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

Gene ID: 293684, updated on 2-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 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 protein phosphorylation IEA
Inferred from Electronic Annotation
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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