Gldc (glycine decarboxylase) - Rat Genome Database

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Gene: Gldc (glycine decarboxylase) Rattus norvegicus
Analyze
Symbol: Gldc
Name: glycine decarboxylase
RGD ID: 1308660
Description: Enables anion binding activity; enzyme binding activity; and glycine dehydrogenase (decarboxylating) activity. Involved in glycine decarboxylation via glycine cleavage system and protein-containing complex assembly. Part of glycine cleavage complex. Human ortholog(s) of this gene implicated in glycine encephalopathy. Orthologous to human GLDC (glycine decarboxylase); PARTICIPATES IN dihydropyrimidine dehydrogenase deficiency pathway; dimethylglycine dehydrogenase deficiency pathway; folate cycle metabolic pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17beta-estradiol; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: glycine decarboxylase, glycine cleavage system protein P); glycine dehydrogenase (decarboxylating); glycine dehydrogenase (decarboxylating), mitochondrial; glycine dehydrogenase (decarboxylating), mitochondrial-like; glycine dehydrogenase (decarboxylating, glycine decarboxylase, glycine cleavage system protein P); glycine dehydrogenase [decarboxylating], mitochondrial; glycine dehydrogenase [decarboxylating], mitochondrial-like; LOC100911814
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
GRCr81237,296,753 - 237,375,620 (-)NCBIGRCr8
mRatBN7.21227,883,249 - 227,962,119 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1227,883,249 - 227,962,097 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1236,285,270 - 236,364,242 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01243,214,954 - 243,293,934 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01236,037,217 - 236,116,284 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01248,295,140 - 248,377,122 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1248,297,331 - 248,377,093 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01255,544,863 - 255,624,599 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41233,846,690 - 233,925,736 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11234,011,236 - 234,089,583 (-)NCBI
Celera1225,029,994 - 225,108,807 (-)NCBICelera
Cytogenetic Map1q52NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
3-chloropropane-1,2-diol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
antimycin A  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
buspirone  (EXP)
butan-1-ol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
coumarin  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
deguelin  (ISO)
diclofenac  (ISO)
diquat  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenpyroximate  (ISO)
fentin chloride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glycidyl methacrylate  (ISO)
GW 4064  (ISO)
HC toxin  (ISO)
indole-3-methanol  (EXP)
indometacin  (EXP)
isobutanol  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
menadione  (ISO)
mercury dichloride  (EXP)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (ISO)
naphthalene  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
O-methyleugenol  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pravastatin  (EXP,ISO)
progesterone  (ISO)
propanal  (ISO)
pyrimidifen  (ISO)
quercetin  (ISO)
rotenone  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
sotorasib  (ISO)
sunitinib  (ISO)
tacedinaline  (ISO)
tacrolimus hydrate  (ISO)
tebufenpyrad  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thifluzamide  (ISO)
thioacetamide  (EXP)
trametinib  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
zaragozic acid A  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. Flusser H, etal., Neurology. 2005 Apr 26;64(8):1426-30.
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. Purification and properties of glycine decarboxylase, a component of the glycine cleavage system, from rat liver mitochondria and immunochemical comparison of this enzyme from various sources. Hayasaka K, etal., J Biochem (Tokyo). 1980 Oct;88(4):1193-9.
5. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. Kanno J, etal., J Med Genet. 2007 Mar;44(3):e69.
6. Epigenetic Silencing of the Putative Tumor Suppressor Gene GLDC (Glycine Dehydrogenase) in Gastric Carcinoma. Min HL, etal., Anticancer Res. 2016 Jan;36(1):179-87.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. Glycine decarboxylase deficiency causes neural tube defects and features of non-ketotic hyperglycinemia in mice. Pai YJ, etal., Nat Commun. 2015 Mar 4;6:6388. doi: 10.1038/ncomms7388.
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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.
Additional References at PubMed
PMID:18614015   PMID:20439489   PMID:28244183  


Genomics

Comparative Map Data
Gldc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81237,296,753 - 237,375,620 (-)NCBIGRCr8
mRatBN7.21227,883,249 - 227,962,119 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1227,883,249 - 227,962,097 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1236,285,270 - 236,364,242 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01243,214,954 - 243,293,934 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01236,037,217 - 236,116,284 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01248,295,140 - 248,377,122 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1248,297,331 - 248,377,093 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01255,544,863 - 255,624,599 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41233,846,690 - 233,925,736 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11234,011,236 - 234,089,583 (-)NCBI
Celera1225,029,994 - 225,108,807 (-)NCBICelera
Cytogenetic Map1q52NCBI
GLDC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3896,532,467 - 6,645,729 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl96,532,467 - 6,645,729 (-)EnsemblGRCh38hg38GRCh38
GRCh3796,532,467 - 6,645,729 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3696,522,464 - 6,635,692 (-)NCBINCBI36Build 36hg18NCBI36
Build 3496,522,468 - 6,635,650NCBI
Celera96,469,938 - 6,583,174 (-)NCBICelera
Cytogenetic Map9p24.1NCBI
HuRef96,487,440 - 6,600,082 (-)NCBIHuRef
CHM1_196,533,234 - 6,646,419 (-)NCBICHM1_1
T2T-CHM13v2.096,537,521 - 6,650,780 (-)NCBIT2T-CHM13v2.0
Gldc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391930,075,847 - 30,152,829 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1930,075,847 - 30,152,829 (-)EnsemblGRCm39 Ensembl
GRCm381930,098,441 - 30,175,441 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1930,098,447 - 30,175,429 (-)EnsemblGRCm38mm10GRCm38
MGSCv371930,172,937 - 30,249,908 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361930,164,444 - 30,241,415 (-)NCBIMGSCv36mm8
Celera1930,873,665 - 30,951,190 (-)NCBICelera
Cytogenetic Map19C1NCBI
cM Map1924.87NCBI
Gldc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543410,431,983 - 10,533,002 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543410,431,434 - 10,533,118 (-)NCBIChiLan1.0ChiLan1.0
GLDC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v211117,935,713 - 118,045,297 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan19117,941,661 - 118,051,245 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v096,347,381 - 6,456,042 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.196,527,242 - 6,635,778 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl96,527,242 - 6,635,779 (-)Ensemblpanpan1.1panPan2
GLDC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11127,491,639 - 27,584,450 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1127,414,834 - 27,584,450 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1126,274,927 - 26,367,677 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01128,350,544 - 28,443,332 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1128,265,114 - 28,443,675 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11127,074,254 - 27,167,008 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01126,893,508 - 26,986,195 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01127,562,632 - 27,654,945 (-)NCBIUU_Cfam_GSD_1.0
Gldc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947142,555,653 - 142,642,377 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365391,007,820 - 1,095,054 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365391,008,340 - 1,095,044 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GLDC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1215,608,849 - 215,715,059 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11215,608,854 - 215,715,062 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
GLDC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11272,876,992 - 72,990,671 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1272,877,017 - 72,990,668 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603861,215,190 - 61,329,981 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gldc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473611,022,691 - 11,134,377 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473611,022,691 - 11,133,950 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gldc
586 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:488
Count of miRNA genes:251
Interacting mature miRNAs:300
Transcripts:ENSRNOT00000067612
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1207702246228581766Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210702053240947965Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1214537555238757011Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1224054293243747962Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1224054293243747962Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat

Markers in Region
BE118980  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21227,894,395 - 227,894,559 (+)MAPPERmRatBN7.2
Rnor_6.01248,308,478 - 248,308,641NCBIRnor6.0
Rnor_5.01255,556,011 - 255,556,174UniSTSRnor5.0
RGSC_v3.41233,857,837 - 233,858,000UniSTSRGSC3.4
Celera1225,041,143 - 225,041,306UniSTS
RH 3.4 Map11614.5UniSTS
Cytogenetic Map1q52UniSTS


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 41 41 41 69 29 12
Low 14 11 15 2 2 5 6 27 6 2
Below cutoff 2 20 5 4 6 6 2 4 6

Sequence


RefSeq Acc Id: ENSRNOT00000067612   ⟹   ENSRNOP00000059355
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1227,883,249 - 227,962,097 (-)Ensembl
Rnor_6.0 Ensembl1248,297,331 - 248,377,093 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089073   ⟹   ENSRNOP00000069291
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1227,883,249 - 227,962,097 (-)Ensembl
Rnor_6.0 Ensembl1248,297,656 - 248,376,750 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104658   ⟹   ENSRNOP00000095648
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1227,883,260 - 227,936,782 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110722   ⟹   ENSRNOP00000093309
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1227,883,249 - 227,962,097 (-)Ensembl
RefSeq Acc Id: NM_001415944   ⟹   NP_001402873
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81237,296,753 - 237,375,604 (-)NCBI
mRatBN7.21227,883,249 - 227,962,109 (-)NCBI
RefSeq Acc Id: XM_006231211   ⟹   XP_006231273
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81237,307,686 - 237,375,620 (-)NCBI
mRatBN7.21227,894,186 - 227,962,119 (-)NCBI
Rnor_6.01248,310,183 - 248,377,122 (-)NCBI
Rnor_5.01255,544,863 - 255,624,599 (-)NCBI
Sequence:
RefSeq Acc Id: XP_006231273   ⟸   XM_006231211
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JUZ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069291   ⟸   ENSRNOT00000089073
RefSeq Acc Id: ENSRNOP00000059355   ⟸   ENSRNOT00000067612
RefSeq Acc Id: ENSRNOP00000093309   ⟸   ENSRNOT00000110722
RefSeq Acc Id: ENSRNOP00000095648   ⟸   ENSRNOT00000104658
RefSeq Acc Id: NP_001402873   ⟸   NM_001415944
- UniProtKB: A0A0G2JUZ5 (UniProtKB/TrEMBL)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JUZ5-F1-model_v2 AlphaFold A0A0G2JUZ5 1-943 view protein structure

Transcriptome

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

Promoters
RGD ID:13690851
Promoter ID:EPDNEW_R1376
Type:single initiation site
Name:Gldc_1
Description:glycine decarboxylase
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_6.01248,377,101 - 248,377,161EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308660 AgrOrtholog
BioCyc Gene G2FUF-55943 BioCyc
BioCyc Pathway GLYCINE-SYN2-PWY [glycine biosynthesis II] BioCyc
  GLYCLEAV-PWY [glycine cleavage] BioCyc
BioCyc Pathway Image GLYCINE-SYN2-PWY BioCyc
  GLYCLEAV-PWY BioCyc
Ensembl Genes ENSRNOG00000011599 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067612.3 UniProtKB/TrEMBL
  ENSRNOT00000089073 ENTREZGENE
  ENSRNOT00000089073.2 UniProtKB/TrEMBL
  ENSRNOT00000104658.1 UniProtKB/TrEMBL
  ENSRNOT00000110722.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/TrEMBL
InterPro ArAA_b-elim_lyase/Thr_aldolase UniProtKB/TrEMBL
  GcvP UniProtKB/TrEMBL
  GDC-P-like UniProtKB/TrEMBL
  GDC-P_C UniProtKB/TrEMBL
  GDC-P_N UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major_dom UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major_sub1 UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_sub2 UniProtKB/TrEMBL
KEGG Report rno:309312 UniProtKB/TrEMBL
NCBI Gene 309312 ENTREZGENE
PANTHER GDC-P UniProtKB/TrEMBL
  GLYCINE DEHYDROGENASE (DECARBOXYLATING), MITOCHONDRIAL UniProtKB/TrEMBL
Pfam Beta_elim_lyase UniProtKB/TrEMBL
  GcvP2_C UniProtKB/TrEMBL
  GDC-P UniProtKB/TrEMBL
PhenoGen Gldc PhenoGen
RatGTEx ENSRNOG00000011599 RatGTEx
Superfamily-SCOP PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
UniProt A0A0G2JUZ5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AP64_RAT UniProtKB/TrEMBL
  A0A8I6AWV3_RAT UniProtKB/TrEMBL
  D4A5Q9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Gldc  glycine decarboxylase  LOC100911814  glycine dehydrogenase [decarboxylating], mitochondrial-like  Data merged from RGD:6490472 737654 PROVISIONAL
2016-03-22 Gldc  glycine decarboxylase  Gldc  glycine dehydrogenase (decarboxylating)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911814  glycine dehydrogenase [decarboxylating], mitochondrial-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-08-29 Gldc  glycine dehydrogenase (decarboxylating)  Gldc  glycine decarboxylase   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Gldc  glycine decarboxylase   Gldc_predicted  glycine decarboxylase (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Gldc_predicted  glycine decarboxylase (predicted)    glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P) (predicted)  Name updated 1299863 APPROVED
2005-01-12 Gldc_predicted  glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P) (predicted)      Symbol and Name status set to approved 70820 APPROVED