Sftpd (surfactant protein D) - Rat Genome Database

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Gene: Sftpd (surfactant protein D) Rattus norvegicus
Analyze
Symbol: Sftpd
Name: surfactant protein D
RGD ID: 3667
Description: Enables identical protein binding activity; lipopolysaccharide binding activity; and monosaccharide binding activity. Involved in several processes, including negative regulation of interleukin-2 production; opsonization; and regulation of phagocytosis. Located in extracellular space; multivesicular body; and rough endoplasmic reticulum. Biomarker of Coronavirus infectious disease; asthma; bacterial pneumonia; lung disease; and newborn respiratory distress syndrome. Human ortholog(s) of this gene implicated in asthma; lung disease (multiple); respiratory syncytial virus infectious disease; and rhinitis. Orthologous to human SFTPD (surfactant protein D); PARTICIPATES IN surfactant homeostasis pathway; forkhead class A signaling pathway; phagocytosis pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CP4; lung surfactant protein D; PSP-D; pulmonary surfactant protein D; pulmonary surfactant-associated protein D; SP-D; SPD; surfactant associated protein D; surfactant pulmonary-associated protein D; surfactant, pulmonary-associated protein D
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21617,046,491 - 17,058,968 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1617,046,483 - 17,059,927 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1617,110,520 - 17,122,892 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01618,238,920 - 18,251,351 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01617,163,418 - 17,175,790 (-)NCBIRnor_WKY
Rnor_6.01618,753,535 - 18,766,100 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1618,745,458 - 18,766,174 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01618,621,441 - 18,633,581 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1617,272,045 - 17,284,082 (-)NCBICelera
RH 3.4 Map16167.0RGD
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Pneumocystis carinii pneumonia alters expression and distribution of lung collectins SP-A and SP-D. Atochina EN, etal., J Lab Clin Med. 2001 Jun;137(6):429-39.
2. Attenuated allergic airway hyperresponsiveness in C57BL/6 mice is associated with enhanced surfactant protein (SP)-D production following allergic sensitization. Atochina EN, etal., Respir Res. 2003 Dec 8;4:15. Print 2003.
3. Immune reconstitution during Pneumocystis lung infection: disruption of surfactant component expression and function by S-nitrosylation. Atochina-Vasserman EN, etal., J Immunol. 2009 Feb 15;182(4):2277-87.
4. Recombinant rat surfactant-associated protein D inhibits human T lymphocyte proliferation and IL-2 production. Borron PJ, etal., J Immunol. 1998 Nov 1;161(9):4599-603.
5. Patterns of neutrophil serine protease-dependent cleavage of surfactant protein D in inflammatory lung disease. Cooley J, etal., J Leukoc Biol. 2008 Apr;83(4):946-55. Epub 2008 Jan 22.
6. Association between single nucleotide polymorphisms of surfactant protein D and allergic rhinitis in Chinese patients. Deng YQ, etal., Tissue Antigens. 2009 Jun;73(6):546-52.
7. Regulation of surfactant protein D expression by glucocorticoids in vitro and in vivo. Deterding RR, etal., Am J Respir Cell Mol Biol. 1994 Jan;10(1):30-7.
8. Sivelestat sodium hydrate improves septic acute lung injury by reducing alveolar dysfunction. Endo S, etal., Res Commun Mol Pathol Pharmacol. 2006;119(1-6):53-65.
9. Surfactant protein levels in bronchoalveolar lavage after segmental allergen challenge in patients with asthma. Erpenbeck VJ, etal., Allergy. 2006 May;61(5):598-604.
10. Surfactant protein D increases phagocytosis and aggregation of pollen-allergen starch granules. Erpenbeck VJ, etal., Am J Physiol Lung Cell Mol Physiol. 2005 Apr;288(4):L692-8. Epub 2004 Dec 10.
11. Surfactant protein D inhibits early airway response in Aspergillus fumigatus-sensitized mice. Erpenbeck VJ, etal., Clin Exp Allergy. 2006 Jul;36(7):930-40.
12. Pulmonary-specific expression of SP-D corrects pulmonary lipid accumulation in SP-D gene-targeted mice. Fisher JH, etal., Am J Physiol Lung Cell Mol Physiol. 2000 Feb;278(2):L365-73.
13. Polymorphisms in Surfactant Protein D are Associated with COPD. Foreman MG, etal., Am J Respir Cell Mol Biol. 2010 May 6.
14. Serum surfactant protein D is increased in acute and chronic inflammation in mice. Fujita M, etal., Cytokine. 2005 Jul 7;31(1):25-33.
15. Rat respiratory coronavirus infection: replication in airway and alveolar epithelial cells and the innate immune response. Funk CJ, etal., J Gen Virol. 2009 Dec;90(Pt 12):2956-64. Epub 2009 Sep 9.
16. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
17. Relationship between pulmonary surfactant protein and lipid peroxidation in lung injury due to paraquat intoxication in rats. Gil HW, etal., Korean J Intern Med. 2007 Jun;22(2):67-72.
18. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
19. Serial changes in surfactant-associated proteins in lung and serum before and after onset of ARDS. Greene KE, etal., Am J Respir Crit Care Med. 1999 Dec;160(6):1843-50.
20. Pulmonary surfactant, lung function, and endobronchial inflammation in cystic fibrosis. Griese M, etal., Am J Respir Crit Care Med. 2004 Nov 1;170(9):1000-5. Epub 2004 Jul 21.
21. Children with absent surfactant protein D in bronchoalveolar lavage have more frequently pneumonia. Griese M, etal., Pediatr Allergy Immunol. 2008 Nov;19(7):639-47. Epub 2008 Feb 11.
22. S-nitrosylation of surfactant protein-D controls inflammatory function. Guo CJ, etal., PLoS Biol. 2008 Nov 11;6(11):e266. doi: 10.1371/journal.pbio.0060266.
23. Aspergillus fumigatus-induced allergic airway inflammation alters surfactant homeostasis and lung function in BALB/c mice. Haczku A, etal., Am J Respir Cell Mol Biol. 2001 Jul;25(1):45-50.
24. Surfactant protein D and KL-6 as serum biomarkers of interstitial lung disease in patients with scleroderma. Hant FN, etal., J Rheumatol. 2009 Apr;36(4):773-80. Epub 2009 Mar 13.
25. Circulating surfactant protein D is decreased in systemic lupus erythematosus. Hoegh SV, etal., J Rheumatol. 2009 Nov;36(11):2449-53. Epub 2009 Oct 15.
26. Nihon Kyobu Shikkan Gakkai zasshi Honda Y Nihon Kyobu Shikkan Gakkai Zasshi. 1996 Dec;34 Suppl:181-5.
27. Surfactant protein-D and surfactant inhibit endotoxin-induced pulmonary inflammation. Ikegami M, etal., Chest. 2007 Nov;132(5):1447-54. Epub 2007 Oct 9.
28. SP-D-deficient mice are resistant to hyperoxia. Jain D, etal., Am J Physiol Lung Cell Mol Physiol. 2007 Apr;292(4):L861-71. Epub 2006 Dec 8.
29. Surfactant protein D protects against acute hyperoxic lung injury. Jain D, etal., Am J Respir Crit Care Med. 2008 Oct 15;178(8):805-13. Epub 2008 Jul 17.
30. The role of surfactant protein D in the colonisation of the respiratory tract and onset of bacteraemia during pneumococcal pneumonia. Jounblat R, etal., Respir Res. 2005 Oct 28;6:126.
31. Eosinophilic inclusions in rat Clara cells and the effect of an inhaled corticosteroid. Kambara T, etal., Toxicol Pathol. 2009;37(3):315-23.
32. Surfactant protein levels in severe respiratory syncytial virus infection. Kerr MH and Paton JY, Am J Respir Crit Care Med. 1999 Apr;159(4 Pt 1):1115-8.
33. Surfactant Protein D Deficiency Increases Lung Injury during Endotoxemia. King BA and Kingma PS, Am J Respir Cell Mol Biol. 2010 Jul 16.
34. Correction of pulmonary abnormalities in Sftpd-/- mice requires the collagenous domain of surfactant protein D. Kingma PS, etal., J Biol Chem. 2006 Aug 25;281(34):24496-505. Epub 2006 Jun 20.
35. Elevation of surfactant protein D, a pulmonary disease biomarker, in the sera of uveitis patients with sarcoidosis. Kitaichi N, etal., Jpn J Ophthalmol. 2010 Jan;54(1):81-4. Epub 2010 Feb 12.
36. Pulmonary collectins enhance phagocytosis of Mycobacterium avium through increased activity of mannose receptor. Kudo K, etal., J Immunol. 2004 Jun 15;172(12):7592-602.
37. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
38. Characterization of the rat pulmonary surfactant protein A promoter. Lacaze-Masmonteil T, etal., Eur J Biochem 1992 Jun 15;206(3):613-23.
39. Clinical importance of bronchoalveolar lavage fluid and blood cytokines, surfactant protein D, and Kerbs von Lungren 6 antigen in idiopathic pulmonary alveolar proteinosis. Lin FC, etal., Mayo Clin Proc. 2008 Dec;83(12):1344-9.
40. Heterogeneous allele expression of pulmonary SP-D gene in rat large intestine and other tissues. Lin Z and Floros J, Physiol Genomics 2002 Dec 3;11(3):235-43.
41. Susceptibility of mice genetically deficient in SP-A or SP-D gene to invasive pulmonary aspergillosis. Madan T, etal., Mol Immunol. 2010 Jun;47(10):1923-30. Epub 2010 Apr 21.
42. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
43. Prognostic value of serum surfactant protein D level prior to transplant for the development of bronchiolitis obliterans syndrome and idiopathic pneumonia syndrome following allogeneic hematopoietic stem cell transplantation. Nakane T, etal., Bone Marrow Transplant. 2008 Jul;42(1):43-9. Epub 2008 Mar 17.
44. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
45. Genetic variants of surfactant proteins A, B, C, and D in bronchopulmonary dysplasia. Pavlovic J, etal., Dis Markers. 2006;22(5-6):277-91.
46. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
47. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
48. GOA pipeline RGD automated data pipeline
49. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
50. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
51. Total extracellular surfactant is increased but abnormal in a rat model of gram-negative bacterial pneumonia. Russo TA, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Sep;283(3):L655-63.
52. Respiratory distress after intratracheal bleomycin: selective deficiency of surfactant proteins B and C. Savani RC, etal., Am J Physiol Lung Cell Mol Physiol. 2001 Sep;281(3):L685-96.
53. Pulmonary surfactant in patients with Pneumocystis pneumonia and acquired immunodeficiency syndrome. Schmidt R, etal., Crit Care Med. 2006 Sep;34(9):2370-6.
54. Distribution of surfactant proteins in type II pneumocytes of newborn, 14-day old, and adult rats: an immunoelectron microscopic and stereological study. Schmiedl A, etal., Histochem Cell Biol. 2005 Dec;124(6):465-76. Epub 2005 Sep 27.
55. Increased surfactant protein a and d expression in acute ovalbumin-induced allergic airway inflammation in brown norway rats. Schmiedl A, etal., Int Arch Allergy Immunol. 2009;148(2):118-26. Epub 2008 Sep 19.
56. Serum surfactant protein D during acute exacerbations of chronic obstructive pulmonary disease. Shakoori TA, etal., Dis Markers. 2009;27(6):287-94.
57. Primary structure of rat pulmonary surfactant protein D. cDNA and deduced amino acid sequence. Shimizu H, etal., J Biol Chem 1992 Jan 25;267(3):1853-7.
58. The effects of fluticasone with or without salmeterol on systemic biomarkers of inflammation in chronic obstructive pulmonary disease. Sin DD, etal., Am J Respir Crit Care Med. 2008 Jun 1;177(11):1207-14. Epub 2008 Feb 28.
59. Surfactant protein D and bronchial dysplasia in smokers at high risk of lung cancer. Sin DD, etal., Chest. 2008 Sep;134(3):582-8.
60. The association between BMI and plasma cytokine levels in patients with acute lung injury. Stapleton RD, etal., Chest. 2010 Sep;138(3):568-77. Epub 2010 Apr 30.
61. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
62. Surfactant protein D regulates airway function and allergic inflammation through modulation of macrophage function. Takeda K, etal., Am J Respir Crit Care Med. 2003 Oct 1;168(7):783-9. Epub 2003 Jul 25.
63. Adsorption of pulmonary surfactant protein D to phospholipid monolayers at the air-water interface. Taneva S, etal., Biochemistry. 1997 Jul 1;36(26):8173-9.
64. Haplotypes of the surfactant protein genes A and D as susceptibility factors for the development of respiratory distress syndrome. Thomas NJ, etal., Acta Paediatr. 2007 Jul;96(7):985-9. Epub 2007 May 24.
65. Transmission of surfactant protein variants and haplotypes in children hospitalized with respiratory syncytial virus. Thomas NJ, etal., Pediatr Res. 2009 Jul;66(1):70-3.
66. Novel strategy to identify genetic risk factors for COPD severity: a genetic isolate. van Diemen CC, etal., Eur Respir J. 2010 Apr;35(4):768-75. Epub 2009 Sep 24.
67. Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d. Wang H, etal., Biochemistry. 2008 Jan 15;47(2):710-20. Epub 2007 Dec 20.
68. Elevated expression of surfactant proteins in newborn rats during adaptation to hyperoxia. White CW, etal., Am J Respir Cell Mol Biol. 2001 Jul;25(1):51-9.
69. Multimerization of surfactant protein D, but not its collagen domain, is required for antiviral and opsonic activities related to influenza virus. White M, etal., J Immunol. 2008 Dec 1;181(11):7936-43.
70. Sinonasal surfactant protein A1, A2, and D gene expression in cystic fibrosis: a preliminary report. Woodworth BA, etal., Otolaryngol Head Neck Surg. 2007 Jul;137(1):34-8.
71. Serum levels of surfactant protein D predict the anti-tumor activity of gefitinib in patients with advanced non-small cell lung cancer. Yamaguchi H, etal., Cancer Chemother Pharmacol. 2010 Apr 17.
72. Prescreening based on the presence of CT-scan abnormalities and biomarkers (KL-6 and SP-D) may reduce severe radiation pneumonitis after stereotactic radiotherapy. Yamashita H, etal., Radiat Oncol. 2010 May 9;5:32.
73. KGF regulates pulmonary epithelial proliferation and surfactant protein gene expression in adult rat lung. Yano T, etal., Am J Physiol Lung Cell Mol Physiol. 2000 Dec;279(6):L1146-58.
74. Surfactant protein D-mediated aggregation of Pneumocystis carinii impairs phagocytosis by alveolar macrophages. Yong SJ, etal., Infect Immun. 2003 Apr;71(4):1662-71.
75. Reversibility of pulmonary abnormalities by conditional replacement of surfactant protein D (SP-D) in vivo. Zhang L, etal., J Biol Chem 2002 Oct 11;277(41):38709-13.
Additional References at PubMed
PMID:2675969   PMID:9751757   PMID:10542261   PMID:12750409   PMID:12857753   PMID:15075250   PMID:15123664   PMID:16500946   PMID:16514117   PMID:17267143   PMID:18302538   PMID:19080379  
PMID:20228064   PMID:20569420   PMID:20601494   PMID:21408140   PMID:22296755   PMID:22892325   PMID:27541374   PMID:28228557   PMID:28719181   PMID:30422021   PMID:34777371   PMID:35865531  


Genomics

Comparative Map Data
Sftpd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21617,046,491 - 17,058,968 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1617,046,483 - 17,059,927 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1617,110,520 - 17,122,892 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01618,238,920 - 18,251,351 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01617,163,418 - 17,175,790 (-)NCBIRnor_WKY
Rnor_6.01618,753,535 - 18,766,100 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1618,745,458 - 18,766,174 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01618,621,441 - 18,633,581 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1617,272,045 - 17,284,082 (-)NCBICelera
RH 3.4 Map16167.0RGD
Cytogenetic Map16p14NCBI
SFTPD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381079,937,740 - 79,982,383 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1079,937,467 - 79,982,614 (-)EnsemblGRCh38hg38GRCh38
GRCh371081,697,496 - 81,708,861 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361081,687,476 - 81,698,841 (-)NCBINCBI36Build 36hg18NCBI36
Build 341081,687,486 - 81,698,836NCBI
Celera1075,688,432 - 75,699,799 (-)NCBICelera
Cytogenetic Map10q22.3NCBI
HuRef1075,540,246 - 75,551,613 (-)NCBIHuRef
CHM1_11081,980,534 - 81,991,901 (-)NCBICHM1_1
T2T-CHM13v2.01080,806,973 - 80,818,340 (-)NCBIT2T-CHM13v2.0
Sftpd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391440,894,169 - 40,907,155 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1440,894,171 - 40,907,106 (-)EnsemblGRCm39 Ensembl
GRCm381441,172,212 - 41,185,198 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1441,172,214 - 41,185,149 (-)EnsemblGRCm38mm10GRCm38
MGSCv371441,985,501 - 41,998,487 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361440,080,927 - 40,093,876 (-)NCBIMGSCv36mm8
Celera1437,332,219 - 37,345,205 (-)NCBICelera
Cytogenetic Map14BNCBI
cM Map1422.36NCBI
Sftpd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955510213,438 - 225,896 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955510213,468 - 226,096 (+)NCBIChiLan1.0ChiLan1.0
SFTPD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11078,965,252 - 78,974,181 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1078,965,252 - 78,974,181 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01076,275,147 - 76,318,952 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SFTPD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1429,394,755 - 29,407,499 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl429,394,678 - 29,407,293 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha429,519,118 - 29,533,724 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0429,696,757 - 29,711,366 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl429,696,745 - 29,709,347 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1429,566,382 - 29,580,989 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0429,769,003 - 29,783,612 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0430,123,008 - 30,137,617 (+)NCBIUU_Cfam_GSD_1.0
Sftpd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721351,337,526 - 51,349,920 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493671660,754 - 73,010 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SFTPD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1482,051,451 - 82,067,976 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11482,051,400 - 82,069,258 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21488,660,094 - 88,675,023 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SFTPD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1951,809,241 - 51,820,974 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl951,811,052 - 51,820,650 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604812,161,420 - 12,172,864 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sftpd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248416,916,849 - 6,936,077 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248416,917,067 - 6,938,594 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sftpd
146 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:232
Count of miRNA genes:91
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000070955, ENSRNOT00000074559
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat

Markers in Region
D16Wox24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21617,058,975 - 17,059,157 (+)MAPPERmRatBN7.2
Rnor_6.01618,766,108 - 18,766,289NCBIRnor6.0
Rnor_5.01618,633,589 - 18,633,770UniSTSRnor5.0
Celera1617,284,090 - 17,284,265UniSTS
Cytogenetic Map16p14UniSTS
AI573415  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21617,046,668 - 17,046,804 (+)MAPPERmRatBN7.2
Rnor_6.01618,753,713 - 18,753,848NCBIRnor6.0
Rnor_5.01618,621,619 - 18,621,754UniSTSRnor5.0
Celera1617,272,223 - 17,272,358UniSTS
Cytogenetic Map16p14UniSTS
RH94509  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21617,046,492 - 17,046,598 (+)MAPPERmRatBN7.2
Rnor_6.01618,753,537 - 18,753,642NCBIRnor6.0
Rnor_5.01618,621,443 - 18,621,548UniSTSRnor5.0
Celera1617,272,047 - 17,272,152UniSTS
RH 3.4 Map16167.0UniSTS
Cytogenetic Map16p14UniSTS
Sftpd  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21617,051,323 - 17,051,671 (+)MAPPERmRatBN7.2
Rnor_6.01618,758,327 - 18,758,674NCBIRnor6.0
Rnor_5.01618,625,808 - 18,626,155UniSTSRnor5.0
Celera1617,276,468 - 17,276,815UniSTS
Cytogenetic Map16p14UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 11
Low 1 4 8 5 4 5 2 3 8 2
Below cutoff 2 10 43 30 15 30 6 7 13 11 15 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000084172   ⟹   ENSRNOP00000074951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1617,046,483 - 17,058,978 (-)Ensembl
Rnor_6.0 Ensembl1618,753,643 - 18,757,918 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084813   ⟹   ENSRNOP00000069079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1617,046,483 - 17,059,927 (-)Ensembl
Rnor_6.0 Ensembl1618,745,458 - 18,766,174 (-)Ensembl
RefSeq Acc Id: NM_012878   ⟹   NP_037010
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21617,046,491 - 17,058,968 (-)NCBI
Rnor_6.01618,753,535 - 18,766,100 (-)NCBI
Rnor_5.01618,621,441 - 18,633,581 (-)NCBI
Celera1617,272,045 - 17,284,082 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037010 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42170 (Get FASTA)   NCBI Sequence Viewer  
  AAH70507 (Get FASTA)   NCBI Sequence Viewer  
  EDL90867 (Get FASTA)   NCBI Sequence Viewer  
  P35248 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037010   ⟸   NM_012878
- Peptide Label: precursor
- UniProtKB: P35248 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069079   ⟸   ENSRNOT00000084813
RefSeq Acc Id: ENSRNOP00000074951   ⟸   ENSRNOT00000084172
Protein Domains
C-type lectin   Collagen-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35248-F1-model_v2 AlphaFold P35248 1-374 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699977
Promoter ID:EPDNEW_R10499
Type:single initiation site
Name:Sftpd_1
Description:surfactant protein D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01618,766,126 - 18,766,186EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3667 AgrOrtholog
BioCyc Gene G2FUF-11904 BioCyc
Ensembl Genes ENSRNOG00000056001 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069079.2 UniProtKB/TrEMBL
  ENSRNOP00000074951 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084172 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOT00000084813.2 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7098194 IMAGE-MGC_LOAD
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Surfac_D-trimer UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25350 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91760 IMAGE-MGC_LOAD
NCBI Gene 25350 ENTREZGENE
Pfam Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Surfac_D-trimer UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sftpd PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CLECT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JUF5_RAT UniProtKB/TrEMBL
  A0A0G2K9D1_RAT UniProtKB/TrEMBL
  P35248 ENTREZGENE
  Q6IRS7_RAT UniProtKB/TrEMBL
  SFTPD_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-30 Sftpd  surfactant protein D  Sftpd  surfactant associated protein D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2001-07-23 Sftpd  Pulmonary surfactant protein D      Name withdrawn 67952 WITHDRAWN
2001-07-23 Sftpd  surfactant, pulmonary-associated protein D      Name updated to reflect Human and Mouse nomenclature 67952 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression synthesized by alveolar type II epithelial cells 729918