Mouse Gene Sftpd (ENSMUST00000077136.4) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus surfactant associated protein D (Sftpd), mRNA. (from RefSeq NM_009160)
Gencode Transcript: ENSMUST00000077136.4
Gencode Gene: ENSMUSG00000021795.10
Transcript (Including UTRs)
   Position: mm10 chr14:41,172,214-41,185,149 Size: 12,936 Total Exon Count: 8 Strand: -
Coding Region
   Position: mm10 chr14:41,172,336-41,183,132 Size: 10,797 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:41,172,214-41,185,149)mRNA (may differ from genome)Protein (374 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SFTPD_MOUSE
DESCRIPTION: RecName: Full=Pulmonary surfactant-associated protein D; Short=PSP-D; Short=SP-D; AltName: Full=Lung surfactant protein D; Flags: Precursor;
FUNCTION: Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
SUBUNIT: Oligomeric complex of 4 set of homotrimers.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix. Secreted, extracellular space, surface film.
MISCELLANEOUS: Pulmonary surfactant consists of 90% lipid and 10% protein. There are 4 surfactant-associated proteins: 2 collagenous, carbohydrate-binding glycoproteins (SP-A and SP-D) and 2 small hydrophobic proteins (SP-B and SP-C).
SIMILARITY: Belongs to the SFTPD family.
SIMILARITY: Contains 1 C-type lectin domain.
SIMILARITY: Contains 1 collagen-like domain.
WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=Pulmonary surfactant protein SP-D; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_mou_Ctlect_170";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.4028-0.086 Picture PostScript Text
3' UTR -20.50122-0.168 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR018378 - C-type_lectin_CS
IPR016187 - C-type_lectin_fold
IPR008160 - Collagen
IPR023350 - Lung_SPD-like_multimerisation
IPR015097 - Surfac_D-trimer

Pfam Domains:
PF00059 - Lectin C-type domain
PF01391 - Collagen triple helix repeat (20 copies)
PF09006 - Lung surfactant protein D coiled-coil trimerisation

SCOP Domains:
56436 - C-type lectin-like
57944 - Triple coiled coil domain of C-type lectins

ModBase Predicted Comparative 3D Structure on P50404
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001530 lipopolysaccharide binding
GO:0030246 carbohydrate binding
GO:0042802 identical protein binding
GO:0048029 monosaccharide binding

Biological Process:
GO:0002376 immune system process
GO:0007585 respiratory gaseous exchange
GO:0008228 opsonization
GO:0032703 negative regulation of interleukin-2 production
GO:0042130 negative regulation of T cell proliferation
GO:0043129 surfactant homeostasis
GO:0043152 induction of bacterial agglutination
GO:0045087 innate immune response
GO:0048286 lung alveolus development
GO:0050765 negative regulation of phagocytosis
GO:0050766 positive regulation of phagocytosis
GO:0050828 regulation of liquid surface tension
GO:0052405 negative regulation by host of symbiont molecular function
GO:1905226 regulation of adhesion of symbiont to host epithelial cell

Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005771 multivesicular body
GO:0005791 rough endoplasmic reticulum
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  L40156 - Mus musculus (clones 12.1, 2.1 and 4.1) surfactant protein D (Sftp4) mRNA, complete cds.
BC003705 - Mus musculus surfactant associated protein D, mRNA (cDNA clone MGC:5668 IMAGE:3601620), complete cds.
BC012896 - Mus musculus surfactant associated protein D, mRNA (cDNA clone IMAGE:3964084), with apparent retained intron.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04145 - Phagosome

Reactome (by CSHL, EBI, and GO)

Protein P50404 (Reactome details) participates in the following event(s):

R-MMU-8961021 SFTPD binds with itself to form SFTPD 12mer
R-MMU-5686335 CSF2RA:CSF2RB binds SFTPs
R-MMU-5686359 SFTPs translocate from extracellular region to clathrin-coated vesicle
R-MMU-5687284 DMBT1 binds SFTPD 12mer, SFTPAs
R-MMU-5683826 Surfactant metabolism
R-MMU-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_009160, P50404, Sftp4, SFTPD_MOUSE, uc007tcr.1, uc007tcr.2, uc007tcr.3
UCSC ID: uc007tcr.3
RefSeq Accession: NM_009160
Protein: P50404 (aka SFTPD_MOUSE or PSPD_MOUSE)
CCDS: CCDS26962.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.