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

Summary

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, Dec 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

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

RH127141 (e-PCR)
- UniSTS:209413

RH134508 (e-PCR)
- UniSTS:217788

RH142164 (e-PCR)
- UniSTS:231416

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)

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]