Shmt2 (serine hydroxymethyltransferase 2) - Rat Genome Database

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Gene: Shmt2 (serine hydroxymethyltransferase 2) Rattus norvegicus
Analyze
Symbol: Shmt2
Name: serine hydroxymethyltransferase 2
RGD ID: 1308582
Description: Enables several functions, including L-allo-threonine aldolase activity; anion binding activity; and glycine hydroxymethyltransferase activity. Involved in L-serine biosynthetic process; glycine biosynthetic process from serine; and positive regulation of cell population proliferation. Located in mitochondrial inner membrane and mitochondrial matrix. Orthologous to human SHMT2 (serine hydroxymethyltransferase 2); PARTICIPATES IN folate mediated one-carbon metabolic pathway; glycine metabolic pathway; glycine, serine and threonine metabolic pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC299857; MGC105820; serine hydroxymethyl transferase 2 (mitochondrial); serine hydroxymethyltransferase 2 (mitochondrial); serine hydroxymethyltransferase, mitochondrial
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8765,244,247 - 65,249,580 (-)NCBIGRCr8
mRatBN7.2763,358,961 - 63,364,293 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl763,358,961 - 63,364,236 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx765,248,234 - 65,253,554 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0767,450,661 - 67,455,981 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0767,251,885 - 67,257,207 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0770,824,718 - 70,829,822 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl770,824,715 - 70,829,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0770,998,103 - 71,003,197 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4767,494,470 - 67,499,540 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1767,515,199 - 67,520,270 (-)NCBI
Celera760,498,180 - 60,503,250 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP)
amitrole  (EXP)
amphetamine  (EXP)
ampicillin  (EXP)
arsenite(3-)  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (EXP,ISO)
Brodifacoum  (EXP)
buspirone  (EXP)
butan-1-ol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
carnosic acid  (ISO)
chlordecone  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dopamine  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
epoxiconazole  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
glyphosate  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-ethionine  (EXP)
lead diacetate  (EXP,ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
metronidazole  (EXP)
N(4)-hydroxycytidine  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
neomycin  (EXP,ISO)
nickel dichloride  (ISO)
O-methyleugenol  (ISO)
omeprazole  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP)
Soman  (EXP)
sulindac  (EXP)
sunitinib  (ISO)
tanespimycin  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
triptonide  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vancomycin  (EXP,ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Affinity purification and characterization of serine hydroxymethyltransferases from rat liver. Masuda T, etal., J Biochem. 1987 Mar;101(3):643-52.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Glycine metabolism in rat liver mitochondria. V. Intramitochondrial localization of the reversible glycine cleavage system and serine hydroxymethyltransferase. Motokawa Y and Kikuchi G, Arch Biochem Biophys. 1971 Oct;146(2):461-4.
6. A functional screen for Myc-responsive genes reveals serine hydroxymethyltransferase, a major source of the one-carbon unit for cell metabolism. Nikiforov MA, etal., Mol Cell Biol. 2002 Aug;22(16):5793-800.
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Activities of hepatic cytosolic and mitochondrial forms of serine hydroxymethyltransferase and hepatic glycine concentration are affected by vitamin B-6 intake in rats. Scheer JB, etal., J Nutr 2005 Feb;135(2):233-8.
12. Trafficking of intracellular folates. Stover PJ and Field MS, Adv Nutr. 2011 Jul;2(4):325-31. doi: 10.3945/┬┐an.111.000596. Epub 2011 Jun 28.
13. Compartmentalization of Mammalian folate-mediated one-carbon metabolism. Tibbetts AS and Appling DR, Annu Rev Nutr. 2010 Aug 21;30:57-81. doi: 10.1146/annurev.nutr.012809.104810.
14. Rapid uptake and degradation of glycine by astroglial cells in culture: synthesis and release of serine and lactate. Verleysdonk S, etal., Glia. 1999 Sep;27(3):239-48.
15. Update and new concepts in vitamin responsive disorders of folate transport and metabolism. Watkins D and Rosenblatt DS, J Inherit Metab Dis. 2012 Jul;35(4):665-70. doi: 10.1007/s10545-011-9418-1. Epub 2011 Nov 23.
Additional References at PubMed
PMID:8505317   PMID:11516159   PMID:12477932   PMID:12865426   PMID:14651853   PMID:17482557   PMID:18063578   PMID:18614015   PMID:19056867   PMID:19513116   PMID:20458337   PMID:21876188  
PMID:24075985   PMID:25619277   PMID:29180469   PMID:29323231   PMID:29364879   PMID:29452640  


Genomics

Comparative Map Data
Shmt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8765,244,247 - 65,249,580 (-)NCBIGRCr8
mRatBN7.2763,358,961 - 63,364,293 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl763,358,961 - 63,364,236 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx765,248,234 - 65,253,554 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0767,450,661 - 67,455,981 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0767,251,885 - 67,257,207 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0770,824,718 - 70,829,822 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl770,824,715 - 70,829,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0770,998,103 - 71,003,197 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4767,494,470 - 67,499,540 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1767,515,199 - 67,520,270 (-)NCBI
Celera760,498,180 - 60,503,250 (-)NCBICelera
Cytogenetic Map7q22NCBI
SHMT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381257,229,711 - 57,234,935 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1257,229,573 - 57,234,935 (+)EnsemblGRCh38hg38GRCh38
GRCh371257,623,494 - 57,628,718 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,909,819 - 55,914,981 (+)NCBINCBI36Build 36hg18NCBI36
Build 341255,909,818 - 55,914,981NCBI
Celera1257,277,587 - 57,282,945 (+)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1254,662,237 - 54,667,595 (+)NCBIHuRef
CHM1_11257,591,454 - 57,596,816 (+)NCBICHM1_1
T2T-CHM13v2.01257,197,949 - 57,203,173 (+)NCBIT2T-CHM13v2.0
Shmt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910127,352,992 - 127,358,313 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10127,352,992 - 127,358,313 (-)EnsemblGRCm39 Ensembl
GRCm3810127,517,123 - 127,522,444 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10127,517,123 - 127,522,444 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710126,954,195 - 126,959,491 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610126,920,088 - 126,925,384 (-)NCBIMGSCv36mm8
Celera10129,908,893 - 129,914,189 (-)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1074.51NCBI
Shmt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554584,957,602 - 4,962,691 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554584,957,614 - 4,962,691 (+)NCBIChiLan1.0ChiLan1.0
SHMT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21037,106,967 - 37,112,419 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11237,103,737 - 37,108,804 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01231,692,451 - 31,697,727 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11231,944,787 - 31,950,138 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1231,944,785 - 31,950,138 (-)Ensemblpanpan1.1panPan2
SHMT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1101,357,347 - 1,362,511 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl101,356,706 - 1,362,305 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha101,421,107 - 1,426,256 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0101,367,808 - 1,372,957 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl101,367,831 - 1,372,939 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1101,344,398 - 1,349,547 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0101,586,394 - 1,591,543 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0101,711,303 - 1,716,453 (+)NCBIUU_Cfam_GSD_1.0
Shmt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494557,442,306 - 57,447,426 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366461,422,817 - 1,429,037 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366461,422,844 - 1,427,929 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHMT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl522,532,894 - 22,540,319 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1522,535,780 - 22,540,322 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2524,368,828 - 24,374,450 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHMT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11153,141,435 - 53,146,625 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1153,141,462 - 53,147,795 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037192,825,670 - 192,831,284 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shmt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480210,713,276 - 10,719,253 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480210,713,276 - 10,718,391 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shmt2
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:230
Count of miRNA genes:158
Interacting mature miRNAs:171
Transcripts:ENSRNOT00000011082
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)753612714103945643Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)759238038104238038Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)761074194106074194Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)762004452101773158Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)762004452101773158Rat

Markers in Region
RH125781  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2763,359,160 - 63,359,280 (+)MAPPERmRatBN7.2
Rnor_6.0770,824,724 - 70,824,843NCBIRnor6.0
Rnor_5.0770,998,109 - 70,998,228UniSTSRnor5.0
RGSC_v3.4767,494,475 - 67,494,594UniSTSRGSC3.4
Celera760,498,185 - 60,498,304UniSTS
Cytogenetic Map7q22UniSTS
PMC133987P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2763,363,767 - 63,364,116 (+)MAPPERmRatBN7.2
Rnor_6.0770,829,330 - 70,829,678NCBIRnor6.0
Rnor_5.0771,002,715 - 71,003,063UniSTSRnor5.0
RGSC_v3.4767,499,081 - 67,499,429UniSTSRGSC3.4
Celera760,502,791 - 60,503,139UniSTS
Cytogenetic Map7q22UniSTS
RH137111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2763,359,237 - 63,359,440 (+)MAPPERmRatBN7.2
Rnor_6.0770,824,801 - 70,825,003NCBIRnor6.0
Rnor_5.0770,998,186 - 70,998,388UniSTSRnor5.0
RGSC_v3.4767,494,552 - 67,494,754UniSTSRGSC3.4
Celera760,498,262 - 60,498,464UniSTS
Cytogenetic Map7q22UniSTS
Shmt2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2763,361,279 - 63,361,349 (+)MAPPERmRatBN7.2
Rnor_6.0770,826,843 - 70,826,912NCBIRnor6.0
Rnor_5.0771,000,228 - 71,000,297UniSTSRnor5.0
RGSC_v3.4767,496,594 - 67,496,663UniSTSRGSC3.4
Celera760,500,304 - 60,500,373UniSTS
Cytogenetic Map7q22UniSTS


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 43 57 41 19 41 8 11 74 35 39 11 8
Low 2
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000011082   ⟹   ENSRNOP00000011082
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl763,358,961 - 63,364,236 (-)Ensembl
Rnor_6.0 Ensembl770,824,715 - 70,829,815 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118611   ⟹   ENSRNOP00000089446
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl763,358,961 - 63,363,681 (-)Ensembl
RefSeq Acc Id: NM_001008322   ⟹   NP_001008323
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8765,244,247 - 65,249,567 (-)NCBI
mRatBN7.2763,358,961 - 63,364,282 (-)NCBI
Rnor_6.0770,824,719 - 70,829,789 (-)NCBI
Rnor_5.0770,998,103 - 71,003,197 (-)NCBI
RGSC_v3.4767,494,470 - 67,499,540 (-)RGD
Celera760,498,180 - 60,503,250 (-)RGD
Sequence:
RefSeq Acc Id: NM_001393833   ⟹   NP_001380762
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8765,244,247 - 65,249,567 (-)NCBI
mRatBN7.2763,358,961 - 63,364,282 (-)NCBI
RefSeq Acc Id: NM_001393834   ⟹   NP_001380763
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8765,244,247 - 65,249,567 (-)NCBI
mRatBN7.2763,358,961 - 63,364,282 (-)NCBI
RefSeq Acc Id: XM_039078757   ⟹   XP_038934685
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8765,246,274 - 65,249,580 (-)NCBI
mRatBN7.2763,360,988 - 63,364,293 (-)NCBI
RefSeq Acc Id: XM_039078758   ⟹   XP_038934686
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8765,244,442 - 65,246,663 (-)NCBI
mRatBN7.2763,358,961 - 63,361,385 (-)NCBI
RefSeq Acc Id: XM_063263240   ⟹   XP_063119310
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8765,244,442 - 65,249,524 (-)NCBI
RefSeq Acc Id: NP_001008323   ⟸   NM_001008322
- Peptide Label: isoform 1
- UniProtKB: Q5U3Z7 (UniProtKB/TrEMBL),   A6HQW0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011082   ⟸   ENSRNOT00000011082
RefSeq Acc Id: XP_038934686   ⟸   XM_039078758
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934685   ⟸   XM_039078757
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000089446   ⟸   ENSRNOT00000118611
RefSeq Acc Id: NP_001380762   ⟸   NM_001393833
- Peptide Label: isoform 2
- UniProtKB: A6HQW0 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001380763   ⟸   NM_001393834
- Peptide Label: isoform 3
- UniProtKB: A6HQW0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119310   ⟸   XM_063263240
- Peptide Label: isoform X1
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U3Z7-F1-model_v2 AlphaFold Q5U3Z7 1-504 view protein structure

Transcriptome

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

Promoters
RGD ID:13695264
Promoter ID:EPDNEW_R5788
Type:initiation region
Name:Shmt2_1
Description:serine hydroxymethyltransferase 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_6.0770,829,808 - 70,829,868EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308582 AgrOrtholog
BioCyc Gene G2FUF-33736 BioCyc
BioCyc Pathway 1CMET2-PWY [folate transformations III (E. coli)] BioCyc
  GLYSYN-PWY [glycine biosynthesis I] BioCyc
  PWY-2161 [folate polyglutamylation] BioCyc
  PWY-3661 [glycine betaine degradation I] BioCyc
  PWY-3661-1 [glycine betaine degradation II (mammalian)] BioCyc
  PWY66-385 [dTMP de novo biosynthesis (mitochondrial)] BioCyc
BioCyc Pathway Image 1CMET2-PWY BioCyc
  GLYSYN-PWY BioCyc
  PWY-2161 BioCyc
  PWY-3661 BioCyc
  PWY-3661-1 BioCyc
  PWY66-385 BioCyc
Ensembl Genes ENSRNOG00000008106 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011082 ENTREZGENE
  ENSRNOT00000011082.5 UniProtKB/TrEMBL
  ENSRNOT00000118611 ENTREZGENE
  ENSRNOT00000118611.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7106911 IMAGE-MGC_LOAD
InterPro PyrdxlP-dep_Trfase_major_dom UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major_sub1 UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major_sub2 UniProtKB/TrEMBL
  Ser_HO-MeTrfase UniProtKB/TrEMBL
  Ser_HO-MeTrfase_PLP_BS UniProtKB/TrEMBL
  SHMT-like_dom UniProtKB/TrEMBL
KEGG Report rno:299857 UniProtKB/TrEMBL
MGC_CLONE MGC:105820 IMAGE-MGC_LOAD
NCBI Gene 299857 ENTREZGENE
PANTHER PTHR11680 UniProtKB/TrEMBL
  SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL UniProtKB/TrEMBL
Pfam SHMT UniProtKB/TrEMBL
PhenoGen Shmt2 PhenoGen
PIRSF SHMT UniProtKB/TrEMBL
PROSITE SHMT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008106 RatGTEx
Superfamily-SCOP PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
UniProt A0A8I6GI43_RAT UniProtKB/TrEMBL
  A6HQW0 ENTREZGENE, UniProtKB/TrEMBL
  Q5U3Z7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Shmt2  serine hydroxymethyltransferase 2  Shmt2  serine hydroxymethyltransferase 2 (mitochondrial)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-01-30   serine hydroxymethyltransferase 2 (mitochondrial)  Shmt2  serine hydroxymethyl transferase 2 (mitochondrial)  Name updated 1299863 APPROVED
2005-12-06 Shmt2  serine hydroxymethyl transferase 2 (mitochondrial)  Shmt2_predicted  serine hydroxymethyl transferase 2 (mitochondrial) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Shmt2_predicted  serine hydroxymethyl transferase 2 (mitochondrial) (predicted)      Symbol and Name status set to approved 70820 APPROVED