Human Gene SFTPA1 (uc009xry.3)
  Description: Homo sapiens surfactant protein A1 (SFTPA1), transcript variant 2, mRNA.
RefSeq Summary (NM_001093770): This gene encodes a lung surfactant protein that is a member of a subfamily of C-type lectins called collectins. The encoded protein binds specific carbohydrate moieties found on lipids and on the surface of microorganisms. This protein plays an essential role in surfactant homeostasis and in the defense against respiratory pathogens. Mutations in this gene are associated with idiopathic pulmonary fibrosis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010].
Transcript (Including UTRs)
   Position: hg19 chr10:81,370,695-81,375,199 Size: 4,505 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr10:81,371,376-81,373,869 Size: 2,494 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:81,370,695-81,375,199)mRNA (may differ from genome)Protein (263 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMalacardsMGI
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: G5E9J3_HUMAN
DESCRIPTION: SubName: Full=Pulmonary surfactant-associated protein A1; SubName: Full=Surfactant, pulmonary-associated protein A1, isoform CRA_a;
SIMILARITY: Contains 1 C-type lectin domain.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SFTPA1
CDC HuGE Published Literature: SFTPA1
Positive Disease Associations: bronchopulmonary aspergillosis , bronchopulmonary dysplasia , cystic fibrosis , respiratory distress syndrome , respiratory syncytial virus infection , respiratory-distress syndrome
Related Studies:
  1. bronchopulmonary aspergillosis
    Saxena, S. et al. 2003, Association of polymorphisms in the collagen region of SP-A2 with increased levels of total IgE antibodies and eosinophilia in patients with allergic bronchopulmonary aspergillosis., The Journal of allergy and clinical immunology. 2003 May;111(5):1001-7. [PubMed 12743564]
    The results indicated that SP-A2 G1649C and SP-A2 A1660G, polymorphisms in the collagen region of SP-A2, might be one of the contributing factors to genetic predisposition and severity of clinical markers of ABPA.
  2. bronchopulmonary dysplasia
    Weber, B. et al. 2000, Polymorphisms of surfactant protein A genes and the risk of bronchopulmonary dysplasia in preterm infants, The Turkish journal of pediatrics. 2000 Jul-Sep;42(3):181-5. [PubMed 11105614]
    In addition to previously established risk factors for BPD, 6A6 polymorphism for SP-A1 gene is an independent co-factor. We believe treatment of neonatal RDS should also include stratification according to genetic risk factors.
  3. cystic fibrosis
    , Association of Common Haplotypes of Surfactant Protein A1 and A2 (SFTPA1 and SFTPA2) Genes with Severity of Lung Disease in Cystic Fibrosis, Pediatr Pulmonol 2006. [PubMed 16429424]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SFTPA1
Diseases sorted by gene-association score: pulmonary fibrosis, idiopathic* (346), pulmonary fibrosis, idiopathic susceptibility* (100), pulmonary fibrosis (17), lung sarcoma (11), acute interstitial pneumonia (11), respiratory distress syndrome in premature infants (10), lung disease (10), thymus adenocarcinoma (8), poland syndrome (8), surfactant dysfunction (7), idiopathic interstitial pneumonia (7), pulmonary surfactant metabolism dysfunction (7), splenic artery aneurysm (6)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1402.16 RPKM in Lung
Total median expression: 1406.97 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.7082-0.338 Picture PostScript Text
3' UTR -428.201330-0.322 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

Pfam Domains:
PF00059 - Lectin C-type domain

SCOP Domains:
56436 - C-type lectin-like

ModBase Predicted Comparative 3D Structure on G5E9J3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  S69686 - SP-A1=SP-A1 beta {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 137 nt].
AK290703 - Homo sapiens cDNA FLJ77898 complete cds, highly similar to Homo sapiens surfactant, pulmonary-associated protein A1 (SFTPA1), mRNA.
AK298002 - Homo sapiens cDNA FLJ54288 complete cds, moderately similar to Pulmonary surfactant-associated protein A1 precursor.
AK298034 - Homo sapiens cDNA FLJ50593 complete cds, moderately similar to Pulmonary surfactant-associated protein A1 precursor.
AK298029 - Homo sapiens cDNA FLJ51913 complete cds, highly similar to Pulmonary surfactant-associated protein A1 precursor.
LQ270737 - Sequence 65 from Patent WO2016071350.
LQ270739 - Sequence 67 from Patent WO2016071350.
LQ270741 - Sequence 69 from Patent WO2016071350.
LQ270743 - Sequence 71 from Patent WO2016071350.
LQ270745 - Sequence 73 from Patent WO2016071350.
LQ270747 - Sequence 75 from Patent WO2016071350.
S69680 - SP-A2=SP-A2 alpha {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 167 nt].
S69681 - SP-A2=SP-2A beta {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 170 nt].
AK316196 - Homo sapiens cDNA, FLJ79095 complete cds, highly similar to Pulmonary surfactant-associated protein A2 precursor.
HQ021433 - Homo sapiens surfactant protein A1 variant AD' 6A (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021434 - Homo sapiens surfactant protein A1 variant AD' 6A2 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021435 - Homo sapiens surfactant protein A1 variant AD' 6A3 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021436 - Homo sapiens surfactant protein A1 variant AD' 6A4 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021437 - Homo sapiens surfactant protein A1 variant AB'D' 6A2 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021438 - Homo sapiens surfactant protein A1 variant AB'D' 6A3 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021439 - Homo sapiens surfactant protein A1 variant AB'D' 6A4 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021440 - Homo sapiens surfactant protein A1 variant ACD' 6A2 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021441 - Homo sapiens surfactant protein A1 variant ACD' 6A3 (SFTPA1) mRNA, complete cds, alternatively spliced.
HQ021442 - Homo sapiens surfactant protein A1 variant ACD' 6A4 (SFTPA1) mRNA, complete cds, alternatively spliced.
JX502764 - Homo sapiens surfactant protein A1 variant AB'D' 6A (SFTPA1) mRNA, complete cds, alternatively spliced.
JX502765 - Homo sapiens surfactant protein A1 variant ACD' 6A (SFTPA1) mRNA, complete cds, alternatively spliced.
AK298092 - Homo sapiens cDNA FLJ61144 complete cds, highly similar to Pulmonary surfactant-associated protein A1 precursor.
S69685 - SP-A1=SP-A1 alpha {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 132 nt].
S69687 - SP-A1=SP-A1 gamma {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 192 nt].
S69688 - SP-A1=SP-A1 delta {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 195 nt].
S69690 - SP-A1=SP-A1 epsilon {5' region, alternatively spliced} [human, fetal lung explants, mRNA Partial, 203 nt].
AK309518 - Homo sapiens cDNA, FLJ99559.
BC026229 - Homo sapiens surfactant protein A1B, mRNA (cDNA clone IMAGE:4704021).
M13686 - Human pulmonary surfactant-associated protein mRNA, complete cds, clone MPSAP-6A.
BC111570 - Homo sapiens surfactant protein A1B, mRNA (cDNA clone MGC:133365 IMAGE:40069324), complete cds.
BC029913 - Homo sapiens surfactant protein A1B, mRNA (cDNA clone IMAGE:5175402), partial cds.
AB590481 - Synthetic construct DNA, clone: pFN21AE1222, Homo sapiens SFTPA1 gene for surfactant protein A1, without stop codon, in Flexi system.
AK309522 - Homo sapiens cDNA, FLJ99563.
JD061994 - Sequence 43018 from Patent EP1572962.
JD392583 - Sequence 373607 from Patent EP1572962.
JD133953 - Sequence 114977 from Patent EP1572962.
JD252344 - Sequence 233368 from Patent EP1572962.
JD370114 - Sequence 351138 from Patent EP1572962.
JD244670 - Sequence 225694 from Patent EP1572962.
JD142136 - Sequence 123160 from Patent EP1572962.
JD498464 - Sequence 479488 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: G5E9J3, G5E9J3_HUMAN, hCG_2025128, NM_001093770, NP_005402
UCSC ID: uc009xry.3
RefSeq Accession: NM_001093770
Protein: G5E9J3 CCDS: CCDS44444.2

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SFTPA1:
pf (Pulmonary Fibrosis Predisposition Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001093770.2
exon count: 6CDS single in 3' UTR: no RNA size: 2219
ORF size: 792CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1739.00frame shift in genome: no % Coverage: 99.32
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.