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    Sdk2 sidekick cell adhesion molecule 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360652, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Sdk2provided by RGD
    Official Full Name
    sidekick cell adhesion molecule 2provided by RGD
    Primary source
    RGD:1310397
    See related
    EnsemblRapid:ENSRNOG00000024711 AllianceGenome:RGD:1310397
    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 be involved in homophilic cell adhesion via plasma membrane adhesion molecules; retina morphogenesis in camera-type eye; and synapse assembly. Predicted to be located in membrane. Predicted to be active in synapse. Orthologous to human SDK2 (sidekick cell adhesion molecule 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 20.4), Lung (RPKM 14.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sdk2 in Genome Data Viewer
    Location:
    10q32.1
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (99324047..99601683, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (98824916..99102590, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (102299593..102576554, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene CDC42 effector protein 4 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase-like Neighboring gene uncharacterized LOC102547853 Neighboring gene uncharacterized LOC102547687 Neighboring gene uncharacterized LOC120095211 Neighboring gene uncharacterized LOC102548022

    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. Sidekick 2 directs formation of a retinal circuit that detects differential motion. Krishnaswamy A, et al. Nature, 2015 Aug 27. PMID 26287463, Free PMC Article
    2. The complexity of PDZ domain-mediated interactions at glutamatergic synapses: a case study on neuroligin. Meyer G, et al. Neuropharmacology, 2004 Oct. PMID 15458844
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    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

    Process Evidence Code Pubs
    involved_in camera-type eye photoreceptor cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retina layer formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein sidekick-2
    Names
    sidekick 2
    sidekick homolog 2

    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_001413325.2 → NP_001400254.1  protein sidekick-2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      Related
      ENSRNOP00000062573.2, ENSRNOT00000065145.4

    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_086028.1 Reference GRCr8

      Range
      99324047..99601683 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006247693.5 → XP_006247755.1  protein sidekick-2 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K999, A6HKH5, D3ZDA6
      Related
      ENSRNOP00000074916.1, ENSRNOT00000091129.3
      Conserved Domains (6) summary
      cd00096
      Location:329 → 397
      Ig; Immunoglobulin domain
      smart00408
      Location:236 → 289
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:505 → 589
      IG_like; Immunoglobulin like
      cd00063
      Location:1629 → 1722
      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:405 → 495
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:419 → 495
      Ig; Immunoglobulin domain

    2. XM_063269472.1 → XP_063125542.1  protein sidekick-2 isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108303.2: Suppressed sequence

      Description
      NM_001108303.2: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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