Sgms2 (sphingomyelin synthase 2) - Rat Genome Database

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Gene: Sgms2 (sphingomyelin synthase 2) Rattus norvegicus
Analyze
Symbol: Sgms2
Name: sphingomyelin synthase 2
RGD ID: 1305778
Description: Predicted to enable ceramide cholinephosphotransferase activity; ceramide phosphoethanolamine synthase activity; and sphingomyelin synthase activity. Predicted to be involved in ceramide biosynthetic process; regulation of bone mineralization; and sphingomyelin biosynthetic process. Predicted to act upstream of or within ceramide phosphoethanolamine biosynthetic process. Located in plasma membrane. Human ortholog(s) of this gene implicated in calvarial doughnut lesions with bone fragility. Orthologous to human SGMS2 (sphingomyelin synthase 2); PARTICIPATES IN sphingolipid metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC310849; phosphatidylcholine:ceramide cholinephosphotransferase 2; RGD1305778; similar to RIKEN cDNA 4933405A16; Sms2; spermatin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82222,567,661 - 222,641,804 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2222,567,664 - 222,590,807 (-)EnsemblGRCr8
mRatBN7.22219,889,809 - 219,967,704 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2219,893,572 - 219,967,546 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2227,549,778 - 227,572,764 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02225,449,445 - 225,472,435 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02220,307,074 - 220,330,066 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02236,458,276 - 236,530,667 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2236,458,279 - 236,480,502 (-)Ensemblrn6Rnor6.0
Rnor_5.02255,006,742 - 255,078,076 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42228,815,312 - 228,838,295 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2212,149,475 - 212,172,550 (-)NCBICelera
RGSC_v3.12228,802,052 - 228,825,035 (-)NCBI
Cytogenetic Map2q43NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
2-palmitoylglycerol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
Benzo[ghi]perylene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
Dibutyl phosphate  (ISO)
dicrotophos  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
fenamidone  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
geldanamycin  (ISO)
gentamycin  (EXP)
glycidol  (EXP)
indometacin  (ISO)
inulin  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP,ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
okadaic acid  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
poly(I:C)  (ISO)
rac-lactic acid  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thiram  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
endoplasmic reticulum membrane  (IBA)
Golgi apparatus  (IEA,ISO)
Golgi membrane  (IBA,IEA,ISO)
membrane  (IEA)
plasma membrane  (IBA,IDA,IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Cellular localization of sphingomyelin synthase 2 in the seminiferous epithelium of adult rat testes. Lee NP, etal., J Endocrinol. 2007 Jan;192(1):17-32.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:14685263   PMID:21980337   PMID:25605874   PMID:25667419   PMID:29294205   PMID:30779713  


Genomics

Comparative Map Data
Sgms2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82222,567,661 - 222,641,804 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2222,567,664 - 222,590,807 (-)EnsemblGRCr8
mRatBN7.22219,889,809 - 219,967,704 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2219,893,572 - 219,967,546 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2227,549,778 - 227,572,764 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02225,449,445 - 225,472,435 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02220,307,074 - 220,330,066 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02236,458,276 - 236,530,667 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2236,458,279 - 236,480,502 (-)Ensemblrn6Rnor6.0
Rnor_5.02255,006,742 - 255,078,076 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42228,815,312 - 228,838,295 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2212,149,475 - 212,172,550 (-)NCBICelera
RGSC_v3.12228,802,052 - 228,825,035 (-)NCBI
Cytogenetic Map2q43NCBI
SGMS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384107,824,563 - 107,915,047 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4107,824,563 - 107,915,047 (+)Ensemblhg38GRCh38
GRCh374108,745,719 - 108,836,203 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364109,033,879 - 109,051,558 (+)NCBIBuild 36Build 36hg18NCBI36
Celera4106,040,532 - 106,131,005 (+)NCBICelera
Cytogenetic Map4q25NCBI
HuRef4104,477,295 - 104,567,792 (+)NCBIHuRef
CHM1_14108,722,193 - 108,812,665 (+)NCBICHM1_1
T2T-CHM13v2.04111,126,863 - 111,217,333 (+)NCBIT2T-CHM13v2.0
Sgms2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393131,112,634 - 131,197,204 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3131,112,634 - 131,197,172 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm383131,318,985 - 131,491,443 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3131,318,985 - 131,491,411 (-)Ensemblmm10GRCm38
MGSCv373131,021,903 - 131,047,841 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv363131,311,893 - 131,334,090 (-)NCBIMGSCv36mm8
Celera3137,840,788 - 137,866,755 (-)NCBICelera
Cytogenetic Map3G3NCBI
cM Map360.91NCBI
Sgms2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554961,905,517 - 1,947,009 (-)Ensembl
ChiLan1.0NW_0049554961,909,347 - 1,955,004 (-)NCBIChiLan1.0ChiLan1.0
SGMS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23105,921,036 - 106,029,587 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14106,217,864 - 106,324,239 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04100,329,642 - 100,420,398 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14110,902,572 - 110,992,887 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4110,936,358 - 110,992,887 (+)EnsemblpanPan2panpan1.1
SGMS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13228,277,195 - 28,407,761 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3228,354,116 - 28,403,734 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3213,614,373 - 13,744,831 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03228,506,826 - 28,637,140 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3228,615,734 - 28,637,123 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13228,500,149 - 28,630,561 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03228,244,646 - 28,375,083 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03211,481,938 - 11,612,641 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sgms2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530112,714,369 - 12,756,874 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936818683,659 - 726,174 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936818687,695 - 726,123 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SGMS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8114,057,603 - 114,076,154 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.18114,052,726 - 114,145,946 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28122,315,213 - 122,407,118 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SGMS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1755,752,419 - 55,843,408 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl755,753,270 - 55,838,914 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603734,378,008 - 34,468,860 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sgms2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248301,502,336 - 1,542,134 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248301,498,700 - 1,543,112 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Sgms2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1327,471,366 - 27,542,695 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sgms2
666 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:163
Count of miRNA genes:126
Interacting mature miRNAs:139
Transcripts:ENSRNOT00000015020
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2163997722225110681Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2212145502231732847Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2184482291229482291Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2202029709236904960Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2210956252251712708Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2219814164239320906Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2214404877251712708Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845370229470703Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2205135267225627153Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283465462229820014Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2204795005249795005Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2214404877251712708Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2218051934251712708Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2186850607231850607Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2192287802237287802Rat
1302789Stl26Serum triglyceride level QTL 263.10.0035blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)2206613059226891081Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2214404877251712708Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2196140964251540988Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2214404877251712708Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660223841096Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2205135267250135267Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2188565047233565047Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2192287802229609668Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2221088977243501206Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2184856304229856304Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2184856304229856304Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2182635347227635347Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283465462225110681Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2184856304229856304Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2203664411248664411Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2214404877251712708Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283400752223709938Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166372086229820014Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2184856304229856304Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2192287802237287802Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2182024327227024327Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2159440760228950743Rat
1359019Hrtrt19Heart rate QTL 192.9heart pumping trait (VT:2000009)heart rate (CMO:0000002)2221270493228950743Rat

Markers in Region
UniSTS:498418  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22219,893,918 - 219,893,992 (+)MAPPERmRatBN7.2
Rnor_6.02236,458,640 - 236,458,713NCBIRnor6.0
Rnor_5.02255,007,107 - 255,007,180UniSTSRnor5.0
RGSC_v3.42228,815,676 - 228,815,749UniSTSRGSC3.4
Celera2212,149,839 - 212,149,912UniSTS
Cytogenetic Map2q43UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 13 68 182 91 90 59 107 59 6 392 209 13 164 100 97 31 24 24

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001014043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001439804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001439805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001439806 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063281956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063281957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC085803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ071571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU840804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU840805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000015020   ⟹   ENSRNOP00000015020
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2222,567,664 - 222,590,807 (-)Ensembl
mRatBN7.2 Ensembl2219,893,572 - 219,967,546 (-)Ensembl
Rnor_6.0 Ensembl2236,458,279 - 236,480,502 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097097   ⟹   ENSRNOP00000097001
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2222,567,664 - 222,590,807 (-)Ensembl
mRatBN7.2 Ensembl2219,893,572 - 219,967,546 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000106830   ⟹   ENSRNOP00000080237
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2219,893,668 - 219,967,020 (-)Ensembl
RefSeq Acc Id: NM_001014043   ⟹   NP_001014065
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,590,807 (-)NCBI
mRatBN7.22219,893,555 - 219,916,698 (-)NCBI
Rnor_6.02236,458,276 - 236,480,502 (-)NCBI
Rnor_5.02255,006,742 - 255,078,076 (-)NCBI
RGSC_v3.42228,815,312 - 228,838,295 (-)RGD
Celera2212,149,475 - 212,172,550 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233311   ⟹   XP_006233373
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,590,954 (-)NCBI
mRatBN7.22219,889,809 - 219,917,532 (-)NCBI
Rnor_6.02236,458,276 - 236,480,555 (-)NCBI
Rnor_5.02255,006,742 - 255,078,076 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590934   ⟹   XP_017446423
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,641,004 (-)NCBI
mRatBN7.22219,893,561 - 219,965,883 (-)NCBI
Rnor_6.02236,458,276 - 236,530,667 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039102450   ⟹   XP_038958378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,641,804 (-)NCBI
mRatBN7.22219,893,561 - 219,967,704 (-)NCBI
RefSeq Acc Id: XM_039102451   ⟹   XP_038958379
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,641,207 (-)NCBI
mRatBN7.22219,893,561 - 219,967,058 (-)NCBI
RefSeq Acc Id: XM_039102452   ⟹   XP_038958380
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,628,717 (-)NCBI
mRatBN7.22219,893,561 - 219,953,833 (-)NCBI
RefSeq Acc Id: XM_039102453   ⟹   XP_038958381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,602,072 (-)NCBI
mRatBN7.22219,893,561 - 219,946,906 (-)NCBI
RefSeq Acc Id: XM_063281956   ⟹   XP_063138026
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,641,004 (-)NCBI
RefSeq Acc Id: XM_063281957   ⟹   XP_063138027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82222,567,661 - 222,590,930 (-)NCBI
RefSeq Acc Id: NP_001014065   ⟸   NM_001014043
- UniProtKB: A0A0G2JSK7 (UniProtKB/TrEMBL),   A6HVS9 (UniProtKB/TrEMBL),   A0A8I5ZQ87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233373   ⟸   XM_006233311
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JSK7 (UniProtKB/TrEMBL),   A6HVS9 (UniProtKB/TrEMBL),   A0A8I5ZQ87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017446423   ⟸   XM_017590934
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000015020   ⟸   ENSRNOT00000015020
RefSeq Acc Id: XP_038958378   ⟸   XM_039102450
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038958379   ⟸   XM_039102451
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038958380   ⟸   XM_039102452
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JSK7 (UniProtKB/TrEMBL),   A6HVS9 (UniProtKB/TrEMBL),   A0A8I5ZQ87 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038958381   ⟸   XM_039102453
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JSK7 (UniProtKB/TrEMBL),   A6HVS9 (UniProtKB/TrEMBL),   A0A8I5ZQ87 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000097001   ⟸   ENSRNOT00000097097
Ensembl Acc Id: ENSRNOP00000080237   ⟸   ENSRNOT00000106830
RefSeq Acc Id: XP_063138026   ⟸   XM_063281956
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JSK7 (UniProtKB/TrEMBL),   A6HVS9 (UniProtKB/TrEMBL),   A0A8I5ZQ87 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063138027   ⟸   XM_063281957
- Peptide Label: isoform X2
Protein Domains
Sphingomyelin synthase-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4JM44-F1-model_v2 AlphaFold Q4JM44 1-365 view protein structure

Transcriptome

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

Promoters
RGD ID:13691761
Promoter ID:EPDNEW_R2285
Type:initiation region
Name:Sgms2_1
Description:sphingomyelin synthase 2
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_6.02236,480,591 - 236,480,651EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305778 AgrOrtholog
BioCyc Gene G2FUF-51206 BioCyc
Ensembl Genes ENSRNOG00000011284 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000015020 ENTREZGENE
IMAGE_CLONE IMAGE:7111151 IMAGE-MGC_LOAD
InterPro Sphingomyelin_synth-like UniProtKB/Swiss-Prot
  Sphingomyelin_synth-like_dom UniProtKB/Swiss-Prot
KEGG Report rno:310849 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93838 IMAGE-MGC_LOAD
NCBI Gene 310849 ENTREZGENE
PANTHER PHOSPHATIDYLCHOLINE:CERAMIDE CHOLINEPHOSPHOTRANSFERASE 2 UniProtKB/Swiss-Prot
  PTHR21290 UniProtKB/Swiss-Prot
Pfam PAP2_C UniProtKB/Swiss-Prot
PhenoGen Sgms2 PhenoGen
RatGTEx ENSRNOG00000011284 RatGTEx
UniProt A0A0G2JSK7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZQ87 ENTREZGENE
  A0A8I6AUC3_RAT UniProtKB/TrEMBL
  A6HVS9 ENTREZGENE, UniProtKB/TrEMBL
  Q4JM44 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5U2Z1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Sgms2  sphingomyelin synthase 2  RGD1305778  similar to RIKEN cDNA 4933405A16  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1305778  similar to RIKEN cDNA 4933405A16  RGD1305778_predicted  similar to RIKEN cDNA 4933405A16 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305778_predicted  similar to RIKEN cDNA 4933405A16 (predicted)  LOC310849_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC310849_predicted  similar to RIKEN cDNA 4933405A16 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL