SCLY: view

Variants for SCLY Gene

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

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
716841 Likely Benign: not provided 238,096,853(+) G/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
775836 Benign: not provided 238,083,297(+) T/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
782740 Benign: not provided 238,098,250(+) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
785025 Benign: not provided 238,068,120(+) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
785026 Benign: not provided 238,081,843(+) C/T

Additional dbSNP identifiers (rs#s) for SCLY Gene

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

Variant ID Type Subtype PubMed ID
dgv4193n100 CNV gain 25217958
esv1081669 CNV insertion 17803354
esv2721746 CNV deletion 23290073
nsv1000252 CNV loss 25217958
nsv1119483 CNV insertion 24896259
nsv508894 CNV insertion 20534489
nsv953215 CNV deletion 24416366

Variation tolerance for SCLY Gene

Residual Variation Intolerance Score: 69.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.83; 79.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCLY Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for SCLY Gene

MalaCards: The human disease database

(14) MalaCards diseases for SCLY Gene - From: DISEASES

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

Additional Disease Information for SCLY

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SCLY: view

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

Publications for SCLY Gene

  1. cDNA cloning, purification, and characterization of mouse liver selenocysteine lyase. Candidate for selenium delivery protein in selenoprotein synthesis. (PMID: 10692412) Mihara H … Esaki N (The Journal of biological chemistry 2000) 2 3 4 23
  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 41
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Characterization of selenocysteine lyase in human tissues and its relationship to tissue selenium concentrations. (PMID: 1483038) Daher R … Van Lente F (Journal of trace elements and electrolytes in health and disease 1992) 3 23
  5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. (PMID: 31515488) Fragoza R … Yu H (Nature communications 2019) 3

Products for SCLY Gene

  • Signalway Proteins for SCLY

Sources for SCLY Gene