Shmt1 (serine hydroxymethyltransferase 1) - Rat Genome Database

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Pathways
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; anion binding activity; and glycine hydroxymethyltransferase activity. Involved in glycine biosynthetic process from serine. Predicted to be located in nucleoplasm. Predicted to be active in cytosol 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 Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21045,468,698 - 45,490,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1050,170,944 - 50,199,114 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01049,661,340 - 49,689,514 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01045,164,929 - 45,193,103 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01047,030,813 - 47,059,216 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01046,802,986 - 46,831,051 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41046,936,605 - 46,964,779 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11046,948,782 - 46,971,713 (-)NCBI
Celera1044,724,251 - 44,752,341 (-)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
2,3,7,8-tetrabromodibenzodioxine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,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)
bisphenol A  (EXP,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) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP,ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
dioxygen  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
epoxiconazole  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
gentamycin  (EXP)
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)
ozone  (ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic 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)
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)

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
mRatBN7.21045,468,698 - 45,490,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1050,170,944 - 50,199,114 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01049,661,340 - 49,689,514 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01045,164,929 - 45,193,103 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01047,030,813 - 47,059,216 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01046,802,986 - 46,831,051 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41046,936,605 - 46,964,779 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11046,948,782 - 46,971,713 (-)NCBI
Celera1044,724,251 - 44,752,341 (-)NCBICelera
Cytogenetic Map10q22NCBI
SHMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381718,327,873 - 18,363,550 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1718,327,860 - 18,363,563 (-)EnsemblGRCh38hg38GRCh38
GRCh371718,231,187 - 18,266,864 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361718,171,912 - 18,207,581 (-)NCBINCBI36Build 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
GRCm391160,678,933 - 60,702,091 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1160,678,930 - 60,702,544 (-)EnsemblGRCm39 Ensembl
GRCm381160,788,897 - 60,811,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,788,104 - 60,811,718 (-)EnsemblGRCm38mm10GRCm38
MGSCv371160,602,399 - 60,624,767 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547810,972,791 - 11,001,535 (+)NCBIChiLan1.0ChiLan1.0
SHMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha541,361,842 - 41,388,892 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBIROS_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_1.0
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
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248493,108,875 - 3,146,669 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shmt1
63 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
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)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
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)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat

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
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 22 57 41 19 41 2 2 20 35 41 11 2
Low 21 6 9 54 6
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000007092   ⟹   ENSRNOP00000007092
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)Ensembl
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105169   ⟹   ENSRNOP00000078307
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1045,468,700 - 45,490,901 (-)Ensembl
RefSeq Acc Id: NM_001413151   ⟹   NP_001400080
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21045,469,448 - 45,490,833 (-)NCBI
RefSeq Acc Id: XM_039085404   ⟹   XP_038941332
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
  ENSRNOP00000078307.1
RefSeq Acc Id: ENSRNOP00000007092   ⟸   ENSRNOT00000007092
RefSeq Acc Id: XP_038941332   ⟸   XM_039085404
- Peptide Label: isoform X2
- UniProtKB: A6HF57 (UniProtKB/TrEMBL),   Q4KLG7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000078307   ⟸   ENSRNOT00000105169
RefSeq Acc Id: NP_001400080   ⟸   NM_001413151
- UniProtKB: A0A8I5ZKU9 (UniProtKB/TrEMBL)
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
Ensembl Genes ENSRNOG00000005275 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007092.6 UniProtKB/TrEMBL
  ENSRNOT00000105169 ENTREZGENE
  ENSRNOT00000105169.1 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_PLP_BS UniProtKB/TrEMBL
  SHMT-like_dom UniProtKB/TrEMBL
KEGG Report rno:287379 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
  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