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    SCYL3 SCY1 like pseudokinase 3 [ Homo sapiens (human) ]

    Gene ID: 57147, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SCYL3provided by HGNC
    Official Full Name
    SCY1 like pseudokinase 3provided by HGNC
    Primary source
    HGNC:HGNC:19285
    See related
    Ensembl:ENSG00000000457 MIM:608192; AllianceGenome:HGNC:19285
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PACE1; PACE-1
    Summary
    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]
    Expression
    Ubiquitous expression in lymph node (RPKM 4.6), testis (RPKM 4.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q24.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (169849631..169894268, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (169205381..169249993, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (169818772..169863037, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928628 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:169751147-169751648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2079 Neighboring gene FIGNL1 interacting regulator of recombination and mitosis Neighboring gene methyltransferase 18, RPL3 N3(tau)-histidine Neighboring gene MPRA-validated peak450 silencer Neighboring gene RNA, 7SL, cytoplasmic 333, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:169862205-169862792 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:169862793-169863380 Neighboring gene VISTA enhancer hs1442 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:169914181-169914349 Neighboring gene kinesin associated protein 3 Neighboring gene RNA, 7SL, cytoplasmic 269, pseudogene Neighboring gene mitochondrial ribosomal protein S10 pseudogene 1

    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. Analysis on the susceptibility genes in two chinese pedigrees with familial Parkinson's disease. Xu C, et al. Neurol Res Int, 2010. PMID 21188226, Free PMC Article
    2. MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Maurer-Stroh S, et al. Genome Biol, 2004. PMID 15003124, Free PMC Article
    3. PACE-1, a novel protein that interacts with the C-terminal domain of ezrin. Sullivan A, et al. Exp Cell Res, 2003 Apr 1. PMID 12651155
    4. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. Cheung CL, et al. Hum Mol Genet, 2009 Feb 15. PMID 19064610
    5. BioID reveals an ATG9A interaction with ATG13-ATG101 in the degradation of p62/SQSTM1-ubiquitin clusters. Kannangara AR, et al. EMBO Rep, 2021 Oct 5. PMID 34369648, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT enables kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell migration NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spinal cord motor neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in lamellipodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein-associating with the carboxyl-terminal domain of ezrin
    Names
    SCY1-like 3
    SCY1-like protein 3
    SCY1-like, kinase-like 3
    ezrin-binding partner PACE-1 (PACE-1)
    ezrin-binding protein PACE-1

    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_020423.7 → NP_065156.5  protein-associating with the carboxyl-terminal domain of ezrin isoform 1

      See identical proteins and their annotated locations for NP_065156.5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AL031297, AL117233, DA449356
      Consensus CDS
      CCDS1286.1
      UniProtKB/TrEMBL
      X6RHX1
      Related
      ENSP00000356745.5, ENST00000367771.11
      Conserved Domains (3) summary
      cd14011
      Location:9 → 247
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      pfam00069
      Location:26 → 245
      Pkinase; Protein kinase domain
      sd00044
      Location:294 → 319
      HEAT; HEAT repeat [structural motif]

    2. NM_181093.4 → NP_851607.2  protein-associating with the carboxyl-terminal domain of ezrin isoform 2

      See identical proteins and their annotated locations for NP_851607.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2, which is longer than isoform 1.
      Source sequence(s)
      AK292507, AL031297, AL117233
      Consensus CDS
      CCDS1287.1
      UniProtKB/Swiss-Prot
      A8K8Z2, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6
      Related
      ENSP00000356746.4, ENST00000367772.8
      Conserved Domains (3) summary
      cd14011
      Location:9 → 247
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      pfam00069
      Location:26 → 245
      Pkinase; Protein kinase domain
      sd00044
      Location:294 → 319
      HEAT; HEAT repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      169849631..169894268 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001863.2 → XP_016857352.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X2

      UniProtKB/TrEMBL
      X6RHX1
      Related
      ENSP00000407993.1, ENST00000423670.1
      Conserved Domains (3) summary
      cd14011
      Location:9 → 247
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      pfam00069
      Location:26 → 245
      Pkinase; Protein kinase domain
      sd00044
      Location:294 → 319
      HEAT; HEAT repeat [structural motif]

    2. XM_011509801.2 → XP_011508103.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X1

      See identical proteins and their annotated locations for XP_011508103.1

      UniProtKB/Swiss-Prot
      A8K8Z2, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6
      Conserved Domains (3) summary
      cd14011
      Location:9 → 247
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      pfam00069
      Location:26 → 245
      Pkinase; Protein kinase domain
      sd00044
      Location:294 → 319
      HEAT; HEAT repeat [structural motif]

    3. XM_017001862.2 → XP_016857351.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X2

      UniProtKB/TrEMBL
      X6RHX1
      Conserved Domains (3) summary
      cd14011
      Location:9 → 247
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      pfam00069
      Location:26 → 245
      Pkinase; Protein kinase domain
      sd00044
      Location:294 → 319
      HEAT; HEAT repeat [structural motif]

    4. XM_006711465.2 → XP_006711528.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X1

      See identical proteins and their annotated locations for XP_006711528.1

      UniProtKB/Swiss-Prot
      A8K8Z2, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6
      Conserved Domains (3) summary
      cd14011
      Location:9 → 247
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      pfam00069
      Location:26 → 245
      Pkinase; Protein kinase domain
      sd00044
      Location:294 → 319
      HEAT; HEAT repeat [structural motif]

    5. XM_011509802.2 → XP_011508104.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X3

      See identical proteins and their annotated locations for XP_011508104.1

      Conserved Domains (2) summary
      sd00044
      Location:152 → 177
      HEAT; HEAT repeat [structural motif]
      cl21453
      Location:1 → 105
      PKc_like; Protein Kinases, catalytic domain

    6. XM_047425909.1 → XP_047281865.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      169205381..169249993 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337795.1 → XP_054193770.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X2

    2. XM_054337793.1 → XP_054193768.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X1

    3. XM_054337792.1 → XP_054193767.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X1

    4. XM_054337794.1 → XP_054193769.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X2

    5. XM_054337796.1 → XP_054193771.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X3

    6. XM_054337797.1 → XP_054193772.1  protein-associating with the carboxyl-terminal domain of ezrin isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IZE3.3 GenPept UniProtKB/Swiss-Prot:Q8IZE3

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