Abat (4-aminobutyrate aminotransferase) - Rat Genome Database

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Gene: Abat (4-aminobutyrate aminotransferase) Rattus norvegicus
Analyze
Symbol: Abat
Name: 4-aminobutyrate aminotransferase
RGD ID: 620948
Description: Exhibits 4-aminobutyrate transaminase activity. Involved in several processes, including gamma-aminobutyric acid biosynthetic process; positive regulation of inhibitory postsynaptic potential; and regulation of secretion. Localizes to mitochondrial matrix and neuron projection. Used to study several diseases, including Huntington's disease; epilepsy (multiple); heroin dependence; ischemia; and mental depression. Human ortholog(s) of this gene implicated in Alzheimer's disease; GABA aminotransferase deficiency; and Huntington's disease. Orthologous to human ABAT (4-aminobutyrate aminotransferase); PARTICIPATES IN 2-hydroxyglutaric aciduria pathway; 3-hydroxy-3-methylglutaryl-CoA lyase deficiency pathway; 3-hydroxyisobutyric aciduria pathway; INTERACTS WITH (+)-schisandrin B; (aminooxy)acetic acid; 1,3-dinitrobenzene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: (S)-3-amino-2-methylpropionate transaminase; 4-aminobutyrate aminotransferase, mitochondrial; beta-AlaAT; GABA aminotransferase; GABA transaminase; GABA-AT; GABA-T; Gabat; gamma-amino-N-butyrate transaminase; L-AIBAT; MGC93392
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: AbatTn(sb-T2/Bart3)2.163Mcwi  
Genetic Models: F344-AbatTn(sb-T2/Bart3)2.163Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2106,996,688 - 7,092,835 (-)NCBI
Rnor_6.0 Ensembl107,093,405 - 7,200,499 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0107,093,406 - 7,200,439 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0105,894,187 - 6,002,068 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4107,040,725 - 7,137,154 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1107,040,724 - 7,137,154 (-)NCBI
Celera105,995,207 - 6,088,218 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(aminooxy)acetic acid  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1-bromopropane  (EXP)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
amitriptyline  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
Butylparaben  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
disulfiram  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzacamene  (EXP)
ethanol  (EXP,ISO)
finasteride  (EXP)
folic acid  (ISO)
furan  (EXP)
gamma-aminobutyric acid  (EXP,ISO)
genistein  (ISO)
glafenine  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
lithium chloride  (ISO)
methapyrilene  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
O-methyleugenol  (ISO)
ochratoxin A  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
pentetrazol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (EXP)
phenylmercury acetate  (ISO)
phlorizin  (ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
propanal  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vigabatrin  (EXP,ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Briggs SW, etal., Epilepsia. 2014 Jan;55(1):94-102. doi: 10.1111/epi.12424. Epub 2013 Oct 28.
2. Brozoski TJ, etal., J Assoc Res Otolaryngol. 2007 Mar;8(1):105-18. Epub 2007 Jan 13.
3. Carter CJ Neurosci Lett. 1984 Aug 10;48(3):339-42.
4. Coscina DV and Nobrega JN, Int J Obes. 1984;8 Suppl 1:191-200.
5. Dewey SL, etal., Synapse. 1999 Jan;31(1):76-86.
6. Dieb W and Hafidi A, Eur J Pain. 2014 May 28. doi: 10.1002/ejp.525.
7. Duvilanski BH, etal., Eur J Pharmacol. 1985 Sep 10;115(1):65-9.
8. Engelborghs S, etal., Arzneimittelforschung. 1998 Jul;48(7):713-6.
9. Gardner EL, etal., Synapse. 2002 Dec 15;46(4):240-50.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Gerasimov MR, etal., Eur J Pharmacol. 2001 Mar 2;414(2-3):205-9.
12. GOA data from the GO Consortium
13. Hirayama T, etal., Hepatology. 2006 Sep;44(3):602-11.
14. Honda M, etal., Kobe J Med Sci. 1998 Feb;44(1):1-8.
15. KEGG
16. Kobayashi N, etal., Exp Eye Res. 1999 Jul;69(1):91-6.
17. Kontani Y, etal., Eur J Biochem 1999 Aug;264(1):218-22.
18. Kraus P and Noack G, J Enzyme Inhib. 1996;10(2):125-33.
19. Kubo T, etal., Naunyn Schmiedebergs Arch Pharmacol. 1990 Mar;341(3):221-4.
20. Li D Hokkaido Igaku Zasshi. 1998 May;73(3):215-25.
21. Loscher W Neurosci Lett. 1993 Oct 1;160(2):177-80.
22. Madl JE and Royer SM, Neuroscience. 2000;96(4):657-64.
23. Martinez-Rodriguez R, etal., Cell Mol Biol. 1982;28(6):513-20.
24. McKenna KF, etal., J Neural Transm Suppl. 1994;41:115-22.
25. Mecarelli O, etal., Pharmacol Res. 1997 Aug;36(2):87-93.
26. Medina-Kauwe LK, etal., J Neurochem 1994 Apr;62(4):1267-75.
27. MGD data from the GO Consortium
28. Miller JW, etal., Epilepsia. 1989 Jul-Aug;30(4):493-500.
29. Mishra N, etal., J Ethnopharmacol. 2010 Mar 24;128(2):533-6. doi: 10.1016/j.jep.2010.01.042. Epub 2010 Jan 28.
30. Nasreen Z, etal., Neurochem Res. 2012 Jan;37(1):202-4. doi: 10.1007/s11064-011-0603-2. Epub 2011 Sep 21.
31. NCBI rat LocusLink and RefSeq merged data July 26, 2002
32. Nikolov RP and Yakimova KS, Amino Acids. 2011 May;40(5):1441-5. doi: 10.1007/s00726-010-0754-5. Epub 2010 Sep 28.
33. OMIM Disease Annotation Pipeline
34. Overstreet LS and Westbrook GL, J Neurophysiol. 2001 Aug;86(2):596-603.
35. Pan Y, etal., J Med Chem. 2012 Jan 12;55(1):357-66. doi: 10.1021/jm201231w. Epub 2011 Dec 30.
36. Paredes RG, etal., Behav Neural Biol. 1993 Sep;60(2):118-22.
37. Pipeline to import KEGG annotations from KEGG into RGD
38. Pipeline to import SMPDB annotations from SMPDB into RGD
39. Pizarro-Delgado J, etal., Biochem J. 2010 Nov 1;431(3):381-9. doi: 10.1042/BJ20100714.
40. Qume M, etal., J Neurochem. 1995 May;64(5):2256-61.
41. Raza M and Al-Shabanah OA, Pharmacol Res. 2003 Jun;47(6):477-83.
42. RGD automated data pipeline
43. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
44. RGD automated import pipeline for gene-chemical interactions
45. Robin MM, etal., Eur J Pharmacol. 1980 Apr 4;62(4):319-27.
46. Schwarcz R, etal., Ann Neurol. 1977 Oct;2(4):299-303.
47. Seiler N, etal., Pharmacol Biochem Behav. 1995 Feb;50(2):181-9.
48. Sherif F and Oreland L, Behav Brain Res. 1994 Jul 29;63(1):11-5.
49. Sherif F and Oreland L, Behav Brain Res. 1995 Dec 14;72(1-2):135-40.
50. Sherif F, etal., J Neural Transm Gen Sect. 1991;84(1-2):95-102.
51. Sherif F, etal., J Neural Transm Gen Sect. 1994;98(1):69-79.
52. Sherif F, etal., J Neural Transm Park Dis Dement Sect. 1992;4(3):227-40.
53. Singewald N, etal., Naunyn Schmiedebergs Arch Pharmacol. 1992 Feb;345(2):181-6.
54. Skirzewski M, etal., Neuroscience. 2011 Nov 24;196:131-46. doi: 10.1016/j.neuroscience.2011.08.058. Epub 2011 Aug 30.
55. Stoof JC and Mulder AH, Eur J Pharmacol. 1977 Nov 15;46(2):177-80.
56. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
57. Tamaki N, etal., J Nutr Sci Vitaminol (Tokyo). 1987 Dec;33(6):439-49.
58. Tamaki N, etal., Methods Enzymol 2000;324:376-89.
59. Tsukamoto K and Sved AF, Neuropharmacology. 1993 Jun;32(6):575-9.
60. Wang QP, etal., Eur J Neurosci. 2008 Apr;27(8):2177-87. doi: 10.1111/j.1460-9568.2008.06175.x.
61. Xi ZX and Stein EA, J Pharmacol Exp Ther. 2000 Aug;294(2):613-9.
62. Yang J, etal., J Neurosci Methods. 2009 Sep 15;182(2):236-43. doi: 10.1016/j.jneumeth.2009.06.015. Epub 2009 Jun 21.
63. Yu X, etal., Life Sci. 2012 Jul 26;91(1-2):5-13. doi: 10.1016/j.lfs.2012.05.005. Epub 2012 May 23.
Additional References at PubMed
PMID:648527   PMID:6470007   PMID:10850552   PMID:11561735   PMID:14651853   PMID:15489334   PMID:15528998   PMID:15650327   PMID:18614015   PMID:23376485   PMID:24809054   PMID:31534049  


Genomics

Comparative Map Data
Abat
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2106,996,688 - 7,092,835 (-)NCBI
Rnor_6.0 Ensembl107,093,405 - 7,200,499 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0107,093,406 - 7,200,439 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0105,894,187 - 6,002,068 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4107,040,725 - 7,137,154 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1107,040,724 - 7,137,154 (-)NCBI
Celera105,995,207 - 6,088,218 (-)NCBICelera
Cytogenetic Map10q12NCBI
ABAT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl168,674,596 - 8,784,575 (+)EnsemblGRCh38hg38GRCh38
GRCh38168,674,617 - 8,784,570 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37168,768,474 - 8,878,427 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36168,675,928 - 8,785,933 (+)NCBINCBI36hg18NCBI36
Build 34168,675,945 - 8,785,932NCBI
Celera168,937,805 - 9,047,806 (+)NCBI
Cytogenetic Map16p13.2NCBI
HuRef168,691,116 - 8,800,895 (+)NCBIHuRef
CHM1_1168,768,357 - 8,878,342 (+)NCBICHM1_1
Abat
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39168,331,293 - 8,439,432 (+)NCBIGRCm39mm39
GRCm39 Ensembl168,331,293 - 8,439,432 (+)Ensembl
GRCm38168,513,429 - 8,621,568 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl168,513,429 - 8,621,568 (+)EnsemblGRCm38mm10GRCm38
MGSCv37168,513,522 - 8,621,661 (+)NCBIGRCm37mm9NCBIm37
MGSCv36168,428,810 - 8,536,889 (+)NCBImm8
Celera169,158,444 - 9,266,822 (+)NCBICelera
Cytogenetic Map16A1NCBI
Abat
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554429,422,849 - 9,516,103 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554429,422,849 - 9,516,054 (-)NCBIChiLan1.0ChiLan1.0
ABAT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1168,850,010 - 8,958,420 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl168,888,178 - 8,958,420 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0167,609,282 - 7,718,049 (+)NCBIMhudiblu_PPA_v0panPan3
ABAT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1633,385,779 - 33,471,348 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl633,376,996 - 33,471,326 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha634,776,452 - 34,862,027 (-)NCBI
ROS_Cfam_1.0633,584,479 - 33,670,069 (-)NCBI
UMICH_Zoey_3.1633,386,823 - 33,472,421 (-)NCBI
UNSW_CanFamBas_1.0633,256,654 - 33,342,147 (-)NCBI
UU_Cfam_GSD_1.0633,678,493 - 33,764,059 (-)NCBI
Abat
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344109,698,256 - 109,775,982 (+)NCBI
SpeTri2.0NW_0049365307,543,743 - 7,621,392 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABAT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl333,908,965 - 34,015,469 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1333,913,068 - 33,960,804 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2334,642,449 - 34,682,257 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ABAT
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.158,274,310 - 8,380,973 (+)NCBI
ChlSab1.1 Ensembl58,315,952 - 8,379,549 (+)Ensembl
Vero_WHO_p1.0NW_02366606821,840,065 - 21,946,865 (-)NCBI
Abat
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248246,112,644 - 6,202,936 (+)NCBI

Position Markers
STS-Z39377  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2107,091,152 - 7,091,407 (+)MAPPER
Rnor_6.0107,198,754 - 7,199,008NCBIRnor6.0
Rnor_5.0106,000,383 - 6,000,637UniSTSRnor5.0
RGSC_v3.4107,135,469 - 7,135,723UniSTSRGSC3.4
Celera106,086,536 - 6,086,790UniSTS
Cytogenetic Map10q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129592136Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135538813Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10483563820170031Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719917555534Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719919591669Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10546011921524070Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10546011921524070Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10546011921524070Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10546011921524070Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10546011921524070Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
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)10622909575983805Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10622928936185929Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat


Genetic Models
This gene Abat is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:24
Count of miRNA genes:21
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000003633
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 37 37 37 74 35 25
Low 2 20 20 4 11 4 7 7 16 9 7
Below cutoff 1 20 8 1 4 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003633   ⟹   ENSRNOP00000003633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl107,093,405 - 7,200,499 (-)Ensembl
RefSeq Acc Id: NM_031003   ⟹   NP_112265
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2106,999,819 - 7,092,835 (-)NCBI
Rnor_6.0107,094,258 - 7,200,439 (-)NCBI
Rnor_5.0105,894,187 - 6,002,068 (-)NCBI
RGSC_v3.4107,040,725 - 7,137,154 (-)RGD
Celera105,995,207 - 6,088,218 (-)RGD
Sequence:
RefSeq Acc Id: XM_006245760   ⟹   XP_006245822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2106,996,688 - 7,053,104 (-)NCBI
Rnor_6.0107,093,406 - 7,146,498 (-)NCBI
Rnor_5.0105,894,187 - 6,002,068 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112265   ⟸   NM_031003
- UniProtKB: P50554 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245822   ⟸   XM_006245760
- Peptide Label: isoform X1
- UniProtKB: P50554 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003633   ⟸   ENSRNOT00000003633

Transcriptome

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

Promoters
RGD ID:13696954
Promoter ID:EPDNEW_R7479
Type:multiple initiation site
Name:Abat_1
Description:4-aminobutyrate aminotransferase
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_6.0107,200,476 - 7,200,536EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620948 AgrOrtholog
Ensembl Genes ENSRNOG00000002636 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003633 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003633 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot
  3.90.1150.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7109775 IMAGE-MGC_LOAD
InterPro 4NH2But_aminotransferase_euk UniProtKB/Swiss-Prot
  Aminotrans_3 UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot
KEGG Report rno:81632 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93392 IMAGE-MGC_LOAD
NCBI Gene 81632 ENTREZGENE
Pfam Aminotran_3 UniProtKB/Swiss-Prot
PharmGKB ABAT RGD
PhenoGen Abat PhenoGen
PIRSF Transaminase_4ab_Lys_Orn UniProtKB/Swiss-Prot
PROSITE AA_TRANSFER_CLASS_3 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot
TIGRFAMs GABAtrns_euk UniProtKB/Swiss-Prot
Transposagen Abat Transposagen
UniProt GABT_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O70539 UniProtKB/Swiss-Prot
  Q66HM1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Abat  4-aminobutyrate aminotransferase      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Abat  4-aminobutyrate aminotransferase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in brain, cerebellar cortex ,liver, kidney, and testis 631979
gene_protein 466 amino acids 631980
gene_protein proteolytically cleaved in two steps in the mitochondria to produce brain- and liver-specific forms 631979
gene_protein proteolytically cleaved in two steps in the mitochondria to produce brain- and liver-specific forms 631980
gene_regulation active enzyme in brain is larger than in liver due to use of a second proteolytic cleavage site