Sftpa1 (surfactant protein A1) - Rat Genome Database

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Gene: Sftpa1 (surfactant protein A1) Rattus norvegicus
Analyze
Symbol: Sftpa1
Name: surfactant protein A1
RGD ID: 3665
Description: Predicted to enable carbohydrate binding activity and metal ion binding activity. Involved in several processes, including cellular response to mechanical stimulus; cellular response to nitric oxide; and response to vitamin A. Located in extracellular space; multivesicular body; and rough endoplasmic reticulum. Biomarker of asthma; bacterial pneumonia; lung disease; newborn respiratory distress syndrome; and obesity. Human ortholog(s) of this gene implicated in lung disease (multiple) and respiratory syncytial virus infectious disease. Orthologous to several human genes including SFTPA1 (surfactant protein A1); PARTICIPATES IN forkhead class A signaling pathway; phagocytosis pathway; INTERACTS WITH (R)-lipoic acid; 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC100364823; LOC102557073; MGC105453; PSAP; PSP-A; pulmonary surfactant-associated protein A; pulmonary surfactant-associated protein A-like; Sftp1; Sftpa; Sftpl; SP-A; surfactant associated protein A; surfactant, pulmonary-associated protein A1; Surfactant-associated protein 1 (pulmonary surfactant protein SP-A); Surfactant-associated protein 1 (pulmonary surfactant protein, SP-A)
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21617,008,180 - 17,011,686 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1617,008,180 - 17,011,685 (+)Ensembl
Rnor_6.01618,716,019 - 18,719,404 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1618,716,019 - 18,719,403 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01618,585,631 - 18,589,016 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41617,570,887 - 17,574,389 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1617,235,343 - 17,236,847 (+)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway 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. Beharka AA, etal., J Immunol 2002 Oct 1;169(7):3565-73.
5. Boon K, etal., PLoS One. 2009;4(4):e5134. Epub 2009 Apr 6.
6. Cai XX, etal., Zhonghua Er Ke Za Zhi. 2003 Mar;41(3):208-11.
7. Chailley-Heu B, etal., Am J Respir Cell Mol Biol. 1999 Jul;21(1):89-96.
8. Choi EH, etal., Pediatr Pulmonol. 2006 Mar;41(3):255-62.
9. Cleary GM, etal., Pediatrics. 1997 Dec;100(6):998-1003.
10. Erpenbeck VJ, etal., Allergy. 2006 May;61(5):598-604.
11. Fisher JH, etal., Biochim Biophys Acta 1988 Sep 7;950(3):338-45.
12. Fujita M, etal., Cytokine. 2005 Jul 7;31(1):25-33.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. Gil HW, etal., Korean J Intern Med. 2007 Jun;22(2):67-72.
15. Greene KE, etal., Am J Respir Crit Care Med. 1999 Dec;160(6):1843-50.
16. Griese M, etal., Am J Respir Crit Care Med. 2004 Nov 1;170(9):1000-5. Epub 2004 Jul 21.
17. Gunther A, etal., Am J Respir Crit Care Med. 1996 Jan;153(1):176-84.
18. Gunther A, etal., Eur Respir J. 1999 Sep;14(3):565-73.
19. Guo X, etal., Eur Respir J. 2001 Sep;18(3):482-90.
20. Gutierrez JA, etal., Am J Respir Cell Mol Biol. 2003 Jul;29(1):81-7. Epub 2003 Jan 31.
21. Haataja R, etal., Hum Mol Genet. 2000 Nov 1;9(18):2751-60.
22. Hattori A, etal., Am J Respir Cell Mol Biol. 1996 Jun;14(6):608-19.
23. Honda Y Nihon Kyobu Shikkan Gakkai Zasshi. 1996 Dec;34 Suppl:181-5.
24. Hull J, etal., Am J Respir Crit Care Med. 1997 Jul;156(1):161-5.
25. Ikegami T, etal., Eur J Obstet Gynecol Reprod Biol. 2000 Nov;93(1):97-103.
26. Inselman LS, etal., Lung. 2004;182(2):101-17.
27. Jennings VM, etal., Am J Respir Cell Mol Biol. 1995 Sep;13(3):297-306.
28. Kerr MH and Paton JY, Am J Respir Crit Care Med. 1999 Apr;159(4 Pt 1):1115-8.
29. Kim CM, etal., Korean J Intern Med. 2003 Jun;18(2):76-82.
30. Kudo K, etal., J Immunol. 2004 Jun 15;172(12):7592-602.
31. Lee JW, etal., Am J Physiol Lung Cell Mol Physiol. 2005 May;288(5):L950-7. Epub 2005 Jan 7.
32. Ma L, etal., Chin Med J (Engl). 2009 Sep 5;122(17):2013-6.
33. Madan T, etal., Clin Chem Lab Med. 2002 Oct;40(10):1002-8.
34. Madan T, etal., Mol Immunol. 2010 Jun;47(10):1923-30. Epub 2010 Apr 21.
35. Malik S, etal., Hum Genet. 2006 Feb;118(6):752-9. Epub 2005 Nov 15.
36. MGD data from the GO Consortium
37. NCBI rat LocusLink and RefSeq merged data July 26, 2002
38. Ohlmeier S, etal., J Proteome Res. 2008 Oct 30.
39. OMIM Disease Annotation Pipeline
40. Oshika E, etal., Pediatr Res. 1998 Mar;43(3):315-24.
41. Pavlovic J, etal., Dis Markers. 2006;22(5-6):277-91.
42. Pettigrew MM, etal., BMC Med Genet. 2007 Apr 2;8:15.
43. Pipeline to import KEGG annotations from KEGG into RGD
44. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
45. Ramadurai SM, etal., Exp Lung Res. 1998 Sep-Oct;24(5):641-57.
46. RGD automated data pipeline
47. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
48. RGD automated import pipeline for gene-chemical interactions
49. Russo TA, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Sep;283(3):L655-63.
50. Savani RC, etal., Am J Physiol Lung Cell Mol Physiol. 2001 Sep;281(3):L685-96.
51. Saxena S, etal., Chest. 2005 Sep;128(3):1611-9.
52. Schellhase DE and Shannon JM, Am J Respir Cell Mol Biol. 1991 Apr;4(4):304-12.
53. Schmidt R, etal., Respir Res. 2007 Jul 27;8:55.
54. Schmiedl A, etal., Exp Toxicol Pathol. 2005 Mar;56(4-5):265-72.
55. Schmiedl A, etal., Histochem Cell Biol. 2005 Dec;124(6):465-76. Epub 2005 Sep 27.
56. Schmiedl A, etal., Int Arch Allergy Immunol. 2009;148(2):118-26. Epub 2008 Sep 19.
57. Selman M, etal., Hum Genet. 2003 Nov;113(6):542-50. Epub 2003 Sep 6.
58. Seymour JF, etal., Thorax. 2003 Mar;58(3):252-7.
59. Smith CI, etal., Am J Physiol 1995 Nov;269(5 Pt 1):L603-12.
60. Stamme C, etal., Am J Respir Cell Mol Biol 2002 Sep;27(3):353-60.
61. Sugahara K, etal., Lab Invest. 1996 Jan;74(1):209-20.
62. ter Horst SA, etal., BMC Pulm Med. 2006 Apr 18;6:8.
63. Thomas NJ, etal., Pediatr Res. 2009 Jul;66(1):70-3.
64. Toki N, etal., Hum Pathol. 1995 Nov;26(11):1252-9.
65. van Diemen CC, etal., Eur Respir J. 2010 Apr;35(4):768-75. Epub 2009 Sep 24.
66. Venkatraman Girija U, etal., J Biol Chem. 2010 Apr 2;285(14):10546-52. doi: 10.1074/jbc.M109.097493. Epub 2010 Jan 29.
67. Weber B, etal., Turk J Pediatr. 2000 Jul-Sep;42(3):181-5.
68. White CW, etal., Am J Respir Cell Mol Biol. 2001 Jul;25(1):51-9.
69. Woodworth BA, etal., Otolaryngol Head Neck Surg. 2007 Jul;137(1):34-8.
70. Yu ZW and Zhang JH, Allergy Asthma Proc. 2008 Sep-Oct;29(5):486-92.
Additional References at PubMed
PMID:3579914   PMID:12477932   PMID:12600986   PMID:12857753   PMID:12882765   PMID:12904592   PMID:12913002   PMID:14993215   PMID:15482851   PMID:15489334   PMID:15969762   PMID:16081790  
PMID:16207426   PMID:16330552   PMID:16500946   PMID:17202387   PMID:17220308   PMID:17469149   PMID:18344412   PMID:18480979   PMID:20382745   PMID:20473679   PMID:20663300   PMID:20688121  
PMID:21047777   PMID:21123169   PMID:21166190   PMID:21248257   PMID:23894445   PMID:25242514   PMID:26196539   PMID:27660222   PMID:28719181   PMID:30055742   PMID:33267655  


Genomics

Comparative Map Data
Sftpa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21617,008,180 - 17,011,686 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1617,008,180 - 17,011,685 (+)Ensembl
Rnor_6.01618,716,019 - 18,719,404 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1618,716,019 - 18,719,403 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01618,585,631 - 18,589,016 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41617,570,887 - 17,574,389 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1617,235,343 - 17,236,847 (+)NCBICelera
Cytogenetic Map16p14NCBI
SFTPA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1079,610,939 - 79,615,455 (+)EnsemblGRCh38hg38GRCh38
GRCh381079,610,939 - 79,615,455 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371081,370,695 - 81,375,211 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361081,040,722 - 81,045,208 (+)NCBINCBI36hg18NCBI36
Build 341081,360,663 - 81,363,921NCBI
Celera1074,655,786 - 74,660,290 (+)NCBI
Cytogenetic Map10q22.3NCBI
HuRef1075,365,719 - 75,370,230 (+)NCBIHuRef
CHM1_11081,653,316 - 81,657,819 (+)NCBICHM1_1
Sftpa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391440,853,745 - 40,858,330 (+)NCBIGRCm39mm39
GRCm39 Ensembl1440,853,739 - 40,858,409 (+)Ensembl
GRCm381441,131,788 - 41,136,373 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1441,131,782 - 41,136,452 (+)EnsemblGRCm38mm10GRCm38
MGSCv371441,945,077 - 41,949,662 (+)NCBIGRCm37mm9NCBIm37
MGSCv361440,040,501 - 40,045,086 (+)NCBImm8
Celera1437,291,836 - 37,296,421 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1422.36NCBI
SFTPA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11080,176,241 - 80,177,151 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01076,571,312 - 76,575,820 (-)NCBIMhudiblu_PPA_v0panPan3
LOC610540
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1429,430,139 - 29,434,640 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha429,554,528 - 29,559,038 (-)NCBI
ROS_Cfam_1.0429,732,348 - 29,736,864 (-)NCBI
UMICH_Zoey_3.1429,601,811 - 29,606,320 (-)NCBI
UNSW_CanFamBas_1.0429,804,500 - 29,809,005 (-)NCBI
UU_Cfam_GSD_1.0430,158,495 - 30,163,007 (-)NCBI
SFTPA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1482,091,178 - 82,107,675 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11482,091,178 - 82,095,393 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21488,698,851 - 88,702,099 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
D16Mgh2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21617,007,576 - 17,007,744 (+)MAPPERmRatBN7.2
Rnor_6.01618,715,416 - 18,715,583NCBIRnor6.0
Rnor_5.01618,585,028 - 18,585,195UniSTSRnor5.0
RGSC_v3.41617,570,282 - 17,570,449UniSTSRGSC3.4
RGSC_v3.41617,570,281 - 17,570,446RGDRGSC3.4
RGSC_v3.11617,570,279 - 17,570,444RGD
RH 3.4 Map16170.6UniSTS
RH 3.4 Map16170.6RGD
RH 2.0 Map16142.7RGD
SHRSP x BN Map165.71RGD
FHH x ACI Map1612.1799RGD
Cytogenetic Map16p14UniSTS
RH136969  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21617,011,434 - 17,011,625 (+)MAPPERmRatBN7.2
Rnor_6.01618,719,153 - 18,719,343NCBIRnor6.0
Rnor_5.01618,588,765 - 18,588,955UniSTSRnor5.0
RGSC_v3.41617,574,140 - 17,574,330UniSTSRGSC3.4
Celera1617,236,596 - 17,236,786UniSTS
RH 3.4 Map16167.1UniSTS
Cytogenetic Map16p14UniSTS
Sftpa1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01618,717,098 - 18,717,980NCBIRnor6.0
Rnor_5.01618,586,710 - 18,587,592UniSTSRnor5.0
RGSC_v3.41617,571,964 - 17,572,967UniSTSRGSC3.4
Cytogenetic Map16p14UniSTS


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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:220
Count of miRNA genes:148
Interacting mature miRNAs:166
Transcripts:ENSRNOT00000047870
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
Low 11 23 8 15 8 8 9 8 7 9 8
Below cutoff 1 5 27 26 1 26 4 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000047870   ⟹   ENSRNOP00000039850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1617,008,180 - 17,011,685 (+)Ensembl
Rnor_6.0 Ensembl1618,716,019 - 18,719,403 (+)Ensembl
RefSeq Acc Id: NM_001270645   ⟹   NP_001257574
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21617,008,180 - 17,011,686 (+)NCBI
Rnor_6.01618,716,019 - 18,719,404 (+)NCBI
Rnor_5.01618,585,631 - 18,589,016 (+)NCBI
Celera1617,235,343 - 17,236,847 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270647   ⟹   NP_001257576
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21617,008,180 - 17,011,686 (+)NCBI
Rnor_6.01618,716,019 - 18,719,404 (+)NCBI
Rnor_5.01618,585,631 - 18,589,016 (+)NCBI
Celera1617,235,343 - 17,236,847 (+)NCBI
Sequence:
RefSeq Acc Id: NM_017329   ⟹   NP_059025
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21617,008,180 - 17,011,686 (+)NCBI
Rnor_6.01618,716,019 - 18,719,404 (+)NCBI
Rnor_5.01618,585,631 - 18,589,016 (+)NCBI
RGSC_v3.41617,570,887 - 17,574,389 (+)RGD
Celera1617,235,343 - 17,236,847 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094199   ⟹   XP_038950127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21617,008,293 - 17,011,686 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_059025   ⟸   NM_017329
- Peptide Label: isoform 2 precursor
- UniProtKB: P08427 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257574   ⟸   NM_001270645
- Peptide Label: isoform 1 precursor
- UniProtKB: P08427 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257576   ⟸   NM_001270647
- Peptide Label: isoform 3 precursor
- UniProtKB: P08427 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039850   ⟸   ENSRNOT00000047870
RefSeq Acc Id: XP_038950127   ⟸   XM_039094199
- Peptide Label: isoform X1
Protein Domains
C-type lectin   Collagen-like

Transcriptome

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

Promoters
RGD ID:13699975
Promoter ID:EPDNEW_R10497
Type:multiple initiation site
Name:Sftpa1_1
Description:surfactant protein A1
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_6.01618,716,010 - 18,716,070EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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
F344/NRrrc (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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/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)
FHH/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
FHL/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)
FHL/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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: 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)
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: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:3665 AgrOrtholog
Ensembl Genes ENSRNOG00000011438 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000039850 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000047870 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7121530 IMAGE-MGC_LOAD
InterPro C-type_lectin-like UniProtKB/Swiss-Prot
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot
  C-type_lectin_CS UniProtKB/Swiss-Prot
  Collectin_CTLD UniProtKB/Swiss-Prot
  CTDL_fold UniProtKB/Swiss-Prot
KEGG Report rno:24773 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105453 IMAGE-MGC_LOAD
NCBI Gene 24773 ENTREZGENE
Pfam Lectin_C UniProtKB/Swiss-Prot
PhenoGen Sftpa1 PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/Swiss-Prot
  C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot
SMART CLECT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot
UniProt P08427 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-05-18 Sftpa1  surfactant protein A1  LOC102557073  pulmonary surfactant-associated protein A-like  Data Merged 737654 APPROVED
2013-12-18 LOC102557073  pulmonary surfactant-associated protein A-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-03-29 Sftpa1  surfactant protein A1  LOC100364823  pulmonary surfactant-associated protein A-like  Data Merged 737654 PROVISIONAL
2010-05-05 LOC100364823  pulmonary surfactant-associated protein A-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-02-26 Sftpa1  surfactant protein A1  Sftpa1  surfactant, pulmonary-associated protein A1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Sftpa1  surfactant, pulmonary-associated protein A1    Surfactant-associated protein 1 (pulmonary surfactant protein, SP-A)  Name updated 629478 APPROVED