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    SCLY selenocysteine lyase [ Homo sapiens (human) ]

    Gene ID: 51540, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SCLYprovided by HGNC
    Official Full Name
    selenocysteine lyaseprovided by HGNC
    Primary source
    HGNC:HGNC:18161
    See related
    Ensembl:ENSG00000132330 MIM:611056; AllianceGenome:HGNC:18161
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCL; hSCL
    Summary
    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]
    Expression
    Ubiquitous expression in kidney (RPKM 6.4), liver (RPKM 4.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCLY in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (238061001..238099413)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (238550904..238589302)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (238969642..239008054)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124908001 Neighboring gene CRISPRi-validated cis-regulatory element chr2.7218 Neighboring gene CRISPRi-validated cis-regulatory element chr2.7219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12483 Neighboring gene UBE2F-SCLY readthrough (NMD candidate) Neighboring gene ubiquitin conjugating enzyme E2 F (putative) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238936739-238937352 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:238941390-238941585 Neighboring gene RNA, U6 small nuclear 1333, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:238948423-238948923 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:238951349-238951541 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12485 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239002815-239003484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239003485-239004152 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239004821-239005488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239005489-239006157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239006158-239006825 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239006826-239007494 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239014380-239015290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239015291-239016200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239016201-239017111 Neighboring gene espin like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239039005-239039675 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239049565-239050078 Neighboring gene kelch like family member 30

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase. Collins R, et al. PLoS One, 2012. PMID 22295093, Free PMC Article
    2. Characterization of selenocysteine lyase in human tissues and its relationship to tissue selenium concentrations. Daher R, et al. J Trace Elem Electrolytes Health Dis, 1992 Sep. PMID 1483038
    3. Selenocysteine lyase, a novel enzyme that specifically acts on selenocysteine. Mammalian distribution and purification and properties of pig liver enzyme. Esaki N, et al. J Biol Chem, 1982 Apr 25. PMID 6461656
    4. Biochemical discrimination between selenium and sulfur 2: mechanistic investigation of the selenium specificity of human selenocysteine lyase. Johansson AL, et al. PLoS One, 2012. PMID 22291978, Free PMC Article
    5. [Differential display of messenger RNA and identification of selenocysteine lyase gene in hepatocellular carcinoma cells transiently expressing hepatitis C virus core protein]. Yepes JO, et al. Biomedica, 2006 Jun. PMID 16925092

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the X-ray crystal structure of human selenocysteine lyase and the key residue that provides the selenocysteine specificity
      Title: Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.
    2. A reaction mechanism whereby the Selenocysteine over Cysteine specificity is achieved using a combination of chemical and physico-mechanical control mechanisms.
      Title: Biochemical discrimination between selenium and sulfur 2: mechanistic investigation of the selenium specificity of human selenocysteine lyase.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Results confirm that HCV core protein is associated with specific changes in mRNA expression, including the gene for selenocysteine lyase, which may be involved in the pathophysiology of hepatocellular carcinoma.
      Title: [Differential display of messenger RNA and identification of selenocysteine lyase gene in hepatocellular carcinoma cells transiently expressing hepatitis C virus core protein].
    5. PMID:10692412 concerns mostly mouse selenocysteine lyase, however, refers to the sequence of the N-terminal region of putative human protein.
      Title: cDNA cloning, purification, and characterization of mouse liver selenocysteine lyase. Candidate for selenium delivery protein in selenoprotein synthesis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough UBE2F-SCLY

    Readthrough gene: UBE2F-SCLY, Included gene: UBE2F

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables amino acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables selenocysteine lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables vitamin B6 binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in amino acid metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in selenocysteine catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    part_of catalytic complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    selenocysteine lyase
    NP_057594.5

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_016510.7 → NP_057594.5  selenocysteine lyase

      Status: VALIDATED

      Source sequence(s)
      AB209458, AC016757, AK293283, BC007891, BC018966
      Consensus CDS
      CCDS2524.3
      UniProtKB/Swiss-Prot
      B9A068, J3KN06, Q53SN1, Q53SN8, Q7L670, Q96I15, Q9NVT7, Q9NZR7
      UniProtKB/TrEMBL
      A0A0A0MQU4
      Related
      ENSP00000254663.7, ENST00000254663.12
      Conserved Domains (1) summary
      COG1104
      Location:30 → 441
      NifS; Cysteine sulfinate desulfinase/cysteine desulfurase or related enzyme [Amino acid transport and metabolism]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      238061001..238099413
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      238550904..238589302
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96I15.4 GenPept UniProtKB/Swiss-Prot:Q96I15

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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