Cst3 (cystatin C) - Rat Genome Database
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Gene: Cst3 (cystatin C) Rattus norvegicus
Analyze
Symbol: Cst3
Name: cystatin C
RGD ID: 2432
Description: Exhibits peptidase inhibitor activity and protease binding activity. Involved in several processes, including animal organ development; circadian sleep/wake cycle, REM sleep; and embryo implantation. Localizes to several cellular components, including multivesicular body; neuronal cell body; and nuclear membrane. Biomarker of intracranial aneurysm; iron deficiency anemia; and obesity. Human ortholog(s) of this gene implicated in CST3-related cerebral amyloid angiopathy and age related macular degeneration 11. Orthologous to several human genes including CST3 (cystatin C); INTERACTS WITH 17alpha-ethynylestradiol; 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CYSC; cystatin 3; Cystatin C (cysteine proteinase inhibitor); cystatin-3; cystatin-C; MGC105556
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: Cst3Tn(sb-T2/Bart3)2.172Mcwi   Cst3em1Mcwi   Cst3em3Mcwi  
Genetic Models: F344-Cst3Tn(sb-T2/Bart3)2.172Mcwi SS-Cst3em1Mcwi SS-Cst3em3Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23136,336,923 - 136,340,796 (-)NCBI
Rnor_6.0 Ensembl3143,219,686 - 143,223,615 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03143,219,671 - 143,223,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03149,628,692 - 149,632,565 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43137,650,903 - 137,654,776 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13137,556,481 - 137,560,243 (-)NCBI
Celera3135,178,032 - 135,181,905 (-)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-chloropropane-1,2-diol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
calcium dichloride  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
cholesterol  (EXP)
choline  (ISO)
cimetidine  (ISO)
cisplatin  (ISO)
clozapine  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fipronil  (EXP)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (EXP)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP,ISO)
haloperidol  (ISO)
Hexachloro-1,3-butadiene  (EXP)
isotretinoin  (ISO)
metformin  (EXP)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
Nandrolone decanoate  (EXP)
nicotine  (ISO)
ochratoxin A  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
rotenone  (ISO)
sarin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sodium cholate  (EXP)
sodium fluoride  (EXP,ISO)
streptozocin  (EXP)
succimer  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
theophylline  (EXP)
triclosan  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Aoki T, etal., Stroke. 2008 Sep;39(9):2603-10. Epub 2008 Jul 17.
2. Barka T and van der Noen H, J Histochem Cytochem. 1993 Dec;41(12):1863-7.
3. Bedi GS Arch Biochem Biophys 1989 Aug 15;273(1):245-53.
4. Borges RL, etal., Nephron Clin Pract. 2009 Nov 3;114(2):c127-c134.
5. Carlson ES, etal., Brain Res. 2008 Aug 7.
6. Cole T, etal., Eur J Biochem 1989 Dec 8;186(1-2):35-42.
7. Derzhko R, etal., Coron Artery Dis. 2009 Nov;20(7):453-61.
8. Engelsberg K, etal., Graefes Arch Clin Exp Ophthalmol. 2004 Mar;242(3):229-39. Epub 2004 Jan 27.
9. Favis R, etal., Pharmacogenet Genomics. 2011 Mar;21(3):121-9.
10. Franceschini N, etal., Ren Fail. 2008;30(1):89-95.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Ghiso J, etal., Proc Natl Acad Sci U S A. 1986 May;83(9):2974-8.
13. GOA data from the GO Consortium
14. Gonzalez-Rivera R, etal., Neurosci Lett. 2006 Nov 20;408(3):178-82. Epub 2006 Oct 5.
15. Gressner AM, etal., World J Gastroenterol. 2006 Feb 7;12(5):731-8.
16. Hakansson K, etal., Comp Biochem Physiol B Biochem Mol Biol. 1996 Jul;114(3):303-11.
17. Hirasawa Y, etal., Exp Anim. 2008 Oct;57(5):423-32.
18. Huaux F, etal., Toxicol Appl Pharmacol. 1995 May;132(1):53-62.
19. Ix JH, etal., J Am Coll Cardiol. 2009 Sep 22;54(13):1176-84.
20. James AB, etal., J Neurochem. 2005 Nov;95(3):796-810.
21. Katakai K, etal., J Neuroendocrinol. 1997 Apr;9(4):247-53.
22. Kravaritou M, etal., Diabetes Res Clin Pract. 2009 Sep;85(3):317-21. Epub 2009 Jul 10.
23. Lee DC, etal., Neurochem Res. 2007 Sep;32(9):1499-510. Epub 2007 Apr 18.
24. Lee DC, etal., Neurotoxicology. 2006 Mar;27(2):260-76. Epub 2006 Jan 18.
25. Lee SH, etal., Metabolism. 2009 Sep 16.
26. Ma J, etal., Neurochem Res. 2007 Feb;32(2):311-20. Epub 2006 Nov 4.
27. Manzano-Fernandez S, etal., Am J Cardiol. 2009 Jun 15;103(12):1753-9.
28. McNamara NV, etal., Pathology. 2009;41(3):269-75.
29. MGD data from the GO Consortium
30. Miyake T, etal., Brain Res Mol Brain Res. 1996 Apr;37(1-2):273-82.
31. Moroi R, etal., Arch Oral Biol. 1997 Apr;42(4):305-15.
32. Mruk D, etal., J Androl. 1997 Nov-Dec;18(6):612-22.
33. Muntner P, etal., Am J Med. 2008 Apr;121(4):341-8.
34. Nagai A, etal., Clin Chim Acta. 2003 Mar;329(1-2):53-60.
35. Nagai A, etal., Neurology. 2000 Dec 26;55(12):1828-32.
36. NCBI rat LocusLink and RefSeq merged data July 26, 2002
37. Niccoli G, etal., Atherosclerosis. 2008 Jun;198(2):373-80. Epub 2007 Nov 5.
38. Nishikawa S and Sasaki F, J Histochem Cytochem. 2000 Sep;48(9):1243-55.
39. Nishikawa S J Histochem Cytochem. 2005 May;53(5):643-51.
40. Nishio C, etal., Brain Res. 2000 Aug 11;873(2):252-62.
41. Nishiura T and Abe K, Arch Oral Biol. 1999 Jan;44(1):15-26.
42. Nishiyama K, etal., Brain Res Bull. 2005 Sep 30;67(1-2):94-9.
43. OMIM Disease Annotation Pipeline
44. Online Mendelian Inheritance in Man, OMIM (TM).
45. Palm DE, etal., Brain Res. 1995 Sep 11;691(1-2):1-8.
46. Parikh NI, etal., Am J Cardiol. 2008 Nov 1;102(9):1194-8. Epub 2008 Sep 12.
47. Pirttila TJ and Pitkanen A, Neurosci Lett. 2006 Mar 6;395(2):108-13. Epub 2005 Nov 23.
48. Quinn CE, etal., Biochem Biophys Res Commun. 2006 Oct 13;349(1):236-44. Epub 2006 Aug 18.
49. RGD automated data pipeline
50. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
51. RGD automated import pipeline for gene-chemical interactions
52. Snell-Bergeon JK, etal., Diabetes Technol Ther. 2009 Jan;11(1):1-9.
53. Straface E, etal., FEBS Lett 2005 May 23;579(13):2759-66. Epub 2005 Apr 19.
54. Sundelof J, etal., Neurology. 2008 Sep 30;71(14):1072-9.
55. Taupin P, etal., Neuron. 2000 Nov;28(2):385-97.
56. Tavera C, etal., Biochem Biophys Res Commun. 1992 Feb 14;182(3):1082-8.
57. Tavera C, etal., Prep Biochem. 1989;19(4):279-91.
58. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
59. Thomas T, etal., Dev Biol. 1989 Jul;134(1):38-47.
60. Tsuruta JK, etal., Biol Reprod. 1993 Nov;49(5):1045-54.
61. Umegae N, etal., Acta Neurol Scand. 2008 Jul;118(1):60-7.
62. Wasselius J, etal., Acta Ophthalmol Scand. 2004 Feb;82(1):68-75.
63. Wasselius J, etal., Invest Ophthalmol Vis Sci. 2001 Jul;42(8):1901-6.
64. Yang HY, etal., Neuroscience. 2001;103(2):493-502.
65. Ying GX, etal., Neuroscience. 2002;112(2):289-98.
Additional References at PubMed
PMID:1563513   PMID:2400577   PMID:3044831   PMID:3488317   PMID:6203523   PMID:7890620   PMID:8999869   PMID:10545518   PMID:12477932   PMID:15127951   PMID:15197734   PMID:15212960  
PMID:15489334   PMID:16502470   PMID:17241700   PMID:17462596   PMID:18026102   PMID:18256700   PMID:18613859   PMID:19056867   PMID:19199708   PMID:20352108   PMID:20489058   PMID:21551085  
PMID:22360852   PMID:22365146   PMID:23376485   PMID:23533145   PMID:24006456   PMID:25479090   PMID:26715107   PMID:26865059   PMID:28053285   PMID:28904096   PMID:29755460   PMID:30052474  
PMID:31801142  


Genomics

Comparative Map Data
Cst3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23136,336,923 - 136,340,796 (-)NCBI
Rnor_6.0 Ensembl3143,219,686 - 143,223,615 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03143,219,671 - 143,223,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03149,628,692 - 149,632,565 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43137,650,903 - 137,654,776 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13137,556,481 - 137,560,243 (-)NCBI
Celera3135,178,032 - 135,181,905 (-)NCBICelera
Cytogenetic Map3q41NCBI
CST3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2023,626,706 - 23,638,473 (-)EnsemblGRCh38hg38GRCh38
GRCh382023,626,706 - 23,637,955 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372023,607,343 - 23,618,592 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362023,562,294 - 23,566,574 (-)NCBINCBI36hg18NCBI36
Build 342023,562,293 - 23,566,574NCBI
Celera2023,687,561 - 23,691,841 (-)NCBI
Cytogenetic Map20p11.21NCBI
HuRef2023,574,763 - 23,578,930 (-)NCBIHuRef
CHM1_12023,608,570 - 23,618,721 (-)NCBICHM1_1
Cst3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392148,713,642 - 148,717,432 (-)NCBIGRCm39mm39
GRCm39 Ensembl2148,713,642 - 148,717,612 (-)Ensembl
GRCm382148,871,722 - 148,875,512 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2148,871,722 - 148,875,692 (-)EnsemblGRCm38mm10GRCm38
MGSCv372148,697,468 - 148,701,204 (-)NCBIGRCm37mm9NCBIm37
MGSCv362148,563,173 - 148,566,909 (-)NCBImm8
Celera2150,137,951 - 150,141,688 (-)NCBICelera
Cytogenetic Map2G3NCBI
cM Map273.6NCBI
Cst3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541530,507,972 - 30,512,109 (-)NCBIChiLan1.0ChiLan1.0
CST3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12023,935,942 - 23,940,420 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2023,935,942 - 23,940,425 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02023,583,043 - 23,587,399 (-)NCBIMhudiblu_PPA_v0panPan3
LOC607874
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12349,562 - 53,618 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CST3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1730,470,855 - 30,474,590 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11730,471,056 - 30,474,486 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21734,560,206 - 34,563,637 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CST3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1252,834,497 - 52,838,785 (-)NCBI
ChlSab1.1 Ensembl252,832,181 - 52,838,865 (-)Ensembl

Position Markers
RH127375  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03143,219,780 - 143,219,981NCBIRnor6.0
Rnor_6.07140,286,211 - 140,286,412NCBIRnor6.0
Rnor_5.03149,628,801 - 149,629,002UniSTSRnor5.0
Rnor_5.0X114,789,909 - 114,790,110UniSTSRnor5.0
RGSC_v3.47137,355,452 - 137,355,653UniSTSRGSC3.4
RGSC_v3.43137,651,012 - 137,651,213UniSTSRGSC3.4
Celera7126,248,838 - 126,249,039UniSTS
Celera3135,178,141 - 135,178,342UniSTS
Cytogenetic Map3q41UniSTS
Cytogenetic Map7q36UniSTS
UniSTS:532125  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07140,286,067 - 140,286,273NCBIRnor6.0
Rnor_5.0X114,789,765 - 114,789,971UniSTSRnor5.0
Celera7126,248,694 - 126,248,900UniSTS
Cytogenetic Map3q41UniSTS
Cytogenetic Map7q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat


Genetic Models
This gene Cst3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:38
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000007175
Prediction methods: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 29 3 3
Medium 3 43 57 41 19 41 8 11 45 35 38 8 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC087591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB314369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB608544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB692474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X16957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000007175   ⟹   ENSRNOP00000007175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3143,219,686 - 143,223,615 (-)Ensembl
RefSeq Acc Id: NM_012837   ⟹   NP_036969
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23136,336,923 - 136,340,796 (-)NCBI
Rnor_6.03143,219,671 - 143,223,544 (-)NCBI
Rnor_5.03149,628,692 - 149,632,565 (-)NCBI
RGSC_v3.43137,650,903 - 137,654,776 (-)RGD
Celera3135,178,032 - 135,181,905 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036969 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87591 (Get FASTA)   NCBI Sequence Viewer  
  CAA34831 (Get FASTA)   NCBI Sequence Viewer  
  EDL95078 (Get FASTA)   NCBI Sequence Viewer  
  EDL95079 (Get FASTA)   NCBI Sequence Viewer  
  P14841 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036969   ⟸   NM_012837
- Peptide Label: precursor
- UniProtKB: P14841 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007175   ⟸   ENSRNOT00000007175

Transcriptome

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

Promoters
RGD ID:13692506
Promoter ID:EPDNEW_R3030
Type:initiation region
Name:Cst3_1
Description:cystatin C
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_6.03143,223,497 - 143,223,557EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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)
ACI/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
ACI/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
BBDP/Wor (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
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)
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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
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)
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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
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:2432 AgrOrtholog
Ensembl Genes ENSRNOG00000005195 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007175 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007175 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7307694 IMAGE-MGC_LOAD
InterPro Cystatin_dom UniProtKB/Swiss-Prot
  Prot_inh_cystat_CS UniProtKB/Swiss-Prot
KEGG Report rno:25307 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105556 IMAGE-MGC_LOAD
NCBI Gene 25307 ENTREZGENE
Pfam Cystatin UniProtKB/Swiss-Prot
PharmGKB CST3 RGD
PhenoGen Cst3 PhenoGen
PROSITE CYSTATIN UniProtKB/Swiss-Prot
SMART SM00043 UniProtKB/Swiss-Prot
TIGR TC216467
UniProt CYTC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5M968 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Cst3  cystatin C    cystatin 3  Name updated 625702 APPROVED
2002-06-10 Cst3  cystatin 3      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization extracellular protein 728248
gene_expression expressed in choroid plexus of brain, cerebrospinal fluid, plasma, testis, epididymis, seminal vesicles, prostate, ovary, submandibular gland and small amounts in liver 728248
gene_protein contains 120 amino acids and a potential N-linked glycosylation site 728248