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    Sftpd surfactant protein D [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25350, updated on 22-Apr-2017
    Official Symbol
    Sftpdprovided by RGD
    Official Full Name
    surfactant protein Dprovided by RGD
    Primary source
    RGD:3667
    See related
    Ensembl:ENSRNOG00000056001
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    SPD; SP-D
    Summary
    binds carbohydrates; may play a role in defense response in the lung [RGD, Feb 2006]
    Annotation information
    Annotation category: suggests misassembly
    Orthologs
    Location:
    16p14
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (18753535..18766100, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 16 NC_005115.3 (18621441..18633581, complement)

    Chromosome 16 - NC_005115.4Genomic Context describing neighboring genes Neighboring gene similar to phafin 2 Neighboring gene mannose-binding lectin (protein A) 1 Neighboring gene uncharacterized LOC102548312 Neighboring gene unconventional myosin-IXb-like

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • Phagosome, organism-specific biosystem (from KEGG)
      Phagosome, organism-specific biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
    • Phagosome, conserved biosystem (from KEGG)
      Phagosome, conserved biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lipopolysaccharide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    monosaccharide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    lung alveolus development IEA
    Inferred from Electronic Annotation
    more info
     
    lung alveolus development ISO
    Inferred from Sequence Orthology
    more info
     
    lung alveolus development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of T cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of interleukin-2 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of phagocytosis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    opsonization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of phagocytosis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of liquid surface tension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    respiratory gaseous exchange IEA
    Inferred from Electronic Annotation
    more info
     
    response to corticosteroid IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to glucocorticoid IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to growth factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to hyperoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    surfactant homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    surfactant homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    surfactant homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    surfactant homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    multivesicular body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    proteinaceous extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
     
    rough endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    pulmonary surfactant-associated protein D
    Names
    CP4
    PSP-D
    lung surfactant protein D
    pulmonary surfactant protein D
    surfactant associated protein D
    surfactant, pulmonary-associated protein D

    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_012878.2NP_037010.1  pulmonary surfactant-associated protein D precursor

      See identical proteins and their annotated locations for NP_037010.1

      Status: PROVISIONAL

      Source sequence(s)
      M81231
      UniProtKB/Swiss-Prot
      P35248
      Related
      ENSRNOP00000069079.1, ENSRNOT00000084813.1
      Conserved Domains (3) summary
      pfam01391
      Location:66124
      Collagen; Collagen triple helix repeat (20 copies)
      pfam09006
      Location:223268
      Surfac_D-trimer; Lung surfactant protein D coiled-coil trimerization
      cl02432
      Location:261374
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005115.4 Reference Rnor_6.0 Primary Assembly

      Range
      18753535..18766100 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000084.1 Alternate Rn_Celera

      Range
      17272045..17284082 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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