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Sdk1 sidekick cell adhesion molecule 1 [ Mus musculus (house mouse) ]

Gene ID: 330222, updated on 28-Apr-2024

Summary

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Official Symbol
Sdk1provided by MGI
Official Full Name
sidekick cell adhesion molecule 1provided by MGI
Primary source
MGI:MGI:2444413
See related
Ensembl:ENSMUSG00000039683 AllianceGenome:MGI:2444413
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
5330440E10; 6720466O15Rik
Summary
Acts upstream of or within behavioral response to cocaine and regulation of dendritic spine development. Predicted to be located in cell junction and plasma membrane. Predicted to be integral component of membrane. Predicted to be active in synapse. Is expressed in ganglia; metanephros; and sensory organ. Orthologous to human SDK1 (sidekick cell adhesion molecule 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal adult (RPKM 2.6), limb E14.5 (RPKM 2.3) and 25 other tissues See more
Orthologs
human all
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Genomic context

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Location:
5 G2; 5 79.81 cM
Exon count:
45
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (141227252..142201377)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (141241497..142215586)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E10362 Neighboring gene predicted gene, 38730 Neighboring gene predicted gene, 30866 Neighboring gene STARR-seq mESC enhancer starr_14727 Neighboring gene STARR-seq mESC enhancer starr_14728 Neighboring gene predicted gene, 54309 Neighboring gene 40S ribosomal protein S2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_14729 Neighboring gene predicted gene, 57842 Neighboring gene predicted gene 16035 Neighboring gene STARR-seq mESC enhancer starr_14730 Neighboring gene predicted gene, 24131 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:142515845-142516174 Neighboring gene STARR-seq mESC enhancer starr_14733 Neighboring gene predicted gene, 52792 Neighboring gene predicted gene, 30998 Neighboring gene predicted gene, 31068

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges. Rochon PL, et al. Elife, 2021 Sep 21. PMID 34545809, Free PMC Article
  2. Architecture of cell-cell adhesion mediated by sidekicks. Tang H, et al. Proc Natl Acad Sci U S A, 2018 Sep 11. PMID 30150416, Free PMC Article
  3. Molecular basis of sidekick-mediated cell-cell adhesion and specificity. Goodman KM, et al. Elife, 2016 Sep 19. PMID 27644106, Free PMC Article
  4. The homophilic adhesion molecule sidekick-1 contributes to augmented podocyte aggregation in HIV-associated nephropathy. Kaufman L, et al. FASEB J, 2007 May. PMID 17307840
  5. Definition of the critical domains required for homophilic targeting of mouse sidekick molecules. Hayashi K, et al. FASEB J, 2005 Apr. PMID 15703275

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges.
    Title: The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges.
  2. The results suggest that the Ig-like domains and the fibronectin III (FnIII) domains of Sidekicks play different roles in cell adhesion. The Ig-like domains mediate the homophilic transinteractions bridging adjacent cells, while the FnIII domains interact with membranes, resulting in a tight adhesion interface between cells
    Title: Architecture of cell-cell adhesion mediated by sidekicks.
  3. Here the authors report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1-4), arranged in a horseshoe conformation.
    Title: Molecular basis of sidekick-mediated cell-cell adhesion and specificity.
  4. Data conclude that the up-regulation of sdk-1 in podocytes is an important pathogenic factor in glomerulosclerosis and that the mechanism involves disruption of the actin cytoskeleton possibly via alterations in MAGI-1 function.
    Title: Up-regulation of the homophilic adhesion molecule sidekick-1 in podocytes contributes to glomerulosclerosis.
  5. -1 is an important mediator of cellular adhesion in HIV-infected podocytes and may contribute to podocyte clustering that is characteristic of pseudocrescent formation in HIV-associated nephropathy
    Title: The homophilic adhesion molecule sidekick-1 contributes to augmented podocyte aggregation in HIV-associated nephropathy.
  6. sidekick is expressed in ureteric bud and ureteric bud-derived tissues and may play a role in branching morphogenesis
    Title: Sidekick-1 is upregulated in glomeruli in HIV-associated nephropathy.
  7. results establish that the first and second immunoglobulin domains of sidekick-1 and -2 are necessary and sufficient to mediate and target homophilic adhesion
    Title: Definition of the critical domains required for homophilic targeting of mouse sidekick molecules.
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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

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

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within behavioral response to cocaine IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of dendritic spine development IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein sidekick-1
Names
sidekick homolog 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_177879.5 → NP_808547.3  protein sidekick-1

    See identical proteins and their annotated locations for NP_808547.3

    Status: VALIDATED

    Source sequence(s)
    AK086302, AK147578
    Consensus CDS
    CCDS39360.2
    UniProtKB/Swiss-Prot
    Q3UFD1, Q3UH53, Q6PAL2, Q6V3A4, Q8BMC2, Q8BZI1
    UniProtKB/TrEMBL
    B2RRK2
    Related
    ENSMUSP00000082928.5, ENSMUST00000085774.11
    Conserved Domains (8) summary
    cd00096
    Location:388 → 454
    Ig; Immunoglobulin domain
    smart00408
    Location:294 → 347
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:281 → 357
    IG_like; Immunoglobulin like
    cd00063
    Location:1686 → 1779
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:462 → 552
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:753 → 839
    fn3; Fibronectin type III domain
    pfam13895
    Location:94 → 169
    Ig_2; Immunoglobulin domain
    cl11960
    Location:476 → 552
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    141227252..142201377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006504712.2 → XP_006504775.1  protein sidekick-1 isoform X1

    UniProtKB/TrEMBL
    B2RRK2
    Conserved Domains (6) summary
    smart00409
    Location:100 → 169
    IG; Immunoglobulin
    cd00063
    Location:1621 → 1714
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:688 → 771
    fn3; Fibronectin type III domain
    pfam07679
    Location:397 → 487
    I-set; Immunoglobulin I-set domain
    pfam13927
    Location:275 → 347
    Ig_3; Immunoglobulin domain
    cl11960
    Location:492 → 581
    Ig; Immunoglobulin domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3UH53.1 GenPept UniProtKB/Swiss-Prot:Q3UH53

Gene LinkOut

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