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    Scyl1 SCY1 like pseudokinase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 293684, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Scyl1provided by RGD
    Official Full Name
    SCY1 like pseudokinase 1provided by RGD
    Primary source
    RGD:1307330
    See related
    EnsemblRapid:ENSRNOG00000023668 AllianceGenome:RGD:1307330
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable ATP binding activity and protein kinase activity. Predicted to be involved in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Predicted to act upstream of or within inflammatory response; neuron differentiation; and protein localization. Predicted to be located in cis-Golgi network; cytosol; and endoplasmic reticulum-Golgi intermediate compartment. Predicted to be part of COPI vesicle coat. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 21. Orthologous to human SCYL1 (SCY1 like pseudokinase 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 169.9), Muscle (RPKM 165.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Scyl1 in Genome Data Viewer
    Location:
    1q43
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (212475198..212489285, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (203045776..203059550, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (221115992..221129668, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene EH domain binding protein 1-like 1 Neighboring gene family with sequence similarity 89, member B Neighboring gene zinc ribbon domain containing 2 Neighboring gene latent transforming growth factor beta binding protein 3 Neighboring gene uncharacterized LOC120097381 Neighboring gene nuclear paraspeckle assembly transcript 1 Neighboring gene FERM domain containing 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Scyl1, mutated in a recessive form of spinocerebellar neurodegeneration, regulates COPI-mediated retrograde traffic. Burman JL, et al. J Biol Chem, 2008 Aug 15. PMID 18556652
    2. Cloning and characterization of a novel gene which encodes a protein interacting with the mitosis-associated kinase-like protein NTKL. Di Y, et al. J Hum Genet, 2003. PMID 12783284
    3. GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation. Witkos TM, et al. Nat Commun, 2019 Jan 10. PMID 30631079, Free PMC Article
    4. Overlapping Role of SCYL1 and SCYL3 in Maintaining Motor Neuron Viability. Kuliyev E, et al. J Neurosci, 2018 Mar 7. PMID 29437892, Free PMC Article
    5. Role of the AP2 beta-appendage hub in recruiting partners for clathrin-coated vesicle assembly. Schmid EM, et al. PLoS Biol, 2006 Sep. PMID 16903783, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data demonstrate a function for Scyl1 as an accessory factor in COPI trafficking and suggest that alterations in the COPI pathway result in neurodegenerative disease.
      Title: Scyl1, mutated in a recessive form of spinocerebellar neurodegeneration, regulates COPI-mediated retrograde traffic.
    Submit: New GeneRIF Correction

    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 RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within spinal cord motor neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of COPI vesicle coat ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cis-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cis-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    N-terminal kinase-like protein
    Names
    SCY1-like protein 1
    SCY1-like, kinase-like 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_001011938.2 → NP_001011938.1  N-terminal kinase-like protein

      See identical proteins and their annotated locations for NP_001011938.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      Q5M9F8
      UniProtKB/TrEMBL
      A6HZ98, A6HZ99
      Related
      ENSRNOP00000105478.1, ENSRNOT00000172302.1
      Conserved Domains (2) summary
      cd14011
      Location:29 → 296
      PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
      sd00044
      Location:351 → 372
      HEAT; HEAT repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      212475198..212489285 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006230749.5 → XP_006230811.3  N-terminal kinase-like protein isoform X1

      Related
      ENSRNOP00000030146.6, ENSRNOT00000032387.9

    2. XM_063286864.1 → XP_063142934.1  N-terminal kinase-like protein isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5M9F8.1 GenPept UniProtKB/Swiss-Prot:Q5M9F8

    Gene LinkOut

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

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