Shmt1 (serine hydroxymethyltransferase 1) - Rat Genome Database

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Gene: Shmt1 (serine hydroxymethyltransferase 1) Rattus norvegicus
Analyze
Symbol: Shmt1
Name: serine hydroxymethyltransferase 1
RGD ID: 1312011
Description: Enables several functions, including L-allo-threonine aldolase activity; glycine hydroxymethyltransferase activity; and pyridoxal phosphate binding activity. Involved in glycine biosynthetic process from serine. Predicted to be located in cytosol. Predicted to be active in mitochondrion and nucleus. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1); PARTICIPATES IN folate mediated one-carbon metabolic pathway; glycine metabolic pathway; glycine, serine and threonine metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC287379; LRRGT00032; mShmt; serine hydroxymethyl transferase 1 (soluble); serine hydroxymethyltransferase 1 (soluble); serine hydroxymethyltransferase, cytosolic; Shmt
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81045,968,959 - 45,990,341 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1045,960,434 - 45,997,326 (-)EnsemblGRCr8
mRatBN7.21045,468,698 - 45,490,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1050,170,944 - 50,199,114 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01049,661,340 - 49,689,514 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01045,164,929 - 45,193,103 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01047,030,813 - 47,059,216 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)Ensemblrn6Rnor6.0
Rnor_5.01046,802,986 - 46,831,051 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41046,936,605 - 46,964,779 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1044,724,251 - 44,752,341 (-)NCBICelera
RGSC_v3.11046,948,782 - 46,971,713 (-)NCBI
Cytogenetic Map10q22NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrabromodibenzodioxine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-hydroxypropanoic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-tert-Octylphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amitrole  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
auramine O  (ISO)
azathioprine  (ISO)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP,ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
epoxiconazole  (ISO)
erianin  (ISO)
Evodiamine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
gentamycin  (EXP)
GSK-J4  (ISO)
indometacin  (EXP,ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
lidocaine  (EXP)
lipopolysaccharide  (ISO)
methidathion  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
okadaic acid  (ISO)
ozone  (ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
pyridoxine  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
sulfadimethoxine  (EXP)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
cytosol  (ISO)
mitochondrion  (IBA)
nucleus  (IBA,IEA,ISO)
replication fork  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Polymorphism of cytosolic serine hydroxymethyltransferase, estrogen and breast cancer risk among Chinese women in Taiwan. Cheng CW, etal., Breast Cancer Res Treat. 2008 Sep;111(1):145-55. Epub 2007 Sep 22.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Genetic polymorphisms in the one-carbon metabolism pathway and breast cancer risk: a population-based case-control study and meta-analyses. Lissowska J, etal., Int J Cancer. 2007 Jun 15;120(12):2696-703.
5. Affinity purification and characterization of serine hydroxymethyltransferases from rat liver. Masuda T, etal., J Biochem. 1987 Mar;101(3):643-52.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. 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.
13. Proteomics success story. Towards early detection of breast and ovarian cancer: plasma proteomics as a tool to find novel markers. Souchelnytskyi S, etal., Proteomics. 2006 Sep;6 Suppl 2:65-8.
14. 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.
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:627563   PMID:8505317   PMID:9753690   PMID:10995219   PMID:11278996   PMID:11516159   PMID:12138190   PMID:12477932   PMID:14651853   PMID:15598699   PMID:17482557   PMID:18614015  
PMID:19056867   PMID:19513116   PMID:20439489   PMID:23106098   PMID:23376485   PMID:23533145   PMID:24698160   PMID:25416956   PMID:36735737  


Genomics

Comparative Map Data
Shmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81045,968,959 - 45,990,341 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1045,960,434 - 45,997,326 (-)EnsemblGRCr8
mRatBN7.21045,468,698 - 45,490,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1050,170,944 - 50,199,114 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01049,661,340 - 49,689,514 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01045,164,929 - 45,193,103 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01047,030,813 - 47,059,216 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)Ensemblrn6Rnor6.0
Rnor_5.01046,802,986 - 46,831,051 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41046,936,605 - 46,964,779 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1044,724,251 - 44,752,341 (-)NCBICelera
RGSC_v3.11046,948,782 - 46,971,713 (-)NCBI
Cytogenetic Map10q22NCBI
SHMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381718,327,873 - 18,363,550 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1718,327,686 - 18,363,550 (-)Ensemblhg38GRCh38
GRCh371718,231,187 - 18,266,864 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361718,171,912 - 18,207,581 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341718,171,912 - 18,207,581NCBI
Celera1719,172,258 - 19,207,893 (-)NCBICelera
Cytogenetic Map17p11.2NCBI
HuRef1717,984,719 - 18,020,240 (-)NCBIHuRef
CHM1_11718,239,946 - 18,275,839 (-)NCBICHM1_1
T2T-CHM13v2.01718,274,679 - 18,310,356 (-)NCBIT2T-CHM13v2.0
Shmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391160,679,723 - 60,702,062 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1160,678,930 - 60,702,544 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381160,788,897 - 60,811,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,788,104 - 60,811,718 (-)Ensemblmm10GRCm38
MGSCv371160,602,399 - 60,624,767 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361161,219,982 - 61,242,350 (-)NCBIMGSCv36mm8
MGSCv361160,605,092 - 60,627,460 (-)NCBIMGSCv36mm8
Cytogenetic Map11B2NCBI
cM Map1137.84NCBI
Shmt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547810,978,139 - 11,001,202 (+)Ensembl
ChiLan1.0NW_00495547810,972,791 - 11,001,535 (+)NCBIChiLan1.0ChiLan1.0
SHMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21952,905,330 - 52,940,088 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11757,616,479 - 57,650,574 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01732,870,949 - 32,905,690 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11737,849,206 - 37,884,220 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1737,849,206 - 37,884,220 (+)EnsemblpanPan2panpan1.1
SHMT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1541,221,531 - 41,248,653 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl541,221,562 - 41,253,166 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha541,361,842 - 41,388,892 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0541,435,940 - 41,463,042 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Shmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560260,989,489 - 61,018,689 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367411,849,609 - 1,877,727 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367411,849,239 - 1,877,724 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHMT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1260,416,463 - 60,435,450 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11260,414,421 - 60,435,451 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SHMT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11617,371,704 - 17,408,499 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660593,494,856 - 3,535,333 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shmt1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248493,114,876 - 3,146,248 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248493,108,875 - 3,146,669 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Shmt1
156 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:43
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000007092
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103589345164140567Rat
152025229Scl83Serum cholesterol level QTL 834.33blood cholesterol amount (VT:0000180)103621155669161158Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103179628176796281Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)102744378772443787Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)101993920764939207Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104183127886831278Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104493935989939359Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104552916496099749Rat
11528628Bss116Bone structure and strength QTL 1166.464e-07femur morphology trait (VT:0000559)femur length (CMO:0000442)104467931246132467Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101866841963668419Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102183375861843633Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102895035373950353Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103589326364653589Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102980091064653589Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102744378772443787Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14282327487823274Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104493935989939359Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104282327487823274Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102466212373695339Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102702353561843633Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103550938380509383Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)102011061465110614Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103589326352293000Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)102758722696099902Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102907697874076978Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104360879388608793Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)102744378772443787Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102937704652699134Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103112911376129113Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104493935989939359Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)103950348784503487Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)102011061465110614Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

Markers in Region
AI385541  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21045,469,694 - 45,469,844 (+)MAPPERmRatBN7.2
Rnor_6.01047,031,059 - 47,031,208NCBIRnor6.0
Rnor_5.01046,803,235 - 46,803,384UniSTSRnor5.0
RGSC_v3.41046,936,614 - 46,936,763UniSTSRGSC3.4
Celera1044,724,260 - 44,724,409UniSTS
Cytogenetic Map10q22UniSTS
RH128681  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21045,468,624 - 45,468,814 (+)MAPPERmRatBN7.2
Rnor_6.01047,029,989 - 47,030,178NCBIRnor6.0
Rnor_5.01046,802,165 - 46,802,354UniSTSRnor5.0
RGSC_v3.41046,935,544 - 46,935,733UniSTSRGSC3.4
Celera1044,723,190 - 44,723,379UniSTS
RH 3.4 Map10526.48UniSTS
Cytogenetic Map10q22UniSTS
RH142767  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21045,474,240 - 45,474,437 (+)MAPPERmRatBN7.2
Rnor_6.01047,035,641 - 47,035,837NCBIRnor6.0
Rnor_5.01046,807,476 - 46,807,672UniSTSRnor5.0
RGSC_v3.41046,941,203 - 46,941,399UniSTSRGSC3.4
Celera1044,728,765 - 44,728,961UniSTS
RH 3.4 Map10528.49UniSTS
Cytogenetic Map10q22UniSTS


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 12 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000007092   ⟹   ENSRNOP00000007092
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1045,968,959 - 45,997,326 (-)Ensembl
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)Ensembl
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105169   ⟹   ENSRNOP00000078307
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1045,960,434 - 45,990,334 (-)Ensembl
mRatBN7.2 Ensembl1045,468,700 - 45,490,901 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000156060   ⟹   ENSRNOP00000105844
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1045,968,959 - 45,990,334 (-)Ensembl
RefSeq Acc Id: NM_001413151   ⟹   NP_001400080
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81045,968,959 - 45,990,341 (-)NCBI
mRatBN7.21045,469,448 - 45,490,833 (-)NCBI
RefSeq Acc Id: XM_039085404   ⟹   XP_038941332
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81045,968,960 - 45,981,116 (-)NCBI
mRatBN7.21045,468,698 - 45,481,601 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001400080 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941332 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99219 (Get FASTA)   NCBI Sequence Viewer  
  AAQ96245 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000007092.4
  ENSRNOP00000078307.2
  ENSRNOP00000105844
  ENSRNOP00000105844.1
Ensembl Acc Id: ENSRNOP00000007092   ⟸   ENSRNOT00000007092
RefSeq Acc Id: XP_038941332   ⟸   XM_039085404
- Peptide Label: isoform X1
- UniProtKB: A6HF57 (UniProtKB/TrEMBL),   Q4KLG7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000078307   ⟸   ENSRNOT00000105169
RefSeq Acc Id: NP_001400080   ⟸   NM_001413151
- UniProtKB: A0A8I5ZKU9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000105844   ⟸   ENSRNOT00000156060
Protein Domains
Serine hydroxymethyltransferase-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6TXG7-F1-model_v2 AlphaFold Q6TXG7 1-681 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1312011 AgrOrtholog
BioCyc Gene G2FUF-24841 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 ENSRNOG00000005275 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007092.7 UniProtKB/TrEMBL
  ENSRNOT00000105169.2 UniProtKB/TrEMBL
  ENSRNOT00000156060 ENTREZGENE
  ENSRNOT00000156060.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7385410 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-like UniProtKB/TrEMBL
  Ser_HO-MeTrfase_PLP_BS UniProtKB/TrEMBL
  SHMT-like_dom UniProtKB/TrEMBL
MGC_CLONE MGC:116396 IMAGE-MGC_LOAD
NCBI Gene 287379 ENTREZGENE
PANTHER PTHR11680 UniProtKB/TrEMBL
  SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC UniProtKB/TrEMBL
Pfam SHMT UniProtKB/TrEMBL
PharmGKB SHMT1 RGD
PhenoGen Shmt1 PhenoGen
PIRSF SHMT UniProtKB/TrEMBL
PROSITE SHMT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005275 RatGTEx
Superfamily-SCOP PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
UniProt A0A8I5ZKU9 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LRM4_RAT UniProtKB/TrEMBL
  A6HF57 ENTREZGENE, UniProtKB/TrEMBL
  Q4KLG7 ENTREZGENE, UniProtKB/TrEMBL
  Q6TXG7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Shmt1  serine hydroxymethyltransferase 1  Shmt1  serine hydroxymethyltransferase 1 (soluble)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-01-30   serine hydroxymethyltransferase 1 (soluble)  Shmt1  serine hydroxymethyl transferase 1 (soluble)  Name updated 1299863 APPROVED
2005-12-06 Shmt1  serine hydroxymethyl transferase 1 (soluble)  Shmt1_predicted  serine hydroxymethyl transferase 1 (soluble) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Shmt1_predicted  serine hydroxymethyl transferase 1 (soluble) (predicted)      Symbol and Name status set to approved 70820 APPROVED