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

    Gene ID: 330222, updated on 27-Nov-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
    Predicted to enable identical protein binding activity. Acts upstream of or within behavioral response to cocaine and regulation of dendritic spine development. Predicted to be located in plasma membrane. Predicted to be active in synapse. Is expressed in several structures, including gut; liver; metanephros; nervous system; and sensory organ. Orthologous to human SDK1 (sidekick cell adhesion molecule 1). [provided by Alliance of Genome Resources, Nov 2024]
    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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    See Sdk1 in Genome Data Viewer
    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. 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
    2. Definition of the critical domains required for homophilic targeting of mouse sidekick molecules. Hayashi K, et al. FASEB J, 2005 Apr. PMID 15703275
    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. Sidekick-1 is upregulated in glomeruli in HIV-associated nephropathy. Kaufman L, et al. J Am Soc Nephrol, 2004 Jul. PMID 15213259

    See all (27) 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.
    Submit: New GeneRIF Correction

    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 identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within regulation of dendritic spine development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in retina layer formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    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

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

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