Sphk2 (sphingosine kinase 2) - Rat Genome Database

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Gene: Sphk2 (sphingosine kinase 2) Rattus norvegicus
Analyze
Symbol: Sphk2
Name: sphingosine kinase 2
RGD ID: 1307757
Description: Predicted to have kinase activity; nucleosomal histone binding activity; and sphingosine-1-phosphate receptor activity. Involved in female pregnancy. Predicted to localize to several cellular components, including mitochondrial inner membrane; nucleoplasm; and nucleosome. Orthologous to human SPHK2 (sphingosine kinase 2); PARTICIPATES IN ceramide signaling pathway; Fabry disease pathway; Gaucher's disease pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC308589
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2196,180,872 - 96,188,592 (-)NCBI
Rnor_6.0 Ensembl1101,692,973 - 101,697,277 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01101,692,972 - 101,700,604 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01102,771,785 - 102,779,436 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4196,178,615 - 96,182,920 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1196,256,726 - 96,261,031 (-)NCBI
Celera190,434,071 - 90,438,377 (-)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blood vessel development  (ISO)
brain development  (ISO)
cellular response to phorbol 13-acetate 12-myristate  (ISO)
female pregnancy  (IEP)
histone H2A-K5 acetylation  (ISO)
histone H2B-K12 acetylation  (ISO)
lipid phosphorylation  (IEA)
negative regulation of cell growth  (ISO)
negative regulation of histone deacetylase activity  (ISO)
negative regulation of histone deacetylation  (ISO)
phosphorylation  (IBA)
positive regulation of apoptotic process  (IBA,ISO)
positive regulation of calcium ion import  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of ceramide biosynthetic process  (ISO)
positive regulation of cytokine production involved in immune response  (IEA,ISO)
positive regulation of gene expression, epigenetic  (ISO)
positive regulation of histone H3-K9 acetylation  (ISO)
positive regulation of interleukin-13 production  (IEA,ISO)
positive regulation of interleukin-6 production  (IEA,ISO)
positive regulation of mast cell activation involved in immune response  (ISO)
positive regulation of mast cell degranulation  (ISO)
positive regulation of protein kinase C signaling  (ISO)
positive regulation of tumor necrosis factor production  (IEA,ISO)
regulation of ATP biosynthetic process  (ISO)
regulation of cytochrome-c oxidase activity  (ISO)
regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
regulation of reactive oxygen species biosynthetic process  (ISO)
sphinganine-1-phosphate biosynthetic process  (IBA,ISO)
sphingolipid metabolic process  (IBA)
sphingosine biosynthetic process  (IBA,ISO)
sphingosine metabolic process  (ISO)
sphingosine-1-phosphate receptor signaling pathway  (IEA)

Cellular Component

References

Additional References at PubMed
PMID:10751414   PMID:12477932   PMID:16093248   PMID:16103110   PMID:16118219   PMID:16314531   PMID:17346996   PMID:17635916   PMID:17897319   PMID:18805787   PMID:19729656   PMID:20371493  
PMID:20959514   PMID:21084291   PMID:23106337   PMID:25637806   PMID:26621495   PMID:29615132  


Genomics

Comparative Map Data
Sphk2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2196,180,872 - 96,188,592 (-)NCBI
Rnor_6.0 Ensembl1101,692,973 - 101,697,277 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01101,692,972 - 101,700,604 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01102,771,785 - 102,779,436 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4196,178,615 - 96,182,920 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1196,256,726 - 96,261,031 (-)NCBI
Celera190,434,071 - 90,438,377 (-)NCBICelera
Cytogenetic Map1q22NCBI
SPHK2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1948,619,291 - 48,630,717 (+)EnsemblGRCh38hg38GRCh38
GRCh381948,619,409 - 48,630,407 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371949,122,763 - 49,133,662 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361953,814,360 - 53,825,474 (+)NCBINCBI36hg18NCBI36
Build 341953,814,359 - 53,825,473NCBI
Celera1945,987,413 - 45,998,527 (+)NCBI
Cytogenetic Map19q13.33NCBI
HuRef1945,501,739 - 45,513,199 (+)NCBIHuRef
CHM1_11949,124,423 - 49,135,537 (+)NCBICHM1_1
Sphk2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39745,358,887 - 45,367,426 (-)NCBIGRCm39mm39
GRCm39 Ensembl745,358,891 - 45,367,426 (-)Ensembl
GRCm38745,709,463 - 45,718,002 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl745,709,467 - 45,718,002 (-)EnsemblGRCm38mm10GRCm38
MGSCv37752,964,833 - 52,973,372 (-)NCBIGRCm37mm9NCBIm37
MGSCv36745,578,303 - 45,585,957 (-)NCBImm8
Celera741,172,020 - 41,180,543 (-)NCBICelera
Cytogenetic Map7B3NCBI
Sphk2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555591,917,301 - 1,928,493 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555591,921,479 - 1,929,450 (-)NCBIChiLan1.0ChiLan1.0
SPHK2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11954,213,166 - 54,224,033 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1954,213,166 - 54,224,767 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01945,620,980 - 45,631,786 (+)NCBIMhudiblu_PPA_v0panPan3
SPHK2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11107,681,425 - 107,689,790 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1107,680,599 - 107,689,707 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1107,202,917 - 107,211,393 (-)NCBI
ROS_Cfam_1.01108,205,468 - 108,213,966 (-)NCBI
UMICH_Zoey_3.11107,872,017 - 107,880,502 (-)NCBI
UNSW_CanFamBas_1.01107,519,318 - 107,527,797 (-)NCBI
UU_Cfam_GSD_1.01108,355,012 - 108,363,506 (-)NCBI
Sphk2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934921,050,633 - 21,058,418 (+)NCBI
SpeTri2.0NW_0049366642,668,708 - 2,676,608 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPHK2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl653,979,012 - 53,986,770 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1653,982,911 - 53,986,779 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2649,726,086 - 49,734,104 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPHK2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1641,865,921 - 41,881,889 (+)NCBI
ChlSab1.1 Ensembl641,867,139 - 41,881,268 (+)Ensembl
Sphk2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248325,246,328 - 5,254,247 (-)NCBI

Position Markers
RH94402  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01101,692,667 - 101,692,825NCBIRnor6.0
Rnor_5.01102,771,499 - 102,771,657UniSTSRnor5.0
RGSC_v3.4196,178,310 - 96,178,468UniSTSRGSC3.4
Celera190,433,766 - 90,433,924UniSTS
RH 3.4 Map1909.3UniSTS
Cytogenetic Map1q22UniSTS
RH141779  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01101,692,514 - 101,692,694NCBIRnor6.0
Rnor_5.01102,771,346 - 102,771,526UniSTSRnor5.0
RGSC_v3.4196,178,157 - 96,178,337UniSTSRGSC3.4
Celera190,433,613 - 90,433,793UniSTS
RH 3.4 Map1909.49UniSTS
Cytogenetic Map1q22UniSTS
RH129117  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01101,693,024 - 101,693,212NCBIRnor6.0
Rnor_5.01102,771,856 - 102,772,044UniSTSRnor5.0
RGSC_v3.4196,178,667 - 96,178,855UniSTSRGSC3.4
Celera190,434,123 - 90,434,311UniSTS
RH 3.4 Map1907.59UniSTS
Cytogenetic Map1q22UniSTS
BF415542  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01101,695,866 - 101,695,959NCBIRnor6.0
Rnor_5.01102,774,698 - 102,774,791UniSTSRnor5.0
RGSC_v3.4196,181,509 - 96,181,602UniSTSRGSC3.4
Celera190,436,966 - 90,437,059UniSTS
RH 3.4 Map1908.9UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)188634585106002500Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)199983293127203999Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:55
Count of miRNA genes:49
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000028549
Prediction methods: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.


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 35 53 37 19 37 1 1 74 35 41 11 1
Low 8 4 4 4 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028549   ⟹   ENSRNOP00000028549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1101,692,973 - 101,697,277 (-)Ensembl
RefSeq Acc Id: NM_001012066   ⟹   NP_001012066
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2196,180,872 - 96,185,177 (-)NCBI
Rnor_6.01101,692,972 - 101,697,277 (-)NCBI
Rnor_5.01102,771,785 - 102,779,436 (-)NCBI
RGSC_v3.4196,178,615 - 96,182,920 (-)RGD
Celera190,434,071 - 90,438,377 (-)RGD
Sequence:
RefSeq Acc Id: XM_006229085   ⟹   XP_006229147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2196,180,872 - 96,188,592 (-)NCBI
Rnor_6.01101,692,972 - 101,700,604 (-)NCBI
Rnor_5.01102,771,785 - 102,779,436 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229088   ⟹   XP_006229150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01101,692,972 - 101,699,139 (-)NCBI
Rnor_5.01102,771,785 - 102,779,436 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759383   ⟹   XP_008757605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2196,180,872 - 96,188,517 (-)NCBI
Rnor_6.01101,692,972 - 101,700,572 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759384   ⟹   XP_008757606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01101,692,972 - 101,699,773 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112297   ⟹   XP_038968225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2196,180,872 - 96,185,771 (-)NCBI
RefSeq Acc Id: XM_039112304   ⟹   XP_038968232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2196,180,872 - 96,186,808 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001012066   ⟸   NM_001012066
- UniProtKB: Q6AYB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229150   ⟸   XM_006229088
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006229147   ⟸   XM_006229085
- Peptide Label: isoform X1
- UniProtKB: Q6AYB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008757606   ⟸   XM_008759384
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008757605   ⟸   XM_008759383
- Peptide Label: isoform X1
- UniProtKB: Q6AYB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028549   ⟸   ENSRNOT00000028549
RefSeq Acc Id: XP_038968232   ⟸   XM_039112304
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968225   ⟸   XM_039112297
- Peptide Label: isoform X1
Protein Domains
DAGKc

Transcriptome

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

Promoters
RGD ID:13690051
Promoter ID:EPDNEW_R575
Type:single initiation site
Name:Sphk2_1
Description:sphingosine kinase 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_6.01101,697,294 - 101,697,354EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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:1307757 AgrOrtholog
Ensembl Genes ENSRNOG00000021032 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028549 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028549 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10330 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7126682 IMAGE-MGC_LOAD
InterPro ATP-NAD_kinase_dom_1 UniProtKB/TrEMBL
  ATP-NAD_kinase_PpnK-typ UniProtKB/TrEMBL
  Diacylglycerol_kinase_cat_dom UniProtKB/TrEMBL
KEGG Report rno:308589 UniProtKB/TrEMBL
MGC_CLONE MGC:94123 IMAGE-MGC_LOAD
NCBI Gene 308589 ENTREZGENE
Pfam DAGK_cat UniProtKB/TrEMBL
PhenoGen Sphk2 PhenoGen
PROSITE DAGK UniProtKB/TrEMBL
SMART DAGKc UniProtKB/TrEMBL
Superfamily-SCOP SSF111331 UniProtKB/TrEMBL
UniProt Q6AYB2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Sphk2  sphingosine kinase 2  Sphk2_predicted  sphingosine kinase 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Sphk2_predicted  sphingosine kinase 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED