Sftpc (surfactant protein C) - Rat Genome Database

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Gene: Sftpc (surfactant protein C) Rattus norvegicus
Analyze
Symbol: Sftpc
Name: surfactant protein C
RGD ID: 3666
Description: Exhibits identical protein binding activity. Involved in several processes, including cellular response to mechanical stimulus; cellular response to nitric oxide; and response to vitamin A. Localizes to alveolar lamellar body; extracellular space; and multivesicular body. Biomarker of bacterial pneumonia and newborn respiratory distress syndrome. Human ortholog(s) of this gene implicated in asthma; lung disease (multiple); and respiratory syncytial virus infectious disease. Orthologous to human SFTPC (surfactant protein C); INTERACTS WITH 3,7-dihydropurine-6-thione; 6-propyl-2-thiouracil; all-trans-retinol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: pulmonary surfactant-associated protein C; pulmonary surfactant-associated proteolipid SPL(Val); SP-C; surfactant associated protein C; Surfactant pulmonary-associated protein C; Surfactant, pulmonary-associated protein C
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21545,596,565 - 45,599,615 (-)NCBI
Rnor_6.0 Ensembl1552,211,544 - 52,214,616 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01552,211,538 - 52,214,480 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01555,935,055 - 55,937,997 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41550,923,105 - 50,926,047 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11550,938,884 - 50,941,827 (-)NCBI
Celera1545,274,971 - 45,277,913 (-)NCBICelera
Cytogenetic Map15p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
1. Amin RS, etal., J Pediatr. 2001 Jul;139(1):85-92.
2. Atochina EN, etal., J Lab Clin Med. 2001 Jun;137(6):429-39.
3. Atochina EN, etal., Respir Res. 2003 Dec 8;4:15. Print 2003.
4. Baekvad-Hansen M, etal., Respir Med. 2010 Mar;104(3):418-25. Epub 2009 Nov 11.
5. Brasch F, etal., Am J Respir Cell Mol Biol 2002 Jun;26(6):659-70.
6. Cameron HS, etal., J Pediatr. 2005 Mar;146(3):370-5.
7. Chailley-Heu B, etal., Am J Respir Cell Mol Biol. 1999 Jul;21(1):89-96.
8. Erpenbeck VJ, etal., Allergy. 2006 May;61(5):598-604.
9. Feng D, etal., Scand J Clin Lab Invest. 2010 Sep;70(5):364-73.
10. Fisher JH, etal., Biochim Biophys Acta 1989 May 1;995(3):225-30.
11. Fujita M, etal., Cytokine. 2005 Jul 7;31(1):25-33.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Glasser SW, etal., Am J Physiol Lung Cell Mol Physiol. 2009 Jul;297(1):L64-72. Epub 2009 Mar 20.
14. Glasser SW, etal., J Biol Chem. 2003 Apr 18;278(16):14291-8. Epub 2003 Jan 7.
15. Glasser SW, etal., J Immunol. 2008 Jul 1;181(1):621-8.
16. GOA data from the GO Consortium
17. Gobran LI and Rooney SA, Am J Physiol Lung Cell Mol Physiol 2001 Dec;281(6):L1413-9.
18. Griese M, etal., Am J Respir Crit Care Med. 2004 Nov 1;170(9):1000-5. Epub 2004 Jul 21.
19. Guillot L, etal., J Med Genet. 2009 Jul;46(7):490-4. Epub 2009 May 13.
20. Gutierrez JA, etal., Am J Respir Cell Mol Biol. 2003 Jul;29(1):81-7. Epub 2003 Jan 31.
21. Guttentag SH, etal., Am J Respir Cell Mol Biol. 2005 Jul;33(1):14-21. Epub 2005 Mar 24.
22. Haczku A, etal., Am J Respir Cell Mol Biol. 2001 Jul;25(1):45-50.
23. Hafner D, etal., Am J Respir Crit Care Med. 1998 Jul;158(1):270-8.
24. Hafner D, etal., Br J Pharmacol. 1998 Jul;124(6):1083-90.
25. Heyen L, etal., Pathog Dis. 2016 Oct;74(7). pii: ftw086. doi: 10.1093/femspd/ftw086. Epub 2016 Sep 4.
26. Ikegami M, etal., J Appl Physiol. 2002 Feb;92(2):519-26.
27. Ikegami T, etal., Eur J Obstet Gynecol Reprod Biol. 2000 Nov;93(1):97-103.
28. Kim CM, etal., Korean J Intern Med. 2003 Jun;18(2):76-82.
29. Lawson WE, etal., Am J Pathol. 2005 Nov;167(5):1267-77.
30. Lee JW, etal., Am J Physiol Lung Cell Mol Physiol. 2005 May;288(5):L950-7. Epub 2005 Jan 7.
31. MGD data from the GO Consortium
32. Mulugeta S and Beers MF, J Biol Chem. 2003 Nov 28;278(48):47979-86. Epub 2003 Aug 21.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Nogee LM, etal., N Engl J Med. 2001 Feb 22;344(8):573-9.
35. OMIM Disease Annotation Pipeline
36. Oosterlaken-Dijksterhuis MA, etal., Biochem J. 1991 Feb 15;274 ( Pt 1):115-9.
37. Oshika E, etal., Pediatr Res. 1998 Mar;43(3):315-24.
38. Paugam-Burtz C, etal., Anesthesiology. 2000 Sep;93(3):805-10.
39. Puthothu B, etal., Pediatr Allergy Immunol. 2006 Dec;17(8):572-7.
40. Ramadurai SM, etal., Exp Lung Res. 1998 Sep-Oct;24(5):641-57.
41. Rayani HH, etal., Exp Lung Res. 1999 Jan-Feb;25(1):69-79.
42. RGD automated data pipeline
43. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
44. RGD automated import pipeline for gene-chemical interactions
45. RGD comprehensive gene curation
46. Russo TA, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Sep;283(3):L655-63.
47. Savani RC, etal., Am J Physiol Lung Cell Mol Physiol. 2001 Sep;281(3):L685-96.
48. Schell HB and Abruzzo TC, N Y State J Med 1977 Nov;77(13):2095-6.
49. Schmidt R, etal., Respir Res. 2007 Jul 27;8:55.
50. Schmiedl A, etal., Histochem Cell Biol. 2005 Dec;124(6):465-76. Epub 2005 Sep 27.
51. Setoguchi Y, etal., Respirology. 2006 Jan;11 Suppl:S41-5.
52. Somaschini M, etal., Pediatr Med Chir. 2005 May-Aug;27(3-4):103-7.
53. Sugahara K, etal., Lab Invest. 1996 Jan;74(1):209-20.
54. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
55. Tsvetkova OA and Veselovskaia MV, Ter Arkh. 2007;79(9):65-9.
56. van Moorsel CH, etal., Am J Respir Crit Care Med. 2010 Jul 23.
57. Veletza SV, etal., Am J Physiol. 1992 Jun;262(6 Pt 1):L684-7.
58. Vorbroker DK, etal., Am J Physiol. 1995 Apr;268(4 Pt 1):L647-56.
59. Wang WJ, etal., J Biol Chem. 2002 May 31;277(22):19929-37. Epub 2002 Mar 20.
60. White CW, etal., Am J Respir Cell Mol Biol. 2001 Jul;25(1):51-9.
61. Yano T, etal., Am J Physiol Lung Cell Mol Physiol. 2000 Dec;279(6):L1146-58.
Additional References at PubMed
PMID:8813084   PMID:9006067   PMID:12477932   PMID:12904592   PMID:16794256   PMID:18239190   PMID:21169555   PMID:24191021   PMID:25416956   PMID:25910212   PMID:27155084   PMID:30341519  
PMID:31515488  


Genomics

Comparative Map Data
Sftpc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21545,596,565 - 45,599,615 (-)NCBI
Rnor_6.0 Ensembl1552,211,544 - 52,214,616 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01552,211,538 - 52,214,480 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01555,935,055 - 55,937,997 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41550,923,105 - 50,926,047 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11550,938,884 - 50,941,827 (-)NCBI
Celera1545,274,971 - 45,277,913 (-)NCBICelera
Cytogenetic Map15p11NCBI
SFTPC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl822,156,913 - 22,164,479 (+)EnsemblGRCh38hg38GRCh38
GRCh38822,157,383 - 22,164,479 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37822,014,896 - 22,021,992 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36822,075,129 - 22,077,937 (+)NCBINCBI36hg18NCBI36
Build 34822,075,112 - 22,077,928NCBI
Celera820,981,168 - 20,983,976 (+)NCBI
Cytogenetic Map8p21.3NCBI
HuRef820,561,488 - 20,564,296 (+)NCBIHuRef
CHM1_1822,220,843 - 22,223,651 (+)NCBICHM1_1
Sftpc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391470,758,381 - 70,761,521 (-)NCBIGRCm39mm39
GRCm39 Ensembl1470,758,389 - 70,761,521 (-)Ensembl
GRCm381470,520,941 - 70,524,081 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1470,520,949 - 70,524,081 (-)EnsemblGRCm38mm10GRCm38
MGSCv371470,920,748 - 70,923,888 (-)NCBIGRCm37mm9NCBIm37
MGSCv361469,256,020 - 69,259,150 (-)NCBImm8
Celera1468,062,491 - 68,065,631 (-)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1436.32NCBI
Sftpc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540345,649,122 - 45,651,837 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540345,649,149 - 45,651,421 (+)NCBIChiLan1.0ChiLan1.0
SFTPC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1818,343,007 - 18,348,764 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl818,345,940 - 18,348,764 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0821,402,060 - 21,409,438 (+)NCBIMhudiblu_PPA_v0panPan3
SFTPC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12535,088,295 - 35,090,995 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2535,088,279 - 35,091,457 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2535,677,864 - 35,680,614 (-)NCBI
ROS_Cfam_1.02535,299,616 - 35,302,366 (-)NCBI
UMICH_Zoey_3.12535,245,093 - 35,247,843 (-)NCBI
UNSW_CanFamBas_1.02535,099,613 - 35,102,363 (-)NCBI
UU_Cfam_GSD_1.02535,255,134 - 35,257,884 (-)NCBI
Sftpc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494312,588,481 - 12,596,579 (-)NCBI
SpeTri2.0NW_0049365555,966,610 - 5,982,083 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SFTPC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl146,440,309 - 6,443,095 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1146,440,309 - 6,443,104 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2146,868,096 - 6,880,564 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SFTPC
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1820,229,756 - 20,233,568 (+)NCBI
ChlSab1.1 Ensembl820,230,870 - 20,234,020 (+)Ensembl
Vero_WHO_p1.0NW_02366605222,002,517 - 22,009,591 (-)NCBI
Sftpc
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475817,742,439 - 17,744,664 (+)NCBI

Position Markers
RH94751  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21545,596,780 - 45,596,906 (+)MAPPER
Rnor_6.01552,211,751 - 52,211,876NCBIRnor6.0
Rnor_5.01555,935,268 - 55,935,393UniSTSRnor5.0
RGSC_v3.41550,923,318 - 50,923,443UniSTSRGSC3.4
Celera1545,275,184 - 45,275,309UniSTS
Cytogenetic Map15p11UniSTS
RH94752  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21545,597,955 - 45,598,125 (+)MAPPER
Rnor_6.01552,212,926 - 52,213,095NCBIRnor6.0
Rnor_5.01555,936,443 - 55,936,612UniSTSRnor5.0
RGSC_v3.41550,924,493 - 50,924,662UniSTSRGSC3.4
Celera1545,276,359 - 45,276,528UniSTS
Cytogenetic Map15p11UniSTS
RH94753  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21545,598,632 - 45,598,824 (+)MAPPER
Rnor_6.01552,213,603 - 52,213,794NCBIRnor6.0
Rnor_5.01555,937,120 - 55,937,311UniSTSRnor5.0
RGSC_v3.41550,925,170 - 50,925,361UniSTSRGSC3.4
Celera1545,277,036 - 45,277,227UniSTS
Cytogenetic Map15p11UniSTS
RH136856  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21545,596,682 - 45,596,873 (+)MAPPER
Rnor_6.01552,211,653 - 52,211,843NCBIRnor6.0
Rnor_5.01555,935,170 - 55,935,360UniSTSRnor5.0
RGSC_v3.41550,923,220 - 50,923,410UniSTSRGSC3.4
Celera1545,275,086 - 45,275,276UniSTS
Cytogenetic Map15p11UniSTS
Sftpc  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21545,597,866 - 45,598,233 (+)MAPPER
Rnor_6.01552,212,837 - 52,213,203NCBIRnor6.0
Rnor_5.01555,936,354 - 55,936,720UniSTSRnor5.0
RGSC_v3.41550,924,404 - 50,924,770UniSTSRGSC3.4
Celera1545,276,270 - 45,276,636UniSTS
Cytogenetic Map15p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154309747052831189Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:94
Count of miRNA genes:80
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000015035
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.


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 11
Medium 1 1 1 1 3 4 2 5 3
Low 1 8 24 8 15 8 5 5 13 9 21 5
Below cutoff 2 7 1 1 3 1 6 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015035   ⟹   ENSRNOP00000015032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1552,211,544 - 52,214,616 (-)Ensembl
RefSeq Acc Id: NM_017342   ⟹   NP_059038
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21545,596,568 - 45,599,512 (-)NCBI
Rnor_6.01552,211,538 - 52,214,480 (-)NCBI
Rnor_5.01555,935,055 - 55,937,997 (-)NCBI
RGSC_v3.41550,923,105 - 50,926,047 (-)RGD
Celera1545,274,971 - 45,277,913 (-)RGD
Sequence:
RefSeq Acc Id: XM_039093609   ⟹   XP_038949537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21545,596,565 - 45,599,615 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_059038   ⟸   NM_017342
- UniProtKB: P11685 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000015032   ⟸   ENSRNOT00000015035
RefSeq Acc Id: XP_038949537   ⟸   XM_039093609
- Peptide Label: isoform X1
Protein Domains
BRICHOS

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3666 AgrOrtholog
Ensembl Genes ENSRNOG00000011177 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015032 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015035 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099876 IMAGE-MGC_LOAD
InterPro BRICHOS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SP-C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SP-C_palmitoylation_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Surfactant_protein_propep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:50683 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91727 IMAGE-MGC_LOAD
NCBI Gene 50683 ENTREZGENE
PANTHER PTHR10800 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BRICHOS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SP_C-Propep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sftpc PhenoGen
PROSITE BRICHOS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SURFACT_PALMITOYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART BRICHOS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SF_P UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204886
UniProt A0A0H2UHI8_RAT UniProtKB/TrEMBL
  P11685 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q52MA6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-30 Sftpc  surfactant protein C  Sftpc  surfactant associated protein C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Sftpc  Surfactant, pulmonary-associated protein C      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process mediates biophysical functions of surfactant 628506
gene_regulation secretion is stimulated by b-adrenergic, adenosine A2B, and purinergic P2Y2 receptor agonists, and by TPA and ionomycin in isolated type II cells 628506
gene_regulation precursor protein undergoes N-terminal processing by cathepsin H 727636